diff --git a/dist/SBMLsqueezer-2.0/SBMLsqueezer_v2.0.zip b/dist/SBMLsqueezer-2.0/SBMLsqueezer_v2.0.zip index 8c4890076..08515af65 100644 Binary files a/dist/SBMLsqueezer-2.0/SBMLsqueezer_v2.0.zip and b/dist/SBMLsqueezer-2.0/SBMLsqueezer_v2.0.zip differ diff --git a/dist/SBMLsqueezer-2.0/SBMLsqueezer_v2.0_Garuda.zip b/dist/SBMLsqueezer-2.0/SBMLsqueezer_v2.0_Garuda.zip index b166bb19b..352890ddf 100644 Binary files a/dist/SBMLsqueezer-2.0/SBMLsqueezer_v2.0_Garuda.zip and b/dist/SBMLsqueezer-2.0/SBMLsqueezer_v2.0_Garuda.zip differ diff --git a/dist/SBMLsqueezer-2.0/SBMLsqueezer_v2.0_incl-libs.jar b/dist/SBMLsqueezer-2.0/SBMLsqueezer_v2.0_incl-libs.jar index 039d0ed54..e8c961454 100644 Binary files a/dist/SBMLsqueezer-2.0/SBMLsqueezer_v2.0_incl-libs.jar and b/dist/SBMLsqueezer-2.0/SBMLsqueezer_v2.0_incl-libs.jar differ diff --git a/doc/api/version_2.0/allclasses-frame.html b/doc/api/version_2.0/allclasses-frame.html index c69be48e0..0f05665ee 100644 --- a/doc/api/version_2.0/allclasses-frame.html +++ b/doc/api/version_2.0/allclasses-frame.html @@ -2,12 +2,12 @@ - + All Classes (SBMLsqueezer 2.0 API Specification) - + diff --git a/doc/api/version_2.0/allclasses-noframe.html b/doc/api/version_2.0/allclasses-noframe.html index d00ef09de..000e6a7b9 100644 --- a/doc/api/version_2.0/allclasses-noframe.html +++ b/doc/api/version_2.0/allclasses-noframe.html @@ -2,12 +2,12 @@ - + All Classes (SBMLsqueezer 2.0 API Specification) - + diff --git a/doc/api/version_2.0/constant-values.html b/doc/api/version_2.0/constant-values.html index 7013fe41a..a538b9279 100644 --- a/doc/api/version_2.0/constant-values.html +++ b/doc/api/version_2.0/constant-values.html @@ -2,12 +2,12 @@ - + Constant Field Values (SBMLsqueezer 2.0 API Specification) - + @@ -217,7 +217,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/deprecated-list.html b/doc/api/version_2.0/deprecated-list.html index 0a97ec5c7..6a0e93b35 100644 --- a/doc/api/version_2.0/deprecated-list.html +++ b/doc/api/version_2.0/deprecated-list.html @@ -2,12 +2,12 @@ - + Deprecated List (SBMLsqueezer 2.0 API Specification) - + @@ -111,7 +111,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/help-doc.html b/doc/api/version_2.0/help-doc.html index ed2b29651..0e10b2b75 100644 --- a/doc/api/version_2.0/help-doc.html +++ b/doc/api/version_2.0/help-doc.html @@ -2,12 +2,12 @@ - + API Help (SBMLsqueezer 2.0 API Specification) - + @@ -188,7 +188,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/index-files/index-1.html b/doc/api/version_2.0/index-files/index-1.html index 07bbf1333..18de50eb9 100644 --- a/doc/api/version_2.0/index-files/index-1.html +++ b/doc/api/version_2.0/index-files/index-1.html @@ -2,12 +2,12 @@ - + A-Index (SBMLsqueezer 2.0 API Specification) - + @@ -191,7 +191,7 @@ -Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/index-files/index-10.html b/doc/api/version_2.0/index-files/index-10.html index b9ea0c189..8d396d9c7 100644 --- a/doc/api/version_2.0/index-files/index-10.html +++ b/doc/api/version_2.0/index-files/index-10.html @@ -2,12 +2,12 @@ - + J-Index (SBMLsqueezer 2.0 API Specification) - + @@ -132,7 +132,7 @@ -Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/index-files/index-11.html b/doc/api/version_2.0/index-files/index-11.html index 1037c322c..47290322e 100644 --- a/doc/api/version_2.0/index-files/index-11.html +++ b/doc/api/version_2.0/index-files/index-11.html @@ -2,12 +2,12 @@ - + K-Index (SBMLsqueezer 2.0 API Specification) - + @@ -230,7 +230,7 @@ -Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/index-files/index-12.html b/doc/api/version_2.0/index-files/index-12.html index 824fb8913..6f5ad269a 100644 --- a/doc/api/version_2.0/index-files/index-12.html +++ b/doc/api/version_2.0/index-files/index-12.html @@ -2,12 +2,12 @@ - + L-Index (SBMLsqueezer 2.0 API Specification) - + @@ -146,7 +146,7 @@ -Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/index-files/index-13.html b/doc/api/version_2.0/index-files/index-13.html index bce1ccf52..8ee278b97 100644 --- a/doc/api/version_2.0/index-files/index-13.html +++ b/doc/api/version_2.0/index-files/index-13.html @@ -2,12 +2,12 @@ - + M-Index (SBMLsqueezer 2.0 API Specification) - + @@ -325,7 +325,7 @@ -Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/index-files/index-14.html b/doc/api/version_2.0/index-files/index-14.html index 9aa497047..8beae5788 100644 --- a/doc/api/version_2.0/index-files/index-14.html +++ b/doc/api/version_2.0/index-files/index-14.html @@ -2,12 +2,12 @@ - + N-Index (SBMLsqueezer 2.0 API Specification) - + @@ -130,7 +130,7 @@ -Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/index-files/index-15.html b/doc/api/version_2.0/index-files/index-15.html index db2279d48..1a4541b29 100644 --- a/doc/api/version_2.0/index-files/index-15.html +++ b/doc/api/version_2.0/index-files/index-15.html @@ -2,12 +2,12 @@ - + O-Index (SBMLsqueezer 2.0 API Specification) - + @@ -152,7 +152,7 @@ -Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/index-files/index-16.html b/doc/api/version_2.0/index-files/index-16.html index d40339d94..124ac5ea5 100644 --- a/doc/api/version_2.0/index-files/index-16.html +++ b/doc/api/version_2.0/index-files/index-16.html @@ -2,12 +2,12 @@ - + P-Index (SBMLsqueezer 2.0 API Specification) - + @@ -433,7 +433,7 @@ -Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/index-files/index-17.html b/doc/api/version_2.0/index-files/index-17.html index 259195298..3c124e2cc 100644 --- a/doc/api/version_2.0/index-files/index-17.html +++ b/doc/api/version_2.0/index-files/index-17.html @@ -2,12 +2,12 @@ - + R-Index (SBMLsqueezer 2.0 API Specification) - + @@ -187,7 +187,7 @@ -Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/index-files/index-18.html b/doc/api/version_2.0/index-files/index-18.html index 8b5685c9b..2f85ed010 100644 --- a/doc/api/version_2.0/index-files/index-18.html +++ b/doc/api/version_2.0/index-files/index-18.html @@ -2,12 +2,12 @@ - + S-Index (SBMLsqueezer 2.0 API Specification) - + @@ -406,7 +406,7 @@ -Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/index-files/index-19.html b/doc/api/version_2.0/index-files/index-19.html index 9967af836..5879583fc 100644 --- a/doc/api/version_2.0/index-files/index-19.html +++ b/doc/api/version_2.0/index-files/index-19.html @@ -2,12 +2,12 @@ - + T-Index (SBMLsqueezer 2.0 API Specification) - + @@ -199,7 +199,7 @@ -Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/index-files/index-2.html b/doc/api/version_2.0/index-files/index-2.html index d8727df16..93c068197 100644 --- a/doc/api/version_2.0/index-files/index-2.html +++ b/doc/api/version_2.0/index-files/index-2.html @@ -2,12 +2,12 @@ - + B-Index (SBMLsqueezer 2.0 API Specification) - + @@ -121,7 +121,7 @@ -Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/index-files/index-20.html b/doc/api/version_2.0/index-files/index-20.html index 56fbe2be2..bc7bed803 100644 --- a/doc/api/version_2.0/index-files/index-20.html +++ b/doc/api/version_2.0/index-files/index-20.html @@ -2,12 +2,12 @@ - + U-Index (SBMLsqueezer 2.0 API Specification) - + @@ -168,7 +168,7 @@ -Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/index-files/index-21.html b/doc/api/version_2.0/index-files/index-21.html index c9f476d65..02a2ce140 100644 --- a/doc/api/version_2.0/index-files/index-21.html +++ b/doc/api/version_2.0/index-files/index-21.html @@ -2,12 +2,12 @@ - + V-Index (SBMLsqueezer 2.0 API Specification) - + @@ -224,7 +224,7 @@ -Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/index-files/index-22.html b/doc/api/version_2.0/index-files/index-22.html index d1f7735c6..20643a55c 100644 --- a/doc/api/version_2.0/index-files/index-22.html +++ b/doc/api/version_2.0/index-files/index-22.html @@ -2,12 +2,12 @@ - + W-Index (SBMLsqueezer 2.0 API Specification) - + @@ -244,7 +244,7 @@ -Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/index-files/index-23.html b/doc/api/version_2.0/index-files/index-23.html index ee0dc32e2..e52fab158 100644 --- a/doc/api/version_2.0/index-files/index-23.html +++ b/doc/api/version_2.0/index-files/index-23.html @@ -2,12 +2,12 @@ - + X-Index (SBMLsqueezer 2.0 API Specification) - + @@ -110,7 +110,7 @@ -Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/index-files/index-24.html b/doc/api/version_2.0/index-files/index-24.html index 6a9cefac6..dd218e618 100644 --- a/doc/api/version_2.0/index-files/index-24.html +++ b/doc/api/version_2.0/index-files/index-24.html @@ -2,12 +2,12 @@ - + Z-Index (SBMLsqueezer 2.0 API Specification) - + @@ -120,7 +120,7 @@ -Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/index-files/index-3.html b/doc/api/version_2.0/index-files/index-3.html index a563bf18c..48a999af9 100644 --- a/doc/api/version_2.0/index-files/index-3.html +++ b/doc/api/version_2.0/index-files/index-3.html @@ -2,12 +2,12 @@ - + C-Index (SBMLsqueezer 2.0 API Specification) - + @@ -279,7 +279,7 @@ -Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/index-files/index-4.html b/doc/api/version_2.0/index-files/index-4.html index 84d102d81..3efa91c4e 100644 --- a/doc/api/version_2.0/index-files/index-4.html +++ b/doc/api/version_2.0/index-files/index-4.html @@ -2,12 +2,12 @@ - + D-Index (SBMLsqueezer 2.0 API Specification) - + @@ -141,7 +141,7 @@ -Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/index-files/index-5.html b/doc/api/version_2.0/index-files/index-5.html index cf47ab1c8..91b7a347a 100644 --- a/doc/api/version_2.0/index-files/index-5.html +++ b/doc/api/version_2.0/index-files/index-5.html @@ -2,12 +2,12 @@ - + E-Index (SBMLsqueezer 2.0 API Specification) - + @@ -110,7 +110,7 @@ -Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/index-files/index-6.html b/doc/api/version_2.0/index-files/index-6.html index 3e4391442..4040cdb3b 100644 --- a/doc/api/version_2.0/index-files/index-6.html +++ b/doc/api/version_2.0/index-files/index-6.html @@ -2,12 +2,12 @@ - + F-Index (SBMLsqueezer 2.0 API Specification) - + @@ -122,7 +122,7 @@ -Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/index-files/index-7.html b/doc/api/version_2.0/index-files/index-7.html index 3935dd667..3b51c4aa4 100644 --- a/doc/api/version_2.0/index-files/index-7.html +++ b/doc/api/version_2.0/index-files/index-7.html @@ -2,12 +2,12 @@ - + G-Index (SBMLsqueezer 2.0 API Specification) - + @@ -998,7 +998,7 @@ -Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/index-files/index-8.html b/doc/api/version_2.0/index-files/index-8.html index 8c97b778b..85d094e7a 100644 --- a/doc/api/version_2.0/index-files/index-8.html +++ b/doc/api/version_2.0/index-files/index-8.html @@ -2,12 +2,12 @@ - + H-Index (SBMLsqueezer 2.0 API Specification) - + @@ -158,7 +158,7 @@ -Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/index-files/index-9.html b/doc/api/version_2.0/index-files/index-9.html index 94d513053..295663e3d 100644 --- a/doc/api/version_2.0/index-files/index-9.html +++ b/doc/api/version_2.0/index-files/index-9.html @@ -2,12 +2,12 @@ - + I-Index (SBMLsqueezer 2.0 API Specification) - + @@ -308,7 +308,7 @@ -Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/index.html b/doc/api/version_2.0/index.html index cce3ca28e..14e1ce85d 100644 --- a/doc/api/version_2.0/index.html +++ b/doc/api/version_2.0/index.html @@ -2,7 +2,7 @@ - + SBMLsqueezer 2.0 API Specification diff --git a/doc/api/version_2.0/org/sbml/squeezer/ConsistencyReportBuilder.html b/doc/api/version_2.0/org/sbml/squeezer/ConsistencyReportBuilder.html index e666e0405..bd37904c0 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/ConsistencyReportBuilder.html +++ b/doc/api/version_2.0/org/sbml/squeezer/ConsistencyReportBuilder.html @@ -2,12 +2,12 @@ - + ConsistencyReportBuilder (SBMLsqueezer 2.0 API Specification) - + @@ -265,7 +265,7 @@

-Generated at April 24 2014
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-Generated at April 24 2014
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-Generated at April 24 2014
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-Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/ParameterFactory.html b/doc/api/version_2.0/org/sbml/squeezer/ParameterFactory.html index 479cffd46..267573c61 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/ParameterFactory.html +++ b/doc/api/version_2.0/org/sbml/squeezer/ParameterFactory.html @@ -2,12 +2,12 @@ - + ParameterFactory (SBMLsqueezer 2.0 API Specification) - + @@ -1422,7 +1422,7 @@

-Generated at April 24 2014
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-Generated at April 24 2014
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-Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/SBMLsqueezer.html b/doc/api/version_2.0/org/sbml/squeezer/SBMLsqueezer.html index e3ee2554d..9c8d70b02 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/SBMLsqueezer.html +++ b/doc/api/version_2.0/org/sbml/squeezer/SBMLsqueezer.html @@ -2,12 +2,12 @@ - + SBMLsqueezer (SBMLsqueezer 2.0 API Specification) - + @@ -116,7 +116,7 @@

Since:
1.0
Version:
-
$Rev: 1092 $
+
$Rev: 1102 $
Author:
Andreas Dräger, Nadine Hassis, Hannes Borch, Sarah R. Müller vom Hagen
See Also:
Serialized Form @@ -865,7 +865,7 @@

-Generated at April 24 2014
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-Generated at April 24 2014
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-Generated at April 24 2014
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-Generated at April 24 2014
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-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/celldesigner/Plugin.html b/doc/api/version_2.0/org/sbml/squeezer/celldesigner/Plugin.html index f4b459b94..a2613c699 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/celldesigner/Plugin.html +++ b/doc/api/version_2.0/org/sbml/squeezer/celldesigner/Plugin.html @@ -2,12 +2,12 @@ - + Plugin (SBMLsqueezer 2.0 API Specification) - + @@ -114,7 +114,7 @@

