10

code/test-xml.rkt

@@ -22,5 +22,5 @@
   (write-file "../html/generated/result.sbgn" af-xml)
 ))
 
-; (test-xml "../examples/metabolismregulation.org_refined/F020-pyrimidine-SBGNv02.sbgn")
-(test-xml "../examples/logical-combination.sbgn")
+(test-xml "../examples/metabolismregulation.org_refined/F003-mevalonate-V002-SBGNv02.sbgn")
+; (test-xml "../examples/logical-combination.sbgn")

html/specification/a-cat-a/af.sbgn

@@ -13,11 +13,11 @@
       <label text="A-active2" />
       <bbox x="360.0" y="230.0" w="80" h="40" />
     </glyph>
-    <arc class="negative influence" id="modulation-358" source="C" target="A1">
+    <arc class="negative influence" id="negative-influence-383" source="C" target="A1">
       <start x="300.0" y="170.0" />
       <end x="200.0" y="230.0" />
     </arc>
-    <arc class="positive influence" id="modulation-359" source="C" target="A2">
+    <arc class="positive influence" id="positive-influence-384" source="C" target="A2">
       <start x="300.0" y="170.0" />
       <end x="400.0" y="230.0" />
     </arc>

html/specification/a-cat-a/pd.sbgn

@@ -8,7 +8,7 @@
     <glyph id="A1" class="macromolecule">
       <label text="A" />
       <bbox x="160.0" y="230.0" w="80" h="40" />
-      <glyph id="A1-state-variable-356" class="state variable">
+      <glyph id="A1-state-variable-381" class="state variable">
         <state value="active1" variable="" />
         <bbox x="230.0" y="222.5" w="15" h="15" />
       </glyph>
@@ -16,7 +16,7 @@
     <glyph id="A2" class="macromolecule">
       <label text="A" />
       <bbox x="360.0" y="230.0" w="80" h="40" />
-      <glyph id="A2-state-variable-357" class="state variable">
+      <glyph id="A2-state-variable-382" class="state variable">
         <state value="active2" variable="" />
         <bbox x="430.0" y="222.5" w="15" h="15" />
       </glyph>
@@ -26,15 +26,15 @@
       <port id="p-in" x="283.0" y="250.0" />
       <port id="p-out" x="317.0" y="250.0" />
     </glyph>
-    <arc class="consumption" id="consumption-353" source="A1" target="p-in">
+    <arc class="consumption" id="consumption-378" source="A1" target="p-in">
       <start x="240.0" y="250.0" />
       <end x="283.0" y="250.0" />
     </arc>
-    <arc class="production" id="production-354" source="p-out" target="A2">
+    <arc class="production" id="production-379" source="p-out" target="A2">
       <start x="317.0" y="250.0" />
       <end x="360.0" y="250.0" />
     </arc>
-    <arc class="catalysis" id="modulation-355" source="C" target="p">
+    <arc class="catalysis" id="catalysis-380" source="C" target="p">
       <start x="300.0" y="170.0" />
       <end x="300.0" y="238.0" />
     </arc>

html/specification/a-cat-i/af.sbgn

@@ -9,7 +9,7 @@
       <label text="A" />
       <bbox x="260.0" y="230.0" w="80" h="40" />
     </glyph>
-    <arc class="negative influence" id="modulation-239" source="C" target="A1">
+    <arc class="negative influence" id="negative-influence-264" source="C" target="A1">
       <start x="300.0" y="170.0" />
       <end x="300.0" y="230.0" />
     </arc>

