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updated samples with the new namespace nwt: for mapProperties and ext…
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…raInfo #712
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@okg21
okg21 committed Jul 12, 2024
1 parent 54d9bea commit 509cb16
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Showing 25 changed files with 263 additions and 242 deletions.
2 changes: 1 addition & 1 deletion app/js/app-menu.js
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Original file line number Diff line number Diff line change
Expand Up @@ -819,7 +819,7 @@ module.exports = function() {
// get and set properties from file
var properties = chiseInstance.getMapProperties();
// init map properties
var mapProperties = ( properties && properties.mapProperties ) ? properties.mapProperties : {};
var mapProperties = ( properties && properties['nwt:mapProperties'] ) ? properties['nwt:mapProperties'] : {};

var urlParams = appUtilities.getScratch(cy, 'urlParams');

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5 changes: 3 additions & 2 deletions app/samples/RTN4-controllers-and-binding-proteins.nwt
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,8 @@
</style>
</listOfStyles>
</renderInformation>
<mapProperties>
<nwt:mapProperties xmlns:nwt="https://newteditor.org/">

<compoundPadding>0</compoundPadding>
<extraCompartmentPadding>14</extraCompartmentPadding>
<extraComplexPadding>10</extraComplexPadding>
Expand All @@ -48,7 +49,7 @@
<mapColorSchemeStyle>solid</mapColorSchemeStyle>
<mapName>RTN4 controllers and binding proteins</mapName>
<mapDescription/>
</mapProperties>
</nwt:mapProperties>
</extension>
<glyph id="nwtN_a02f454b-ac83-4785-bc95-41f7fcc3b317" class="SIF macromolecule">
<label text="RTN4"/>
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16 changes: 8 additions & 8 deletions app/samples/activated_stat1alpha_induction_of_the_irf1_gene.nwt
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@
</style>
</listOfStyles>
</renderInformation>
<mapProperties>
<nwt:mapProperties xmlns:nwt="https://newteditor.org/">
<compoundPadding>0</compoundPadding>
<extraCompartmentPadding>14</extraCompartmentPadding>
<extraComplexPadding>10</extraComplexPadding>
Expand All @@ -71,7 +71,7 @@ using logical operators</mapDescription>
<defaultInfoboxHeight>12</defaultInfoboxHeight>
<defaultInfoboxWidth>30</defaultInfoboxWidth>
<rearrangeAfterExpandCollapse>true</rearrangeAfterExpandCollapse>
</mapProperties>
</nwt:mapProperties>
</extension>
<glyph id="glyph8" class="source and sink">
<bbox x="219.34507961077375" y="426.0211623750535" w="22" h="22"/>
Expand Down Expand Up @@ -115,7 +115,7 @@ using logical operators</mapDescription>
</glyph>
<glyph id="glyph13" class="complex">
<extension>
<extraInfo>
<nwt:extraInfo xmlns:nwt="https://newteditor.org/">
<w>116.5</w>
<h>115.22325353322313</h>
<minW>0</minW>
Expand All @@ -124,13 +124,13 @@ using logical operators</mapDescription>
<WRBias>0</WRBias>
<HTBias>0</HTBias>
<HBBias>0</HBBias>
</extraInfo>
</nwt:extraInfo>
</extension>
<label text="STAT1α"/>
<bbox x="124.28900890905871" y="180.96669449413326" w="136.5" h="135.22325353322313"/>
<glyph id="glyph11" class="complex">
<extension>
<extraInfo>
<nwt:extraInfo xmlns:nwt="https://newteditor.org/">