Since:
1.0
Version:
-
$Rev: 1085 $
+
$Rev: 1097 $
Author:
Nadine Hassis, Andreas Dräger, Hannes Borch
@@ -268,7 +268,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/celldesigner/PluginAction.html b/doc/api/version_2.0/org/sbml/squeezer/celldesigner/PluginAction.html index 2f56aef07..7bc1d3c3f 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/celldesigner/PluginAction.html +++ b/doc/api/version_2.0/org/sbml/squeezer/celldesigner/PluginAction.html @@ -2,12 +2,12 @@ - + PluginAction (SBMLsqueezer 2.0 API Specification) - + @@ -274,7 +274,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/celldesigner/PluginTest.html b/doc/api/version_2.0/org/sbml/squeezer/celldesigner/PluginTest.html index 751957e7e..9f3915cca 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/celldesigner/PluginTest.html +++ b/doc/api/version_2.0/org/sbml/squeezer/celldesigner/PluginTest.html @@ -2,12 +2,12 @@ - + PluginTest (SBMLsqueezer 2.0 API Specification) - + @@ -219,7 +219,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/celldesigner/PluginWorker.html b/doc/api/version_2.0/org/sbml/squeezer/celldesigner/PluginWorker.html index f87df7f4e..201ac4981 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/celldesigner/PluginWorker.html +++ b/doc/api/version_2.0/org/sbml/squeezer/celldesigner/PluginWorker.html @@ -2,12 +2,12 @@ - + PluginWorker (SBMLsqueezer 2.0 API Specification) - + @@ -227,7 +227,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/celldesigner/class-use/Mode.html b/doc/api/version_2.0/org/sbml/squeezer/celldesigner/class-use/Mode.html index 8d6196dd9..8eb9013af 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/celldesigner/class-use/Mode.html +++ b/doc/api/version_2.0/org/sbml/squeezer/celldesigner/class-use/Mode.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.celldesigner.Mode (SBMLsqueezer 2.0 API Specification) - + @@ -178,7 +178,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/celldesigner/class-use/Plugin.html b/doc/api/version_2.0/org/sbml/squeezer/celldesigner/class-use/Plugin.html index 7e168ed0c..8c263f76f 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/celldesigner/class-use/Plugin.html +++ b/doc/api/version_2.0/org/sbml/squeezer/celldesigner/class-use/Plugin.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.celldesigner.Plugin (SBMLsqueezer 2.0 API Specification) - + @@ -151,7 +151,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/celldesigner/class-use/PluginAction.html b/doc/api/version_2.0/org/sbml/squeezer/celldesigner/class-use/PluginAction.html index bc0151cb3..67e1d7b21 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/celldesigner/class-use/PluginAction.html +++ b/doc/api/version_2.0/org/sbml/squeezer/celldesigner/class-use/PluginAction.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.celldesigner.PluginAction (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/celldesigner/class-use/PluginTest.html b/doc/api/version_2.0/org/sbml/squeezer/celldesigner/class-use/PluginTest.html index 92b0b5863..8785446ad 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/celldesigner/class-use/PluginTest.html +++ b/doc/api/version_2.0/org/sbml/squeezer/celldesigner/class-use/PluginTest.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.celldesigner.PluginTest (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/celldesigner/class-use/PluginWorker.html b/doc/api/version_2.0/org/sbml/squeezer/celldesigner/class-use/PluginWorker.html index 83c141ee7..fba5ec77f 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/celldesigner/class-use/PluginWorker.html +++ b/doc/api/version_2.0/org/sbml/squeezer/celldesigner/class-use/PluginWorker.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.celldesigner.PluginWorker (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/celldesigner/package-frame.html b/doc/api/version_2.0/org/sbml/squeezer/celldesigner/package-frame.html index 435fff66d..77f709d4e 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/celldesigner/package-frame.html +++ b/doc/api/version_2.0/org/sbml/squeezer/celldesigner/package-frame.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.celldesigner (SBMLsqueezer 2.0 API Specification) - + diff --git a/doc/api/version_2.0/org/sbml/squeezer/celldesigner/package-summary.html b/doc/api/version_2.0/org/sbml/squeezer/celldesigner/package-summary.html index 44a1838e8..e4d00e6ee 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/celldesigner/package-summary.html +++ b/doc/api/version_2.0/org/sbml/squeezer/celldesigner/package-summary.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.celldesigner (SBMLsqueezer 2.0 API Specification) - + @@ -169,7 +169,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/celldesigner/package-tree.html b/doc/api/version_2.0/org/sbml/squeezer/celldesigner/package-tree.html index bed851f74..3807c7bc4 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/celldesigner/package-tree.html +++ b/doc/api/version_2.0/org/sbml/squeezer/celldesigner/package-tree.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.celldesigner Class Hierarchy (SBMLsqueezer 2.0 API Specification) - + @@ -142,7 +142,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/celldesigner/package-use.html b/doc/api/version_2.0/org/sbml/squeezer/celldesigner/package-use.html index a8d03206c..f5a9af171 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/celldesigner/package-use.html +++ b/doc/api/version_2.0/org/sbml/squeezer/celldesigner/package-use.html @@ -2,12 +2,12 @@ - + Uses of Package org.sbml.squeezer.celldesigner (SBMLsqueezer 2.0 API Specification) - + @@ -142,7 +142,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/class-use/ConsistencyReportBuilder.html b/doc/api/version_2.0/org/sbml/squeezer/class-use/ConsistencyReportBuilder.html index 563799b67..44bdbfd7f 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/class-use/ConsistencyReportBuilder.html +++ b/doc/api/version_2.0/org/sbml/squeezer/class-use/ConsistencyReportBuilder.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.ConsistencyReportBuilder (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/class-use/KineticLawGenerator.html b/doc/api/version_2.0/org/sbml/squeezer/class-use/KineticLawGenerator.html index e88522567..35de73b4c 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/class-use/KineticLawGenerator.html +++ b/doc/api/version_2.0/org/sbml/squeezer/class-use/KineticLawGenerator.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.KineticLawGenerator (SBMLsqueezer 2.0 API Specification) - + @@ -220,7 +220,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/class-use/ModificationException.html b/doc/api/version_2.0/org/sbml/squeezer/class-use/ModificationException.html index 478154244..ac81fdfd8 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/class-use/ModificationException.html +++ b/doc/api/version_2.0/org/sbml/squeezer/class-use/ModificationException.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.ModificationException (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/class-use/OptionsGeneral.html b/doc/api/version_2.0/org/sbml/squeezer/class-use/OptionsGeneral.html index f38aca5ba..0dd497f66 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/class-use/OptionsGeneral.html +++ b/doc/api/version_2.0/org/sbml/squeezer/class-use/OptionsGeneral.html @@ -2,12 +2,12 @@ - + Uses of Interface org.sbml.squeezer.OptionsGeneral (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/class-use/ParameterFactory.html b/doc/api/version_2.0/org/sbml/squeezer/class-use/ParameterFactory.html index bba920cf9..dfc3990dd 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/class-use/ParameterFactory.html +++ b/doc/api/version_2.0/org/sbml/squeezer/class-use/ParameterFactory.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.ParameterFactory (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/class-use/RateLawNotApplicableException.html b/doc/api/version_2.0/org/sbml/squeezer/class-use/RateLawNotApplicableException.html index 4b797d4bc..8faee9946 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/class-use/RateLawNotApplicableException.html +++ b/doc/api/version_2.0/org/sbml/squeezer/class-use/RateLawNotApplicableException.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.RateLawNotApplicableException (SBMLsqueezer 2.0 API Specification) - + @@ -468,7 +468,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/class-use/ReactionType.html b/doc/api/version_2.0/org/sbml/squeezer/class-use/ReactionType.html index 7d304d759..3dfb6a1e2 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/class-use/ReactionType.html +++ b/doc/api/version_2.0/org/sbml/squeezer/class-use/ReactionType.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.ReactionType (SBMLsqueezer 2.0 API Specification) - + @@ -147,7 +147,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/class-use/SBMLsqueezer.html b/doc/api/version_2.0/org/sbml/squeezer/class-use/SBMLsqueezer.html index 9e3b6f6d0..bd10cd042 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/class-use/SBMLsqueezer.html +++ b/doc/api/version_2.0/org/sbml/squeezer/class-use/SBMLsqueezer.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.SBMLsqueezer (SBMLsqueezer 2.0 API Specification) - + @@ -146,7 +146,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/class-use/SubmodelController.html b/doc/api/version_2.0/org/sbml/squeezer/class-use/SubmodelController.html index 7dd82ca7b..6906a8f1d 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/class-use/SubmodelController.html +++ b/doc/api/version_2.0/org/sbml/squeezer/class-use/SubmodelController.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.SubmodelController (SBMLsqueezer 2.0 API Specification) - + @@ -220,7 +220,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/class-use/UnitConsistencyType.html b/doc/api/version_2.0/org/sbml/squeezer/class-use/UnitConsistencyType.html index cbd8d23e0..799eecd98 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/class-use/UnitConsistencyType.html +++ b/doc/api/version_2.0/org/sbml/squeezer/class-use/UnitConsistencyType.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.UnitConsistencyType (SBMLsqueezer 2.0 API Specification) - + @@ -194,7 +194,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/class-use/UnitFactory.html b/doc/api/version_2.0/org/sbml/squeezer/class-use/UnitFactory.html index 36e52cb8d..529a0280e 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/class-use/UnitFactory.html +++ b/doc/api/version_2.0/org/sbml/squeezer/class-use/UnitFactory.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.UnitFactory (SBMLsqueezer 2.0 API Specification) - + @@ -147,7 +147,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/KineticLawGeneratorWorker.html b/doc/api/version_2.0/org/sbml/squeezer/gui/KineticLawGeneratorWorker.html index 41d2acdd3..0355934a6 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/KineticLawGeneratorWorker.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/KineticLawGeneratorWorker.html @@ -2,12 +2,12 @@ - + KineticLawGeneratorWorker (SBMLsqueezer 2.0 API Specification) - + @@ -229,7 +229,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/KineticLawSelectionDialog.html b/doc/api/version_2.0/org/sbml/squeezer/gui/KineticLawSelectionDialog.html index ab1cf4615..7da09ba6d 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/KineticLawSelectionDialog.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/KineticLawSelectionDialog.html @@ -2,12 +2,12 @@ - + KineticLawSelectionDialog (SBMLsqueezer 2.0 API Specification) - + @@ -418,7 +418,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/KineticLawSelectionPanel.html b/doc/api/version_2.0/org/sbml/squeezer/gui/KineticLawSelectionPanel.html index bd7b1adc7..3ca448767 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/KineticLawSelectionPanel.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/KineticLawSelectionPanel.html @@ -2,12 +2,12 @@ - + KineticLawSelectionPanel (SBMLsqueezer 2.0 API Specification) - + @@ -487,7 +487,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/KineticLawTable.html b/doc/api/version_2.0/org/sbml/squeezer/gui/KineticLawTable.html index d241eda8a..f0c423f2e 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/KineticLawTable.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/KineticLawTable.html @@ -2,12 +2,12 @@ - + KineticLawTable (SBMLsqueezer 2.0 API Specification) - + @@ -542,7 +542,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/KineticLawTableCellRenderer.html b/doc/api/version_2.0/org/sbml/squeezer/gui/KineticLawTableCellRenderer.html index 1a8b7b70e..18bad0932 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/KineticLawTableCellRenderer.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/KineticLawTableCellRenderer.html @@ -2,12 +2,12 @@ - + KineticLawTableCellRenderer (SBMLsqueezer 2.0 API Specification) - + @@ -378,7 +378,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/KineticLawTableModel.html b/doc/api/version_2.0/org/sbml/squeezer/gui/KineticLawTableModel.html index 28ca3e3b3..1da6d2e68 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/KineticLawTableModel.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/KineticLawTableModel.html @@ -2,12 +2,12 @@ - + KineticLawTableModel (SBMLsqueezer 2.0 API Specification) - + @@ -477,7 +477,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/KineticLawWindowAdapter.html b/doc/api/version_2.0/org/sbml/squeezer/gui/KineticLawWindowAdapter.html index b1b1aacdb..91d250965 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/KineticLawWindowAdapter.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/KineticLawWindowAdapter.html @@ -2,12 +2,12 @@ - + KineticLawWindowAdapter (SBMLsqueezer 2.0 API Specification) - + @@ -450,7 +450,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/LaTeXRenderer.html b/doc/api/version_2.0/org/sbml/squeezer/gui/LaTeXRenderer.html index c966bd3d6..53cc94058 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/LaTeXRenderer.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/LaTeXRenderer.html @@ -2,12 +2,12 @@ - + LaTeXRenderer (SBMLsqueezer 2.0 API Specification) - + @@ -448,7 +448,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/SBMLsqueezerUI.Command.html b/doc/api/version_2.0/org/sbml/squeezer/gui/SBMLsqueezerUI.Command.html index 355a3e370..fa7574986 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/SBMLsqueezerUI.Command.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/SBMLsqueezerUI.Command.html @@ -2,12 +2,12 @@ - + SBMLsqueezerUI.Command (SBMLsqueezer 2.0 API Specification) - + @@ -368,7 +368,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/SBMLsqueezerUI.html b/doc/api/version_2.0/org/sbml/squeezer/gui/SBMLsqueezerUI.html index bf452189a..9d73b512a 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/SBMLsqueezerUI.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/SBMLsqueezerUI.html @@ -2,12 +2,12 @@ - + SBMLsqueezerUI (SBMLsqueezer 2.0 API Specification) - + @@ -762,7 +762,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/KineticLawGeneratorWorker.html b/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/KineticLawGeneratorWorker.html index 04b5691ef..f3e5691ef 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/KineticLawGeneratorWorker.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/KineticLawGeneratorWorker.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.gui.KineticLawGeneratorWorker (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/KineticLawSelectionDialog.html b/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/KineticLawSelectionDialog.html index 53e63e2b5..5e138853d 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/KineticLawSelectionDialog.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/KineticLawSelectionDialog.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.gui.KineticLawSelectionDialog (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/KineticLawSelectionPanel.html b/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/KineticLawSelectionPanel.html index 16324263a..ac13b9c11 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/KineticLawSelectionPanel.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/KineticLawSelectionPanel.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.gui.KineticLawSelectionPanel (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/KineticLawTable.html b/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/KineticLawTable.html index 9cbd9d198..9bc4862bc 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/KineticLawTable.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/KineticLawTable.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.gui.KineticLawTable (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/KineticLawTableCellRenderer.html b/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/KineticLawTableCellRenderer.html index c1e2f84e4..99cc3df25 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/KineticLawTableCellRenderer.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/KineticLawTableCellRenderer.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.gui.KineticLawTableCellRenderer (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/KineticLawTableModel.html b/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/KineticLawTableModel.html index 7aaf71069..5b363d52a 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/KineticLawTableModel.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/KineticLawTableModel.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.gui.KineticLawTableModel (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/KineticLawWindowAdapter.html b/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/KineticLawWindowAdapter.html index ec5e83409..434d0dcca 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/KineticLawWindowAdapter.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/KineticLawWindowAdapter.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.gui.KineticLawWindowAdapter (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/LaTeXRenderer.html b/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/LaTeXRenderer.html index c87a9561c..60c38a236 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/LaTeXRenderer.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/LaTeXRenderer.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.gui.LaTeXRenderer (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/SBMLsqueezerUI.Command.html b/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/SBMLsqueezerUI.Command.html index c5d36c1fe..c86772eac 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/SBMLsqueezerUI.Command.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/SBMLsqueezerUI.Command.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.gui.SBMLsqueezerUI.Command (SBMLsqueezer 2.0 API Specification) - + @@ -154,7 +154,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/SBMLsqueezerUI.html b/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/SBMLsqueezerUI.html index e9f9ef605..db0f8fb98 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/SBMLsqueezerUI.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/class-use/SBMLsqueezerUI.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.gui.SBMLsqueezerUI (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/locales/package-frame.html b/doc/api/version_2.0/org/sbml/squeezer/gui/locales/package-frame.html index c46a3ae54..c0457acea 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/locales/package-frame.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/locales/package-frame.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.gui.locales (SBMLsqueezer 2.0 API Specification) - + diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/locales/package-summary.html b/doc/api/version_2.0/org/sbml/squeezer/gui/locales/package-summary.html index fcde91825..fbd9f55ba 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/locales/package-summary.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/locales/package-summary.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.gui.locales (SBMLsqueezer 2.0 API Specification) - + @@ -127,7 +127,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/locales/package-tree.html b/doc/api/version_2.0/org/sbml/squeezer/gui/locales/package-tree.html index 19fe09fde..0a6cdcbc2 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/locales/package-tree.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/locales/package-tree.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.gui.locales Class Hierarchy (SBMLsqueezer 2.0 API Specification) - + @@ -111,7 +111,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/locales/package-use.html b/doc/api/version_2.0/org/sbml/squeezer/gui/locales/package-use.html index d92ec8e70..d87911193 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/locales/package-use.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/locales/package-use.html @@ -2,12 +2,12 @@ - + Uses of Package org.sbml.squeezer.gui.locales (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/package-frame.html b/doc/api/version_2.0/org/sbml/squeezer/gui/package-frame.html index dd52bf4b6..baa9eb338 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/package-frame.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/package-frame.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.gui (SBMLsqueezer 2.0 API Specification) - + diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/package-summary.html b/doc/api/version_2.0/org/sbml/squeezer/gui/package-summary.html index 2c9ec106b..d1993444f 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/package-summary.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/package-summary.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.gui (SBMLsqueezer 2.0 API Specification) - + @@ -192,7 +192,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/package-tree.html b/doc/api/version_2.0/org/sbml/squeezer/gui/package-tree.html index 117c01455..75a95c4e6 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/package-tree.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/package-tree.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.gui Class Hierarchy (SBMLsqueezer 2.0 API Specification) - + @@ -180,7 +180,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/package-use.html b/doc/api/version_2.0/org/sbml/squeezer/gui/package-use.html index 1fb96eb28..e66408a17 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/package-use.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/package-use.html @@ -2,12 +2,12 @@ - + Uses of Package org.sbml.squeezer.gui (SBMLsqueezer 2.0 API Specification) - + @@ -135,7 +135,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/KineticLawSelectionEquationPanel.html b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/KineticLawSelectionEquationPanel.html index 058eebe5f..4c8851873 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/KineticLawSelectionEquationPanel.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/KineticLawSelectionEquationPanel.html @@ -2,12 +2,12 @@ - + KineticLawSelectionEquationPanel (SBMLsqueezer 2.0 API Specification) - + @@ -530,7 +530,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/KineticLawSelectionEquationPanelDescriptor.html b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/KineticLawSelectionEquationPanelDescriptor.html index ea29c4465..dcff5daa3 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/KineticLawSelectionEquationPanelDescriptor.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/KineticLawSelectionEquationPanelDescriptor.html @@ -2,12 +2,12 @@ - + KineticLawSelectionEquationPanelDescriptor (SBMLsqueezer 2.0 API Specification) - + @@ -435,7 +435,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/KineticLawSelectionEquationProgressPanelDescriptor.html b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/KineticLawSelectionEquationProgressPanelDescriptor.html index b660b154b..e9dc21f5b 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/KineticLawSelectionEquationProgressPanelDescriptor.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/KineticLawSelectionEquationProgressPanelDescriptor.html @@ -2,12 +2,12 @@ - + KineticLawSelectionEquationProgressPanelDescriptor (SBMLsqueezer 2.0 API Specification) - + @@ -374,7 +374,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/KineticLawSelectionOptionPanel.html b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/KineticLawSelectionOptionPanel.html index 937eb94e8..54e11e539 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/KineticLawSelectionOptionPanel.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/KineticLawSelectionOptionPanel.html @@ -2,12 +2,12 @@ - + KineticLawSelectionOptionPanel (SBMLsqueezer 2.0 API Specification) - + @@ -474,7 +474,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/KineticLawSelectionOptionPanelDescriptor.html b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/KineticLawSelectionOptionPanelDescriptor.html index 88f72b562..06aadab70 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/KineticLawSelectionOptionPanelDescriptor.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/KineticLawSelectionOptionPanelDescriptor.html @@ -2,12 +2,12 @@ - + KineticLawSelectionOptionPanelDescriptor (SBMLsqueezer 2.0 API Specification) - + @@ -387,7 +387,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/KineticLawSelectionWizard.html b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/KineticLawSelectionWizard.html index 63dd24b55..b7e954c68 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/KineticLawSelectionWizard.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/KineticLawSelectionWizard.html @@ -2,12 +2,12 @@ - + KineticLawSelectionWizard (SBMLsqueezer 2.0 API Specification) - + @@ -304,7 +304,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/class-use/KineticLawSelectionEquationPanel.html b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/class-use/KineticLawSelectionEquationPanel.html index ec67d257d..83a39deb4 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/class-use/KineticLawSelectionEquationPanel.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/class-use/KineticLawSelectionEquationPanel.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.gui.wizard.KineticLawSelectionEquationPanel (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/class-use/KineticLawSelectionEquationPanelDescriptor.html b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/class-use/KineticLawSelectionEquationPanelDescriptor.html index f3402dba3..763a14df2 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/class-use/KineticLawSelectionEquationPanelDescriptor.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/class-use/KineticLawSelectionEquationPanelDescriptor.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.gui.wizard.KineticLawSelectionEquationPanelDescriptor (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/class-use/KineticLawSelectionEquationProgressPanelDescriptor.html b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/class-use/KineticLawSelectionEquationProgressPanelDescriptor.html index f3a653b52..4eea08b7c 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/class-use/KineticLawSelectionEquationProgressPanelDescriptor.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/class-use/KineticLawSelectionEquationProgressPanelDescriptor.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.gui.wizard.KineticLawSelectionEquationProgressPanelDescriptor (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/class-use/KineticLawSelectionOptionPanel.html b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/class-use/KineticLawSelectionOptionPanel.html index 06d33ad7d..74e2577b4 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/class-use/KineticLawSelectionOptionPanel.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/class-use/KineticLawSelectionOptionPanel.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.gui.wizard.KineticLawSelectionOptionPanel (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/class-use/KineticLawSelectionOptionPanelDescriptor.html b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/class-use/KineticLawSelectionOptionPanelDescriptor.html index 4f3ed8625..b76033475 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/class-use/KineticLawSelectionOptionPanelDescriptor.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/class-use/KineticLawSelectionOptionPanelDescriptor.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.gui.wizard.KineticLawSelectionOptionPanelDescriptor (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/class-use/KineticLawSelectionWizard.html b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/class-use/KineticLawSelectionWizard.html index c2560a191..da8f70f4b 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/class-use/KineticLawSelectionWizard.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/class-use/KineticLawSelectionWizard.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.gui.wizard.KineticLawSelectionWizard (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/package-frame.html b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/package-frame.html index 65723c8a9..8750707c0 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/package-frame.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/package-frame.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.gui.wizard (SBMLsqueezer 2.0 API Specification) - + diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/package-summary.html b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/package-summary.html index 72269ad0f..3a2ec5456 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/package-summary.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/package-summary.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.gui.wizard (SBMLsqueezer 2.0 API Specification) - + @@ -165,7 +165,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/package-tree.html b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/package-tree.html index acfb29847..30c8566d5 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/package-tree.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/package-tree.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.gui.wizard Class Hierarchy (SBMLsqueezer 2.0 API Specification) - + @@ -140,7 +140,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/package-use.html b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/package-use.html index fa7289006..3b5b2a16e 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/package-use.html +++ b/doc/api/version_2.0/org/sbml/squeezer/gui/wizard/package-use.html @@ -2,12 +2,12 @@ - + Uses of Package org.sbml.squeezer.gui.wizard (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/io/IOOptions.html b/doc/api/version_2.0/org/sbml/squeezer/io/IOOptions.html index 44ce8c84d..6bb3ca1ad 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/io/IOOptions.html +++ b/doc/api/version_2.0/org/sbml/squeezer/io/IOOptions.html @@ -2,12 +2,12 @@ - + IOOptions (SBMLsqueezer 2.0 API Specification) - + @@ -262,7 +262,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/io/SBMLio.html b/doc/api/version_2.0/org/sbml/squeezer/io/SBMLio.html index b72aea4e8..ef0043d3b 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/io/SBMLio.html +++ b/doc/api/version_2.0/org/sbml/squeezer/io/SBMLio.html @@ -2,12 +2,12 @@ - + SBMLio (SBMLsqueezer 2.0 API Specification) - + @@ -121,7 +121,7 @@

Since:
1.3
Version:
-
$Rev: 1091 $
+
$Rev: 1102 $
Author:
Andreas Dräger
@@ -714,7 +714,7 @@

-Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/io/SqSBMLReader.html b/doc/api/version_2.0/org/sbml/squeezer/io/SqSBMLReader.html index e6b5df33a..fe24d5638 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/io/SqSBMLReader.html +++ b/doc/api/version_2.0/org/sbml/squeezer/io/SqSBMLReader.html @@ -2,12 +2,12 @@ - + SqSBMLReader (SBMLsqueezer 2.0 API Specification) - + @@ -405,7 +405,7 @@

-Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/io/SqSBMLWriter.html b/doc/api/version_2.0/org/sbml/squeezer/io/SqSBMLWriter.html index 1b760ddc1..5a61b6007 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/io/SqSBMLWriter.html +++ b/doc/api/version_2.0/org/sbml/squeezer/io/SqSBMLWriter.html @@ -2,12 +2,12 @@ - + SqSBMLWriter (SBMLsqueezer 2.0 API Specification) - + @@ -351,7 +351,7 @@

-Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/io/class-use/IOOptions.html b/doc/api/version_2.0/org/sbml/squeezer/io/class-use/IOOptions.html index bf0d4438e..080963461 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/io/class-use/IOOptions.html +++ b/doc/api/version_2.0/org/sbml/squeezer/io/class-use/IOOptions.html @@ -2,12 +2,12 @@ - + Uses of Interface org.sbml.squeezer.io.IOOptions (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/io/class-use/SBMLio.html b/doc/api/version_2.0/org/sbml/squeezer/io/class-use/SBMLio.html index f6e278637..edf202c41 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/io/class-use/SBMLio.html +++ b/doc/api/version_2.0/org/sbml/squeezer/io/class-use/SBMLio.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.io.SBMLio (SBMLsqueezer 2.0 API Specification) - + @@ -236,7 +236,7 @@

-Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/io/class-use/SqSBMLReader.html b/doc/api/version_2.0/org/sbml/squeezer/io/class-use/SqSBMLReader.html index 4be68db14..5d560a525 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/io/class-use/SqSBMLReader.html +++ b/doc/api/version_2.0/org/sbml/squeezer/io/class-use/SqSBMLReader.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.io.SqSBMLReader (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/io/class-use/SqSBMLWriter.html b/doc/api/version_2.0/org/sbml/squeezer/io/class-use/SqSBMLWriter.html index bf8bddfb7..46ee5a02b 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/io/class-use/SqSBMLWriter.html +++ b/doc/api/version_2.0/org/sbml/squeezer/io/class-use/SqSBMLWriter.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.io.SqSBMLWriter (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/io/package-frame.html b/doc/api/version_2.0/org/sbml/squeezer/io/package-frame.html index 668d34db3..2a8928208 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/io/package-frame.html +++ b/doc/api/version_2.0/org/sbml/squeezer/io/package-frame.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.io (SBMLsqueezer 2.0 API Specification) - + diff --git a/doc/api/version_2.0/org/sbml/squeezer/io/package-summary.html b/doc/api/version_2.0/org/sbml/squeezer/io/package-summary.html index 69a301fe1..785cc3948 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/io/package-summary.html +++ b/doc/api/version_2.0/org/sbml/squeezer/io/package-summary.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.io (SBMLsqueezer 2.0 API Specification) - + @@ -167,7 +167,7 @@

-Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/io/package-tree.html b/doc/api/version_2.0/org/sbml/squeezer/io/package-tree.html index 1098b6c1d..df3497d19 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/io/package-tree.html +++ b/doc/api/version_2.0/org/sbml/squeezer/io/package-tree.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.io Class Hierarchy (SBMLsqueezer 2.0 API Specification) - + @@ -128,7 +128,7 @@

-Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/io/package-use.html b/doc/api/version_2.0/org/sbml/squeezer/io/package-use.html index 6f832b817..954ee12dc 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/io/package-use.html +++ b/doc/api/version_2.0/org/sbml/squeezer/io/package-use.html @@ -2,12 +2,12 @@ - + Uses of Package org.sbml.squeezer.io (SBMLsqueezer 2.0 API Specification) - + @@ -183,7 +183,7 @@

-Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/AdditiveModelLinear.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/AdditiveModelLinear.html index bf0c95759..9c2c0c7d2 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/AdditiveModelLinear.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/AdditiveModelLinear.html @@ -2,12 +2,12 @@ - + AdditiveModelLinear (SBMLsqueezer 2.0 API Specification) - + @@ -376,7 +376,7 @@

-Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/AdditiveModelNonLinear.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/AdditiveModelNonLinear.html index ab0df177b..3aa2e3ef0 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/AdditiveModelNonLinear.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/AdditiveModelNonLinear.html @@ -2,12 +2,12 @@ - + AdditiveModelNonLinear (SBMLsqueezer 2.0 API Specification) - + @@ -377,7 +377,7 @@

-Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/BasicKineticLaw.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/BasicKineticLaw.html index 27aaef9dd..fe5c58d50 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/BasicKineticLaw.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/BasicKineticLaw.html @@ -2,12 +2,12 @@ - + BasicKineticLaw (SBMLsqueezer 2.0 API Specification) - + @@ -446,7 +446,7 @@

-Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/CommonModularRateLaw.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/CommonModularRateLaw.html index 796c691c1..a86f411c3 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/CommonModularRateLaw.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/CommonModularRateLaw.html @@ -2,12 +2,12 @@ - + CommonModularRateLaw (SBMLsqueezer 2.0 API Specification) - + @@ -376,7 +376,7 @@

-Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/ConvenienceKinetics.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/ConvenienceKinetics.html index 477ae3aea..f4f26aa7b 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/ConvenienceKinetics.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/ConvenienceKinetics.html @@ -2,12 +2,12 @@ - + ConvenienceKinetics (SBMLsqueezer 2.0 API Specification) - + @@ -384,7 +384,7 @@

-Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/DirectBindingModularRateLaw.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/DirectBindingModularRateLaw.html index 98f289309..1c21a7b06 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/DirectBindingModularRateLaw.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/DirectBindingModularRateLaw.html @@ -2,12 +2,12 @@ - + DirectBindingModularRateLaw (SBMLsqueezer 2.0 API Specification) - + @@ -375,7 +375,7 @@

-Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/ForceDependentModularRateLaw.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/ForceDependentModularRateLaw.html index ff148cf05..84026988c 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/ForceDependentModularRateLaw.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/ForceDependentModularRateLaw.html @@ -2,12 +2,12 @@ - + ForceDependentModularRateLaw (SBMLsqueezer 2.0 API Specification) - + @@ -374,7 +374,7 @@

-Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/GeneralizedMassAction.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/GeneralizedMassAction.html index 688d5fc5a..665492116 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/GeneralizedMassAction.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/GeneralizedMassAction.html @@ -2,12 +2,12 @@ - + GeneralizedMassAction (SBMLsqueezer 2.0 API Specification) - + @@ -378,7 +378,7 @@

-Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/HSystem.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/HSystem.html index 5a54ad966..cc89f9a64 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/HSystem.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/HSystem.html @@ -2,12 +2,12 @@ - + HSystem (SBMLsqueezer 2.0 API Specification) - + @@ -380,7 +380,7 @@

-Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/HillEquation.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/HillEquation.html index e48e75b57..54de07553 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/HillEquation.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/HillEquation.html @@ -2,12 +2,12 @@ - + HillEquation (SBMLsqueezer 2.0 API Specification) - + @@ -374,7 +374,7 @@

-Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/HillHinzeEquation.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/HillHinzeEquation.html index d8ef5d130..eb7ea58e7 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/HillHinzeEquation.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/HillHinzeEquation.html @@ -2,12 +2,12 @@ - + HillHinzeEquation (SBMLsqueezer 2.0 API Specification) - + @@ -376,7 +376,7 @@

-Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/HillRaddeEquation.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/HillRaddeEquation.html index e22de5aae..03f52afe8 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/HillRaddeEquation.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/HillRaddeEquation.html @@ -2,12 +2,12 @@ - + HillRaddeEquation (SBMLsqueezer 2.0 API Specification) - + @@ -376,7 +376,7 @@

-Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/InterfaceArbitraryEnzymeKinetics.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/InterfaceArbitraryEnzymeKinetics.html index 0524a7e8e..e4bfc0d92 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/InterfaceArbitraryEnzymeKinetics.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/InterfaceArbitraryEnzymeKinetics.html @@ -2,12 +2,12 @@ - + InterfaceArbitraryEnzymeKinetics (SBMLsqueezer 2.0 API Specification) - + @@ -148,7 +148,7 @@

-Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/InterfaceBiBiKinetics.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/InterfaceBiBiKinetics.html index 9744e6739..03af96503 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/InterfaceBiBiKinetics.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/InterfaceBiBiKinetics.html @@ -2,12 +2,12 @@ - + InterfaceBiBiKinetics (SBMLsqueezer 2.0 API Specification) - + @@ -149,7 +149,7 @@

-Generated at April 24 2014
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-Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/InterfaceGeneRegulatoryKinetics.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/InterfaceGeneRegulatoryKinetics.html index 4e6c2a9d5..bd59d1799 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/InterfaceGeneRegulatoryKinetics.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/InterfaceGeneRegulatoryKinetics.html @@ -2,12 +2,12 @@ - + InterfaceGeneRegulatoryKinetics (SBMLsqueezer 2.0 API Specification) - + @@ -146,7 +146,7 @@

-Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/InterfaceIntegerStoichiometry.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/InterfaceIntegerStoichiometry.html index 2fbf86ba8..98d070c47 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/InterfaceIntegerStoichiometry.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/InterfaceIntegerStoichiometry.html @@ -2,12 +2,12 @@ - + InterfaceIntegerStoichiometry (SBMLsqueezer 2.0 API Specification) - + @@ -147,7 +147,7 @@

-Generated at April 24 2014
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-Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/InterfaceKinteticsType.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/InterfaceKinteticsType.html index 0b36c3135..ad252b216 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/InterfaceKinteticsType.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/InterfaceKinteticsType.html @@ -2,12 +2,12 @@ - + InterfaceKinteticsType (SBMLsqueezer 2.0 API Specification) - + @@ -145,7 +145,7 @@

