Biological Pathway Exchange Language

Update of /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/io/sif/level2
In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv30084/paxtools/io/sif/level2

Modified Files:
	ControlRule.java 
Log Message:
Minor change. Variable type correction.

Index: ControlRule.java
===================================================================
RCS file: /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/io/sif/level2/ControlRule.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** ControlRule.java	26 Feb 2008 22:08:19 -0000	1.8
--- ControlRule.java	20 Aug 2008 07:43:22 -0000	1.9
***************
*** 43,52 ****
  		// Iterate over all associated controls
  
! 		for (interaction inter : A.getAllInteractions(control.class))
  		{
  			// Iterate over all affected conversions of this control
  
! 			for (conversion conv : getAffectedConversions((control) inter,
! 				null))
  			{
  				Set<physicalEntity> presenceSet =
--- 43,51 ----
  		// Iterate over all associated controls
  
! 		for (control cont : A.getAllInteractions(control.class))
  		{
  			// Iterate over all affected conversions of this control
  
! 			for (conversion conv : getAffectedConversions(cont, null))
  			{
  				Set<physicalEntity> presenceSet =

Update of /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/impl/level2
In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv28943/paxtools/impl/level2

Modified Files:
	physicalEntityParticipantImpl.java 
Log Message:
Fixed the check in isInEquivalentState method. Previously it was not checking whether the complex members belong to the same complex. Now they are not in equivalent state if they are not members of the same complex.

Index: physicalEntityParticipantImpl.java
===================================================================
RCS file: /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/impl/level2/physicalEntityParticipantImpl.java,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** physicalEntityParticipantImpl.java	6 Mar 2008 22:20:21 -0000	1.10
--- physicalEntityParticipantImpl.java	20 Aug 2008 07:40:44 -0000	1.11
***************
*** 53,57 ****
  					that.getCELLULAR_LOCATION() == null
  					:
! 					CELLULAR_LOCATION.isEquivalent(that.getCELLULAR_LOCATION()));
  	}
  
--- 53,61 ----
  					that.getCELLULAR_LOCATION() == null
  					:
! 					CELLULAR_LOCATION.isEquivalent(that.getCELLULAR_LOCATION()))
! 				&&
! 				(COMPONENTSof == null ?
! 					that.isCOMPONENTof() == null :
! 					COMPONENTSof.equals(that.isCOMPONENTof()));
  	}
  
***************
*** 62,66 ****
  	}
  
- 
  	public int equivalenceCode()
  	{
--- 66,69 ----

Update of /cvsroot/biopax/Paxtools/test/org/biopax/paxtools/model/level3
In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv11582/test/org/biopax/paxtools/model/level3

Modified Files:
	MockFactory.java 
Log Message:
Level 3 support - Mock Factory is up-to-date

Index: MockFactory.java
===================================================================
RCS file: /cvsroot/biopax/Paxtools/test/org/biopax/paxtools/model/level3/MockFactory.java,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** MockFactory.java	18 Aug 2008 00:47:15 -0000	1.12
--- MockFactory.java	18 Aug 2008 14:29:21 -0000	1.13
***************
*** 425,428 ****
--- 425,440 ----
      }
  
+     public TemplateReaction createTemplateReaction() {
+         TemplateReaction bpe = factory.createTemplateReaction();
+         populateMock(bpe);
+         return bpe;
+     }
+ 
+     public TemplateReactionRegulation createTemplateReactionRegulation() {
+         TemplateReactionRegulation bpe = factory.createTemplateReactionRegulation();
+         populateMock(bpe);
+         return bpe;
+     }
+ 
  // -------------------------- OTHER METHODS --------------------------

Update of /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/io/jena
In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv11158/src/org/biopax/paxtools/io/jena

Modified Files:
	JenaIOHandler.java 
Log Message:
Level 3 support - GR implementation is up-to-date, subject to change based on regulon db output.. made all errors logs.. I need to think a way to manage and configure errors.

