Compiled SBMLsqueezer again for release, generated JavaDoc, improved …

…the Users' Guide, implemented example program code, updated figures.
draeger-lab · Jun 2, 2014 · caaf930 · caaf930
1 parent cb23026
commit caaf930
Show file tree

Hide file tree

Showing 407 changed files with 1,714 additions and 1,327 deletions.
diff --git a/dist/SBMLsqueezer-2.0/SBMLsqueezer_v2.0.zip b/dist/SBMLsqueezer-2.0/SBMLsqueezer_v2.0.zip
diff --git a/dist/SBMLsqueezer-2.0/SBMLsqueezer_v2.0_Garuda.zip b/dist/SBMLsqueezer-2.0/SBMLsqueezer_v2.0_Garuda.zip
diff --git a/dist/SBMLsqueezer-2.0/SBMLsqueezer_v2.0_incl-libs.jar b/dist/SBMLsqueezer-2.0/SBMLsqueezer_v2.0_incl-libs.jar
diff --git a/doc/api/version_2.0/allclasses-frame.html b/doc/api/version_2.0/allclasses-frame.html
@@ -2,12 +2,12 @@
 <!--NewPage-->
 <HTML>
 <HEAD>
-<!-- Generated by javadoc (build 1.6.0_65) on Thu Apr 24 17:20:18 PDT 2014 -->
+<!-- Generated by javadoc (build 1.6.0_65) on Mon May 19 11:34:05 PDT 2014 -->
 <TITLE>
 All Classes (SBMLsqueezer 2.0 API Specification)
 </TITLE>
 
-<META NAME="date" CONTENT="2014-04-24">
+<META NAME="date" CONTENT="2014-05-19">
 
 <LINK REL ="stylesheet" TYPE="text/css" HREF="javadoc-style.css" TITLE="Style">
 

diff --git a/doc/api/version_2.0/allclasses-noframe.html b/doc/api/version_2.0/allclasses-noframe.html
@@ -2,12 +2,12 @@
 <!--NewPage-->
 <HTML>
 <HEAD>
-<!-- Generated by javadoc (build 1.6.0_65) on Thu Apr 24 17:20:18 PDT 2014 -->
+<!-- Generated by javadoc (build 1.6.0_65) on Mon May 19 11:34:05 PDT 2014 -->
 <TITLE>
 All Classes (SBMLsqueezer 2.0 API Specification)
 </TITLE>
 
-<META NAME="date" CONTENT="2014-04-24">
+<META NAME="date" CONTENT="2014-05-19">
 
 <LINK REL ="stylesheet" TYPE="text/css" HREF="javadoc-style.css" TITLE="Style">
 

diff --git a/doc/api/version_2.0/constant-values.html b/doc/api/version_2.0/constant-values.html
@@ -2,12 +2,12 @@
 <!--NewPage-->
 <HTML>
 <HEAD>
-<!-- Generated by javadoc (build 1.6.0_65) on Thu Apr 24 17:20:15 PDT 2014 -->
+<!-- Generated by javadoc (build 1.6.0_65) on Mon May 19 11:34:04 PDT 2014 -->
 <TITLE>
 Constant Field Values (SBMLsqueezer 2.0 API Specification)
 </TITLE>
 
-<META NAME="date" CONTENT="2014-04-24">
+<META NAME="date" CONTENT="2014-05-19">
 
 <LINK REL ="stylesheet" TYPE="text/css" HREF="javadoc-style.css" TITLE="Style">
 
@@ -217,7 +217,7 @@ <H1>
 </TABLE>
 </TD>
 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-Generated at April 24 2014<br/>Version 2.0 Revision 1096</EM>
+Generated at May 19 2014<br/>Version 2.0 Revision 1101</EM>
 </TD>
 </TR>
 

diff --git a/doc/api/version_2.0/deprecated-list.html b/doc/api/version_2.0/deprecated-list.html
@@ -2,12 +2,12 @@
 <!--NewPage-->
 <HTML>
 <HEAD>
-<!-- Generated by javadoc (build 1.6.0_65) on Thu Apr 24 17:20:18 PDT 2014 -->
+<!-- Generated by javadoc (build 1.6.0_65) on Mon May 19 11:34:05 PDT 2014 -->
 <TITLE>
 Deprecated List (SBMLsqueezer 2.0 API Specification)
 </TITLE>
 