-Generated at April 24 2014
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-Generated at April 24 2014
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-Generated at April 24 2014
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-Generated at April 24 2014
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-Generated at April 24 2014
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-Generated at April 24 2014
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-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/IrrevCompetNonCooperativeEnzymes.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/IrrevCompetNonCooperativeEnzymes.html index 76d1a9543..d36463d2d 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/IrrevCompetNonCooperativeEnzymes.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/IrrevCompetNonCooperativeEnzymes.html @@ -2,12 +2,12 @@ - + IrrevCompetNonCooperativeEnzymes (SBMLsqueezer 2.0 API Specification) - + @@ -394,7 +394,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/IrrevNonModulatedNonInteractingEnzymes.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/IrrevNonModulatedNonInteractingEnzymes.html index 9db041c25..0aa6b5ed4 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/IrrevNonModulatedNonInteractingEnzymes.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/IrrevNonModulatedNonInteractingEnzymes.html @@ -2,12 +2,12 @@ - + IrrevNonModulatedNonInteractingEnzymes (SBMLsqueezer 2.0 API Specification) - + @@ -395,7 +395,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/MichaelisMenten.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/MichaelisMenten.html index cd426cbc4..520e4a7fb 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/MichaelisMenten.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/MichaelisMenten.html @@ -2,12 +2,12 @@ - + MichaelisMenten (SBMLsqueezer 2.0 API Specification) - + @@ -401,7 +401,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/NetGeneratorLinear.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/NetGeneratorLinear.html index fd3ebf1c5..39f2edc18 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/NetGeneratorLinear.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/NetGeneratorLinear.html @@ -2,12 +2,12 @@ - + NetGeneratorLinear (SBMLsqueezer 2.0 API Specification) - + @@ -377,7 +377,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/NetGeneratorNonLinear.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/NetGeneratorNonLinear.html index 4c4f7977c..14ef071f8 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/NetGeneratorNonLinear.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/NetGeneratorNonLinear.html @@ -2,12 +2,12 @@ - + NetGeneratorNonLinear (SBMLsqueezer 2.0 API Specification) - + @@ -378,7 +378,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/OptionsRateLaws.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/OptionsRateLaws.html index d8f9d0f21..1d63de670 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/OptionsRateLaws.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/OptionsRateLaws.html @@ -2,12 +2,12 @@ - + OptionsRateLaws (SBMLsqueezer 2.0 API Specification) - + @@ -638,7 +638,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/OrderedMechanism.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/OrderedMechanism.html index 6e24b95ca..e9993941f 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/OrderedMechanism.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/OrderedMechanism.html @@ -2,12 +2,12 @@ - + OrderedMechanism (SBMLsqueezer 2.0 API Specification) - + @@ -392,7 +392,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/PingPongMechanism.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/PingPongMechanism.html index 409a0b86a..a143aa26c 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/PingPongMechanism.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/PingPongMechanism.html @@ -2,12 +2,12 @@ - + PingPongMechanism (SBMLsqueezer 2.0 API Specification) - + @@ -393,7 +393,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/PowerLawModularRateLaw.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/PowerLawModularRateLaw.html index 745c04d8a..454a881f9 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/PowerLawModularRateLaw.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/PowerLawModularRateLaw.html @@ -2,12 +2,12 @@ - + PowerLawModularRateLaw (SBMLsqueezer 2.0 API Specification) - + @@ -379,7 +379,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/RandomOrderMechanism.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/RandomOrderMechanism.html index 233e9d750..31d86e2be 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/RandomOrderMechanism.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/RandomOrderMechanism.html @@ -2,12 +2,12 @@ - + RandomOrderMechanism (SBMLsqueezer 2.0 API Specification) - + @@ -394,7 +394,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/RestrictedSpaceKinetics.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/RestrictedSpaceKinetics.html index f5c5d98c3..95cb17a28 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/RestrictedSpaceKinetics.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/RestrictedSpaceKinetics.html @@ -2,12 +2,12 @@ - + RestrictedSpaceKinetics (SBMLsqueezer 2.0 API Specification) - + @@ -368,7 +368,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/SSystem.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/SSystem.html index d744bcae5..ea401fba5 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/SSystem.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/SSystem.html @@ -2,12 +2,12 @@ - + SSystem (SBMLsqueezer 2.0 API Specification) - + @@ -386,7 +386,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/SimultaneousBindingModularRateLaw.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/SimultaneousBindingModularRateLaw.html index d3a2d08e4..41aec0265 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/SimultaneousBindingModularRateLaw.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/SimultaneousBindingModularRateLaw.html @@ -2,12 +2,12 @@ - + SimultaneousBindingModularRateLaw (SBMLsqueezer 2.0 API Specification) - + @@ -375,7 +375,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/TypeStandardVersion.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/TypeStandardVersion.html index 089fc1f75..238c109f5 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/TypeStandardVersion.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/TypeStandardVersion.html @@ -2,12 +2,12 @@ - + TypeStandardVersion (SBMLsqueezer 2.0 API Specification) - + @@ -322,7 +322,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/Vohradsky.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/Vohradsky.html index b662447c5..f29a87ab4 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/Vohradsky.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/Vohradsky.html @@ -2,12 +2,12 @@ - + Vohradsky (SBMLsqueezer 2.0 API Specification) - + @@ -353,7 +353,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/Weaver.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/Weaver.html index 07aa05251..e92b49777 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/Weaver.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/Weaver.html @@ -2,12 +2,12 @@ - + Weaver (SBMLsqueezer 2.0 API Specification) - + @@ -377,7 +377,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/ZerothOrderForwardGMAK.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/ZerothOrderForwardGMAK.html index bf4f886ab..2fdf2cdec 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/ZerothOrderForwardGMAK.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/ZerothOrderForwardGMAK.html @@ -2,12 +2,12 @@ - + ZerothOrderForwardGMAK (SBMLsqueezer 2.0 API Specification) - + @@ -375,7 +375,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/ZerothOrderReverseGMAK.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/ZerothOrderReverseGMAK.html index 3103d7455..91f3fb546 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/ZerothOrderReverseGMAK.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/ZerothOrderReverseGMAK.html @@ -2,12 +2,12 @@ - + ZerothOrderReverseGMAK (SBMLsqueezer 2.0 API Specification) - + @@ -374,7 +374,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/AdditiveModelLinear.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/AdditiveModelLinear.html index 61360de63..df5d65fd1 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/AdditiveModelLinear.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/AdditiveModelLinear.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.kinetics.AdditiveModelLinear (SBMLsqueezer 2.0 API Specification) - + @@ -186,7 +186,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/AdditiveModelNonLinear.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/AdditiveModelNonLinear.html index a05daea8c..c126ef733 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/AdditiveModelNonLinear.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/AdditiveModelNonLinear.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.kinetics.AdditiveModelNonLinear (SBMLsqueezer 2.0 API Specification) - + @@ -167,7 +167,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/BasicKineticLaw.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/BasicKineticLaw.html index 85e137973..e420d3b9c 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/BasicKineticLaw.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/BasicKineticLaw.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.kinetics.BasicKineticLaw (SBMLsqueezer 2.0 API Specification) - + @@ -815,7 +815,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/CommonModularRateLaw.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/CommonModularRateLaw.html index 94841fdcd..3105035cf 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/CommonModularRateLaw.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/CommonModularRateLaw.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.kinetics.CommonModularRateLaw (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/ConvenienceKinetics.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/ConvenienceKinetics.html index 605cc5b1d..2781588fe 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/ConvenienceKinetics.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/ConvenienceKinetics.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.kinetics.ConvenienceKinetics (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/DirectBindingModularRateLaw.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/DirectBindingModularRateLaw.html index d3d41218a..fbd9e819d 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/DirectBindingModularRateLaw.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/DirectBindingModularRateLaw.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.kinetics.DirectBindingModularRateLaw (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/ForceDependentModularRateLaw.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/ForceDependentModularRateLaw.html index 195a49b7f..ef43230db 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/ForceDependentModularRateLaw.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/ForceDependentModularRateLaw.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.kinetics.ForceDependentModularRateLaw (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/GeneralizedMassAction.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/GeneralizedMassAction.html index 52aa6c118..92eb57aaf 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/GeneralizedMassAction.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/GeneralizedMassAction.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.kinetics.GeneralizedMassAction (SBMLsqueezer 2.0 API Specification) - + @@ -224,7 +224,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/HSystem.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/HSystem.html index 7c7a8e668..d2ec35de5 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/HSystem.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/HSystem.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.kinetics.HSystem (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/HillEquation.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/HillEquation.html index 425d5a771..9c9aa9f9d 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/HillEquation.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/HillEquation.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.kinetics.HillEquation (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/HillHinzeEquation.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/HillHinzeEquation.html index 8aa9e8c23..1c9f607e1 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/HillHinzeEquation.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/HillHinzeEquation.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.kinetics.HillHinzeEquation (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/HillRaddeEquation.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/HillRaddeEquation.html index 0371146c9..ec8a3dfbf 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/HillRaddeEquation.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/HillRaddeEquation.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.kinetics.HillRaddeEquation (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceArbitraryEnzymeKinetics.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceArbitraryEnzymeKinetics.html index 8bd68735e..2fc3a80d0 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceArbitraryEnzymeKinetics.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceArbitraryEnzymeKinetics.html @@ -2,12 +2,12 @@ - + Uses of Interface org.sbml.squeezer.kinetics.InterfaceArbitraryEnzymeKinetics (SBMLsqueezer 2.0 API Specification) - + @@ -199,7 +199,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceBiBiKinetics.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceBiBiKinetics.html index 186a7f51f..a022aa8f9 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceBiBiKinetics.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceBiBiKinetics.html @@ -2,12 +2,12 @@ - + Uses of Interface org.sbml.squeezer.kinetics.InterfaceBiBiKinetics (SBMLsqueezer 2.0 API Specification) - + @@ -225,7 +225,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceBiUniKinetics.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceBiUniKinetics.html index 5f60b1652..6bccfcb0a 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceBiUniKinetics.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceBiUniKinetics.html @@ -2,12 +2,12 @@ - + Uses of Interface org.sbml.squeezer.kinetics.InterfaceBiUniKinetics (SBMLsqueezer 2.0 API Specification) - + @@ -225,7 +225,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceGeneRegulatoryKinetics.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceGeneRegulatoryKinetics.html index 3b6118cd2..0de8fe664 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceGeneRegulatoryKinetics.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceGeneRegulatoryKinetics.html @@ -2,12 +2,12 @@ - + Uses of Interface org.sbml.squeezer.kinetics.InterfaceGeneRegulatoryKinetics (SBMLsqueezer 2.0 API Specification) - + @@ -256,7 +256,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceIntegerStoichiometry.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceIntegerStoichiometry.html index 649f5a240..e43cfcbe4 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceIntegerStoichiometry.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceIntegerStoichiometry.html @@ -2,12 +2,12 @@ - + Uses of Interface org.sbml.squeezer.kinetics.InterfaceIntegerStoichiometry (SBMLsqueezer 2.0 API Specification) - + @@ -154,7 +154,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceIrreversibleKinetics.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceIrreversibleKinetics.html index eb8c56083..b7dfedcf9 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceIrreversibleKinetics.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceIrreversibleKinetics.html @@ -2,12 +2,12 @@ - + Uses of Interface org.sbml.squeezer.kinetics.InterfaceIrreversibleKinetics (SBMLsqueezer 2.0 API Specification) - + @@ -360,7 +360,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceKinteticsType.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceKinteticsType.html index 9f1ee9f30..b761312cc 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceKinteticsType.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceKinteticsType.html @@ -2,12 +2,12 @@ - + Uses of Interface org.sbml.squeezer.kinetics.InterfaceKinteticsType (SBMLsqueezer 2.0 API Specification) - + @@ -523,7 +523,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceModulatedKinetics.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceModulatedKinetics.html index 4a1eed174..89bcfaa36 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceModulatedKinetics.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceModulatedKinetics.html @@ -2,12 +2,12 @@ - + Uses of Interface org.sbml.squeezer.kinetics.InterfaceModulatedKinetics (SBMLsqueezer 2.0 API Specification) - + @@ -397,7 +397,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceNonEnzymeKinetics.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceNonEnzymeKinetics.html index ccaee1f53..1971a965d 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceNonEnzymeKinetics.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceNonEnzymeKinetics.html @@ -2,12 +2,12 @@ - + Uses of Interface org.sbml.squeezer.kinetics.InterfaceNonEnzymeKinetics (SBMLsqueezer 2.0 API Specification) - + @@ -233,7 +233,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceReversibleKinetics.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceReversibleKinetics.html index 9247d93ba..8df8d16f3 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceReversibleKinetics.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceReversibleKinetics.html @@ -2,12 +2,12 @@ - + Uses of Interface org.sbml.squeezer.kinetics.InterfaceReversibleKinetics (SBMLsqueezer 2.0 API Specification) - + @@ -397,7 +397,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceUniUniKinetics.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceUniUniKinetics.html index 2dc1fdd30..0281e1de6 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceUniUniKinetics.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceUniUniKinetics.html @@ -2,12 +2,12 @@ - + Uses of Interface org.sbml.squeezer.kinetics.InterfaceUniUniKinetics (SBMLsqueezer 2.0 API Specification) - + @@ -235,7 +235,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceZeroProducts.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceZeroProducts.html index 3ab1d3313..38fe41d79 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceZeroProducts.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceZeroProducts.html @@ -2,12 +2,12 @@ - + Uses of Interface org.sbml.squeezer.kinetics.InterfaceZeroProducts (SBMLsqueezer 2.0 API Specification) - + @@ -264,7 +264,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceZeroReactants.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceZeroReactants.html index 478fc2623..8857aca99 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceZeroReactants.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/InterfaceZeroReactants.html @@ -2,12 +2,12 @@ - + Uses of Interface org.sbml.squeezer.kinetics.InterfaceZeroReactants (SBMLsqueezer 2.0 API Specification) - + @@ -264,7 +264,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/IrrevCompetNonCooperativeEnzymes.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/IrrevCompetNonCooperativeEnzymes.html index ac8379a4a..263720cc3 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/IrrevCompetNonCooperativeEnzymes.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/IrrevCompetNonCooperativeEnzymes.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.kinetics.IrrevCompetNonCooperativeEnzymes (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/IrrevNonModulatedNonInteractingEnzymes.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/IrrevNonModulatedNonInteractingEnzymes.html index 89f786f63..cf8021e7b 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/IrrevNonModulatedNonInteractingEnzymes.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/IrrevNonModulatedNonInteractingEnzymes.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.kinetics.IrrevNonModulatedNonInteractingEnzymes (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/MichaelisMenten.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/MichaelisMenten.html index 300581cd0..c4bd89792 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/MichaelisMenten.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/MichaelisMenten.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.kinetics.MichaelisMenten (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/NetGeneratorLinear.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/NetGeneratorLinear.html index 87ebbc06e..ef9a0bd74 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/NetGeneratorLinear.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/NetGeneratorLinear.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.kinetics.NetGeneratorLinear (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/NetGeneratorNonLinear.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/NetGeneratorNonLinear.html index 6a00dcbf1..aec74140b 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/NetGeneratorNonLinear.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/NetGeneratorNonLinear.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.kinetics.NetGeneratorNonLinear (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/OptionsRateLaws.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/OptionsRateLaws.html index 0742f303f..5ded76d35 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/OptionsRateLaws.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/OptionsRateLaws.html @@ -2,12 +2,12 @@ - + Uses of Interface org.sbml.squeezer.kinetics.OptionsRateLaws (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/OrderedMechanism.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/OrderedMechanism.html index 411c2432d..3ec969375 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/OrderedMechanism.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/OrderedMechanism.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.kinetics.OrderedMechanism (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/PingPongMechanism.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/PingPongMechanism.html index 1c4314752..04a5da629 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/PingPongMechanism.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/PingPongMechanism.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.kinetics.PingPongMechanism (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/PowerLawModularRateLaw.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/PowerLawModularRateLaw.html index a9edddcf3..b211fec0c 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/PowerLawModularRateLaw.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/PowerLawModularRateLaw.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.kinetics.PowerLawModularRateLaw (SBMLsqueezer 2.0 API Specification) - + @@ -173,7 +173,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/RandomOrderMechanism.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/RandomOrderMechanism.html index 1ff75dd00..a4f6bc7af 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/RandomOrderMechanism.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/RandomOrderMechanism.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.kinetics.RandomOrderMechanism (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/RestrictedSpaceKinetics.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/RestrictedSpaceKinetics.html index def86966f..2fab3abe4 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/RestrictedSpaceKinetics.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/RestrictedSpaceKinetics.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.kinetics.RestrictedSpaceKinetics (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/SSystem.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/SSystem.html index e8a8e73b1..3a5c2f330 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/SSystem.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/SSystem.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.kinetics.SSystem (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/SimultaneousBindingModularRateLaw.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/SimultaneousBindingModularRateLaw.html index 3ccab2e53..cf94b3fa2 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/SimultaneousBindingModularRateLaw.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/SimultaneousBindingModularRateLaw.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.kinetics.SimultaneousBindingModularRateLaw (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/TypeStandardVersion.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/TypeStandardVersion.html index 34131b1b2..faff83d5b 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/TypeStandardVersion.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/TypeStandardVersion.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.kinetics.TypeStandardVersion (SBMLsqueezer 2.0 API Specification) - + @@ -208,7 +208,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/Vohradsky.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/Vohradsky.html index da44becfa..5c72170da 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/Vohradsky.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/Vohradsky.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.kinetics.Vohradsky (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/Weaver.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/Weaver.html index aecc0aff5..6ee7fa5c4 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/Weaver.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/Weaver.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.kinetics.Weaver (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/ZerothOrderForwardGMAK.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/ZerothOrderForwardGMAK.html index c1a50700c..a978911b3 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/ZerothOrderForwardGMAK.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/ZerothOrderForwardGMAK.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.kinetics.ZerothOrderForwardGMAK (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/ZerothOrderReverseGMAK.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/ZerothOrderReverseGMAK.html index 6e72e4e9d..8c7ec1abb 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/ZerothOrderReverseGMAK.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/class-use/ZerothOrderReverseGMAK.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.kinetics.ZerothOrderReverseGMAK (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/package-frame.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/package-frame.html index 5c1b6f95a..581077524 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/package-frame.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/package-frame.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.kinetics (SBMLsqueezer 2.0 API Specification) - + diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/package-summary.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/package-summary.html index a5249f1dc..177700cbe 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/package-summary.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/package-summary.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.kinetics (SBMLsqueezer 2.0 API Specification) - + @@ -400,7 +400,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/package-tree.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/package-tree.html index 98e198614..3a406d77e 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/package-tree.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/package-tree.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.kinetics Class Hierarchy (SBMLsqueezer 2.0 API Specification) - + @@ -186,7 +186,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/kinetics/package-use.html b/doc/api/version_2.0/org/sbml/squeezer/kinetics/package-use.html index cc3862ceb..8ebba4ee3 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/kinetics/package-use.html +++ b/doc/api/version_2.0/org/sbml/squeezer/kinetics/package-use.html @@ -2,12 +2,12 @@ - + Uses of Package org.sbml.squeezer.kinetics (SBMLsqueezer 2.0 API Specification) - + @@ -311,7 +311,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/math/GaussianRank.html b/doc/api/version_2.0/org/sbml/squeezer/math/GaussianRank.html index 4424d948e..72b64f28d 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/math/GaussianRank.html +++ b/doc/api/version_2.0/org/sbml/squeezer/math/GaussianRank.html @@ -2,12 +2,12 @@ - + GaussianRank (SBMLsqueezer 2.0 API Specification) - + @@ -257,7 +257,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/math/class-use/GaussianRank.html b/doc/api/version_2.0/org/sbml/squeezer/math/class-use/GaussianRank.html index 076abc7c8..3291278b8 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/math/class-use/GaussianRank.html +++ b/doc/api/version_2.0/org/sbml/squeezer/math/class-use/GaussianRank.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.math.GaussianRank (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/math/package-frame.html b/doc/api/version_2.0/org/sbml/squeezer/math/package-frame.html index 153fd8868..54fe7cea9 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/math/package-frame.html +++ b/doc/api/version_2.0/org/sbml/squeezer/math/package-frame.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.math (SBMLsqueezer 2.0 API Specification) - + diff --git a/doc/api/version_2.0/org/sbml/squeezer/math/package-summary.html b/doc/api/version_2.0/org/sbml/squeezer/math/package-summary.html index c23047121..78ec08b2e 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/math/package-summary.html +++ b/doc/api/version_2.0/org/sbml/squeezer/math/package-summary.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.math (SBMLsqueezer 2.0 API Specification) - + @@ -142,7 +142,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/math/package-tree.html b/doc/api/version_2.0/org/sbml/squeezer/math/package-tree.html index 0d5df2c60..2a4d270eb 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/math/package-tree.html +++ b/doc/api/version_2.0/org/sbml/squeezer/math/package-tree.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.math Class Hierarchy (SBMLsqueezer 2.0 API Specification) - + @@ -118,7 +118,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/math/package-use.html b/doc/api/version_2.0/org/sbml/squeezer/math/package-use.html index b8dee33ff..78e248111 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/math/package-use.html +++ b/doc/api/version_2.0/org/sbml/squeezer/math/package-use.html @@ -2,12 +2,12 @@ - + Uses of Package org.sbml.squeezer.math (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/package-frame.html b/doc/api/version_2.0/org/sbml/squeezer/package-frame.html index 9f71fe1f0..bf337ffac 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/package-frame.html +++ b/doc/api/version_2.0/org/sbml/squeezer/package-frame.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer (SBMLsqueezer 2.0 API Specification) - + diff --git a/doc/api/version_2.0/org/sbml/squeezer/package-summary.html b/doc/api/version_2.0/org/sbml/squeezer/package-summary.html index 8ca05aa2d..8bdaed0c4 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/package-summary.html +++ b/doc/api/version_2.0/org/sbml/squeezer/package-summary.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer (SBMLsqueezer 2.0 API Specification) - + @@ -230,7 +230,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/package-tree.html b/doc/api/version_2.0/org/sbml/squeezer/package-tree.html index 96258b1c5..16d2588e7 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/package-tree.html +++ b/doc/api/version_2.0/org/sbml/squeezer/package-tree.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer Class Hierarchy (SBMLsqueezer 2.0 API Specification) - + @@ -145,7 +145,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/package-use.html b/doc/api/version_2.0/org/sbml/squeezer/package-use.html index 350f7428a..f9126ad48 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/package-use.html +++ b/doc/api/version_2.0/org/sbml/squeezer/package-use.html @@ -2,12 +2,12 @@ - + Uses of Package org.sbml.squeezer (SBMLsqueezer 2.0 API Specification) - + @@ -333,7 +333,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/resources/html/package-frame.html b/doc/api/version_2.0/org/sbml/squeezer/resources/html/package-frame.html index 7f8d684a8..7cba579f6 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/resources/html/package-frame.html +++ b/doc/api/version_2.0/org/sbml/squeezer/resources/html/package-frame.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.resources.html (SBMLsqueezer 2.0 API Specification) - + diff --git a/doc/api/version_2.0/org/sbml/squeezer/resources/html/package-summary.html b/doc/api/version_2.0/org/sbml/squeezer/resources/html/package-summary.html index 9f09227a0..77ff3b8a7 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/resources/html/package-summary.html +++ b/doc/api/version_2.0/org/sbml/squeezer/resources/html/package-summary.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.resources.html (SBMLsqueezer 2.0 API Specification) - + @@ -129,7 +129,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/resources/html/package-tree.html b/doc/api/version_2.0/org/sbml/squeezer/resources/html/package-tree.html index 84aab79da..5dfee60b9 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/resources/html/package-tree.html +++ b/doc/api/version_2.0/org/sbml/squeezer/resources/html/package-tree.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.resources.html Class Hierarchy (SBMLsqueezer 2.0 API Specification) - + @@ -111,7 +111,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/resources/html/package-use.html b/doc/api/version_2.0/org/sbml/squeezer/resources/html/package-use.html index 301ba2bd7..29764a7b1 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/resources/html/package-use.html +++ b/doc/api/version_2.0/org/sbml/squeezer/resources/html/package-use.html @@ -2,12 +2,12 @@ - + Uses of Package org.sbml.squeezer.resources.html (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/resources/img/package-frame.html b/doc/api/version_2.0/org/sbml/squeezer/resources/img/package-frame.html index a6286b850..943691ed6 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/resources/img/package-frame.html +++ b/doc/api/version_2.0/org/sbml/squeezer/resources/img/package-frame.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.resources.img (SBMLsqueezer 2.0 API Specification) - + diff --git a/doc/api/version_2.0/org/sbml/squeezer/resources/img/package-summary.html b/doc/api/version_2.0/org/sbml/squeezer/resources/img/package-summary.html index 82cde0e9e..04fd5d069 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/resources/img/package-summary.html +++ b/doc/api/version_2.0/org/sbml/squeezer/resources/img/package-summary.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.resources.img (SBMLsqueezer 2.0 API Specification) - + @@ -129,7 +129,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/resources/img/package-tree.html b/doc/api/version_2.0/org/sbml/squeezer/resources/img/package-tree.html index 0ea615899..ce70903fd 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/resources/img/package-tree.html +++ b/doc/api/version_2.0/org/sbml/squeezer/resources/img/package-tree.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.resources.img Class Hierarchy (SBMLsqueezer 2.0 API Specification) - + @@ -111,7 +111,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/resources/img/package-use.html b/doc/api/version_2.0/org/sbml/squeezer/resources/img/package-use.html index 74b107af5..f78a035a8 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/resources/img/package-use.html +++ b/doc/api/version_2.0/org/sbml/squeezer/resources/img/package-use.html @@ -2,12 +2,12 @@ - + Uses of Package org.sbml.squeezer.resources.img (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/resources/package-frame.html b/doc/api/version_2.0/org/sbml/squeezer/resources/package-frame.html index 03662154c..1f0f72c7f 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/resources/package-frame.html +++ b/doc/api/version_2.0/org/sbml/squeezer/resources/package-frame.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.resources (SBMLsqueezer 2.0 API Specification) - + diff --git a/doc/api/version_2.0/org/sbml/squeezer/resources/package-summary.html b/doc/api/version_2.0/org/sbml/squeezer/resources/package-summary.html index a8cdf8c11..ccb3f2767 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/resources/package-summary.html +++ b/doc/api/version_2.0/org/sbml/squeezer/resources/package-summary.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.resources (SBMLsqueezer 2.0 API Specification) - + @@ -131,7 +131,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/resources/package-tree.html b/doc/api/version_2.0/org/sbml/squeezer/resources/package-tree.html index de109de19..cc7d9f322 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/resources/package-tree.html +++ b/doc/api/version_2.0/org/sbml/squeezer/resources/package-tree.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.resources Class Hierarchy (SBMLsqueezer 2.0 API Specification) - + @@ -111,7 +111,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/resources/package-use.html b/doc/api/version_2.0/org/sbml/squeezer/resources/package-use.html index 5c4a262ba..c127cdf32 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/resources/package-use.html +++ b/doc/api/version_2.0/org/sbml/squeezer/resources/package-use.html @@ -2,12 +2,12 @@ - + Uses of Package org.sbml.squeezer.resources (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/AutomaticSearch.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/AutomaticSearch.html index 48f178805..e66855f2d 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/AutomaticSearch.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/AutomaticSearch.html @@ -2,12 +2,12 @@ - + AutomaticSearch (SBMLsqueezer 2.0 API Specification) - + @@ -275,7 +275,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/SABIORK.QueryField.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/SABIORK.QueryField.html index 5d1f212d5..593c09653 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/SABIORK.QueryField.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/SABIORK.QueryField.html @@ -2,12 +2,12 @@ - + SABIORK.QueryField (SBMLsqueezer 2.0 API Specification) - + @@ -866,7 +866,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/SABIORK.Resource.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/SABIORK.Resource.html index 77f0289b0..5a41d7132 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/SABIORK.Resource.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/SABIORK.Resource.html @@ -2,12 +2,12 @@ - + SABIORK.Resource (SBMLsqueezer 2.0 API Specification) - + @@ -546,7 +546,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/SABIORK.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/SABIORK.html index 481b1f02c..9b079b044 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/SABIORK.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/SABIORK.html @@ -2,12 +2,12 @@ - + SABIORK (SBMLsqueezer 2.0 API Specification) - + @@ -629,7 +629,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/SABIORKOptions.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/SABIORKOptions.html index 068de200d..cefa26eb4 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/SABIORKOptions.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/SABIORKOptions.html @@ -2,12 +2,12 @@ - + SABIORKOptions (SBMLsqueezer 2.0 API Specification) - + @@ -293,7 +293,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/SABIORKPreferences.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/SABIORKPreferences.html index 093bd01a8..e15d55bfb 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/SABIORKPreferences.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/SABIORKPreferences.html @@ -2,12 +2,12 @@ - + SABIORKPreferences (SBMLsqueezer 2.0 API Specification) - + @@ -555,7 +555,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/class-use/AutomaticSearch.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/class-use/AutomaticSearch.html index 7ffbc01a4..2b7712756 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/class-use/AutomaticSearch.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/class-use/AutomaticSearch.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.AutomaticSearch (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/class-use/SABIORK.QueryField.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/class-use/SABIORK.QueryField.html index de82c9853..87529214d 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/class-use/SABIORK.QueryField.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/class-use/SABIORK.QueryField.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.SABIORK.QueryField (SBMLsqueezer 2.0 API Specification) - + @@ -291,7 +291,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/class-use/SABIORK.Resource.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/class-use/SABIORK.Resource.html index 11a852a32..702b457b9 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/class-use/SABIORK.Resource.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/class-use/SABIORK.Resource.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.SABIORK.Resource (SBMLsqueezer 2.0 API Specification) - + @@ -155,7 +155,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/class-use/SABIORK.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/class-use/SABIORK.html index 1bb6aacf8..c04862b8d 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/class-use/SABIORK.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/class-use/SABIORK.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.SABIORK (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/class-use/SABIORKOptions.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/class-use/SABIORKOptions.html index 6beb19dda..2bdddf067 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/class-use/SABIORKOptions.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/class-use/SABIORKOptions.html @@ -2,12 +2,12 @@ - + Uses of Interface org.sbml.squeezer.sabiork.SABIORKOptions (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/class-use/SABIORKPreferences.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/class-use/SABIORKPreferences.html index 96067bc29..60c16074b 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/class-use/SABIORKPreferences.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/class-use/SABIORKPreferences.html @@ -2,12 +2,12 @@ - + Uses of Interface org.sbml.squeezer.sabiork.SABIORKPreferences (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/package-frame.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/package-frame.html index 54e365b35..36e82beef 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/package-frame.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/package-frame.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.sabiork (SBMLsqueezer 2.0 API Specification) - + diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/package-summary.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/package-summary.html index c5d18fd53..9941c5152 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/package-summary.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/package-summary.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.sabiork (SBMLsqueezer 2.0 API Specification) - + @@ -187,7 +187,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/package-tree.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/package-tree.html index 6c0f0c28c..1b93705a0 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/package-tree.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/package-tree.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.sabiork Class Hierarchy (SBMLsqueezer 2.0 API Specification) - + @@ -135,7 +135,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/package-use.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/package-use.html index 8592a1db4..bd8484f86 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/package-use.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/package-use.html @@ -2,12 +2,12 @@ - + Uses of Package org.sbml.squeezer.sabiork (SBMLsqueezer 2.0 API Specification) - + @@ -162,7 +162,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/WebServiceConnectException.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/WebServiceConnectException.html index e1a681368..eff25d757 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/WebServiceConnectException.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/WebServiceConnectException.html @@ -2,12 +2,12 @@ - + WebServiceConnectException (SBMLsqueezer 2.0 API Specification) - + @@ -259,7 +259,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/WebServiceResponseException.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/WebServiceResponseException.html index a04e528e0..740c33e98 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/WebServiceResponseException.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/WebServiceResponseException.html @@ -2,12 +2,12 @@ - + WebServiceResponseException (SBMLsqueezer 2.0 API Specification) - + @@ -296,7 +296,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/XMLParser.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/XMLParser.html index 5194f5a3a..240812ec6 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/XMLParser.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/XMLParser.html @@ -2,12 +2,12 @@ - + XMLParser (SBMLsqueezer 2.0 API Specification) - + @@ -266,7 +266,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/class-use/WebServiceConnectException.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/class-use/WebServiceConnectException.html index 7b2098de1..8e80df58d 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/class-use/WebServiceConnectException.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/class-use/WebServiceConnectException.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.util.WebServiceConnectException (SBMLsqueezer 2.0 API Specification) - + @@ -231,7 +231,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/class-use/WebServiceResponseException.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/class-use/WebServiceResponseException.html index 26fbdb035..9f33e7eee 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/class-use/WebServiceResponseException.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/class-use/WebServiceResponseException.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.util.WebServiceResponseException (SBMLsqueezer 2.0 API Specification) - + @@ -231,7 +231,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/class-use/XMLParser.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/class-use/XMLParser.html index a87010633..4543efe58 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/class-use/XMLParser.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/class-use/XMLParser.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.util.XMLParser (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/package-frame.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/package-frame.html index 28c941914..9b71191ad 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/package-frame.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/package-frame.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.sabiork.util (SBMLsqueezer 2.0 API Specification) - + diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/package-summary.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/package-summary.html index 777ad1009..009daeb11 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/package-summary.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/package-summary.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.sabiork.util (SBMLsqueezer 2.0 API Specification) - + @@ -163,7 +163,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/package-tree.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/package-tree.html index ec882509f..2e241f59f 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/package-tree.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/package-tree.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.sabiork.util Class Hierarchy (SBMLsqueezer 2.0 API Specification) - + @@ -123,7 +123,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/package-use.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/package-use.html index ff617cb9a..a16971e49 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/package-use.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/util/package-use.html @@ -2,12 +2,12 @@ - + Uses of Package org.sbml.squeezer.sabiork.util (SBMLsqueezer 2.0 API Specification) - + @@ -168,7 +168,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/SABIORKWizard.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/SABIORKWizard.html index b27a05548..77997f1a4 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/SABIORKWizard.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/SABIORKWizard.html @@ -2,12 +2,12 @@ - + SABIORKWizard (SBMLsqueezer 2.0 API Specification) - + @@ -320,7 +320,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/class-use/SABIORKWizard.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/class-use/SABIORKWizard.html index 33c8154b6..335346689 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/class-use/SABIORKWizard.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/class-use/SABIORKWizard.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.SABIORKWizard (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/ConsoleWizard.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/ConsoleWizard.html index 44c8a9cfc..12be2b132 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/ConsoleWizard.