html/specification/a-cat-i/pd.sbgn

@@ -8,7 +8,7 @@
     <glyph id="A1" class="macromolecule">
       <label text="A" />
       <bbox x="160.0" y="230.0" w="80" h="40" />
-      <glyph id="A1-state-variable-237" class="state variable">
+      <glyph id="A1-state-variable-262" class="state variable">
         <state value="active" variable="" />
         <bbox x="230.0" y="222.5" w="15" h="15" />
       </glyph>
@@ -16,7 +16,7 @@
     <glyph id="A2" class="macromolecule">
       <label text="A" />
       <bbox x="360.0" y="230.0" w="80" h="40" />
-      <glyph id="A2-state-variable-238" class="state variable">
+      <glyph id="A2-state-variable-263" class="state variable">
         <state value="inactive" variable="" />
         <bbox x="430.0" y="222.5" w="15" h="15" />
       </glyph>
@@ -26,15 +26,15 @@
       <port id="p-in" x="283.0" y="250.0" />
       <port id="p-out" x="317.0" y="250.0" />
     </glyph>
-    <arc class="consumption" id="consumption-234" source="A1" target="p-in">
+    <arc class="consumption" id="consumption-259" source="A1" target="p-in">
       <start x="240.0" y="250.0" />
       <end x="283.0" y="250.0" />
     </arc>
-    <arc class="production" id="production-235" source="p-out" target="A2">
+    <arc class="production" id="production-260" source="p-out" target="A2">
       <start x="317.0" y="250.0" />
       <end x="360.0" y="250.0" />
     </arc>
-    <arc class="catalysis" id="modulation-236" source="C" target="p">
+    <arc class="catalysis" id="catalysis-261" source="C" target="p">
       <start x="300.0" y="170.0" />
       <end x="300.0" y="238.0" />
     </arc>

html/specification/a-cat-ss/af.sbgn

+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
+  <map language="activity flow">
+    <glyph id="C" class="biological activity">
+      <label text="C" />
+      <bbox x="260.0" y="130.0" w="80" h="40" />
+    </glyph>
+    <glyph id="A" class="biological activity">
+      <label text="A" />
+      <bbox x="260.0" y="230.0" w="80" h="40" />
+    </glyph>
+    <arc class="negative influence" id="negative-influence-844" source="C" target="A">
+      <start x="300.0" y="170.0" />
+      <end x="300.0" y="230.0" />
+    </arc>
+  </map>
+</sbgn>
\ No newline at end of file

html/specification/a-cat-ss/pd.sbgn

+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
+  <map language="process description">
+    <glyph id="C" class="macromolecule">
+      <label text="C" />
+      <bbox x="260.0" y="130.0" w="80" h="40" />
+    </glyph>
+    <glyph id="A" class="macromolecule">
+      <label text="A" />
+      <bbox x="160.0" y="230.0" w="80" h="40" />
+      <glyph id="A-state-variable-843" class="state variable">
+        <state value="active" variable="" />
+        <bbox x="230.0" y="222.5" w="15" h="15" />
+      </glyph>
+    </glyph>
+    <glyph id="S" class="source and sink">
+      <bbox x="375.0" y="225.0" w="50" h="50" />
+    </glyph>
+    <glyph id="p" class="process">
+      <bbox x="288.0" y="238.0" w="24" h="24" />
+      <port id="p-in" x="283.0" y="250.0" />
+      <port id="p-out" x="317.0" y="250.0" />
+    </glyph>
+    <arc class="consumption" id="consumption-840" source="A" target="p-in">
+      <start x="240.0" y="250.0" />
+      <end x="283.0" y="250.0" />
+    </arc>
+    <arc class="production" id="production-841" source="p-out" target="S">
+      <start x="317.0" y="250.0" />
+      <end x="375.0" y="250.0" />
+    </arc>
+    <arc class="catalysis" id="catalysis-842" source="C" target="p">
+      <start x="300.0" y="170.0" />
+      <end x="300.0" y="238.0" />
+    </arc>
+  </map>
+</sbgn>
\ No newline at end of file

html/specification/a-catr-a/af.sbgn

@@ -13,11 +13,11 @@
       <label text="C" />
       <bbox x="260.0" y="130.0" w="80" h="40" />
     </glyph>
-    <arc class="positive influence" id="modulation-694" source="C" target="A1">
+    <arc class="positive influence" id="positive-influence-721" source="C" target="A1">
       <start x="300.0" y="170.0" />
       <end x="200.0" y="230.0" />
     </arc>
-    <arc class="positive influence" id="modulation-695" source="C" target="A2">
+    <arc class="positive influence" id="positive-influence-722" source="C" target="A2">
       <start x="300.0" y="170.0" />
       <end x="400.0" y="230.0" />
     </arc>