-<META NAME="date" CONTENT="2014-04-24">
+<META NAME="date" CONTENT="2014-05-19">
 
 <LINK REL ="stylesheet" TYPE="text/css" HREF="javadoc-style.css" TITLE="Style">
 
@@ -111,7 +111,7 @@ <H2>
 </TABLE>
 </TD>
 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-Generated at April 24 2014<br/>Version 2.0 Revision 1096</EM>
+Generated at May 19 2014<br/>Version 2.0 Revision 1101</EM>
 </TD>
 </TR>
 

diff --git a/doc/api/version_2.0/help-doc.html b/doc/api/version_2.0/help-doc.html
@@ -2,12 +2,12 @@
 <!--NewPage-->
 <HTML>
 <HEAD>
-<!-- Generated by javadoc (build 1.6.0_65) on Thu Apr 24 17:20:18 PDT 2014 -->
+<!-- Generated by javadoc (build 1.6.0_65) on Mon May 19 11:34:05 PDT 2014 -->
 <TITLE>
 API Help (SBMLsqueezer 2.0 API Specification)
 </TITLE>
 
-<META NAME="date" CONTENT="2014-04-24">
+<META NAME="date" CONTENT="2014-05-19">
 
 <LINK REL ="stylesheet" TYPE="text/css" HREF="javadoc-style.css" TITLE="Style">
 
@@ -188,7 +188,7 @@ <H3>
 </TABLE>
 </TD>
 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-Generated at April 24 2014<br/>Version 2.0 Revision 1096</EM>
+Generated at May 19 2014<br/>Version 2.0 Revision 1101</EM>
 </TD>
 </TR>
 

diff --git 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 @@
 <!--NewPage-->
 <HTML>
 <HEAD>
-<!-- Generated by javadoc (build 1.6.0_65) on Thu Apr 24 17:20:17 PDT 2014 -->
+<!-- Generated by javadoc (build 1.6.0_65) on Mon May 19 11:34:05 PDT 2014 -->
 <TITLE>
 A-Index (SBMLsqueezer 2.0 API Specification)
 </TITLE>
 
-<META NAME="date" CONTENT="2014-04-24">
+<META NAME="date" CONTENT="2014-05-19">
 
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../javadoc-style.css" TITLE="Style">
 
@@ -191,7 +191,7 @@
 </TABLE>
 </TD>
 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-Generated at April 24 2014<br/>Version 2.0 Revision 1096</EM>
+Generated at May 19 2014<br/>Version 2.0 Revision 1101</EM>
 </TD>
 </TR>
 

diff --git 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 @@
 <!--NewPage-->
 <HTML>
 <HEAD>
-<!-- Generated by javadoc (build 1.6.0_65) on Thu Apr 24 17:20:18 PDT 2014 -->
+<!-- Generated by javadoc (build 1.6.0_65) on Mon May 19 11:34:05 PDT 2014 -->
 <TITLE>
 J-Index (SBMLsqueezer 2.0 API Specification)
 </TITLE>
 
-<META NAME="date" CONTENT="2014-04-24">
+<META NAME="date" CONTENT="2014-05-19">
 
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../javadoc-style.css" TITLE="Style">
 
@@ -132,7 +132,7 @@
 </TABLE>
 </TD>
 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-Generated at April 24 2014<br/>Version 2.0 Revision 1096</EM>
+Generated at May 19 2014<br/>Version 2.0 Revision 1101</EM>
 </TD>
 </TR>
 

diff --git 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 @@
 <!--NewPage-->
 <HTML>
 <HEAD>
-<!-- Generated by javadoc (build 1.6.0_65) on Thu Apr 24 17:20:18 PDT 2014 -->
+<!-- Generated by javadoc (build 1.6.0_65) on Mon May 19 11:34:05 PDT 2014 -->
 <TITLE>
 K-Index (SBMLsqueezer 2.0 API Specification)
 </TITLE>
 
-<META NAME="date" CONTENT="2014-04-24">
+<META NAME="date" CONTENT="2014-05-19">
 
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../javadoc-style.css" TITLE="Style">
 