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/ConsoleWizard.html @@ -2,12 +2,12 @@ - + ConsoleWizard (SBMLsqueezer 2.0 API Specification) - + @@ -262,7 +262,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/SearchAResult.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/SearchAResult.html index 3357733d4..97bff4e6b 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/SearchAResult.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/SearchAResult.html @@ -2,12 +2,12 @@ - + SearchAResult (SBMLsqueezer 2.0 API Specification) - + @@ -326,7 +326,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/class-use/ConsoleWizard.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/class-use/ConsoleWizard.html index 71f955e1a..673c8362b 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/class-use/ConsoleWizard.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/class-use/ConsoleWizard.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.console.ConsoleWizard (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/class-use/SearchAResult.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/class-use/SearchAResult.html index bf43b1887..c38c9321a 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/class-use/SearchAResult.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/class-use/SearchAResult.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.console.SearchAResult (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/package-frame.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/package-frame.html index 0ff5916d6..33af91363 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/package-frame.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/package-frame.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.sabiork.wizard.console (SBMLsqueezer 2.0 API Specification) - + diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/package-summary.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/package-summary.html index f836eee8f..08fbd680e 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/package-summary.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/package-summary.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.sabiork.wizard.console (SBMLsqueezer 2.0 API Specification) - + @@ -147,7 +147,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/package-tree.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/package-tree.html index a14d85bc5..dae2148e1 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/package-tree.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/package-tree.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.sabiork.wizard.console Class Hierarchy (SBMLsqueezer 2.0 API Specification) - + @@ -118,7 +118,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/package-use.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/package-use.html index 7e6cc9d9d..2a37bad2f 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/package-use.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/console/package-use.html @@ -2,12 +2,12 @@ - + Uses of Package org.sbml.squeezer.sabiork.wizard.console (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/Card.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/Card.html index 67711ae11..cd465156e 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/Card.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/Card.html @@ -2,12 +2,12 @@ - + Card (SBMLsqueezer 2.0 API Specification) - + @@ -448,7 +448,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardMatching.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardMatching.html index 9ff4e2956..5147e82ff 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardMatching.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardMatching.html @@ -2,12 +2,12 @@ - + CardMatching (SBMLsqueezer 2.0 API Specification) - + @@ -429,7 +429,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardMethod.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardMethod.html index 22d194d9b..9c93c0632 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardMethod.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardMethod.html @@ -2,12 +2,12 @@ - + CardMethod (SBMLsqueezer 2.0 API Specification) - + @@ -404,7 +404,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardReactionsA.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardReactionsA.html index 5b0beca20..282fca9cd 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardReactionsA.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardReactionsA.html @@ -2,12 +2,12 @@ - + CardReactionsA (SBMLsqueezer 2.0 API Specification) - + @@ -470,7 +470,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardReactionsM.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardReactionsM.html index 36626b1e0..bf539be78 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardReactionsM.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardReactionsM.html @@ -2,12 +2,12 @@ - + CardReactionsM (SBMLsqueezer 2.0 API Specification) - + @@ -490,7 +490,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSearchA.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSearchA.html index ef47d0537..e79eb5c6e 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSearchA.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSearchA.html @@ -2,12 +2,12 @@ - + CardSearchA (SBMLsqueezer 2.0 API Specification) - + @@ -538,7 +538,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSearchM.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSearchM.html index 29e7d62c0..8c8184669 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSearchM.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSearchM.html @@ -2,12 +2,12 @@ - + CardSearchM (SBMLsqueezer 2.0 API Specification) - + @@ -538,7 +538,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSearchResultsA.SearchState.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSearchResultsA.SearchState.html index cb97672ca..2e3d38d4e 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSearchResultsA.SearchState.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSearchResultsA.SearchState.html @@ -2,12 +2,12 @@ - + CardSearchResultsA.SearchState (SBMLsqueezer 2.0 API Specification) - + @@ -284,7 +284,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSearchResultsA.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSearchResultsA.html index 4c1be125e..415fb4d2d 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSearchResultsA.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSearchResultsA.html @@ -2,12 +2,12 @@ - + CardSearchResultsA (SBMLsqueezer 2.0 API Specification) - + @@ -504,7 +504,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSearchResultsM.SearchState.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSearchResultsM.SearchState.html index a6ef11fa6..bfd06d28d 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSearchResultsM.SearchState.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSearchResultsM.SearchState.html @@ -2,12 +2,12 @@ - + CardSearchResultsM.SearchState (SBMLsqueezer 2.0 API Specification) - + @@ -316,7 +316,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSearchResultsM.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSearchResultsM.html index 37a44dbfc..1c408377d 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSearchResultsM.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSearchResultsM.html @@ -2,12 +2,12 @@ - + CardSearchResultsM (SBMLsqueezer 2.0 API Specification) - + @@ -564,7 +564,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSummaryA.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSummaryA.html index 92621ce8c..8d8ad9b06 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSummaryA.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSummaryA.html @@ -2,12 +2,12 @@ - + CardSummaryA (SBMLsqueezer 2.0 API Specification) - + @@ -404,7 +404,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSummaryM.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSummaryM.html index d45aefc3d..9c50cd499 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSummaryM.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/CardSummaryM.html @@ -2,12 +2,12 @@ - + CardSummaryM (SBMLsqueezer 2.0 API Specification) - + @@ -404,7 +404,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/ComboBoxModelCaptions.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/ComboBoxModelCaptions.html index 35f13e58a..eb68c587a 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/ComboBoxModelCaptions.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/ComboBoxModelCaptions.html @@ -2,12 +2,12 @@ - + ComboBoxModelCaptions (SBMLsqueezer 2.0 API Specification) - + @@ -394,7 +394,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/ComboBoxModelConstraints.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/ComboBoxModelConstraints.html index 99260de44..53587cb78 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/ComboBoxModelConstraints.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/ComboBoxModelConstraints.html @@ -2,12 +2,12 @@ - + ComboBoxModelConstraints (SBMLsqueezer 2.0 API Specification) - + @@ -287,7 +287,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/ComboBoxModelReactionFilters.ReactionFilter.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/ComboBoxModelReactionFilters.ReactionFilter.html index 1dd9ae38f..51b4fc1e6 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/ComboBoxModelReactionFilters.ReactionFilter.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/ComboBoxModelReactionFilters.ReactionFilter.html @@ -2,12 +2,12 @@ - + ComboBoxModelReactionFilters.ReactionFilter (SBMLsqueezer 2.0 API Specification) - + @@ -392,7 +392,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/ComboBoxModelReactionFilters.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/ComboBoxModelReactionFilters.html index e9cf5631c..0d16a4cd0 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/ComboBoxModelReactionFilters.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/ComboBoxModelReactionFilters.html @@ -2,12 +2,12 @@ - + ComboBoxModelReactionFilters (SBMLsqueezer 2.0 API Specification) - + @@ -284,7 +284,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/ComboBoxModelSearchItems.SearchItem.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/ComboBoxModelSearchItems.SearchItem.html index 8d0fb61d0..fc00598db 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/ComboBoxModelSearchItems.SearchItem.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/ComboBoxModelSearchItems.SearchItem.html @@ -2,12 +2,12 @@ - + ComboBoxModelSearchItems.SearchItem (SBMLsqueezer 2.0 API Specification) - + @@ -290,7 +290,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/ComboBoxModelSearchItems.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/ComboBoxModelSearchItems.html index b033644b1..f3eb5f598 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/ComboBoxModelSearchItems.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/ComboBoxModelSearchItems.html @@ -2,12 +2,12 @@ - + ComboBoxModelSearchItems (SBMLsqueezer 2.0 API Specification) - + @@ -334,7 +334,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JComboBoxInterval.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JComboBoxInterval.html index 6cef03d76..6978d9d41 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JComboBoxInterval.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JComboBoxInterval.html @@ -2,12 +2,12 @@ - + JComboBoxInterval (SBMLsqueezer 2.0 API Specification) - + @@ -417,7 +417,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JComboBoxSearchField.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JComboBoxSearchField.html index 2fbaa87ca..36b284d32 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JComboBoxSearchField.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JComboBoxSearchField.html @@ -2,12 +2,12 @@ - + JComboBoxSearchField (SBMLsqueezer 2.0 API Specification) - + @@ -487,7 +487,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JComponentEtchedLine.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JComponentEtchedLine.html index 12d9c0ec5..dcd82eac6 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JComponentEtchedLine.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JComponentEtchedLine.html @@ -2,12 +2,12 @@ - + JComponentEtchedLine (SBMLsqueezer 2.0 API Specification) - + @@ -293,7 +293,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JDialogWizard.Actions.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JDialogWizard.Actions.html index ec6d12dc4..0fb021708 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JDialogWizard.Actions.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JDialogWizard.Actions.html @@ -2,12 +2,12 @@ - + JDialogWizard.Actions (SBMLsqueezer 2.0 API Specification) - + @@ -306,7 +306,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JDialogWizard.ButtonState.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JDialogWizard.ButtonState.html index 89cf139cb..8031d4289 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JDialogWizard.ButtonState.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JDialogWizard.ButtonState.html @@ -2,12 +2,12 @@ - + JDialogWizard.ButtonState (SBMLsqueezer 2.0 API Specification) - + @@ -338,7 +338,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JDialogWizard.CardID.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JDialogWizard.CardID.html index fab0632ff..e43ba210e 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JDialogWizard.CardID.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JDialogWizard.CardID.html @@ -2,12 +2,12 @@ - + JDialogWizard.CardID (SBMLsqueezer 2.0 API Specification) - + @@ -450,7 +450,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JDialogWizard.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JDialogWizard.html index e04a0a9ca..db064a55f 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JDialogWizard.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JDialogWizard.html @@ -2,12 +2,12 @@ - + JDialogWizard (SBMLsqueezer 2.0 API Specification) - + @@ -770,7 +770,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JPanelFilterOptions.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JPanelFilterOptions.html index b2a8e49ef..3ad954079 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JPanelFilterOptions.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/JPanelFilterOptions.html @@ -2,12 +2,12 @@ - + JPanelFilterOptions (SBMLsqueezer 2.0 API Specification) - + @@ -389,7 +389,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableCellRendererBooleans.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableCellRendererBooleans.html index 45bdd949b..803a165fc 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableCellRendererBooleans.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableCellRendererBooleans.html @@ -2,12 +2,12 @@ - + TableCellRendererBooleans (SBMLsqueezer 2.0 API Specification) - + @@ -239,7 +239,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableCellRendererColorGradient.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableCellRendererColorGradient.html index 4448d1238..de25216fb 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableCellRendererColorGradient.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableCellRendererColorGradient.html @@ -2,12 +2,12 @@ - + TableCellRendererColorGradient (SBMLsqueezer 2.0 API Specification) - + @@ -210,7 +210,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableCellRendererReactions.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableCellRendererReactions.html index e1bb5fff2..69bc3d68b 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableCellRendererReactions.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableCellRendererReactions.html @@ -2,12 +2,12 @@ - + TableCellRendererReactions (SBMLsqueezer 2.0 API Specification) - + @@ -239,7 +239,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableCellRendererSearchAResults.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableCellRendererSearchAResults.html index 3c03ff36b..6d50ad99b 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableCellRendererSearchAResults.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableCellRendererSearchAResults.html @@ -2,12 +2,12 @@ - + TableCellRendererSearchAResults (SBMLsqueezer 2.0 API Specification) - + @@ -240,7 +240,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableCellRendererTemperature.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableCellRendererTemperature.html index e64cf5153..44bbdff81 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableCellRendererTemperature.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableCellRendererTemperature.html @@ -2,12 +2,12 @@ - + TableCellRendererTemperature (SBMLsqueezer 2.0 API Specification) - + @@ -237,7 +237,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableCellRendererpHValues.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableCellRendererpHValues.html index 985b38d85..b7ea674b8 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableCellRendererpHValues.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableCellRendererpHValues.html @@ -2,12 +2,12 @@ - + TableCellRendererpHValues (SBMLsqueezer 2.0 API Specification) - + @@ -237,7 +237,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableModelReactions.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableModelReactions.html index 479fe7d42..4205fc344 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableModelReactions.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableModelReactions.html @@ -2,12 +2,12 @@ - + TableModelReactions (SBMLsqueezer 2.0 API Specification) - + @@ -383,7 +383,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableModelSearchAResults.SearchAResult.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableModelSearchAResults.SearchAResult.html index cdd66581c..6967f6156 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableModelSearchAResults.SearchAResult.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableModelSearchAResults.SearchAResult.html @@ -2,12 +2,12 @@ - + TableModelSearchAResults.SearchAResult (SBMLsqueezer 2.0 API Specification) - + @@ -309,7 +309,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableModelSearchAResults.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableModelSearchAResults.html index 9f182b64a..2c4157ffb 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableModelSearchAResults.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableModelSearchAResults.html @@ -2,12 +2,12 @@ - + TableModelSearchAResults (SBMLsqueezer 2.0 API Specification) - + @@ -464,7 +464,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableModelSearchMResults.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableModelSearchMResults.html index 9edd02e1a..948c7812b 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableModelSearchMResults.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableModelSearchMResults.html @@ -2,12 +2,12 @@ - + TableModelSearchMResults (SBMLsqueezer 2.0 API Specification) - + @@ -421,7 +421,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableModelSearchTerms.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableModelSearchTerms.html index 470536ebe..c0752aa02 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableModelSearchTerms.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/TableModelSearchTerms.html @@ -2,12 +2,12 @@ - + TableModelSearchTerms (SBMLsqueezer 2.0 API Specification) - + @@ -530,7 +530,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/Card.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/Card.html index 7cd861f6c..4e332018c 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/Card.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/Card.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.Card (SBMLsqueezer 2.0 API Specification) - + @@ -222,7 +222,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardMatching.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardMatching.html index 10dfa1a20..f00cc6874 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardMatching.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardMatching.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.CardMatching (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardMethod.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardMethod.html index d0043f980..c95e23994 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardMethod.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardMethod.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.CardMethod (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardReactionsA.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardReactionsA.html index a0e16bf09..f48880722 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardReactionsA.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardReactionsA.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.CardReactionsA (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardReactionsM.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardReactionsM.html index a62debd69..ee33b2a29 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardReactionsM.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardReactionsM.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.CardReactionsM (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSearchA.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSearchA.html index 83cb1136b..c0ebc66b4 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSearchA.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSearchA.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.CardSearchA (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSearchM.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSearchM.html index 84c8ee53e..6fb904350 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSearchM.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSearchM.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.CardSearchM (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSearchResultsA.SearchState.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSearchResultsA.SearchState.html index 18e9d483b..2401d9f81 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSearchResultsA.SearchState.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSearchResultsA.SearchState.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.CardSearchResultsA.SearchState (SBMLsqueezer 2.0 API Specification) - + @@ -155,7 +155,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSearchResultsA.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSearchResultsA.html index e046d3881..d8ef9a2a4 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSearchResultsA.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSearchResultsA.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.CardSearchResultsA (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSearchResultsM.SearchState.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSearchResultsM.SearchState.html index 40d44d21b..c01a2521d 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSearchResultsM.SearchState.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSearchResultsM.SearchState.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.CardSearchResultsM.SearchState (SBMLsqueezer 2.0 API Specification) - + @@ -155,7 +155,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSearchResultsM.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSearchResultsM.html index 12335a553..f6e0a6a62 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSearchResultsM.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSearchResultsM.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.CardSearchResultsM (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSummaryA.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSummaryA.html index 1f5e1b3bc..69139fd18 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSummaryA.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSummaryA.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.CardSummaryA (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSummaryM.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSummaryM.html index 99ea77ce8..d1a36d94d 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSummaryM.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/CardSummaryM.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.CardSummaryM (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/ComboBoxModelCaptions.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/ComboBoxModelCaptions.html index d5f76e61e..63c5a71c9 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/ComboBoxModelCaptions.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/ComboBoxModelCaptions.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.ComboBoxModelCaptions (SBMLsqueezer 2.0 API Specification) - + @@ -165,7 +165,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/ComboBoxModelConstraints.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/ComboBoxModelConstraints.html index 662acc234..26e625acf 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/ComboBoxModelConstraints.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/ComboBoxModelConstraints.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.ComboBoxModelConstraints (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/ComboBoxModelReactionFilters.ReactionFilter.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/ComboBoxModelReactionFilters.ReactionFilter.html index 1946a55ae..deacb0cdb 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/ComboBoxModelReactionFilters.ReactionFilter.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/ComboBoxModelReactionFilters.ReactionFilter.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.ComboBoxModelReactionFilters.ReactionFilter (SBMLsqueezer 2.0 API Specification) - + @@ -179,7 +179,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/ComboBoxModelReactionFilters.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/ComboBoxModelReactionFilters.html index efee08d13..bff078078 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/ComboBoxModelReactionFilters.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/ComboBoxModelReactionFilters.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.ComboBoxModelReactionFilters (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/ComboBoxModelSearchItems.SearchItem.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/ComboBoxModelSearchItems.SearchItem.html index 93e9542a8..fdb47fb3f 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/ComboBoxModelSearchItems.SearchItem.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/ComboBoxModelSearchItems.SearchItem.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.ComboBoxModelSearchItems.SearchItem (SBMLsqueezer 2.0 API Specification) - + @@ -155,7 +155,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/ComboBoxModelSearchItems.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/ComboBoxModelSearchItems.html index af3e177d9..2c0e7c2ab 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/ComboBoxModelSearchItems.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/ComboBoxModelSearchItems.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.ComboBoxModelSearchItems (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JComboBoxInterval.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JComboBoxInterval.html index 22942761e..2496fa88c 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JComboBoxInterval.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JComboBoxInterval.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.JComboBoxInterval (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JComboBoxSearchField.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JComboBoxSearchField.html index 180e73080..f40bb4d96 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JComboBoxSearchField.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JComboBoxSearchField.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.JComboBoxSearchField (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JComponentEtchedLine.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JComponentEtchedLine.html index aa13ba0e3..ee0f14d33 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JComponentEtchedLine.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JComponentEtchedLine.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.JComponentEtchedLine (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JDialogWizard.Actions.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JDialogWizard.Actions.html index 8cb1a308a..76f69ea90 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JDialogWizard.Actions.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JDialogWizard.Actions.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.JDialogWizard.Actions (SBMLsqueezer 2.0 API Specification) - + @@ -155,7 +155,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JDialogWizard.ButtonState.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JDialogWizard.ButtonState.html index 9dc68ecb9..b87fa392c 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JDialogWizard.ButtonState.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JDialogWizard.ButtonState.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.JDialogWizard.ButtonState (SBMLsqueezer 2.0 API Specification) - + @@ -172,7 +172,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JDialogWizard.CardID.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JDialogWizard.CardID.html index 3c0947163..b1a5ed593 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JDialogWizard.CardID.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JDialogWizard.CardID.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.JDialogWizard.CardID (SBMLsqueezer 2.0 API Specification) - + @@ -331,7 +331,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JDialogWizard.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JDialogWizard.html index bf5519458..531eeead4 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JDialogWizard.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JDialogWizard.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.JDialogWizard (SBMLsqueezer 2.0 API Specification) - + @@ -215,7 +215,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JPanelFilterOptions.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JPanelFilterOptions.html index d0bf1d2f8..1b3650549 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JPanelFilterOptions.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/JPanelFilterOptions.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.JPanelFilterOptions (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableCellRendererBooleans.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableCellRendererBooleans.html index 2c98a6fd9..1435697b4 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableCellRendererBooleans.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableCellRendererBooleans.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.TableCellRendererBooleans (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableCellRendererColorGradient.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableCellRendererColorGradient.html index 3c8651907..a36259f6e 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableCellRendererColorGradient.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableCellRendererColorGradient.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.TableCellRendererColorGradient (SBMLsqueezer 2.0 API Specification) - + @@ -154,7 +154,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableCellRendererReactions.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableCellRendererReactions.html index 10c9526c3..2e79bca02 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableCellRendererReactions.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableCellRendererReactions.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.TableCellRendererReactions (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableCellRendererSearchAResults.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableCellRendererSearchAResults.html index 9cf4eee5d..49c79b7ff 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableCellRendererSearchAResults.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableCellRendererSearchAResults.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.TableCellRendererSearchAResults (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableCellRendererTemperature.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableCellRendererTemperature.html index 6636f05df..ab42900c9 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableCellRendererTemperature.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableCellRendererTemperature.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.TableCellRendererTemperature (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableCellRendererpHValues.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableCellRendererpHValues.html index 8ad0dfbb8..15a2514cb 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableCellRendererpHValues.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableCellRendererpHValues.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.TableCellRendererpHValues (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableModelReactions.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableModelReactions.html index da8318bab..626f9c772 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableModelReactions.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableModelReactions.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.TableModelReactions (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableModelSearchAResults.SearchAResult.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableModelSearchAResults.SearchAResult.html index 722d1e891..6724dd346 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableModelSearchAResults.SearchAResult.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableModelSearchAResults.SearchAResult.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.TableModelSearchAResults.SearchAResult (SBMLsqueezer 2.0 API Specification) - + @@ -197,7 +197,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableModelSearchAResults.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableModelSearchAResults.html index d0baa031f..9ab18e703 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableModelSearchAResults.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableModelSearchAResults.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.TableModelSearchAResults (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableModelSearchMResults.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableModelSearchMResults.html index d0b338ae1..054e140cf 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableModelSearchMResults.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableModelSearchMResults.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.TableModelSearchMResults (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableModelSearchTerms.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableModelSearchTerms.html index 1543d04db..8592e9845 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableModelSearchTerms.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/class-use/TableModelSearchTerms.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.gui.TableModelSearchTerms (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/package-frame.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/package-frame.html index 27c7442c0..2c73c0f4e 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/package-frame.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/package-frame.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.sabiork.wizard.gui (SBMLsqueezer 2.0 API Specification) - + diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/package-summary.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/package-summary.html index 91c445dc7..b66d9689f 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/package-summary.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/package-summary.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.sabiork.wizard.gui (SBMLsqueezer 2.0 API Specification) - + @@ -311,7 +311,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/package-tree.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/package-tree.html index 32182f3ae..51c445ff2 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/package-tree.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/package-tree.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.sabiork.wizard.gui Class Hierarchy (SBMLsqueezer 2.0 API Specification) - + @@ -183,7 +183,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/package-use.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/package-use.html index 345bdfff6..0a91386e2 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/package-use.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/gui/package-use.html @@ -2,12 +2,12 @@ - + Uses of Package org.sbml.squeezer.sabiork.wizard.gui (SBMLsqueezer 2.0 API Specification) - + @@ -203,7 +203,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/KineticLawImporter.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/KineticLawImporter.html index f55a97d3d..45657195d 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/KineticLawImporter.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/KineticLawImporter.html @@ -2,12 +2,12 @@ - + KineticLawImporter (SBMLsqueezer 2.0 API Specification) - + @@ -622,7 +622,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/WizardModel.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/WizardModel.html index edaa73ea1..5a89e3a71 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/WizardModel.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/WizardModel.html @@ -2,12 +2,12 @@ - + WizardModel (SBMLsqueezer 2.0 API Specification) - + @@ -913,7 +913,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/WizardProperties.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/WizardProperties.html index 22e4869c2..40b18526c 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/WizardProperties.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/WizardProperties.html @@ -2,12 +2,12 @@ - + WizardProperties (SBMLsqueezer 2.0 API Specification) - + @@ -248,7 +248,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/class-use/KineticLawImporter.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/class-use/KineticLawImporter.html index 1d8a0b485..782a03d95 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/class-use/KineticLawImporter.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/class-use/KineticLawImporter.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.model.KineticLawImporter (SBMLsqueezer 2.0 API Specification) - + @@ -428,7 +428,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/class-use/WizardModel.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/class-use/WizardModel.html index f7b04d119..98403ff40 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/class-use/WizardModel.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/class-use/WizardModel.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.model.WizardModel (SBMLsqueezer 2.0 API Specification) - + @@ -215,7 +215,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/class-use/WizardProperties.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/class-use/WizardProperties.html index 89f099831..394582e7c 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/class-use/WizardProperties.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/class-use/WizardProperties.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.sabiork.wizard.model.WizardProperties (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/package-frame.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/package-frame.html index 094bd536e..0b60514a3 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/package-frame.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/package-frame.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.sabiork.wizard.model (SBMLsqueezer 2.0 API Specification) - + diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/package-summary.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/package-summary.html index 5927012f6..6f9e46860 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/package-summary.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/package-summary.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.sabiork.wizard.model (SBMLsqueezer 2.0 API Specification) - + @@ -152,7 +152,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/package-tree.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/package-tree.html index a004ee1d2..9a5235035 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/package-tree.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/package-tree.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.sabiork.wizard.model Class Hierarchy (SBMLsqueezer 2.0 API Specification) - + @@ -119,7 +119,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/package-use.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/package-use.html index 3a4a83c7e..2950abed2 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/package-use.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/model/package-use.html @@ -2,12 +2,12 @@ - + Uses of Package org.sbml.squeezer.sabiork.wizard.model (SBMLsqueezer 2.0 API Specification) - + @@ -183,7 +183,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/package-frame.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/package-frame.html index e2a76f477..c18f6b7b0 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/package-frame.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/package-frame.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.sabiork.wizard (SBMLsqueezer 2.0 API Specification) - + diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/package-summary.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/package-summary.html index f040897b7..6507e92f1 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/package-summary.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/package-summary.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.sabiork.wizard (SBMLsqueezer 2.0 API Specification) - + @@ -146,7 +146,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/package-tree.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/package-tree.html index 71cfece22..618fde7f8 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/package-tree.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/package-tree.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.sabiork.wizard Class Hierarchy (SBMLsqueezer 2.0 API Specification) - + @@ -118,7 +118,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/package-use.html b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/package-use.html index 9e04d8ceb..24228a189 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/package-use.html +++ b/doc/api/version_2.0/org/sbml/squeezer/sabiork/wizard/package-use.html @@ -2,12 +2,12 @@ - + Uses of Package org.sbml.squeezer.sabiork.wizard (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/util/Bundles.html b/doc/api/version_2.0/org/sbml/squeezer/util/Bundles.html index 11472aed2..84ed05411 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/util/Bundles.html +++ b/doc/api/version_2.0/org/sbml/squeezer/util/Bundles.html @@ -2,12 +2,12 @@ - + Bundles (SBMLsqueezer 2.0 API Specification) - + @@ -303,7 +303,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/util/ConnectToSABIORK.html b/doc/api/version_2.0/org/sbml/squeezer/util/ConnectToSABIORK.html index 1bfa71a7c..414811c17 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/util/ConnectToSABIORK.html +++ b/doc/api/version_2.0/org/sbml/squeezer/util/ConnectToSABIORK.html @@ -2,12 +2,12 @@ - + ConnectToSABIORK (SBMLsqueezer 2.0 API Specification) - + @@ -319,7 +319,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/util/ModelChangeListener.html b/doc/api/version_2.0/org/sbml/squeezer/util/ModelChangeListener.html index 309ea6b3a..aff4f4b52 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/util/ModelChangeListener.html +++ b/doc/api/version_2.0/org/sbml/squeezer/util/ModelChangeListener.html @@ -2,12 +2,12 @@ - + ModelChangeListener (SBMLsqueezer 2.0 API Specification) - + @@ -269,7 +269,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/util/ProgressAdapter.TypeOfProgress.html b/doc/api/version_2.0/org/sbml/squeezer/util/ProgressAdapter.TypeOfProgress.html index 4874d85fd..997b4d57f 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/util/ProgressAdapter.TypeOfProgress.html +++ b/doc/api/version_2.0/org/sbml/squeezer/util/ProgressAdapter.TypeOfProgress.html @@ -2,12 +2,12 @@ - + ProgressAdapter.TypeOfProgress (SBMLsqueezer 2.0 API Specification) - + @@ -332,7 +332,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/util/ProgressAdapter.html b/doc/api/version_2.0/org/sbml/squeezer/util/ProgressAdapter.html index 70c51ee7f..5acd133f5 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/util/ProgressAdapter.html +++ b/doc/api/version_2.0/org/sbml/squeezer/util/ProgressAdapter.html @@ -2,12 +2,12 @@ - + ProgressAdapter (SBMLsqueezer 2.0 API Specification) - + @@ -334,7 +334,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/util/class-use/Bundles.html b/doc/api/version_2.0/org/sbml/squeezer/util/class-use/Bundles.html index de7de090e..4db68ee39 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/util/class-use/Bundles.html +++ b/doc/api/version_2.0/org/sbml/squeezer/util/class-use/Bundles.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.util.Bundles (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/util/class-use/ConnectToSABIORK.html b/doc/api/version_2.0/org/sbml/squeezer/util/class-use/ConnectToSABIORK.html index 9e64e4562..2c62e391d 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/util/class-use/ConnectToSABIORK.html +++ b/doc/api/version_2.0/org/sbml/squeezer/util/class-use/ConnectToSABIORK.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.util.ConnectToSABIORK (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/util/class-use/ModelChangeListener.html b/doc/api/version_2.0/org/sbml/squeezer/util/class-use/ModelChangeListener.html index 662668a4a..fdae8b77d 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/util/class-use/ModelChangeListener.html +++ b/doc/api/version_2.0/org/sbml/squeezer/util/class-use/ModelChangeListener.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.util.ModelChangeListener (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/util/class-use/ProgressAdapter.TypeOfProgress.html b/doc/api/version_2.0/org/sbml/squeezer/util/class-use/ProgressAdapter.TypeOfProgress.html index c69f4724b..176d94db8 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/util/class-use/ProgressAdapter.TypeOfProgress.html +++ b/doc/api/version_2.0/org/sbml/squeezer/util/class-use/ProgressAdapter.TypeOfProgress.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.util.ProgressAdapter.TypeOfProgress (SBMLsqueezer 2.0 API Specification) - + @@ -169,7 +169,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/util/class-use/ProgressAdapter.html b/doc/api/version_2.0/org/sbml/squeezer/util/class-use/ProgressAdapter.html index bdadfd2e9..0f983c5b6 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/util/class-use/ProgressAdapter.html +++ b/doc/api/version_2.0/org/sbml/squeezer/util/class-use/ProgressAdapter.html @@ -2,12 +2,12 @@ - + Uses of Class org.sbml.squeezer.util.ProgressAdapter (SBMLsqueezer 2.0 API Specification) - + @@ -109,7 +109,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/util/package-frame.html b/doc/api/version_2.0/org/sbml/squeezer/util/package-frame.html index 8e734546f..7d049eb6f 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/util/package-frame.html +++ b/doc/api/version_2.0/org/sbml/squeezer/util/package-frame.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.util (SBMLsqueezer 2.0 API Specification) - + diff --git a/doc/api/version_2.0/org/sbml/squeezer/util/package-summary.html b/doc/api/version_2.0/org/sbml/squeezer/util/package-summary.html index 0f6ba8270..5ddcb25b0 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/util/package-summary.html +++ b/doc/api/version_2.0/org/sbml/squeezer/util/package-summary.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.util (SBMLsqueezer 2.0 API Specification) - + @@ -169,7 +169,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/util/package-tree.html b/doc/api/version_2.0/org/sbml/squeezer/util/package-tree.html index 054dcfddf..4deb5ddc7 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/util/package-tree.html +++ b/doc/api/version_2.0/org/sbml/squeezer/util/package-tree.html @@ -2,12 +2,12 @@ - + org.sbml.squeezer.util Class Hierarchy (SBMLsqueezer 2.0 API Specification) - + @@ -129,7 +129,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/org/sbml/squeezer/util/package-use.html b/doc/api/version_2.0/org/sbml/squeezer/util/package-use.html index 5540c7712..43ff2319b 100644 --- a/doc/api/version_2.0/org/sbml/squeezer/util/package-use.html +++ b/doc/api/version_2.0/org/sbml/squeezer/util/package-use.html @@ -2,12 +2,12 @@ - + Uses of Package org.sbml.squeezer.util (SBMLsqueezer 2.0 API Specification) - + @@ -135,7 +135,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/overview-frame.html b/doc/api/version_2.0/overview-frame.html index eed7a9cbb..67ea993e7 100644 --- a/doc/api/version_2.0/overview-frame.html +++ b/doc/api/version_2.0/overview-frame.html @@ -2,12 +2,12 @@ - + Overview List (SBMLsqueezer 2.0 API Specification) - + diff --git a/doc/api/version_2.0/overview-summary.html b/doc/api/version_2.0/overview-summary.html index dd2d327e4..3cb0f02ea 100644 --- a/doc/api/version_2.0/overview-summary.html +++ b/doc/api/version_2.0/overview-summary.html @@ -2,12 +2,12 @@ - + Overview (SBMLsqueezer 2.0 API Specification) - + @@ -229,7 +229,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/overview-tree.html b/doc/api/version_2.0/overview-tree.html index e494ef99f..e3e925f06 100644 --- a/doc/api/version_2.0/overview-tree.html +++ b/doc/api/version_2.0/overview-tree.html @@ -2,12 +2,12 @@ - + Class Hierarchy (SBMLsqueezer 2.0 API Specification) - + @@ -304,7 +304,7 @@