html/specification/a-catr-a/pd.sbgn

@@ -4,7 +4,7 @@
     <glyph id="A1" class="macromolecule">
       <label text="A" />
       <bbox x="160.0" y="230.0" w="80" h="40" />
-      <glyph id="A1-state-variable-692" class="state variable">
+      <glyph id="A1-state-variable-719" class="state variable">
         <state value="active1" variable="" />
         <bbox x="230.0" y="222.5" w="15" h="15" />
       </glyph>
@@ -12,7 +12,7 @@
     <glyph id="A2" class="macromolecule">
       <label text="A" />
       <bbox x="360.0" y="230.0" w="80" h="40" />
-      <glyph id="A2-state-variable-693" class="state variable">
+      <glyph id="A2-state-variable-720" class="state variable">
         <state value="active2" variable="" />
         <bbox x="430.0" y="222.5" w="15" h="15" />
       </glyph>
@@ -26,15 +26,15 @@
       <port id="p-in" x="283.0" y="250.0" />
       <port id="p-out" x="317.0" y="250.0" />
     </glyph>
-    <arc class="production" id="production-689" source="p-in" target="A1">
+    <arc class="production" id="production-716" source="p-in" target="A1">
       <start x="317.0" y="250.0" />
       <end x="240.0" y="250.0" />
     </arc>
-    <arc class="production" id="production-690" source="p-out" target="A2">
+    <arc class="production" id="production-717" source="p-out" target="A2">
       <start x="317.0" y="250.0" />
       <end x="360.0" y="250.0" />
     </arc>
-    <arc class="catalysis" id="modulation-691" source="C" target="p">
+    <arc class="catalysis" id="catalysis-718" source="C" target="p">
       <start x="300.0" y="170.0" />
       <end x="300.0" y="238.0" />
     </arc>

html/specification/a-inh-a/af.sbgn

@@ -13,11 +13,11 @@
       <label text="A-active2" />
       <bbox x="360.0" y="230.0" w="80" h="40" />
     </glyph>
-    <arc class="positive influence" id="modulation-439" source="C" target="A1">
+    <arc class="positive influence" id="positive-influence-464" source="C" target="A1">
       <start x="300.0" y="170.0" />
       <end x="200.0" y="230.0" />
     </arc>
-    <arc class="negative influence" id="modulation-440" source="C" target="A2">
+    <arc class="negative influence" id="negative-influence-465" source="C" target="A2">
       <start x="300.0" y="170.0" />
       <end x="400.0" y="230.0" />
     </arc>

html/specification/a-inh-a/pd.sbgn

@@ -8,7 +8,7 @@
     <glyph id="A1" class="macromolecule">
       <label text="A" />
       <bbox x="160.0" y="230.0" w="80" h="40" />
-      <glyph id="A1-state-variable-437" class="state variable">
+      <glyph id="A1-state-variable-462" class="state variable">
         <state value="active1" variable="" />
         <bbox x="230.0" y="222.5" w="15" h="15" />
       </glyph>
@@ -16,7 +16,7 @@
     <glyph id="A2" class="macromolecule">
       <label text="A" />
       <bbox x="360.0" y="230.0" w="80" h="40" />
-      <glyph id="A2-state-variable-438" class="state variable">
+      <glyph id="A2-state-variable-463" class="state variable">
         <state value="active2" variable="" />
         <bbox x="430.0" y="222.5" w="15" h="15" />
       </glyph>
@@ -26,15 +26,15 @@
       <port id="p-in" x="283.0" y="250.0" />
       <port id="p-out" x="317.0" y="250.0" />
     </glyph>
-    <arc class="consumption" id="consumption-434" source="A1" target="p-in">
+    <arc class="consumption" id="consumption-459" source="A1" target="p-in">
       <start x="240.0" y="250.0" />
       <end x="283.0" y="250.0" />
     </arc>
-    <arc class="production" id="production-435" source="p-out" target="A2">
+    <arc class="production" id="production-460" source="p-out" target="A2">
       <start x="317.0" y="250.0" />
       <end x="360.0" y="250.0" />
     </arc>
-    <arc class="inhibition" id="modulation-436" source="C" target="p">
+    <arc class="inhibition" id="inhibition-461" source="C" target="p">
       <start x="300.0" y="170.0" />
       <end x="300.0" y="238.0" />
     </arc>

html/specification/a-inh-i/af.sbgn

@@ -9,7 +9,7 @@
       <label text="A" />
       <bbox x="260.0" y="230.0" w="80" h="40" />
     </glyph>
-    <arc class="positive influence" id="modulation-305" source="C" target="A1">
+    <arc class="positive influence" id="positive-influence-330" source="C" target="A1">
       <start x="300.0" y="170.0" />
       <end x="300.0" y="230.0" />
     </arc>