Index: JenaIOHandler.java
===================================================================
RCS file: /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/io/jena/JenaIOHandler.java,v
retrieving revision 1.23
retrieving revision 1.24
diff -C2 -d -r1.23 -r1.24
*** JenaIOHandler.java	18 Aug 2008 00:47:15 -0000	1.23
--- JenaIOHandler.java	18 Aug 2008 14:28:19 -0000	1.24
***************
*** 300,305 ****
  		throws IllegalAccessException, InvocationTargetException
  	{
! 		OntProperty ontProperty =
  			((OntProperty) predicate.as(OntProperty.class));
          String localName = ontProperty.getLocalName();
          PropertyEditor editor = editorMap.getEditorForProperty(
--- 300,315 ----
  		throws IllegalAccessException, InvocationTargetException
  	{
! 		 OntProperty ontProperty;
!         try
!         {
!         ontProperty =
  			((OntProperty) predicate.as(OntProperty.class));
+         }
+         catch (ConversionException e)
+         {
+            log.error("Unknown property");
+            log.error(predicate + "bpe:" +bpe.getRDFId());
+            return;
+         }
          String localName = ontProperty.getLocalName();
          PropertyEditor editor = editorMap.getEditorForProperty(
***************
*** 388,392 ****
  			editor.setPropertyToBean(bpe, value);
  		}
! 		catch (IllegalBioPAXArgumentException e)
  		{
  			log.error(e);
--- 398,402 ----
  			editor.setPropertyToBean(bpe, value);
  		}
! 		catch (Exception e)
  		{
  			log.error(e);

Update of /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/proxy/level3
In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv11158/src/org/biopax/paxtools/proxy/level3

Modified Files:
	BioPAXFactoryForPersistence.java 
Log Message:
Level 3 support - GR implementation is up-to-date, subject to change based on regulon db output.. made all errors logs.. I need to think a way to manage and configure errors.

Index: BioPAXFactoryForPersistence.java
===================================================================
RCS file: /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/proxy/level3/BioPAXFactoryForPersistence.java,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** BioPAXFactoryForPersistence.java	17 Aug 2008 23:04:08 -0000	1.14
--- BioPAXFactoryForPersistence.java	18 Aug 2008 14:28:19 -0000	1.15
***************
*** 254,257 ****
--- 254,261 ----
  	}
  
+     public TemplateReactionRegulation createTemplateReactionRegulation() {
+         return new TemplateReactionRegulationProxy();
+     }
+ 
      public TissueVocabulary createTissueVocabulary() {
           return new TissueVocabularyProxy();

Update of /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/impl/level3
In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv11158/src/org/biopax/paxtools/impl/level3

Modified Files:
	Level3FactoryImpl.java 
Added Files:
	TemplateReactionRegulationImpl.java 
Log Message:
Level 3 support - GR implementation is up-to-date, subject to change based on regulon db output.. made all errors logs.. I need to think a way to manage and configure errors.

Index: Level3FactoryImpl.java
===================================================================
RCS file: /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/impl/level3/Level3FactoryImpl.java,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** Level3FactoryImpl.java	17 Aug 2008 23:04:07 -0000	1.14
--- Level3FactoryImpl.java	18 Aug 2008 14:28:19 -0000	1.15
***************
*** 297,300 ****
--- 297,308 ----
      }
  
+     public TemplateReaction createTemplateReaction() {
+         return new TemplateReactionImpl();
+     }
+ 
+     public TemplateReactionRegulation createTemplateReactionRegulation() {
+         return new TemplateReactionRegulationImpl();
+     }
+ 
  
  }

--- NEW FILE: TemplateReactionRegulationImpl.java ---
package org.biopax.paxtools.impl.level3;

import org.biopax.paxtools.model.level3.TemplateReactionRegulation;

/**
 * Created by IntelliJ IDEA.
 * User: demir
 * Date: Aug 18, 2008
 * Time: 10:13:08 AM
 * To change this template use File | Settings | File Templates.
 */
public class TemplateReactionRegulationImpl extends ControlImpl implements TemplateReactionRegulation
{
}

Update of /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/model/level3
In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv11158/src/org/biopax/paxtools/model/level3

Modified Files:
	Level3Factory.java 
Log Message:
Level 3 support - GR implementation is up-to-date, subject to change based on regulon db output.. made all errors logs.. I need to think a way to manage and configure errors.

Index: Level3Factory.java
===================================================================
RCS file: /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/model/level3/Level3Factory.java,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** Level3Factory.java	17 Aug 2008 23:04:07 -0000	1.10
--- Level3Factory.java	18 Aug 2008 14:28:19 -0000	1.11
***************
*** 117,119 ****
--- 117,125 ----
      public FragmentFeature createFragmentFeature();
  
+     public TemplateReaction createTemplateReaction();
+ 
+     public TemplateReactionRegulation createTemplateReactionRegulation();
+ 
+ 
+ 
  }

Update of /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/io/simpleIO
In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv7777/src/org/biopax/paxtools/io/simpleIO

Modified Files:
	Level1Editor.properties Level2Editor.properties 
	Level3Editor.properties 
Log Message:
Updates properties and jenaIOHandlerTest