-Generated at April 24 2014
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Version 2.0 Revision 1101 diff --git a/doc/api/version_2.0/serialized-form.html b/doc/api/version_2.0/serialized-form.html index d705f57f7..7928f421e 100644 --- a/doc/api/version_2.0/serialized-form.html +++ b/doc/api/version_2.0/serialized-form.html @@ -2,12 +2,12 @@ - + Serialized Form (SBMLsqueezer 2.0 API Specification) - + @@ -2856,7 +2856,7 @@

-Generated at April 24 2014
Version 2.0 Revision 1096 +Generated at May 19 2014
Version 2.0 Revision 1101 diff --git a/doc/tutorials/user_guide/UT.sty b/doc/tutorials/user_guide/UT.sty index 5c0fc7d36..120955f38 100644 --- a/doc/tutorials/user_guide/UT.sty +++ b/doc/tutorials/user_guide/UT.sty @@ -31,7 +31,7 @@ % rotate text. % Some color in the document -\RequirePackage{color} +\RequirePackage[usenames,dvipsnames]{color} % Source code and pseudo code \RequirePackage{listings} % Source code listing support diff --git a/doc/tutorials/user_guide/UserGuide.tex b/doc/tutorials/user_guide/UserGuide.tex index 356bfb2d2..d49f793d0 100644 --- a/doc/tutorials/user_guide/UserGuide.tex +++ b/doc/tutorials/user_guide/UserGuide.tex @@ -15,6 +15,9 @@ ]{scrreprt} \usepackage{UT} + +\usepackage{pdfcomment} + \usepackage{wrapfig} \usepackage{textcomp} \usepackage{cleveref} @@ -84,7 +87,7 @@ \author{Andreas Dr\"ager$^{1,2,}$\thanks{Corresponding author: \href{mailto:andraeger@eng.ucsd.edu}{\url{andraeger@eng.ucsd.edu}}} \and Roland Keller$^{1}$\and -%Matthias Rall\and +Matthias Rall$^{1}$\and Johannes Eichner$^{1}$\and Andreas Zell$^{1}$} \date{\today} @@ -135,7 +138,7 @@ % \listoffigures % \listoftables -\cleardoublepage % Erzeugt neue Leerseite. Muss ggf. auskommentiert werden. +%\cleardoublepage % Erzeugt neue Leerseite. 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If you encounter any difficulties or bugs, please do not hesitate to contact -the mailing list, +the mailing list, \ding{41} \href{mailto:sbmlsqueezer@googlegroups.com}{\texttt{sbmlsqueezer@google\-groups.com}}. \section{General program features} @@ -433,6 +433,7 @@ \section{Starting the application} \section{Adjusting the preferences} \label{sec:GUIPrefs} + \begin{SCfigure} \shadowimage[width=.5\textwidth]{prefs/Basic_configuration} \caption[Basic configuration]{Basic configuration. @@ -454,6 +455,20 @@ \section{Adjusting the preferences} can here select those types of species that should be considered enzymes.} \label{fig:Basic_Configuration} \end{SCfigure} +The program SBMLsqueezer offers a large number of options to configure how +kinetic equations are generated. +All options described in this section can also be applied using SBMLsqueezer's +command-line interface (see \vref{chap:CMD} for details). +This means that you can already upon launching the program define with which +options it should be initialized. +Your configuration can always be set back to the default options if desired. +SBMLsqueezer stores its configuration in the system's preferences of your \OS. +This means that when launching the program for the next time, you can directly +continue with your previous configuration. +Furthermore, there are no configuration files generated by SBMLsqueezer in +addition to those maintained by your \OS. +Hence, SBMLsqueezer integrates well into your working environment. + \begin{SCfigure} \shadowimage[width=.5\textwidth]{prefs/Rate_law_selection} \caption[Rate law selection]{Rate law selection. @@ -472,20 +487,6 @@ \section{Adjusting the preferences} its corresponding command-line options in \vref{sec:Rate_law_selection}.} \label{fig:Rate_law_selection} \end{SCfigure} -The program SBMLsqueezer offers a large number of options to configure how -kinetic equations are generated. -All options described in this section can also be applied using SBMLsqueezer's -command-line interface (see \vref{chap:CMD} for details). -This means that you can already upon launching the program define with which -options it should be initialized. -Your configuration can always be set back to the default options if desired. -SBMLsqueezer stores its configuration in the system's preferences of your \OS. -This means that when launching the program for the next time, you can directly -continue with your previous configuration. -Furthermore, there are no configuration files generated by SBMLsqueezer in -addition to those maintained by your \OS. -Hence, SBMLsqueezer integrates well into your working environment. - \begin{wrapfigure}{O}{.9cm} \vspace{\wrapfigspace} \includegraphics[width=16px]{settings_64} @@ -498,6 +499,7 @@ \section{Adjusting the preferences} \menu{Edit > Preferences}, whereas under \MacOSX, these can be found under \menu{SBMLsqueezer > Preferences\dots} or by using the keystroke combination \keys{\cmd + {$,$}}. + \begin{SCfigure} \shadowimage[width=.5\textwidth]{prefs/SABIO-RK_search_options} \caption[\SABIO search options]{\SABIO search options. @@ -509,6 +511,20 @@ \section{Adjusting the preferences} Of course, you can also restrict your search to an organism of choice.} \label{fig:SABIO-RK_search_options} \end{SCfigure} +On the bottom panel of the preferences dialog you can see the four buttons +\keys{Cancel}, \keys{Defaults}, \keys{Apply}, and \keys{OK} as this is displayed in +\vrefrange{fig:Basic_Configuration}{fig:LaTeX_Options}. +The \keys{Cancel} button has the same effect as a click at the close button on the +top of the window or hitting the \keys{\escwin} key: all of your changes will be +disregarded and the window will be closed. +The \keys{Defaults} button restores the standard settings of SBMLsqueezer. +With \keys{Apply} you can persistently save your current settings. +The \keys{OK} button is a combination of \keys{Apply} and close, i.e., it makes your +settings persistent and closes the window. +Hitting the \keys{\return} key has the same effect as clicking at the \keys{OK} button. +Note that the dialog is structured with multiple tabs. When clicking at +\keys{Defaults} the preferences in all tabs will be restored, even if those are not +active at the time when you hit that button. \begin{SCfigure} \shadowimage[width=.5\textwidth]{prefs/SABIO-RK_search_preferences} \caption[\SABIO search preferences]{\SABIO search preferences. @@ -525,7 +541,6 @@ \section{Adjusting the preferences} more appropriate settings for just this reaction.} \label{fig:SABIO-RK_search_preferences} \end{SCfigure} - \begin{SCfigure} \shadowimage[width=.5\textwidth]{prefs/LaTeX_Options} \caption[\LaTeX{} options]{\LaTeX{} options. @@ -542,20 +557,6 @@ \section{Adjusting the preferences} For more information about \SBMLLaTeX see the documentation of this project.} \label{fig:LaTeX_Options} \end{SCfigure} -On the bottom panel of the preferences dialog you can see the four buttons -\keys{Cancel}, \keys{Defaults}, \keys{Apply}, and \keys{OK} as this is displayed in -\vrefrange{fig:Basic_Configuration}{fig:LaTeX_Options}. -The \keys{Cancel} button has the same effect as a click at the close button on the -top of the window or hitting the \keys{\escwin} key: all of your changes will be -disregarded and the window will be closed. -The \keys{Defaults} button restores the standard settings of SBMLsqueezer. -With \keys{Apply} you can persistently save your current settings. -The \keys{OK} button is a combination of \keys{Apply} and close, i.e., it makes your -settings persistent and closes the window. -Hitting the \keys{\return} key has the same effect as clicking at the \keys{OK} button. -Note that the dialog is structured with multiple tabs. When clicking at -\keys{Defaults} the preferences in all tabs will be restored, even if those are not -active at the time when you hit that button. \section{Open a model} @@ -569,7 +570,7 @@ \section{Open a model} If you prefer keystroke combinations, you can use \keys{\cmd + O} on \MacOSX or \keys{\ctrlwin + O} on \Windows and \Linux computers. The \GUI can open multiple \SBML files in parallel. -SBMLsqueezer arranges these \SBML documents in tabs. +SBMLsqueezer arranges these \SBML documents in tabs, whose order can be changed by dragging and dropping the tabs. Furthermore, you can also open one ore multiple models in SBMLsqueezer via drag and drop, i.e., just select one or multiple \SBML files in an arbitrary file browser of your \OS and drag these into SBMLsqueezer's \GUI. When starting SBMLsqueezer from the command line, you can directly pass a model @@ -617,8 +618,25 @@ \section{Equation generation one by one} In all cases, the same dialog window will appear, which offers you a selection of appropriate rate laws for the particular reaction and gives you the opportunity to choose between those, or to discard the dialog. No change will be performed to your model when canceling the dialog (either by pushing \keys{\escwin} or by clicking at \keys{Cancel}. -We here use biomodel \numero~390 from \BioModels \citep{Li2010a} as an illustrative example model. -\TODO{Modell zitieren!} +We here use biomodel \numero~390 from \BioModels \citep{Li2010a, Arnold2011} as an illustrative example model. +\begin{SCfigure} +\includegraphics[width=.54\textwidth]{CellDesigner/reaction_context_menu.png} +\caption[Reaction context menu in \CellDesigner]{Reaction context menu in \CellDesigner. +After installing SBMLsqueezer as a plug-in, its functionality will be incorporated into \CellDesigner's reaction context menu. +If you right-click at an arbitrary reaction, it allows you to create a kinetic equation for this reaction (with the dialog in \namecref{fig:RateLawDialog}~\ref{fig:RateLawDialog}), or to generate a \LaTeX{} model report that only involves the details relevant for the selected reaction.} +\label{fig:ReactionContextMenu} +\end{SCfigure} +\begin{figure}[b!] +\shadowimage[width=\textwidth]{Screenshot_2} +\caption[Generating a kinetic equation for a single reaction]{Generating a kinetic equation for a single reaction. +This dialog can be opened by right-clicking on an individual reaction in your active model and selecting \menu{Squeeze} in the pop-up menu. +%The equation preview displays how the rate law will look like, where zooming in and out can give you a better %overview. +The directionality of the reaction and the enzyme property can be altered. +%In most cases you can also decide if the reaction should be considered an enzyme reaction or not. +Both options possibly influence the selection of rate laws. +To abort this dialog, click at \keys{Cancel} or hit the \keys{\escwin} key.} +\label{fig:RateLawDialog} +\end{figure} In case that you are working with \CellDesigner, right-click at the reaction of interest as this is displayed in \vref{fig:ReactionContextMenu} and select the menu item \menu{Squeeze kinetic law}. When using SBMLsqueezer as a stand-alone program, you can generate kinetic equations for a selected reaction by right-clicking at the reaction of interest. @@ -637,23 +655,6 @@ \section{Equation generation one by one} Just note, that there are some parameters, which cannot be stored locally because they represent recurrent properties of some reactive species and are needed across several rate laws (e.g., energy constants). -\begin{SCfigure} -\includegraphics[width=.6\textwidth]{CellDesigner/reaction_context_menu.png} -\caption[Reaction context menu in \CellDesigner]{Reaction context menu in \CellDesigner. -After installing SBMLsqueezer as a plug-in, its functionality will be incorporated into \CellDesigner's reaction context menu. -If you right-click at an arbitrary reaction, it allows you to create a kinetic equation for this reaction (with the dialog in \namecref{fig:RateLawDialog}~\ref{fig:RateLawDialog}), or to generate a \LaTeX{} model report that only involves the details relevant for the selected reaction.} -\label{fig:ReactionContextMenu} -\end{SCfigure} -\begin{figure}[b!] -\shadowimage[width=\textwidth]{Screenshot_2} -\caption[Generating a kinetic equation for a single reaction]{Generating a kinetic equation for a single reaction. -This dialog can be opened by right-clicking on an individual reaction in your active model. -%The equation preview displays how the rate law will look like, where zooming in and out can give you a better %overview. -The directionality of the reaction and the enzyme property can be altered. -%In most cases you can also decide if the reaction should be considered an enzyme reaction or not. -Both options possibly influence the selection of rate laws.} -\label{fig:RateLawDialog} -\end{figure} \section{Generate kinetic equations in a single step} @@ -671,8 +672,7 @@ \section{Generate kinetic equations in a single step} In the \CellDesigner plug-in version, just click at \menu{Plugin > SBMLsqueezer 2.0 > Squeeze kinetic laws} to launch the kinetics wizard. In the stand-alone version, you can either right-click at the model in the \SBML tree, the lemon icon in the tool bar (see the symbol next to this text), or \menu{Edit > Squeeze} in the menu bar. -We again use biomodel \numero~390 from \BioModels \citep{Li2010a} as an example model. -\TODO{Modell zitieren!} +We again use biomodel \numero~390 from \BioModels \citep{Li2010a, Arnold2011} as an example model. The usage of the kinetics wizard is identical, irrespective of how you launched it. You can see how this wizard looks like in \vref{fig:KineticLawWizard}. @@ -688,13 +688,13 @@ \section{Generate kinetic equations in a single step} When you hit the button \keys{Finish}, the created rate equations, units, and parameter objects will be incorporated into your original model. \begin{SCfigure} -\includegraphics[width=.6\textwidth]{CellDesigner/plugin_menu} +\includegraphics[width=.54\textwidth]{CellDesigner/plugin_menu} \caption[Launching SBMLsqueezer in \CellDesigner]{Launching SBMLsqueezer in \CellDesigner. The \menu{Plugin > SBMLsqueezer 2.0} gives you access to nearly all functions of the program. You can launch the kinetics wizard, adjust your preferences, export a \LaTeX{} report, open a help browser, or just look at how SBMLsqueezer internally represents \CellDesigner's data structure.} \label{fig:PluginMenu} \end{SCfigure} -\begin{figure}[t!] +\begin{figure} \shadowimage[width=\textwidth]{Screenshot_4} \caption[Generating kinetic equations in one single step with the kinetic law wizard]{Generating kinetic equations in one single step with the kinetic law wizard. This screen-shot shows the Kinetic Law Wizard (here shown with the user interface @@ -704,7 +704,7 @@ \section{Generate kinetic equations in a single step} \begin{figure} \shadowimage[width=\textwidth]{wizard_results_table} \caption[Results of the kinetics wizard displayed in a table]{Results of the kinetics wizard displayed in a table. -In this example two rows are highlighted in \textcolor{red}{red}. +In this example two rows are highlighted in \colorbox{red}{red}. The reason is that these reactions involve an unrealistically high number of reactant molecules, or are reversible with a high number of products, respectively. SBMLsqueezer displays these warnings to indicate that the generated rate law might neglect several intermediate steps. In this table, you can review all generated rate law. @@ -735,8 +735,7 @@ \section{Extraction of rate laws from \SABIO} Furthermore, this feature requires an active internet connection and can therefore not be used in an off-line mode. This section describes how to use SBMLsqueezer's \GUI to extract information from \SABIO. -As an example model we pick biomodel \numero~206 from \BioModels \citep{Li2010a}. -\TODO{Modell zitieren!} +As an example model we pick biomodel \numero~206 from \BioModels \citep{Li2010a, Wolf2000}. You can also do this on the command line, which allows you batch processing of multiple \SBML files as this has been done by \citet{Buechel2013}. For more information about the command-line options for \SABIO see \vref{chap:CMD}. @@ -744,42 +743,38 @@ \section{Extraction of rate laws from \SABIO} \subsection{Rate laws from \SABIO for an entire network} -\begin{figure}[t] -\shadowimage[width=\textwidth]{SABIO_automatic_1} +\begin{SCfigure} +\includegraphics[width=.45\textwidth]{SABIO_automatic_1compact1} \caption[Starting the \SABIO wizard]{Starting the \SABIO wizard. After opening a model in SBMLsqueezer, the \SABIO button will become active in the tool-bar (see the black fringe). A tool-tip will display more information about this button when moving the mouse over it. You can click at this button to launch the \SABIO wizard. Alternatively, you can also click at \menu{Edit > SABIO-RK}.} \label{fig:startAutomatic} -\end{figure} -\begin{figure}[t!] -\shadowimage[width=\textwidth]{SABIO_automatic_2} +\end{SCfigure} +\begin{SCfigure} +\shadowimage[width=.54\textwidth]{SABIO_automatic_2} \caption[Selection of reactions in the \SABIO wizard]{Selection of reactions in the \SABIO wizard. On the first window you can select which reactions you want to equip with kinetic equations from \SABIO. In order to select multiple reactions in the table hold the \keys{\ctrlwin} key pressed while clicking on the desired reactions. You can abort the wizard by either clicking at the \keys{Cancel} button or by hitting the \keys{\escwin} key. When finished click on the button \keys{Next}. -\TODO{Warum ist das Menu oben aufgeklappt und was kann man da einstellen? Das ist hier nicht erklaert!} -\TODO{Da ist so viel grauer Platz rechts, aber die Tabelle ist so klein, dass man die Eintraege in manchen Spalten gar nicht lesen kann!}} +\TODO{Warum ist das Menu oben aufgeklappt und was kann man da einstellen? Das ist hier nicht erklaert!}} \label{fig:selectReations} -\end{figure} -\begin{figure}[t!] -\shadowimage[width=\textwidth]{SABIO_automatic_5} +\end{SCfigure} +\begin{SCfigure} +\shadowimage[width=.54\textwidth]{SABIO_automatic_5} \caption[Selection of search terms for \SABIO]{Selection of search terms for \SABIO. On the next window you can add categories for search terms together with their values. These terms are used to select only reactions and rate laws from \SABIO, whose annotation contains these terms. An example is the organism, in which this reaction takes place. You can choose ``organism" from the provided terms and type the desired name as value of the term in the text field. By clicking at button \keys{Add} (black fringe), the term will be added to the table on the left-hand side of the dialog window. -The \KEGG identifier of a reaction is always included in the respective search, \TODO{because the \API simultaneously searches for rate equations for several reactions.} -Your search can be further restricted by changing the bounds of pH, temperature, etc. in the right panel. -Whenever a search term is added. See \vref{fig:removeSearchTerms} for an example how to remove a term again.} \label{fig:searchTerms} -\end{figure} -\begin{figure}[t!] -\shadowimage[width=\textwidth]{SABIO_automatic_6} +\end{SCfigure} +\begin{SCfigure} +\shadowimage[width=.54\textwidth]{SABIO_automatic_6} \caption[Removal of search terms for \SABIO]{Removal of search terms for \SABIO. You can remove a query field again by clicking on the check box button in the right-most column. When you are done with selecting appropriate search terms, click button \keys{Next} to see the results of your query. \Cref{fig:foundEquations} displays an example who this overview can look like. @@ -787,36 +782,37 @@ \subsection{Rate laws from \SABIO for an entire network} As before, you can abort the dialog by either hitting the key \keys{\escwin} or by clicking at the \keys{Cancel} button. \TODO{Auch hier sind die Tabellenspalten so unguenstig zusammengerutscht, dass man den Inhalt nicht erkennen kann.}} \label{fig:removeSearchTerms} -\end{figure} -\begin{figure}[t!] -\shadowimage[width=\textwidth]{SABIO_automatic_8} +\end{SCfigure} +\begin{figure} +\shadowimage[width=\textwidth]{SABIO_automatic_8compact} \caption[Window with found kinetic equations]{Window with found kinetic equations. -On the following window all reactions are listed. -If a matching rate equation has been found, the respective reaction is marked in \textcolor{green}{green}. -A reaction is highlighted in \textcolor{yellow}{yellow} if the found rate equations do not exactly fit to your model. -A \textcolor{red}{red} background means that no matching rate equation has been found for the respective reaction. -If you are satisfied with the results, you can click on \keys{Next}. -\TODO{Hier wird der Platz fuer die Tabellenspalten ebenfalls nicht ausgenutzt.}} +The next window lists all reactions whose background color has the following meaning: +A reaction is marked in \colorbox{LimeGreen}{green} if a matching rate equation has been found, +\colorbox{Goldenrod}{yellow} if the found rate equations do not exactly fit to your model, and +\colorbox{red}{red} if no matching rate equation has been found. +If you are satisfied with the results, click \keys{Next}.} \label{fig:foundEquations} \end{figure} \begin{figure}[t!] -\shadowimage[width=\textwidth]{SABIO_automatic_9} +\shadowimage[width=\textwidth]{SABIO_automatic_9compact} \caption[Summary of necessary changes]{Summary of necessary changes. The wizard presents a summary of all required changes to the model that are necessary if you want to transfer the identified rate laws from \SABIO to your active model. This summary lists only changes related to reactions that have been highlighted in green in the previous step (\vref{fig:foundEquations}). -If you now click on \keys{Finish} and hence confirm these changes to be made, the rate -equations will be transferred to your model and all changes will be applied as stated in this summary.} +Upon clicking on \keys{Finish} a pop-up dialog will finally ask you to either confirm these changes to be made or to disregard all results. +If you confirm, the rate equations will be transferred to your model and all changes will be applied as stated in this summary.} \label{fig:changes} \end{figure} \Crefrange{fig:startAutomatic}{fig:changes} show how you can add kinetic equations from \SABIO to several reactions at once. -To this end, SBMLsqueezer provides a wizard that guides you through the selection of relevant reactions and provides several options to restrict the search in \SABIO. +To this end, SBMLsqueezer provides a wizard that guides you through the selection of relevant reactions (\vref{fig:selectReations}) and provides several options to restrict the search in \SABIO (\vref{fig:searchTerms}). The user interface of this wizard is similar to the database web interface provided by \SABIO\footnote{\url{http://sabio.h-its.org}}. To ensure that entries for the reactions of interest can be found in \SABIO, it is important to annotate these reactions with identifiers from the \KEGG database using the \MIRIAM registry. +The \KEGG identifier of a reaction is always included in the respective search, \pdfmarkupcomment[author={Andreas Dr\"ager}, color={yellow}]{because the $\backslash$API simultaneously searches for rate equations for several reactions.}{Unklar.} +You can further restrict your search by changing the bounds of pH, temperature, etc. in the right panel (see \vref{fig:searchTerms}). -\subsection{For a selected reaction} +\subsection{\SABIO for a selected reaction} \begin{figure}[t!] -\shadowimage[width=\textwidth]{SABIO_manual_1} +\shadowimage[width=\textwidth]{SABIO_manual_1compact} \caption[Starting the \SABIO application for a selected reaction]{Starting the \SABIO application for a selected reaction. To find a reaction of interest, you can use the search function at the bottom of the \SBML tree. Just click at the text field and type a part of the reaction's name or identifier. @@ -828,8 +824,8 @@ \subsection{For a selected reaction} This will bring you to the selection of search terms that is described in \vref{fig:searchTermsManual}.} \label{fig:startManual} \end{figure} -\begin{figure}[t!] -\shadowimage[width=\textwidth]{SABIO_manual_3} +\begin{SCfigure} +\shadowimage[width=.54\textwidth]{SABIO_manual_3} \caption[Selection of search terms]{Selection of search terms. You can add search terms such as the organism by choosing from the provided terms and typing in the value of the term. The search can be further restricted by changing the @@ -838,23 +834,21 @@ \subsection{For a selected reaction} This dialog is just the same what has been described in \vrefrange{fig:searchTerms}{fig:removeSearchTerms} when adding kinetic laws to several reactions in a single step. The example continues in \vref{fig:searchTermsQuery}.