<w>93.25</w>
<h>46.5</h>
<minW>0</minW>
Expand All @@ -139,7 +139,7 @@ using logical operators</mapDescription>
<WRBias>0</WRBias>
<HTBias>0</HTBias>
<HBBias>0</HBBias>
</extraInfo>
</nwt:extraInfo>
</extension>
<label text="STAT1α"/>
<bbox x="135.9140089090587" y="192.59169449413324" w="113.25" h="66.5"/>
Expand Down Expand Up @@ -171,7 +171,7 @@ using logical operators</mapDescription>
</glyph>
<glyph id="glyph0" class="complex">
<extension>
<extraInfo>
<nwt:extraInfo xmlns:nwt="https://newteditor.org/">
<w>93.25000000000001</w>
<h>46.5</h>
<minW>0</minW>
Expand All @@ -180,7 +180,7 @@ using logical operators</mapDescription>
<WRBias>0</WRBias>
<HTBias>0</HTBias>
<HBBias>0</HBBias>
</extraInfo>
</nwt:extraInfo>
</extension>
<label text="STAT1α"/>
<bbox x="49.44346744528587" y="28.34609843233484" w="113.25000000000001" h="66.5"/>
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13 changes: 7 additions & 6 deletions app/samples/af_learners_card.nwt
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,8 @@
</style>
</listOfStyles>
</renderInformation>
<mapProperties>
<nwt:mapProperties xmlns:nwt="https://newteditor.org/">

<compoundPadding>0</compoundPadding>
<extraCompartmentPadding>14</extraCompartmentPadding>
<extraComplexPadding>10</extraComplexPadding>
Expand All @@ -79,7 +80,7 @@
<mapColorSchemeStyle>solid</mapColorSchemeStyle>
<mapName>Pathway #sbgn-network-container-0</mapName>
<mapDescription/>
</mapProperties>
</nwt:mapProperties>
</extension>
<glyph id="60a70c60-a024-940a-7aa7-bdc502a4e11c" class="biological activity">
<label text="LOGICAL OPERATORS"/>
Expand Down Expand Up @@ -287,7 +288,7 @@
</glyph>
<glyph id="nwtN_a84230a9-1748-472e-b10c-c9e06317036e" class="compartment">
<extension>
<extraInfo>
<nwt:extraInfo xmlns:nwt="https://newteditor.org/">
<w>86.26289567355363</w>
<h>48.685521632231705</h>
<minW>0</minW>
Expand All @@ -296,14 +297,14 @@
<WRBias>0</WRBias>
<HTBias>0</HTBias>
<HBBias>0</HBBias>
</extraInfo>
</nwt:extraInfo>
</extension>
<label text="LABEL"/>
<bbox x="-508.13144783677683" y="670.6572391838841" w="86.26289567355363" h="48.685521632231705"/>
</glyph>
<glyph id="nwtN_66245041-19e3-4975-b185-6b0cb39421f4" class="submap">
<extension>
<extraInfo>
<nwt:extraInfo xmlns:nwt="https://newteditor.org/">
<w>80</w>
<h>45.55407379545484</h>
<minW>0</minW>
Expand All @@ -312,7 +313,7 @@
<WRBias>0</WRBias>
<HTBias>0</HTBias>
<HBBias>0</HBBias>
</extraInfo>
</nwt:extraInfo>
</extension>
<label text="LABEL"/>
<bbox x="-265" y="672.2229631022726" w="80" h="45.55407379545484"/>
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5 changes: 3 additions & 2 deletions app/samples/apoptotic_reaction_model.nwt
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,8 @@
</style>
</listOfStyles>
</renderInformation>
<mapProperties>
<nwt:mapProperties xmlns:nwt="https://newteditor.org/">

<compoundPadding>0</compoundPadding>
<extraCompartmentPadding>14</extraCompartmentPadding>
<extraComplexPadding>10</extraComplexPadding>
Expand All @@ -49,7 +50,7 @@
<highlightColor>#0B9BCD</highlightColor>
<extraHighlightThickness>2</extraHighlightThickness>
<mapPD2AFConverted>false</mapPD2AFConverted>
</mapProperties>
</nwt:mapProperties>
</extension>
<glyph id="__s0" class="simple molecule">
<label text="L(bf=None)"/>