@@ -230,7 +230,7 @@
 </TABLE>
 </TD>
 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-Generated at April 24 2014<br/>Version 2.0 Revision 1096</EM>
+Generated at May 19 2014<br/>Version 2.0 Revision 1101</EM>
 </TD>
 </TR>
 

diff --git 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 @@
 <!--NewPage-->
 <HTML>
 <HEAD>
-<!-- Generated by javadoc (build 1.6.0_65) on Thu Apr 24 17:20:18 PDT 2014 -->
+<!-- Generated by javadoc (build 1.6.0_65) on Mon May 19 11:34:05 PDT 2014 -->
 <TITLE>
 L-Index (SBMLsqueezer 2.0 API Specification)
 </TITLE>
 
-<META NAME="date" CONTENT="2014-04-24">
+<META NAME="date" CONTENT="2014-05-19">
 
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../javadoc-style.css" TITLE="Style">
 
@@ -146,7 +146,7 @@
 </TABLE>
 </TD>
 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-Generated at April 24 2014<br/>Version 2.0 Revision 1096</EM>
+Generated at May 19 2014<br/>Version 2.0 Revision 1101</EM>
 </TD>
 </TR>
 

diff --git 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 @@
 <!--NewPage-->
 <HTML>
 <HEAD>
-<!-- Generated by javadoc (build 1.6.0_65) on Thu Apr 24 17:20:18 PDT 2014 -->
+<!-- Generated by javadoc (build 1.6.0_65) on Mon May 19 11:34:05 PDT 2014 -->
 <TITLE>
 M-Index (SBMLsqueezer 2.0 API Specification)
 </TITLE>
 
-<META NAME="date" CONTENT="2014-04-24">
+<META NAME="date" CONTENT="2014-05-19">
 
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../javadoc-style.css" TITLE="Style">
 
@@ -325,7 +325,7 @@
 </TABLE>
 </TD>
 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-Generated at April 24 2014<br/>Version 2.0 Revision 1096</EM>
+Generated at May 19 2014<br/>Version 2.0 Revision 1101</EM>
 </TD>
 </TR>
 

diff --git 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 @@
 <!--NewPage-->
 <HTML>
 <HEAD>
-<!-- Generated by javadoc (build 1.6.0_65) on Thu Apr 24 17:20:18 PDT 2014 -->
+<!-- Generated by javadoc (build 1.6.0_65) on Mon May 19 11:34:05 PDT 2014 -->
 <TITLE>
 N-Index (SBMLsqueezer 2.0 API Specification)
 </TITLE>
 
-<META NAME="date" CONTENT="2014-04-24">
+<META NAME="date" CONTENT="2014-05-19">
 
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../javadoc-style.css" TITLE="Style">
 
@@ -130,7 +130,7 @@
 </TABLE>
 </TD>
 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-Generated at April 24 2014<br/>Version 2.0 Revision 1096</EM>
+Generated at May 19 2014<br/>Version 2.0 Revision 1101</EM>
 </TD>
 </TR>
 

diff --git 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 @@
 <!--NewPage-->
 <HTML>
 <HEAD>
-<!-- Generated by javadoc (build 1.6.0_65) on Thu Apr 24 17:20:18 PDT 2014 -->
+<!-- Generated by javadoc (build 1.6.0_65) on Mon May 19 11:34:05 PDT 2014 -->
 <TITLE>
 O-Index (SBMLsqueezer 2.0 API Specification)
 </TITLE>
 
-<META NAME="date" CONTENT="2014-04-24">
+<META NAME="date" CONTENT="2014-05-19">
 
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../javadoc-style.css" TITLE="Style">
 
@@ -152,7 +152,7 @@
 </TABLE>
 </TD>
 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-Generated at April 24 2014<br/>Version 2.0 Revision 1096</EM>
+Generated at May 19 2014<br/>Version 2.0 Revision 1101</EM>
 </TD>
 </TR>
 

diff --git 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 @@
 <!--NewPage-->
 <HTML>
 <HEAD>
-<!-- Generated by javadoc (build 1.6.0_65) on Thu Apr 24 17:20:18 PDT 2014 -->
+<!-- Generated by javadoc (build 1.6.0_65) on Mon May 19 11:34:05 PDT 2014 -->
 <TITLE>
 P-Index (SBMLsqueezer 2.0 API Specification)
 </TITLE>
 