html/specification/a-inh-i/pd.sbgn

@@ -8,7 +8,7 @@
     <glyph id="A1" class="macromolecule">
       <label text="A" />
       <bbox x="160.0" y="230.0" w="80" h="40" />
-      <glyph id="A1-state-variable-303" class="state variable">
+      <glyph id="A1-state-variable-328" class="state variable">
         <state value="active" variable="" />
         <bbox x="230.0" y="222.5" w="15" h="15" />
       </glyph>
@@ -16,7 +16,7 @@
     <glyph id="A2" class="macromolecule">
       <label text="A" />
       <bbox x="360.0" y="230.0" w="80" h="40" />
-      <glyph id="A2-state-variable-304" class="state variable">
+      <glyph id="A2-state-variable-329" class="state variable">
         <state value="inactive" variable="" />
         <bbox x="430.0" y="222.5" w="15" h="15" />
       </glyph>
@@ -26,15 +26,15 @@
       <port id="p-in" x="283.0" y="250.0" />
       <port id="p-out" x="317.0" y="250.0" />
     </glyph>
-    <arc class="consumption" id="consumption-300" source="A1" target="p-in">
+    <arc class="consumption" id="consumption-325" source="A1" target="p-in">
       <start x="240.0" y="250.0" />
       <end x="283.0" y="250.0" />
     </arc>
-    <arc class="production" id="production-301" source="p-out" target="A2">
+    <arc class="production" id="production-326" source="p-out" target="A2">
       <start x="317.0" y="250.0" />
       <end x="360.0" y="250.0" />
     </arc>
-    <arc class="inhibition" id="modulation-302" source="C" target="p">
+    <arc class="inhibition" id="inhibition-327" source="C" target="p">
       <start x="300.0" y="170.0" />
       <end x="300.0" y="238.0" />
     </arc>

html/specification/a-inh-ss/af.sbgn

+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
+  <map language="activity flow">
+    <glyph id="C" class="biological activity">
+      <label text="C" />
+      <bbox x="260.0" y="130.0" w="80" h="40" />
+    </glyph>
+    <glyph id="A" class="biological activity">
+      <label text="A" />
+      <bbox x="260.0" y="230.0" w="80" h="40" />
+    </glyph>
+    <arc class="positive influence" id="positive-influence-864" source="C" target="A">
+      <start x="300.0" y="170.0" />
+      <end x="300.0" y="230.0" />
+    </arc>
+  </map>
+</sbgn>
\ No newline at end of file

html/specification/a-inh-ss/pd.sbgn

+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
+  <map language="process description">
+    <glyph id="C" class="macromolecule">
+      <label text="C" />
+      <bbox x="260.0" y="130.0" w="80" h="40" />
+    </glyph>
+    <glyph id="A" class="macromolecule">
+      <label text="A" />
+      <bbox x="160.0" y="230.0" w="80" h="40" />
+      <glyph id="A-state-variable-863" class="state variable">
+        <state value="active" variable="" />
+        <bbox x="230.0" y="222.5" w="15" h="15" />
+      </glyph>
+    </glyph>
+    <glyph id="S" class="source and sink">
+      <bbox x="375.0" y="225.0" w="50" h="50" />
+    </glyph>
+    <glyph id="p" class="process">
+      <bbox x="288.0" y="238.0" w="24" h="24" />
+      <port id="p-in" x="283.0" y="250.0" />
+      <port id="p-out" x="317.0" y="250.0" />
+    </glyph>
+    <arc class="consumption" id="consumption-860" source="A" target="p-in">
+      <start x="240.0" y="250.0" />
+      <end x="283.0" y="250.0" />
+    </arc>
+    <arc class="production" id="production-861" source="p-out" target="S">
+      <start x="317.0" y="250.0" />
+      <end x="375.0" y="250.0" />
+    </arc>
+    <arc class="inhibition" id="inhibition-862" source="C" target="p">
+      <start x="300.0" y="170.0" />
+      <end x="300.0" y="238.0" />
+    </arc>
+  </map>
+</sbgn>
\ No newline at end of file

