[Sbfc-svn] SF.net SVN: sbfc:[703] trunk/src/org/sbfc/converter/biopax2sbml/BioPAX2SBML .java

[<tra...@us...>]

Revision: 703
          http://sourceforge.net/p/sbfc/code/703
Author:   tramy-nguyen
Date:     2017-01-03 06:43:06 +0000 (Tue, 03 Jan 2017)
Log Message:
-----------
Implemented custom annotation for BioPAX availability property

Modified Paths:
--------------
    trunk/src/org/sbfc/converter/biopax2sbml/BioPAX2SBML.java

Modified: trunk/src/org/sbfc/converter/biopax2sbml/BioPAX2SBML.java
===================================================================
--- trunk/src/org/sbfc/converter/biopax2sbml/BioPAX2SBML.java	2017-01-03 05:54:23 UTC (rev 702)
+++ trunk/src/org/sbfc/converter/biopax2sbml/BioPAX2SBML.java	2017-01-03 06:43:06 UTC (rev 703)
@@ -662,7 +662,7 @@
 				//Hold the custom annotation for xref comment property
 				List<XMLNode> annotatedList = new ArrayList<XMLNode>();
 
-				parseAnnotations(pathway, annotatedList);
+				parseAnnotations(pathway, "pathway", annotatedList);
 
 				if(annotatedList.size() > 0)
 				{
@@ -673,6 +673,22 @@
 					}
 				}
 			}
+			if(pathway.getAvailability() != null && !pathway.getAvailability().isEmpty()){
+				//Hold the custom annotation for xref comment property
+				List<XMLNode> annotatedList = new ArrayList<XMLNode>();
+
+				parseAvailability(pathway, "pathway", annotatedList);
+
+				if(annotatedList.size() > 0)
+				{
+					XMLNode customNode = createCustomBiopaxAnnotation(sbmlModel);
+					for(XMLNode node: annotatedList)
+					{
+						customNode.addChild(node);
+					}
+				}
+			}
+			
 		}
 		else 
 		{
@@ -705,18 +721,18 @@
 	 * @param annotatedList - An empty list of XMLNode to store the SBML annotations in.
 	 * @return
 	 */
-	private List<XMLNode> parseAnnotations(Entity entity, List<XMLNode> annotatedList)
+	private List<XMLNode> parseAnnotations(Entity entity, String entityType, List<XMLNode> annotatedList)
 	{
 		//TODO: Find annotations example for this method.
 		if(entity.getAnnotations() != null && entity.getAnnotations().size() > 0)
 		{
-			for(String annotKey : entity.getAnnotations().keySet())
+			XMLNode xrefNode = createAnnotatedObject(entityType, entity.getRDFId());
+			XMLNode commentNode = createAnnotatedProperty("annotations");
+			xrefNode.addChild(commentNode);
+			for(Object annotObj : entity.getAnnotations().values())
 			{
-				XMLNode xrefNode = createAnnotatedObject("Pathway", annotKey);
-				XMLNode commentNode = createAnnotatedProperty("annotations");
-				xrefNode.addChild(commentNode);
-				
-				String annotValue = entity.getAnnotations().get(annotKey).toString();
+				//TODO: Note, this will ignore all annotation key.
+				String annotValue = annotObj.toString();
 				commentNode.addChild(createAnnotatedValue(annotValue));
 				
 				annotatedList.add(xrefNode);
@@ -726,6 +742,25 @@
 		return annotatedList;
 		
 	}
+	
+	private List<XMLNode> parseAvailability(Entity entity, String entityType, List<XMLNode> annotatedList)
+	{
+		//TODO: Find example for this method.
+		if(entity.getAvailability() != null && entity.getAvailability().size() > 0)
+		{
+			XMLNode xrefNode = createAnnotatedObject(entityType, entity.getRDFId());
+			XMLNode commentNode = createAnnotatedProperty("availability");
+			xrefNode.addChild(commentNode);
+			for(String availability : entity.getAvailability())
+			{
+				commentNode.addChild(createAnnotatedValue(availability));
+			}
+			annotatedList.add(xrefNode);
+		}
+		
+		return annotatedList;
+		
+	}
 
 	/**
 	 * Convert a list of pathway components to its corresponding SBML Elements.
@@ -1345,10 +1380,25 @@
 			parseEvidence(entity.getEvidence(), sbmlSpecies);
 		}
 		if(entity.getAnnotations() != null && !entity.getAnnotations().isEmpty()){
+			
+			List<XMLNode> annotatedList = new ArrayList<XMLNode>();
+
+			parseAnnotations(entity, "PhysicalEntity", annotatedList);
+
+			if(annotatedList.size() > 0)
+			{
+				XMLNode customNode = createCustomBiopaxAnnotation(sbmlSpecies);
+				for(XMLNode node: annotatedList)
+				{
+					customNode.addChild(node);
+				}
+			}
+		}
+		if(entity.getAvailability() != null && !entity.getAvailability().isEmpty()){
 			//Hold the custom annotation for xref comment property
 			List<XMLNode> annotatedList = new ArrayList<XMLNode>();
 
-			parseAnnotations(entity, annotatedList);
+			parseAvailability(entity, "PhysicalEntity", annotatedList);
 
 			if(annotatedList.size() > 0)
 			{
@@ -2054,6 +2104,37 @@
 					{
 						parseXref(control.getXref(), modifierSpecies);
 					}
+					if(control.getAnnotations() != null && !control.getAnnotations().isEmpty()){
+						
+						List<XMLNode> annotatedList = new ArrayList<XMLNode>();
+
+						parseAnnotations(control, "ControlInteractions", annotatedList);
+
+						if(annotatedList.size() > 0)
+						{
+							XMLNode customNode = createCustomBiopaxAnnotation(modifierSpecies);
+							for(XMLNode node: annotatedList)
+							{
+								customNode.addChild(node);
+							}
+						}
+					}
+					if(control.getAvailability() != null && !control.getAvailability().isEmpty()){
+						
+						List<XMLNode> annotatedList = new ArrayList<XMLNode>();
+
+						parseAvailability(control, "ControlInteraction", annotatedList);
+
+						if(annotatedList.size() > 0)
+						{
+							XMLNode customNode = createCustomBiopaxAnnotation(modifierSpecies);
+							for(XMLNode node: annotatedList)
+							{
+								customNode.addChild(node);
+							}
+						}
+					}
+					
 				}
 			}
 		}
@@ -2400,7 +2481,37 @@
 		{
 			parseEvidence(entity.getEvidence(), reaction);
 		}
+		if(entity.getAnnotations() != null && !entity.getAnnotations().isEmpty()){
+			
+			List<XMLNode> annotatedList = new ArrayList<XMLNode>();
 
+			parseAnnotations(entity, "Interactions", annotatedList);
+
+			if(annotatedList.size() > 0)
+			{
+				XMLNode customNode = createCustomBiopaxAnnotation(reaction);
+				for(XMLNode node: annotatedList)
+				{
+					customNode.addChild(node);
+				}
+			}
+		}
+		if(entity.getAvailability() != null && !entity.getAvailability().isEmpty()){
+			//Hold the custom annotation for xref comment property
+			List<XMLNode> annotatedList = new ArrayList<XMLNode>();
+
+			parseAvailability(entity, "Interaction", annotatedList);
+
+			if(annotatedList.size() > 0)
+			{
+				XMLNode customNode = createCustomBiopaxAnnotation(reaction);
+				for(XMLNode node: annotatedList)
+				{
+					customNode.addChild(node);
+				}
+			}
+		}
+
 		return reaction; 
 	}
 

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