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49 changes: 25 additions & 24 deletions app/samples/atm_mediated_phosphorylation_of_repair_proteins.nwt
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,8 @@
</style>
</listOfStyles>
</renderInformation>
<mapProperties>
<nwt:mapProperties xmlns:nwt="https://newteditor.org/">

<compoundPadding>0</compoundPadding>
<extraCompartmentPadding>14</extraCompartmentPadding>
<extraComplexPadding>10</extraComplexPadding>
Expand All @@ -66,11 +67,11 @@
<defaultInfoboxHeight>12</defaultInfoboxHeight>
<defaultInfoboxWidth>30</defaultInfoboxWidth>
<rearrangeAfterExpandCollapse>true</rearrangeAfterExpandCollapse>
</mapProperties>
</nwt:mapProperties>
</extension>
<glyph id="nucleoplasm" class="compartment">
<extension>
<extraInfo>
<nwt:extraInfo xmlns:nwt="https://newteditor.org/">
<w>945.9813811844967</w>
<h>691.7670512250039</h>
<minW>0</minW>
Expand All @@ -79,14 +80,14 @@
<WRBias>0</WRBias>
<HTBias>0</HTBias>
<HBBias>0</HBBias>
</extraInfo>
</nwt:extraInfo>
</extension>
<label text="nucleoplasm"/>
<bbox x="60.21141431603337" y="44.41926938166296" w="973.9813811844967" h="719.7670512250039"/>
</glyph>
<glyph id="http___www.reactome.org_biopax_48887Complex2697" class="complex" compartmentRef="nucleoplasm">
<extension>
<extraInfo>
<nwt:extraInfo xmlns:nwt="https://newteditor.org/">
<w>124.5</w>
<h>139.75</h>
<minW>0</minW>
Expand All @@ -95,7 +96,7 @@
<WRBias>0</WRBias>
<HTBias>0</HTBias>
<HBBias>0</HBBias>
</extraInfo>
</nwt:extraInfo>
</extension>
<label text="53BP1:H2AX complex&#xA;at site of double-strand break"/>
<bbox x="725.05372614112" y="472.4750746025246" w="144.5" h="159.75"/>
Expand All @@ -122,7 +123,7 @@
</glyph>
<glyph id="http___www.reactome.org_biopax_48887Complex2701" class="complex" compartmentRef="nucleoplasm">
<extension>
<extraInfo>
<nwt:extraInfo xmlns:nwt="https://newteditor.org/">
<w>124.5</w>
<h>139.75</h>
<minW>0</minW>
Expand All @@ -131,7 +132,7 @@
<WRBias>0</WRBias>
<HTBias>0</HTBias>
<HBBias>0</HBBias>
</extraInfo>
</nwt:extraInfo>
</extension>
<label text="BRCA1:53BP1 complex&#xA;at site of DNA double-strand break"/>
<bbox x="874.0677955005301" y="305.4589063319209" w="144.5" h="159.75"/>
Expand Down Expand Up @@ -162,7 +163,7 @@
</glyph>
<glyph id="http___www.reactome.org_biopax_48887Complex2695" class="complex" compartmentRef="nucleoplasm">
<extension>
<extraInfo>
<nwt:extraInfo xmlns:nwt="https://newteditor.org/">
<w>63.25</w>
<h>86.5</h>
<minW>0</minW>
Expand All @@ -171,7 +172,7 @@
<WRBias>0</WRBias>
<HTBias>0</HTBias>
<HBBias>0</HBBias>
</extraInfo>
</nwt:extraInfo>
</extension>
<label text="MDC1/NFBD1:gamma&#xA;H2AX complex"/>
<bbox x="591.0707011075036" y="60.044269381662986" w="83.25" h="106.5"/>
Expand All @@ -190,7 +191,7 @@
</glyph>
<glyph id="http___www.reactome.org_biopax_48887Complex2694" class="complex" compartmentRef="nucleoplasm">
<extension>
<extraInfo>
<nwt:extraInfo xmlns:nwt="https://newteditor.org/">
<w>124.5</w>
<h>99.625</h>
<minW>0</minW>
Expand All @@ -199,7 +200,7 @@
<WRBias>0</WRBias>
<HTBias>0</HTBias>
<HBBias>0</HBBias>
</extraInfo>
</nwt:extraInfo>
</extension>
<label text="gamma H2AX:MDC1/NFBD1 complex&#xA;at site of DNA double-strand break"/>
<bbox x="568.3077857135538" y="535.7596450387515" w="144.5" h="119.625"/>