html/specification/a-mod-a/af.sbgn

@@ -13,11 +13,11 @@
       <label text="A-active2" />
       <bbox x="360.0" y="230.0" w="80" h="40" />
     </glyph>
-    <arc class="unknown influence" id="modulation-412" source="C" target="A1">
+    <arc class="unknown influence" id="unknown-influence-437" source="C" target="A1">
       <start x="300.0" y="170.0" />
       <end x="200.0" y="230.0" />
     </arc>
-    <arc class="unknown influence" id="modulation-413" source="C" target="A2">
+    <arc class="unknown influence" id="unknown-influence-438" source="C" target="A2">
       <start x="300.0" y="170.0" />
       <end x="400.0" y="230.0" />
     </arc>

html/specification/a-mod-a/pd.sbgn

@@ -8,7 +8,7 @@
     <glyph id="A1" class="macromolecule">
       <label text="A" />
       <bbox x="160.0" y="230.0" w="80" h="40" />
-      <glyph id="A1-state-variable-410" class="state variable">
+      <glyph id="A1-state-variable-435" class="state variable">
         <state value="active1" variable="" />
         <bbox x="230.0" y="222.5" w="15" h="15" />
       </glyph>
@@ -16,7 +16,7 @@
     <glyph id="A2" class="macromolecule">
       <label text="A" />
       <bbox x="360.0" y="230.0" w="80" h="40" />
-      <glyph id="A2-state-variable-411" class="state variable">
+      <glyph id="A2-state-variable-436" class="state variable">
         <state value="active2" variable="" />
         <bbox x="430.0" y="222.5" w="15" h="15" />
       </glyph>
@@ -26,15 +26,15 @@
       <port id="p-in" x="283.0" y="250.0" />
       <port id="p-out" x="317.0" y="250.0" />
     </glyph>
-    <arc class="consumption" id="consumption-407" source="A1" target="p-in">
+    <arc class="consumption" id="consumption-432" source="A1" target="p-in">
       <start x="240.0" y="250.0" />
       <end x="283.0" y="250.0" />
     </arc>
-    <arc class="production" id="production-408" source="p-out" target="A2">
+    <arc class="production" id="production-433" source="p-out" target="A2">
       <start x="317.0" y="250.0" />
       <end x="360.0" y="250.0" />
     </arc>
-    <arc class="modulation" id="modulation-409" source="C" target="p">
+    <arc class="modulation" id="modulation-434" source="C" target="p">
       <start x="300.0" y="170.0" />
       <end x="300.0" y="238.0" />
     </arc>

html/specification/a-mod-i/af.sbgn

@@ -9,7 +9,7 @@
       <label text="A" />
       <bbox x="260.0" y="230.0" w="80" h="40" />
     </glyph>
-    <arc class="unknown influence" id="modulation-283" source="C" target="A1">
+    <arc class="unknown influence" id="unknown-influence-308" source="C" target="A1">
       <start x="300.0" y="170.0" />
       <end x="300.0" y="230.0" />
     </arc>

html/specification/a-mod-i/pd.sbgn

@@ -8,7 +8,7 @@
     <glyph id="A1" class="macromolecule">
       <label text="A" />
       <bbox x="160.0" y="230.0" w="80" h="40" />
-      <glyph id="A1-state-variable-281" class="state variable">
+      <glyph id="A1-state-variable-306" class="state variable">
         <state value="active" variable="" />
         <bbox x="230.0" y="222.5" w="15" h="15" />
       </glyph>
@@ -16,7 +16,7 @@
     <glyph id="A2" class="macromolecule">
       <label text="A" />
       <bbox x="360.0" y="230.0" w="80" h="40" />
-      <glyph id="A2-state-variable-282" class="state variable">
+      <glyph id="A2-state-variable-307" class="state variable">
         <state value="inactive" variable="" />
         <bbox x="430.0" y="222.5" w="15" h="15" />
       </glyph>
@@ -26,15 +26,15 @@
       <port id="p-in" x="283.0" y="250.0" />
       <port id="p-out" x="317.0" y="250.0" />
     </glyph>
-    <arc class="consumption" id="consumption-278" source="A1" target="p-in">
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html/specification/a-nsti-a/af.sbgn

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html/specification/a-nsti-a/pd.sbgn

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html/specification/a-nsti-i/af.sbgn

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html/specification/a-nsti-i/pd.sbgn

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