} \label{fig:searchTermsManual} -\end{figure} -\begin{figure}[t!] -\shadowimage[width=\textwidth]{SABIO_manual_7} +\end{SCfigure} +\begin{SCfigure} +\shadowimage[width=.54\textwidth]{SABIO_manual_7} \caption[Window with two search terms]{Window with two search terms. Here a search for an organism and an enzyme name has been specified and will be combined to a query when clicking on \keys{Next}. -You will then see the list of reactions as it is displayed in \vref{fig:foundEquationsManual}. -\TODO{Hier wird der Platz fuer die Tabellenspalten ebenfalls nicht ausgenutzt.}} +You will then see the list of reactions as it is displayed in \vref{fig:foundEquationsManual}.} \label{fig:searchTermsQuery} -\end{figure} +\end{SCfigure} As an alternative you can add kinetic equations from \SABIO to a selected individual reaction. How to do this is shown in \vrefrange{fig:startManual}{fig:changesManual}. You should first select the reaction, for which you want to obtain a rate law from \SABIO (\vref{fig:startManual}). All subsequent steps of the procedure are essentially the same as when obtaining rate laws from \SABIO for all reactions in a single step. The only difference is that the \SABIO wizard will be launched for one selected reaction of interest only instead of having all reactions in the model. -We here use biomodel \numero~206 from \BioModels \citep{Li2010a} as an example network. -\TODO{Modell zitieren.} +We here use biomodel \numero~206 from \BioModels \citep{Li2010a, Wolf2000} as an example network. \TODO{Hier muss auch erklaert werden, warum ein Matching mit den Modellelementen noetig ist, wie dies in \vref{fig:matching} dargestellt wird. Warum braucht man sich darum nicht zu kuemmern, wenn man fuer alle Reaktionen kinetische Gleichungen aus SABIO holt, warum aber ist es hier noetig, was passiert hierbei?} \begin{figure}[t!] \shadowimage[width=\textwidth]{SABIO_manual_8} @@ -865,22 +859,22 @@ \subsection{For a selected reaction} \TODO{Hier wird der Platz fuer die Tabellenspalten ebenfalls nicht ausgenutzt.}} \label{fig:foundEquationsManual} \end{figure} -\begin{figure}[t!] -\shadowimage[width=\textwidth]{SABIO_manual_9} +\begin{SCfigure} +\shadowimage[width=.54\textwidth]{SABIO_manual_9compact} \caption[Window for matching elements in the equation to model elements]{Window for matching elements in the equation to model elements. You can choose how to match the species, compartments, etc., contained in the selected rate equation to the respective \SBML elements in your model. The necessary elements to import, such as function definitions contained in the rate equation to add, are also shown.} \label{fig:matching} -\end{figure} -\begin{figure}[t!] -\shadowimage[width=\textwidth]{SABIO_manual_10} +\end{SCfigure} +\begin{SCfigure} +\shadowimage[width=.54\textwidth]{SABIO_manual_10compact} \caption[Summary of necessary changes]{Summary of necessary changes. A summary of all necessary changes to the model for adding the selected rate equation is displayed. Now click on \keys{Finish} and confirm the changes afterwards. \TODO{Was soll das immer mit dem \emph{afterwards}? Muss man denn nachdem auf \emph{Finish} geklickt wurde, noch einmal etwas anklicken? Was kommt denn dann fuer ein Dialog? Oder ist mit dem Klick auf \emph{Finish alles erledigt}? Dann muesste aber der Text dies auch klar beschreiben.} Then the rate equation will be added and the necessary changes will be applied to your model.} \label{fig:changesManual} -\end{figure} +\end{SCfigure} \section{Viewing and saving the results} @@ -956,12 +950,77 @@ \section{Interaction with further \Garuda gadgets} \label{fig:SelectGarudaGadget} \end{SCfigure} + +\section{Using SBMLsqueezer as an on-line program} +\label{sec:SBMLsqueezer_online_version} + +SBMLsqueezer can also be used via the Galaxy web-service facility \citep{Goecks2010} of the University of Tuebingen\footnote{\url{http://webservices.cs.uni-tuebingen.de}\label{fn:Webservices}}. +Since the user interface of this variant greatly differs from all other use-case scenarios, we here give a description of options and functions of the web interface. + +In order to use the on-line version of SBMLsqueezer, open a browser of your choice. +Go to the main portal of all web services provided by the Universtiy of Tuebingen\footref{fn:Webservices}. +There you can either and scroll down until you find the tool SBMLsqueezer and click at the the program's logo, or you can click at the link in the list of tools on the left. +Alternatively, you can go directly to the service SBMLsqueezer\footnote{\url{http://webservices.cs.uni-tuebingen.de/tool_runner?tool_id=sbmlupload2}}. +\Cref{fig:WebserviceLaunch} displays the web interface of the Galaxy framework. +\begin{figure} +\shadowimage[width=\textwidth]{Webservice/SBMLsqueezerWebservice1} +\caption[Starting the on-line version of SBMLsqueezer]{Starting the on-line version of SBMLsqueezer. +This figure displays the Galaxy framework in the browser Firefox version 29.0.1 under \MacOSX version 10.9.3. +You can start working with SBMLsqueezer by either clicking at the program's icon or the link ``Upload SBML file".} +\label{fig:WebserviceLaunch} +\end{figure} + +The first step is now to upload your \SBML file of interest to the on-line program. +To this end, you can either click at the link ``Upload SBML file" on the left-hand side of the browser window, or click at the icon of SBMLsquezeer. +In both cases you should see a browse button that allows you to select an \XML or \SBML file from your local file system. +After selecting the file, hit the button ``Execute" in order to actually upload the file to the Galaxy service. +Galaxy informs you about the progress of the upload in the ``History" column at the right-hand side of the browser window. +You can upload further files if you like, but at least one file is required in order to run SBMLsqueezer. + +Second, click at the link ``Generate kinetic rate equations" on the left-hand side of the browser window. +You should see a view similar to what is displayed in \vref{fig:WebserviceConfiguration}. +Scroll down to see all available options. +At the bottom of this page, there is also a descriptive text explaining how to proceed. +Each option has descriptive text as well. +The on-line version presents all options of the program just as the stand-alone version. +You can therefore go back in this tutorial and look-up the meaning of individual options either in \vref{sec:GUIPrefs} about the graphical user interface of the stand-alone version or in \vref{chap:CMD} where the command-line options are described. +When you scroll down, you can see that this on-line program also offers you to obtain rate laws from \SABIO. +Just one option group is missing, namely \SBMLLaTeX. +The reason is because the Galaxy framework of the University of Tuebingen provides \SBMLLaTeX as a separate on-line program. +When you are happy with the settings, scroll down until you see the ``Execute" button. +When you hit this button, SBMLsqueezer will create kinetic equations for your model according to your preferences. +To this end, a new job to is scheduled that will be displayed in your history. +\begin{figure} +\shadowimage[width=\textwidth]{Webservice/SBMLsqueezerWebservice2} +\caption[Adjusting preferences in the on-line version]{Adjusting preferences in the on-line version. +In this example, three models have been uploaded to the Galaxy service and are shown in the history column in the right-hand side of the browser window. +You can now choose for which file SBMLsqueezer should generate kinetic equations by altering the selected entry in the combo box at the top of the center column. +In the center column, this view offers you all options of the stand-alone version of SBMLsqueezer.} +\label{fig:WebserviceConfiguration} +\end{figure} + +When the job is done, you can obtain the results by first clicking at the link ``Generated kinetics for\ldots", which will appear in the history column. +You can then click on the disk icon below in order to download the \SBML file that contains your results. +If you click at the eye icon, the central column will display a rendered version of your \SBML file, which is the view at all \XHTML notes within your file. +\begin{figure} +\shadowimage[width=\textwidth]{Webservice/SBMLsqueezerWebservice3} +\caption[Obtaining the results from the on-line version]{Obtaining the results from the on-line version. +The history column contains an overview of all files for which kinetic equations have been generated. +You can view the details of each file by clicking at the eye icon, or download the file by first clicking at the link in the headline of the respective entry (``Generated kinetics for\ldots") and then clicking at the disk icon.} +\label{fig:WebserviceResult} +\end{figure} + + \section{Using SBMLsqueezer as an equation generator library} \label{sec:API} We will now discuss how to use the \API of SBMLsqueezer directly in order to generate kinetic equations as part of more complex operations. This function could already be used in version 1.3 of SBMLsqueezer (see \vref{lst:1.3APIUsage}). Since then, the \API has been greatly modified and improved. +We will now discuss important aspects of the new \API of SBMLsqueezer and give use-case examples. + +\subsection{Assignment of kinetic equations to all reactions in an \SBML file} + \Cref{lst:SBMLsqueezer2API1} gives you an example for a simple application that takes the paths to two \SBML files as input and proceeds as follows: \begin{enumerate} \item Changes the preferences of the program by defining several options. @@ -971,7 +1030,9 @@ \section{Using SBMLsqueezer as an equation generator library} \end{enumerate} The paths in this example can also point to a directory instead of a particular file. If this is the case, \texttt{SBMLsqueezer} will recursively traverse all acceptable \SBML files in the given input folder and create a corresponding file with newly created or obtained kinetic equations in the output folder. -\lstinputlisting[caption={Usage of SBMLsqueezer 2 via its \acs{API}}, label={lst:SBMLsqueezer2API1}, firstline={43}]{../../../examples/src/org/sbml/squeezer/test/SBMLsqueezerAPI.java} +\lstinputlisting[caption={Generating rate laws for all reactions in a model via the \acs{API} of SBMLsqueezer 2}, label={lst:SBMLsqueezer2API1}, firstline={45}, lastline={77}]{../../../examples/src/org/sbml/squeezer/test/SqueezeFile.java} + +\subsection{Adjusting configuration and user preferences} While the previous version of SBMLsqueezer stored its preferences in configuration files within the user's home directory, SBMLsqueezer now makes use of the preferences of your \OS. The keywords for the individual options have been slightly changed, but are still very similar. @@ -985,7 +1046,7 @@ \section{Using SBMLsqueezer as an equation generator library} If you are using an \IDE, such as \Eclipse, an auto-complete function will directly show you which options are provided within a particular sub-class of \texttt{KeyProvider}. Such an \IDE will also display the Java documentation to you. You can load the preferences by calling -\begin{lstlisting}[language=Java, numbers=none, caption={Loading preferences in SBMLsqueezer}] +\begin{lstlisting}[language=Java, numbers=none, caption={Loading preferences in SBMLsqueezer 2}] SBPreferences prefs = SBPreferences.getPreferencesFor(MyOptionsClass.class); \end{lstlisting} Here, \texttt{MyOptionsClass} acts as a placeholder for your actual instance of \texttt{KeyProvider} for which you want to load preferences. @@ -1008,9 +1069,12 @@ \section{Using SBMLsqueezer as an equation generator library} In particular, when selecting a specific kind of rate law for a certain type of reaction, SBMLsqueezer expects the class object of that \texttt{KineticLaw}. Note that this is in contrast to version~1.3, which expected the name of the class. -Let us now discuss how you can use SBMLsqueezer's \API with a \libSBML back-end instead of \JSBML. +\subsection{Using SBMLsqueezer with a \libSBML back-end} + + +Let us now discuss how you can use SBMLsqueezer's \API with a \libSBML back-end instead of pure \JSBML. To this end, you only have to change the way how you initialize your instance of \texttt{SBMLsqueezer}: -\begin{lstlisting}[language=Java, numbers=none, caption={Initializing \texttt{SBMLsqueezer} with a \libSBML back-end}] +\begin{lstlisting}[language=Java, numbers=none, caption={Initializing SBMLsqueezer 2 with a \libSBML back-end}] SBMLsqueezer squeezer = new SBMLsqueezer( new org.sbml.jsbml.xml.libsbml.LibSBMLReader(), new org.sbml.jsbml.xml.libsbml.LibSBMLWriter()); @@ -1019,6 +1083,12 @@ \section{Using SBMLsqueezer as an equation generator library} Here, we are initializing \texttt{SBMLsqueezer} based on a \libSBML \texttt{Model} data structure. It is important to use the correct reader and writer from the package \texttt{org.sbml.jsbml.xml.libsbml}, and not to confuse these with the \texttt{LibSBMLReader} and \texttt{LibSBMLWriter} from the \texttt{org.sbml.jsbml.celldesigner.libsbml} package in \JSBML. Otherwise, your application will not function, because the classes in this package are very basic implementation needed for the interface between \JSBML and \CellDesigner. +Please note that SBMLsqueezer can internally only work with the \JSBML data structure. +The \libSBML back-end is used to parse and write \SBML files and also allows for off-line model validation. +However, SBMLsqueezer will convert \libSBML's data structure to \JSBML and synchronize its changes to the original data structure. +When run-time is crucial for your application, this procedure should hence be avoided. + +\subsection{Assignment of specific rate laws to selected reactions} Instead of reading and writing entire files ore recursively walking through a directory structure, it can also be desirable to perform more customized calls to create rate laws for individual reactions only. To this end, a more deeper understanding about the functioning of SBMLsqueezer is required. @@ -1045,44 +1115,39 @@ \section{Using SBMLsqueezer as an equation generator library} \end{description} \renewcommand{\descriptionlabel}[1]{\textcolor{black}{\textbf{#1}}} With these classes at hand, new kinetic equations can be created for arbitrary reactions. -\lstinputlisting[caption={Usage of SBMLsqueezer 2 via its \acs{API}}, label={lst:SBMLsqueezer2API1}, firstline={43}]{../../../examples/src/org/sbml/squeezer/test/SBMLsqueezerAPI2.java} -\TODO{Needs more.} - -\TODO{How can the SABIO-RK interface be utilized via the API?}. - -\section{Using SBMLsqueezer as an on-line program} -\label{sec:SBMLsqueezer_online_version} - -SBMLsqueezer can also be used via the Galaxy web-service facility of the University of Tuebingen. -Since the user interface of this variant greatly differs from all other use-case scenarios, we here give a description of options and functions of the web interface. +The example in \vref{lst:SBMLsqueezer2API1} demonstrates how a convenience rate law \citep{Liebermeister2006} can be assigned to a selected reaction in an \SBML file. +This type of rate equation can be applied to reversible as well as to irreversible enzyme-catalyzed reactions and has been found to be particularly useful when no specific information about reaction mechanisms is known \citep{Draeger2007b, Draeger2009a, Draeger2011a}. +\lstinputlisting[caption={Assignment of a kinetic law to a reaction via the \acs{API} of SBMLsqueezer 2}, label={lst:SBMLsqueezer2API1}, firstline={47}, lastline={76}]{../../../examples/src/org/sbml/squeezer/test/SqueezeReaction.java} -\subsection{Open an \SBML file} -\subsection{Adjust your preferences} -\subsection{Create kinetic equations} -\subsection{Obtain the results} +\subsection{Querying \SABIO and merging the results into a local \SBML document} -\chapter{Example use cases} +\TODO{How can the SABIO-RK interface be utilized via the API?}. -\section{\emph{De-novo} creation of kinetic equations} -\subsection{For an entire network} -Starting from the screen in \vref{fig:KineticLawWizard} you have to click on \keys{Next}. On the next screen you see a table with the reactions and the suggested type of rate equation for each reaction (\vref{fig:suggestedEquations}). You can change a suggested rate law, if you are not satisfied with it (see \vref{fig:changeEquation}). -\begin{figure}[htbp] -\shadowimage[width=\textwidth]{Screenshot_5} -\caption[Table with suggested rate equation types]{Table with suggested rate equation types. -This table is displayed, when you start from the screen in \vref{fig:KineticLawWizard} and click on \keys{Next}. The table shows which type of rate equation SBMLsqueezer suggests to generate for each reaction as well as a preview of the respective formula. You can add the rate laws to the model by clicking on \keys{Finish}.} -\label{fig:suggestedEquations} -\end{figure} -\begin{SCfigure} -\shadowimage[width=.6\textwidth]{Screenshot_6} -\caption[Choosing an alternative rate law]{Choosing an alternative rate law. -If you are not satisfied with a rate law type suggested by SBMLsqueezer, you can click on the respective row in the table in \vref{fig:suggestedEquations}. Then this window is displayed which lets you choose another type of rate law.} -\label{fig:changeEquation} -\end{SCfigure} -\subsection{For selected reactions} -You can generate a rate law for a specific reaction by right-clicking on it. Then a window appears, which lets you choose the type of rate law (see \vref{fig:RateLawDialog} for details). +%\chapter{Example use cases} +% +%\section{\emph{De-novo} creation of kinetic equations} +%\subsection{For an entire network} +%Starting from the screen in \vref{fig:KineticLawWizard} you have to click on \keys{Next}. On the next screen you see a table with the reactions and the suggested type of rate equation for each reaction (\vref{fig:suggestedEquations}). You can change a suggested rate law, if you are not satisfied with it (see \vref{fig:changeEquation}). +% +%\begin{figure}[htbp] +%\shadowimage[width=\textwidth]{Screenshot_5} +%\caption[Table with suggested rate equation types]{Table with suggested rate equation types. +%This table is displayed, when you start from the screen in \vref{fig:KineticLawWizard} and click on \keys{Next}. The table shows which type of rate equation SBMLsqueezer suggests to generate for each reaction as well as a preview of the respective formula. You can add the rate laws to the model by clicking on \keys{Finish}.} +%\label{fig:suggestedEquations} +%\end{figure} +% +%\begin{SCfigure} +%\shadowimage[width=.54\textwidth]{Screenshot_6} +%\caption[Choosing an alternative rate law]{Choosing an alternative rate law. +%If you are not satisfied with a rate law type suggested by SBMLsqueezer, you can click on the respective row in the table in \vref{fig:suggestedEquations}. Then this window is displayed which lets you choose another type of rate law.} +%\label{fig:changeEquation} +%\end{SCfigure} +% +%\subsection{For selected reactions} +%You can generate a rate law for a specific reaction by right-clicking on it. Then a window appears, which lets you choose the type of rate law (see \vref{fig:RateLawDialog} for details). \chapter{Command-line arguments} @@ -1784,7 +1849,7 @@ \subsection{Additional options} Default value: \texttt{INFO} \end{description} -\section{LaTeX Options} +\section{\LaTeX{} options} \label{sec:LaTeX_Options} The program SBMLsqueezer brings with it a full version of the latest development @@ -1794,7 +1859,7 @@ \section{LaTeX Options} \SBMLLaTeX\footnote{\url{http://www.cogsys.cs.uni-tuebingen.de/software/SBML2LaTeX/}} and the corresponding publication \citep{Draeger2009b}. -\subsection{LaTeX compiler location} +\subsection{\LaTeX{} compiler location} \begin{description} \item[--load-latex-compiler{[} |={]}] The path to the \LaTeX{} compiler to generate PDF, DVI or other @@ -1885,9 +1950,9 @@ \subsection{Typographical options} serif) text. All possible values for type \texttt{} are: \begin{itemize} - \item \texttt{avant} {\fontfamily{pag}\selectfont (sample in Avant Garde)}, - \item \texttt{cmss} {\fontfamily{cmss}\selectfont (sample in Computer Modern Sans Serif)}, and - \item \texttt{helvetica} {\fontfamily{phv}\selectfont (sample in Helvetica)}. + \item\texttt{avant} {\fontfamily{pag}\selectfont (sample in Avant Garde)}, + \item\texttt{cmss} {\fontfamily{cmss}\selectfont (sample in Computer Modern Sans Serif)}, and + \item\texttt{helvetica} {\fontfamily{phv}\selectfont (sample in Helvetica)}. \end{itemize} Default value: \texttt{helvetica} @@ -1905,13 +1970,13 @@ \subsection{Typographical options} might not look as nicely as they do when using \texttt{mathptmx}. All possible values for type \texttt{} are: \begin{itemize} - \item \texttt{chancery} {\fontfamily{pzc}\selectfont (sample in Chancery)}, - \item \texttt{charter} {\fontfamily{bch}\selectfont (sample in Charter)}, - \item \texttt{cmr} {\fontfamily{cmr}\selectfont (sample in Computer Modern Roman)}, - \item \texttt{mathptmx} {\fontfamily{ptm}\selectfont (sample in Times for math)}, - \item \texttt{palatino} {\fontfamily{ppl}\selectfont (sample in Palatino)}, - \item \texttt{times} {\fontfamily{ptm}\selectfont (sample in Times)}, and - \item \texttt{utopia} {\fontfamily{put}\selectfont (sample in Utopia)}. + \item\texttt{chancery} {\fontfamily{pzc}\selectfont (sample in Chancery)}, + \item\texttt{charter} {\fontfamily{bch}\selectfont (sample in Charter)}, + \item\texttt{cmr} {\fontfamily{cmr}\selectfont (sample in Computer Modern Roman)}, + \item\texttt{mathptmx} {\fontfamily{ptm}\selectfont (sample in Times for math)}, + \item\texttt{palatino} {\fontfamily{ppl}\selectfont (sample in Palatino)}, + \item\texttt{times} {\fontfamily{ptm}\selectfont (sample in Times)}, and + \item\texttt{utopia} {\fontfamily{put}\selectfont (sample in Utopia)}. \end{itemize} Default value: \texttt{mathptmx} @@ -1921,8 +1986,8 @@ \subsection{Typographical options} also marked with this font. All possible values for type \texttt{} are: \begin{itemize} - \item \texttt{cmt} {\fontfamily{cmt}\selectfont (sample in Computer Modern Typewriter)} and - \item \texttt{courier} {\fontfamily{pcr}\selectfont (sample in Courier)}. + \item\texttt{cmt} {\fontfamily{cmt}\selectfont (sample in Computer Modern Typewriter)} and + \item\texttt{courier} {\fontfamily{pcr}\selectfont (sample in Courier)}. \end{itemize} Default value: \texttt{cmt} @@ -2092,7 +2157,7 @@ \section{Rate laws for metabolic processes} \begin{itemize} \item (Generalized) mass-action rate law with numerous orders \citep[p.~16]{Guldberg1879, Heinrich1996} \item Uni-uni Michaelis-Menten kinetics \citep{Michaelis1913} - \item Irreversible non-modulated non-interacting reactant enzymes (\SBO) + \item Irreversible non-modulated non-interacting reactant enzymes (see \SBO) \item Bi-uni enzyme mechanisms \citep{Segel1993, Bisswanger2000, Cornish-Bowden2004} \begin{itemize} \item Random-order mechanism @@ -2188,17 +2253,17 @@ \section{Rate laws for gene-regulatory processes} \chapter{FAQ and troubleshooting} \label{ch:faq} -TODO: These are some template questions. Add new ones and modify/ remove the -old ones to suit your needs. +\TODO{These are some template questions. Add new ones and modify/ remove the +old ones to suit your needs.} -\noindent \textbf{Where can I get help for a certain component/ option/ checkbox/ etc.?}\newline -Most elements in SBMLsqueezer have tooltips. If you don't understand an option, you +\noindent \textbf{Where can I get help for a certain component, option, check-box etc.?}\newline +Most elements in SBMLsqueezer have tool-tips. If you do not understand an option, you can get help in the first place by just pointing the mouse cursor over it and -wait for the tooltip to show up ($\sim$ 3 seconds).\newline +wait for the tool-tip to show up ($\sim$3 seconds).