[Sbfc-svn] SF.net SVN: sbfc:[641] trunk/test/org/sbfc/test/sbml2biopax/ SBMLSpeciesTests.java

[<nik...@us...>]

Revision: 641
          http://sourceforge.net/p/sbfc/code/641
Author:   niko-rodrigue
Date:     2016-06-09 13:48:53 +0000 (Thu, 09 Jun 2016)
Log Message:
-----------
added a basic reaction in SBMLSpeciesTests

Modified Paths:
--------------
    trunk/test/org/sbfc/test/sbml2biopax/SBMLSpeciesTests.java

Modified: trunk/test/org/sbfc/test/sbml2biopax/SBMLSpeciesTests.java
===================================================================
--- trunk/test/org/sbfc/test/sbml2biopax/SBMLSpeciesTests.java	2016-06-09 13:14:12 UTC (rev 640)
+++ trunk/test/org/sbfc/test/sbml2biopax/SBMLSpeciesTests.java	2016-06-09 13:48:53 UTC (rev 641)
@@ -20,6 +20,7 @@
 import org.sbfc.converter.sbml2biopax.SBML2BioPAX_l3;
 import org.sbml.jsbml.CVTerm;
 import org.sbml.jsbml.Model;
+import org.sbml.jsbml.Reaction;
 import org.sbml.jsbml.SBMLDocument;
 import org.sbml.jsbml.Species;
 
@@ -69,6 +70,7 @@
     Species s3 = m.createSpecies("S3");
     s3.addCVTerm(new CVTerm(CVTerm.Qualifier.BQB_IS, "http://identifiers.org/chebi/CHEBI:15377"));
     s3.setName("SmallMolecule");
+    s3.setCompartment("cell");
     try {
       s3.appendNotes("Adding a small notes to this species"); // The SBML Notes should be somehow stored in the BioPAX comment element.
       s3.appendNotes("Chebi: CHEBI:15377");
@@ -82,37 +84,41 @@
     Species s4 = m.createSpecies("S4");
     s4.addCVTerm(new CVTerm(CVTerm.Qualifier.BQB_IS, "urn:miriam:obo.chebi:CHEBI%3A23436"));
     s4.setName("SmallMolecule");
-
+    s4.setCompartment("cell");
+    
     Species s5 = m.createSpecies("S5");
     s5.addCVTerm(new CVTerm(CVTerm.Qualifier.BQB_IS, "http://purl.obolibrary.org/obo/CHEBI#CHEBI:8116"));
     s5.setName("SmallMolecule");
+    s5.setCompartment("cell");
     
     Species s6 = m.createSpecies("S6");
     s6.addCVTerm(new CVTerm(CVTerm.Qualifier.BQB_IS, "http://identifiers.org/kegg.compound/C00001"));
     s6.setName("SmallMolecule");
+    s6.setCompartment("cell");
     
-    
     // Complex => has an intact annotation or child of SBO 253 (296, 286)    
     Species s7 = m.createSpecies("S7");
     s7.setName("Complex");
     s7.setSBOTerm(253);
+    s7.setCompartment("cell");
     
     Species s8 = m.createSpecies("S8");
     s8.setName("Complex");
     s8.setSBOTerm(296);
+    s8.setCompartment("cell");
     
     Species s9 = m.createSpecies("S9");
     s9.setName("Complex");
     s9.addCVTerm(new CVTerm(CVTerm.Qualifier.BQB_IS, "http://identifiers.org/intact/EBI-9691559"));
+    s9.setCompartment("cell");
     
-    
     // TODO - Protein child of SBO 297 or has annotation to uniprot, urn:miriam:kegg.compound:C00173, interpro, ensembl:ENSRNOP*, ensembl:ENSP*
     Species s10 = m.createSpecies("S10");
     s10.setName("Protein");
     s10.addCVTerm(new CVTerm(CVTerm.Qualifier.BQB_IS, "http://identifiers.org/uniprot/P04156"));
+    s10.setCompartment("cell");
     
     
-    
     // TODO - DNA chebi:CHEBI%3A9160, ensembl:ENSG*, ensembl:ENSRNOG*,  kegg.compound:C00039, child of SBO 251?
     
     
@@ -127,6 +133,20 @@
     
     // Gene=243
     
+    // Reactions
+    Reaction r1 = m.createReaction();
+    r1.createReactant(s1);
+    r1.createReactant(s2);
+    r1.createReactant(s3);
+    r1.createReactant(s4);
+    r1.createReactant(s5);
+    r1.createReactant(s6);
+    
+    r1.createProduct(s7);
+    r1.createProduct(s8);
+    r1.createProduct(s9);
+    r1.createProduct(s10);
+    
         
     SBMLModel sbfcSBMLModel = new SBMLModel(doc);
     SBML2BioPAX sbml2biopax = new SBML2BioPAX_l3();

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