-<META NAME="date" CONTENT="2014-04-24">
+<META NAME="date" CONTENT="2014-05-19">
 
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../javadoc-style.css" TITLE="Style">
 
@@ -433,7 +433,7 @@
 </TABLE>
 </TD>
 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-Generated at April 24 2014<br/>Version 2.0 Revision 1096</EM>
+Generated at May 19 2014<br/>Version 2.0 Revision 1101</EM>
 </TD>
 </TR>
 

diff --git 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 @@
 <!--NewPage-->
 <HTML>
 <HEAD>
-<!-- Generated by javadoc (build 1.6.0_65) on Thu Apr 24 17:20:18 PDT 2014 -->
+<!-- Generated by javadoc (build 1.6.0_65) on Mon May 19 11:34:05 PDT 2014 -->
 <TITLE>
 R-Index (SBMLsqueezer 2.0 API Specification)
 </TITLE>
 
-<META NAME="date" CONTENT="2014-04-24">
+<META NAME="date" CONTENT="2014-05-19">
 
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../javadoc-style.css" TITLE="Style">
 
@@ -187,7 +187,7 @@
 </TABLE>
 </TD>
 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-Generated at April 24 2014<br/>Version 2.0 Revision 1096</EM>
+Generated at May 19 2014<br/>Version 2.0 Revision 1101</EM>
 </TD>
 </TR>
 

diff --git 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 @@
 <!--NewPage-->
 <HTML>
 <HEAD>
-<!-- Generated by javadoc (build 1.6.0_65) on Thu Apr 24 17:20:18 PDT 2014 -->
+<!-- Generated by javadoc (build 1.6.0_65) on Mon May 19 11:34:05 PDT 2014 -->
 <TITLE>
 S-Index (SBMLsqueezer 2.0 API Specification)
 </TITLE>
 
-<META NAME="date" CONTENT="2014-04-24">
+<META NAME="date" CONTENT="2014-05-19">
 
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../javadoc-style.css" TITLE="Style">
 
@@ -406,7 +406,7 @@
 </TABLE>
 </TD>
 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-Generated at April 24 2014<br/>Version 2.0 Revision 1096</EM>
+Generated at May 19 2014<br/>Version 2.0 Revision 1101</EM>
 </TD>
 </TR>
 

diff --git 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 @@
 <!--NewPage-->
 <HTML>
 <HEAD>
-<!-- Generated by javadoc (build 1.6.0_65) on Thu Apr 24 17:20:18 PDT 2014 -->
+<!-- Generated by javadoc (build 1.6.0_65) on Mon May 19 11:34:05 PDT 2014 -->
 <TITLE>
 T-Index (SBMLsqueezer 2.0 API Specification)
 </TITLE>
 
-<META NAME="date" CONTENT="2014-04-24">
+<META NAME="date" CONTENT="2014-05-19">
 
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../javadoc-style.css" TITLE="Style">
 
@@ -199,7 +199,7 @@
 </TABLE>
 </TD>
 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-Generated at April 24 2014<br/>Version 2.0 Revision 1096</EM>
+Generated at May 19 2014<br/>Version 2.0 Revision 1101</EM>
 </TD>
 </TR>
 

diff --git 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 @@
 <!--NewPage-->
 <HTML>
 <HEAD>
-<!-- Generated by javadoc (build 1.6.0_65) on Thu Apr 24 17:20:17 PDT 2014 -->
+<!-- Generated by javadoc (build 1.6.0_65) on Mon May 19 11:34:05 PDT 2014 -->
 <TITLE>
 B-Index (SBMLsqueezer 2.0 API Specification)
 </TITLE>
 
-<META NAME="date" CONTENT="2014-04-24">
+<META NAME="date" CONTENT="2014-05-19">
 
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../javadoc-style.css" TITLE="Style">
 
@@ -121,7 +121,7 @@
 </TABLE>
 </TD>
 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-Generated at April 24 2014<br/>Version 2.0 Revision 1096</EM>
+Generated at May 19 2014<br/>Version 2.0 Revision 1101</EM>
 </TD>
 </TR>