\newline \noindent \textbf{I'm getting a ``java.lang.OutOfMemoryError: Java heap space"}\newline Some operations need a lot of memory. If you simply start SBMLsqueezer, without any -JVM parameters, only 64\,MB of memory are available. Please append the argument +\JVM parameters, only 64\,MB of memory are available. Please append the argument \texttt{-Xmx1024M} to start the application with 1\,GB of main memory. See \vref{startingTheProgram} for a more detailed description of how to start the application with additional memory. If possible, you should give the @@ -2206,24 +2271,18 @@ \chapter{FAQ and troubleshooting} available to the application.\newline \noindent \textbf{Is an internet connection required to run SBMLsqueezer?}\newline -An internet connection is required for most operations. Many identifier mapping -files and pathway-based visualizations require an active internet connection. -However, if you import your data directly with NCBI Entrez Gene IDs and do not -use the pathway-visualization or GO-enrichment, you should be able to run the -application offline.\newline - -\noindent \textbf{Where can I get the latest version?}\newline -Go to \url{http://www.cogsys.cs.uni-tuebingen.de/software/Integrator/}.\newline - -\noindent \textbf{Which \Java version must be installed on my computer to launch -SBMLsqueezer?}\newline SBMLsqueezer requires at least \Java 1.6. Please see -\url{http://www.java.com/de/download/} to download the latest \Java version. - -\noindent -\textbf{Why does SBMLsqueezer not start on my Mac with \MacOSX prior to 10.6 Update 3?}\newline -If you try to launch SBMLsqueezer, but the application does -not start and you receive the following error message on the command-line or -\Java console of your Mac, you need to update your \Java installation: +The vast majority of SBMLsqueezer's functions run in off-line mode. +Features that require an active internet connection are the on-line check for updates and following external links within on-line help. +\newline + +\noindent \textbf{Where can I obtain the latest version?}\newline +Go to \url{http://www.cogsys.cs.uni-tuebingen.de/software/SBMLsqueezer/}.\newline + +\noindent \textbf{Which \Java version must be installed on my computer to launch SBMLsqueezer?}\newline +SBMLsqueezer requires at least \Java 1.6. Please see \url{http://www.java.com/de/download/} to download the latest \Java version. + +\noindent \textbf{Why does SBMLsqueezer not start on my Mac with \MacOSX prior to 10.6 Update 3?}\newline +If you try to launch SBMLsqueezer, but the application does not start and you receive the following error message on the command-line or \Java console of your Mac, you need to update your \Java installation: \begin{verbatim} Exception in thread "AWT-EventQueue-0" java.lang.NoClassDefFoundError: com/apple/eawt/AboutHandler @@ -2231,15 +2290,20 @@ \chapter{FAQ and troubleshooting} at java.lang.ClassLoader.defineClass(ClassLoader.java:703) ... \end{verbatim} -The interface \texttt{com.apple.eawt.AboutHandler} was introduced to \Java for -\MacOSX 10.6 Update 3. If you have an earlier version of \MacOSX or \Java, -please update your OS or \Java installation. Also see the \MacOSX documentation -about the \texttt{AboutHandler} for more information. On a Mac, you can update -your \Java installation through the Software Update menu item in the main Apple -menu. +The interface \texttt{com.apple.eawt.AboutHandler} was introduced to \Java for \MacOSX 10.6 Update 3. If you have an earlier version of \MacOSX or \Java, please update your OS or \Java installation. +Also see the \MacOSX documentation about the \texttt{AboutHandler} for more information. On a Mac, you can update your \Java installation through the Software Update menu item in the main Apple menu. +\newline + +\noindent \textbf{How can I report bugs or get help?}\newline +Just contact the mailing list using the following e-mail address: \ding{41} +\href{mailto:sbmlsqueezer@googlegroups.com}{\texttt{sbmlsqueezer@google\-groups.com}} \chapter{License} +\begin{wrapfigure}{O}{1.5cm} +\vspace{\wrapfigspace} +\includegraphics[width=1.5cm]{lgplv3-147x51} +\end{wrapfigure} SBMLsqueezer is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version~3 of the License, or @@ -2286,7 +2350,7 @@ \section{Core developers} \section{Principal Investigators} \begin{itemize} -\item Bernhard \O. Palsson, +\item Bernhard \O.~Palsson, University of California, San Diego, La Jolla, California, USA \href{mailto:palsson@ucsd.edu}{palsson@ucsd.edu} \item Andreas Zell, @@ -2308,7 +2372,7 @@ \section{Alumni} Oliver Kohlbacher, Sarah Rachel M\"uller vom Hagen, Sebastian Nagel, -Leif J. Pallesen, +Leif J.~Pallesen, Alexander Peltzer, Julianus Pfeuffer, Matthias Rall, @@ -2316,11 +2380,17 @@ \section{Alumni} Simon Sch\"afer, Adrian Schr\"oder, Jochen Supper, -Dieudonn\'e M. Wouamba, -Michael J. Ziller +Dieudonn\'e M.~Wouamba, +Michael J.~Ziller We also thank Shaowu Yang for providing the \Chinese language pack for this program. + \section{Collaborators and partners} The authors are grateful to the \SABIO team, in particular Martin Golebiewski and Wolfgang M\"uller from the Heidelberg Insitute of Technology (HITS). + +%\section{Disclaimer} +% +%This document does not claim affiliation or endorsement of any of the authors with any of the producers of commercial software products that are mentioned throughout this text. +%In particular, none of the authors is affiliated with Apple, Microsoft, Oracle, neither involved in the development, implementation, or distribution of their commercial software products, such as \Java, \Windows, \MacOSX. diff --git a/doc/tutorials/user_guide/tex/Release_Notes.tex b/doc/tutorials/user_guide/tex/Release_Notes.tex index 7b2b57c6d..fd8604ab4 100644 --- a/doc/tutorials/user_guide/tex/Release_Notes.tex +++ b/doc/tutorials/user_guide/tex/Release_Notes.tex @@ -310,7 +310,7 @@ \subsubsection{Improved Systems Biology Ontology support} Whenever possible, SBMLsqueezer annotates newly created objects, such as \texttt{Parameter}s or \texttt{UnitDefinition}s, with \SBO identifiers. -\paragraph{\MIRIAM Support} +\subsubsection{\MIRIAM Support} In contrast to earlier versions, SBMLsqueezer now also interprets and uses \MIRIAM tags. The new command-line and configuration key option @@ -502,7 +502,7 @@ \subsection{Bug fixes} The new plug-in interface in \JSBML provides a much better performance. Errors in kinetic equations and units of parameters have been detected and solved: -\begin{itemize} +\begin{dinglist}{54} \item Sometimes SBMLsqueezer created invalid identifiers for newly introduced units. \item The units of the association and dissociation constant in generalized mass @@ -512,7 +512,7 @@ \subsection{Bug fixes} \item The units of the half saturation constant in the (generalized) Hill equation were not correctly derived. The derivation of units of kinetic parameters has been improved -\end{itemize} +\end{dinglist} Several minor issues with the graphical user interface have been solved. \subsection{Known Issues} diff --git a/doc/tutorials/user_guide/tex/abbreviations.tex b/doc/tutorials/user_guide/tex/abbreviations.tex index 2f461b568..55ea71d05 100644 --- a/doc/tutorials/user_guide/tex/abbreviations.tex +++ b/doc/tutorials/user_guide/tex/abbreviations.tex @@ -16,4 +16,5 @@ \chapter{Acronyms} \acro{SABIO-RK} {System for the Analysis of Biochemical Pathways -- Reaction Kinetics} \acro{SBO} {Systems Biology Ontology} \acro{XHTML} {Extended HTML} + \acro{XML} {Extended Markup Language} \end{acronym} diff --git a/doc/tutorials/user_guide/tex/literature.bib b/doc/tutorials/user_guide/tex/literature.bib index f8dabfda8..960d0c3fe 100644 --- a/doc/tutorials/user_guide/tex/literature.bib +++ b/doc/tutorials/user_guide/tex/literature.bib @@ -1,6 +1,37 @@ % This file was created with JabRef 2.9.2. % Encoding: UTF8 +@ARTICLE{Arnold2011, + author = {Arnold, Anne and Nikoloski, Zoran}, + title = {A quantitative comparison of Calvin-Benson cycle models}, + journal = {Trends Plant Sci}, + year = {2011}, + volume = {16}, + pages = {676--683}, + number = {12}, + month = dec, + abstract = {The Calvin-Benson cycle (CBC) provides the precursors for biomass + synthesis necessary for plant growth. The dynamic behavior and yield + of the CBC depend on the environmental conditions and regulation + of the cellular state. Accurate quantitative models hold the promise + of identifying the key determinants of the tightly regulated CBC + function and their effects on the responses in future climates. We + provide an integrative analysis of the largest compendium of existing + models for photosynthetic processes. Based on the proposed ranking, + our framework facilitates the discovery of best-performing models + with regard to metabolomics data and of candidates for metabolic + engineering.}, + doi = {10.1016/j.tplants.2011.09.004}, + institution = {Institute of Biochemistry and Biology, University of Potsdam, 14476 + Potsdam, Germany.}, + keywords = {Metabolomics; Photosynthesis; Plants, growth /&/ development/metabolism}, + language = {eng}, + medline-pst = {ppublish}, + pii = {S1360-1385(11)00195-6}, + pmid = {22001849}, + url = {http://dx.doi.org/10.1016/j.tplants.2011.09.004} +} + @ARTICLE{Buechel2013, author = {B{\"u}chel, Finja and Rodriguez, Nicolas and Swainston, Neil and Wrzodek, Clemens and Czauderna, Tobias and Keller, Roland and Mittag, @@ -241,6 +272,96 @@ @ARTICLE{Courtot2011 url = {http://dx.doi.org/10.1038/msb.2011.77} } +@INPROCEEDINGS{Draeger2007b, + author = {Dr{\"a}ger, Andreas and Kronfeld, Marcel and Supper, Jochen and Planatscher, + Hannes and Magnus, J{\o}rgen Barsett and Oldiges, Marco and Zell, + Andreas}, + title = {{Benchmarking Evolutionary Algorithms on Convenience Kinetics Models + of the Valine and Leucine Biosynthesis in \emph{C.~glutamicum}}}, + booktitle = {2007 IEEE Congress on Evolutionary Computation}, + year = {2007}, + editor = {Srinivasan, Dipti and Wang, Lipo}, + pages = {896--903}, + address = {Singapore}, + month = {25-28 September}, + organization = {IEEE Computational Intelligence Society}, + publisher = {IEEE Press}, + abstract = {An important problem in systems biology is parameter estimation for + biochemical system models. Our work concentrates on the metabolic + subnetwork of the valine and leucine biosynthesis in Corynebacterium + glutamicum, an anaerobic actinobacterium of high biotechnological + importance. Using data of an in vivo experiment measuring 13 metabolites + during a glucose stimulus-response experiment we investigate the + performance of various Evolutionary Algorithms on the parameter inference + problem in biochemical modeling. Due to the inconclusive information + on the reversibility of the reactions in the pathway, we develop + both a reversible and an irreversible differential equation model + based on the recent convenience kinetics approach. As the reversible + model allows better approximation on the whole, we use it to analyze + the impact of different settings on four especially promising EAs. + We show that Particle Swarm Optimization as well as Differential + Evolution are useful methods for parameter estimation on convenience + kinetics models outperforming Genetic Algorithm and Evolution Strategy + approaches and nearly reaching the quality of independent spline + approximations on the raw data.}, + isbn = {1-4244-1340-0}, + keywords = {systems biology, mathematical modeling, benchmark, evolutionary algorithms, + valine and leucine biosynthesis, Corynebacterium glutamicum, convenience + kinetics} +} + +@ARTICLE{Draeger2009a, + author = {Dr{\"a}ger, Andreas and Kronfeld, Marcel and Ziller, Michael Johannes + and Supper, Jochen and Planatscher, Hannes and Magnus, J{\o}rgen + Barsett and Oldiges, Marco and Kohlbacher, Oliver and Zell, Andreas}, + title = {{Modeling metabolic networks in \emph{C.~glutamicum}: a comparison + of rate laws in combination with various parameter optimization strategies}}, + journal = {BMC Syst Biol}, + year = {2009}, + volume = {3}, + pages = {5}, + month = {January}, + abstract = {Background: To understand the dynamic behavior of cellular systems, + mathematical modeling is often necessary and comprises three steps: + (1) experimental measurement of participating molecules, (2) assignment + of rate laws to each reaction, and (3) parameter calibration with + respect to the measurements. In each of these steps the modeler is + confronted with a plethora of alternative approaches, e. g., the + selection of approximative rate laws in step two as specific equations + are often unknown, or the choice of an estimation procedure with + its specific settings in step three. This overall process with its + numerous choices and the mutual influence between them makes it hard + to single out the best modeling approach for a given problem. + + Results: We investigate the modeling process using multiple kinetic + equations together with various parameter optimization methods for + a well-characterized example network, the biosynthesis of valine + and leucine in C. glutamicum. For this purpose, we derive seven dynamic + models based on generalized mass action, Michaelis-Menten and convenience + kinetics as well as the stochastic Langevin equation. In addition, + we introduce two modeling approaches for feedback inhibition to the + mass action kinetics. The parameters of each model are estimated + using eight optimization strategies. To determine the most promising + modeling approaches together with the best optimization algorithms, + we carry out a two-step benchmark: (1) coarse-grained comparison + of the algorithms on all models and (2) fine-grained tuning of the + best optimization algorithms and models. To analyze the space of + the best parameters found for each model, we apply clustering, variance, + and correlation analysis. + + Conclusions: A mixed model based on the convenience rate law and the + Michaelis-Menten equation, in which all reactions are assumed to + be reversible, is the most suitable deterministic modeling approach + followed by a reversible generalized mass action kinetics model. + A Langevin model is advisable to take stochastic effects into account. + To estimate the model parameters, three algorithms are particularly + useful: For first attempts the settings-free Tribes algorithm yields + valuable results. Particle swarm optimization and differential evolution + provide significantly better results with appropriate settings.}, + doi = {10.1186/1752-0509-3-5}, + url = {http://www.biomedcentral.com/1752-0509/3/5} +} + @PHDTHESIS{Draeger2011a, author = {Dr\"ager, Andreas}, title = {Computational Modeling of Biochemical Networks}, @@ -1729,6 +1850,41 @@ @h-its.org url = {http://dx.doi.org/10.1093/nar/gkr1046} } +@ARTICLE{Wolf2000, + author = {Wolf, Jana and Passarge, Jutta and Somsen, Oscar J. G. and Snoep, + Jacky L. and Heinrich, Reinhart and Westerhoff, Hans V.}, + title = {Transduction of intracellular and intercellular dynamics in yeast + glycolytic oscillations}, + journal = {Biophys J}, + year = {2000}, + volume = {78}, + pages = {1145--1153}, + number = {3}, + month = mar, + abstract = {Under certain well-defined conditions, a population of yeast cells + exhibits glycolytic oscillations that synchronize through intercellular + acetaldehyde. This implies that the dynamic phenomenon of the oscillation + propagates within and between cells. We here develop a method to + establish by which route dynamics propagate through a biological + reaction network. Application of the method to yeast demonstrates + how the oscillations and the synchronization signal can be transduced. + That transduction is not so much through the backbone of glycolysis, + as via the Gibbs energy and redox coenzyme couples (ATP/ADP, and + NADH/NAD), and via both intra- and intercellular acetaldehyde.}, + doi = {10.1016/S0006-3495(00)76672-0}, + institution = {Humboldt University, Institute of Biology, Theoretical Biophysics, + Invalidenstrasse 42, D-10115 Berlin, Germany.}, + keywords = {Acetaldehyde, metabolism; Adenosine Diphosphate, metabolism; Adenosine + Triphosphate, metabolism; Glycolysis; Kinetics; Models, Chemical; + NAD, metabolism; Oscillometry; Oxidation-Reduction; Saccharomyces + cerevisiae, metabolism}, + language = {eng}, + medline-pst = {ppublish}, + pii = {S0006-3495(00)76672-0}, + pmid = {10692304}, + url = {http://dx.doi.org/10.1016/S0006-3495(00)76672-0} +} + @ARTICLE{Wrzodek2013, author = {Wrzodek, Clemens and B\"uchel, Finja and Ruff, Manuel and Dr\"ager, Andreas and Zell, Andreas}, diff --git a/doc/tutorials/user_guide/tex/macros.tex b/doc/tutorials/user_guide/tex/macros.tex index 648ed74bd..71a159d49 100644 --- a/doc/tutorials/user_guide/tex/macros.tex +++ b/doc/tutorials/user_guide/tex/macros.tex @@ -12,7 +12,7 @@ \newcommand{\file} [1]{\texttt{#1}} \newcommand{\wrapfigspace} {-10pt} -\newcommand{\TODO} [1]{\textcolor{red}{#1}} +\newcommand{\TODO} [1]{\pdfcomment{#1}} %\textcolor{red}{#1}} \newcommand{\numero} {N\raisebox{.25em}{\relsize{-2}\underline{o}}\xspace} \newcommand{\itemcolor}[1]{% Update list item colour \renewcommand{\makelabel}[1]{\color{#1}\hfil ##1}} @@ -34,7 +34,7 @@ % E \newcommand{\English} {English\index{Language pack!English}\xspace} -\newcommand{\Eclipse} {Eclipse\index{IDE!Eclipse}\xspace} +\newcommand{\Eclipse} {Eclipse\index{Eclipse}\xspace} % G \newcommand{\Galaxy} {Galaxy\index{Galaxy}\xspace} @@ -78,7 +78,7 @@ \newcommand{\OS} {operating system\index{Operating System}\xspace} % P -\newcommand{\PATH} {\texttt{PATH}\index{Operating System!MS Windows!\texttt{PATH}}\xspace} +\newcommand{\PATH} {\texttt{PATH}\index{Operating System!Microsoft Windows!\texttt{PATH}}\xspace} \newcommand{\pathmodels} {path2models\index{Path to models project}\xspace} \newcommand{\PDF} {\ac{PDF}\index{\acfi{PDF}}\xspace} @@ -92,15 +92,16 @@ \newcommand{\SBMLLaTeXs} {{\sffamily\upshape\raisebox{-.35ex}{S\hspace{-.425ex}BML}\hspace{-0.5ex}\begin{rotate}{-17.5}\raisebox{-.1ex}{2}\end{rotate}\hspace{1ex}\LaTeX}} \newcommand{\SBMLLaTeX} {\SBMLLaTeXs\index{SBML2LaTeX@{SBML2\LaTeX}}\xspace} \newcommand{\SBMLsimulator} {SBMLsimulator\index{SBMLsimulator}\xspace} -\newcommand{\SBO} {\ac{SBO}\index{SBO}\xspace} +\newcommand{\SBO} {\ac{SBO}\index{\acfi{SBO}}\xspace} % U \newcommand{\UbuntuLinux} {Ubuntu Linux\index{Operating System!Linux!Ubuntu}\xspace} \newcommand{\Unix} {Unix\index{Operating System!Unix}\xspace} % W -\newcommand{\WindowsSeven} {Windows~7\index{Operating System!Windows!Windows~7}\xspace} -\newcommand{\Windows} {Microsoft Windows\index{Operating System!MS Windows}\xspace} +\newcommand{\WindowsSeven} {Windows~7\index{Operating System!Microsoft Windows!Windows~7}\xspace} +\newcommand{\Windows} {Microsoft Windows\index{Operating System!Microsoft Windows}\xspace} % X \newcommand{\XHTML} {\ac{XHTML}\index{\acfi{XHTML}}\xspace} +\newcommand{\XML} {\ac{XML}\index{\acfi{XML}}\xspace} diff --git a/examples/src/org/sbml/squeezer/test/SqueezeFile.java b/examples/src/org/sbml/squeezer/test/SqueezeFile.java new file mode 100644 index 000000000..4c7ba4cfa --- /dev/null +++ b/examples/src/org/sbml/squeezer/test/SqueezeFile.java @@ -0,0 +1,78 @@ +/* + * $Id$ + * $URL$ + * --------------------------------------------------------------------- + * This file is part of SBMLsqueezer, a Java program that creates rate + * equations for reactions in SBML files (http://sbml.org). + * + * Copyright (C) 2006-2014 by the University of Tuebingen, Germany. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + * --------------------------------------------------------------------- + */ +package org.sbml.squeezer.test; + +import org.sbml.jsbml.Model; +import org.sbml.squeezer.OptionsGeneral; +import org.sbml.squeezer.SBMLsqueezer; +import org.sbml.squeezer.kinetics.ConvenienceKinetics; +import org.sbml.squeezer.kinetics.MichaelisMenten; +import org.sbml.squeezer.kinetics.OptionsRateLaws; + +import de.zbit.util.prefs.SBPreferences; + +/** + * This is a simple example that displays how to use {@link SBMLsqueezer} as an + * rate equation generating core in a more complex application. + * + * @author Andreas Dräger + * @version $Rev$ + * @since 2.0 + */ +public class SqueezeFile { + + /** + * This program takes the absolute paths to an input file and an output + * file as arguments, configures several preferences for + * {@link SBMLsqueezer}, generates kinetic equations, units, parameters + * etc. and saves the result in the given output file in SBML format. + * + * @param args absolute or relative paths to two SBML files (in and out) + * @throws Throwable if either user preferences cannot be made + * persistent or the creation of rate laws fails. + */ + public static void main(String[] args) throws Throwable { + /* + * Configure user preferences of SBMLsqueezer + */ + // General preferences + SBPreferences prefs = SBPreferences.getPreferencesFor(OptionsGeneral.class); + prefs.put(OptionsGeneral.ALL_REACTIONS_AS_ENZYME_CATALYZED, true); + prefs.put(OptionsGeneral.DEFAULT_COMPARTMENT_SIZE, 1d); + prefs.put(OptionsGeneral.POSSIBLE_ENZYME_RNA, true); + prefs.flush(); + + // Rate law selection + prefs = SBPreferences.getPreferencesFor(OptionsRateLaws.class); + prefs.put(OptionsRateLaws.KINETICS_REVERSIBLE_UNI_UNI_TYPE, MichaelisMenten.class); + prefs.put(OptionsRateLaws.KINETICS_REVERSIBLE_ARBITRARY_ENZYME_REACTIONS, ConvenienceKinetics.class); + prefs.flush(); + + // Initialize SBMLsqueezer with JSBML as its internal SBML library + SBMLsqueezer squeezer = new SBMLsqueezer(); + // Create kinetic equations, parameters, units etc. and save the result + squeezer.squeeze(args[0], args[1]); + } + +} diff --git a/examples/src/org/sbml/squeezer/test/SqueezeReaction.java b/examples/src/org/sbml/squeezer/test/SqueezeReaction.java new file mode 100644 index 000000000..531c84668 --- /dev/null +++ b/examples/src/org/sbml/squeezer/test/SqueezeReaction.java @@ -0,0 +1,78 @@ +/* + * $Id$ + * $URL$ + * --------------------------------------------------------------------- + * This file is part of SBMLsqueezer, a Java program that creates rate + * equations for reactions in SBML files (http://sbml.org). + * + * Copyright (C) 2006-2014 by the University of Tuebingen, Germany. + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + * --------------------------------------------------------------------- + */ +package org.sbml.squeezer.test; + +import java.io.File; + +import org.sbml.jsbml.Model; +import org.sbml.jsbml.Reaction; +import org.sbml.jsbml.SBMLDocument; +import org.sbml.jsbml.SBMLReader; +import org.sbml.jsbml.SBMLWriter; +import org.sbml.squeezer.KineticLawGenerator; +import org.sbml.squeezer.UnitConsistencyType; +import org.sbml.squeezer.kinetics.ConvenienceKinetics; +import org.sbml.squeezer.kinetics.TypeStandardVersion; + +import de.zbit.util.progressbar.ProgressBar; + +/** + * @author Andreas Dräger + * @version $Rev$ + * @since 2.0 + */ +public class SqueezeReaction { + + /** + * Reads a given SBML file, creates a convenience rate law for the first + * reaction within that file, and stores the result in the second file. + * + * @param args absolute or relative paths to two SBML files (in and out) + * @throws Throwable + */ + public static void main(String args[]) throws Throwable { + // Select an SBML reaction object from your SBML document + SBMLDocument doc = SBMLReader.read(new File(args[0])); + Model model = doc.getModel(); + Reaction reaction = model.getReaction(0); + + // Create and run the kinetic law generator + KineticLawGenerator klg = new KineticLawGenerator(model); + // This operates on a copy of the model that only contains one reaction + klg.createKineticLaw( + reaction, // the selected reaction + ConvenienceKinetics.class, // the type of rate law to be created + false, // whether to set the reaction reversible + TypeStandardVersion.cat, // type parameter for modular rate laws + UnitConsistencyType.amount, // how to ensure unit consistency + 1d); // the value for new parameters + + // Transfer the rate law from the model copy to the original model + klg.storeKineticLaws(); + + // Save the result in another file + SBMLWriter.write(doc, new File(args[1]), ' ', (short) 2); + } + +}