Expand All @@ -222,7 +223,7 @@
</glyph>
<glyph id="http___www.reactome.org_biopax_48887Complex2698" class="complex" compartmentRef="nucleoplasm">
<extension>
<extraInfo>
<nwt:extraInfo xmlns:nwt="https://newteditor.org/">
<w>124.5</w>
<h>99.625</h>
<minW>0</minW>
Expand All @@ -231,7 +232,7 @@
<WRBias>0</WRBias>
<HTBias>0</HTBias>
<HBBias>0</HBBias>
</extraInfo>
</nwt:extraInfo>
</extension>
<label text="gamma-H2AX:NBS1 complex&#xA;at the site of double-strand break"/>
<bbox x="297.5287109506822" y="388.92193702165366" w="144.5" h="119.625"/>
Expand Down Expand Up @@ -274,7 +275,7 @@
</glyph>
<glyph id="http___www.reactome.org_biopax_48887Complex465" class="complex" compartmentRef="nucleoplasm">
<extension>
<extraInfo>
<nwt:extraInfo xmlns:nwt="https://newteditor.org/">
<w>112.5</w>
<h>86.5</h>
<minW>0</minW>
Expand All @@ -283,7 +284,7 @@
<WRBias>0</WRBias>
<HTBias>0</HTBias>
<HBBias>0</HBBias>
</extraInfo>
</nwt:extraInfo>
</extension>
<label text="MRN"/>
<bbox x="274.23006591273156" y="248.4785957006104" w="132.5" h="106.5"/>
Expand All @@ -302,7 +303,7 @@
</glyph>
<glyph id="http___www.reactome.org_biopax_48887Complex2700" class="complex" compartmentRef="nucleoplasm">
<extension>
<extraInfo>
<nwt:extraInfo xmlns:nwt="https://newteditor.org/">
<w>124.5</w>
<h>139.75</h>
<minW>0</minW>
Expand All @@ -311,7 +312,7 @@
<WRBias>0</WRBias>
<HTBias>0</HTBias>
<HBBias>0</HBBias>
</extraInfo>
</nwt:extraInfo>
</extension>
<label text="DNA double-strand break&#xA;ends: MRN complex"/>
<bbox x="75.83641431603334" y="356.89462451538236" w="144.5" h="159.75"/>
Expand Down Expand Up @@ -382,7 +383,7 @@
</glyph>
<glyph id="http___www.reactome.org_biopax_48887Complex2696" class="complex" compartmentRef="nucleoplasm">
<extension>
<extraInfo>
<nwt:extraInfo xmlns:nwt="https://newteditor.org/">
<w>124.5</w>
<h>94.62499999999999</h>
<minW>0</minW>
Expand All @@ -391,7 +392,7 @@
<WRBias>0</WRBias>
<HTBias>0</HTBias>
<HBBias>0</HBBias>
</extraInfo>
</nwt:extraInfo>
</extension>
<label text="ATM associated with DNA&#xA;double-strand break ends"/>
<bbox x="703.045283111857" y="65.49784613827416" w="144.5" h="114.62499999999999"/>
Expand Down Expand Up @@ -426,7 +427,7 @@
</glyph>
<glyph id="http___www.reactome.org_biopax_48887Complex2693" class="complex" compartmentRef="nucleoplasm">
<extension>
<extraInfo>
<nwt:extraInfo xmlns:nwt="https://newteditor.org/">
<w>83.25</w>
<h>99.62499999999994</h>
<minW>0</minW>
Expand All @@ -435,7 +436,7 @@
<WRBias>0</WRBias>
<HTBias>0</HTBias>
<HBBias>0</HBBias>
</extraInfo>
</nwt:extraInfo>
</extension>
<label text="gamma H2AX-coated DNA&#xA;double-strand break ends"/>
<bbox x="482.4269164951279" y="415.9274321040441" w="103.25" h="119.62499999999994"/>
Expand All @@ -454,7 +455,7 @@
</glyph>
<glyph id="http___www.reactome.org_biopax_48887Complex2699" class="complex" compartmentRef="nucleoplasm">
<extension>
<extraInfo>
<nwt:extraInfo xmlns:nwt="https://newteditor.org/">
<w>112.5</w>
<h>38.25</h>
<minW>0</minW>
Expand All @@ -463,7 +464,7 @@
<WRBias>0</WRBias>
<HTBias>0</HTBias>
<HBBias>0</HBBias>
</extraInfo>
</nwt:extraInfo>
</extension>
<label text="RAD50:MRE11 complex"/>
<bbox x="354.17466305127505" y="168.8256888954739" w="132.5" h="58.25"/>
Expand Down
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