Index: Level1Editor.properties
===================================================================
RCS file: /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/io/simpleIO/Level1Editor.properties,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** Level1Editor.properties	15 Aug 2008 15:29:46 -0000	1.2
--- Level1Editor.properties	18 Aug 2008 00:47:15 -0000	1.3
***************
*** 1,207 ****
- catalysis entity XREF
  catalysis entity COMMENT
! catalysis entity SHORT-NAME
  catalysis entity AVAILABILITY
  catalysis catalysis DIRECTION
- catalysis entity NAME
- catalysis control CONTROLLER
- catalysis entity DATA-SOURCE
  catalysis entity SYNONYMS
  catalysis control CONTROLLED
! catalysis control CONTROL-TYPE
  catalysis catalysis COFACTOR
! physicalEntityParticipant physicalEntityParticipant STOICHIOMETRIC-COEFFICIENT
  physicalEntityParticipant utilityClass COMMENT
  physicalEntityParticipant physicalEntityParticipant PHYSICAL-ENTITY
! physicalEntityParticipant physicalEntityParticipant CELLULAR-LOCATION
! modulation entity XREF
  modulation entity COMMENT
! modulation entity SHORT-NAME
  modulation entity AVAILABILITY
- modulation entity NAME
- modulation control CONTROLLER
- modulation entity DATA-SOURCE
  modulation entity SYNONYMS
  modulation control CONTROLLED
  modulation control CONTROL-TYPE
- protein entity XREF
- protein protein SEQUENCE
  protein entity COMMENT
! protein entity SHORT-NAME
  protein entity AVAILABILITY
! protein entity NAME
  protein protein ORGANISM
  protein entity DATA-SOURCE
! protein entity SYNONYMS
  dataSource utilityClass COMMENT
  dataSource dataSource NAME
- transport entity XREF
- transport conversion SPONTANEOUS
- transport entity COMMENT
- transport entity SHORT-NAME
- transport entity AVAILABILITY
  transport conversion LEFT
- transport entity NAME
- transport entity DATA-SOURCE
  transport conversion RIGHT
  transport entity SYNONYMS
! complexAssembly entity XREF
! complexAssembly conversion SPONTANEOUS
! complexAssembly entity COMMENT
! complexAssembly entity SHORT-NAME
! complexAssembly entity AVAILABILITY
  complexAssembly conversion LEFT
- complexAssembly entity NAME
- complexAssembly entity DATA-SOURCE
  complexAssembly conversion RIGHT
  complexAssembly entity SYNONYMS
! xref xref DB-VERSION
! xref utilityClass COMMENT
! xref xref DB
! xref xref ID
! xref xref ID-VERSION
! biochemicalReaction conversion SPONTANEOUS
! biochemicalReaction biochemicalReaction DELTA-S
  biochemicalReaction conversion RIGHT
  biochemicalReaction entity SYNONYMS
! biochemicalReaction biochemicalReaction EC-NUMBER
  biochemicalReaction biochemicalReaction KEQ
  biochemicalReaction entity XREF
- biochemicalReaction entity COMMENT
- biochemicalReaction biochemicalReaction DELTA-G
  biochemicalReaction entity AVAILABILITY
! biochemicalReaction entity SHORT-NAME
! biochemicalReaction conversion LEFT
  biochemicalReaction entity NAME
! biochemicalReaction entity DATA-SOURCE
! biochemicalReaction biochemicalReaction DELTA-H
! control entity XREF
  control entity COMMENT
! control entity SHORT-NAME
  control entity AVAILABILITY
- control entity NAME
- control control CONTROLLER
- control entity DATA-SOURCE
  control entity SYNONYMS
  control control CONTROLLED
  control control CONTROL-TYPE
! publicationXref publicationXref YEAR
! publicationXref publicationXref TITLE
  publicationXref publicationXref URL
  publicationXref xref DB-VERSION
! publicationXref publicationXref SOURCE
! publicationXref utilityClass COMMENT
! publicationXref xref DB
! publicationXref xref ID
  publicationXref publicationXref AUTHORS
  publicationXref xref ID-VERSION
! conversion entity XREF
! conversion conversion SPONTANEOUS
! conversion entity COMMENT
! conversion entity SHORT-NAME
! conversion entity AVAILABILITY
  conversion conversion LEFT
- conversion entity NAME
- conversion entity DATA-SOURCE
  conversion conversion RIGHT
  conversion entity SYNONYMS
  bioSource bioSource CELLTYPE
- bioSource bioSource NAME
  bioSource bioSource TAXON-XREF
- bioSource utilityClass COMMENT
  bioSource bioSource TISSUE
! physicalEntity entity XREF
  physicalEntity entity COMMENT
! physicalEntity entity SHORT-NAME
  physicalEntity entity AVAILABILITY
- physicalEntity entity NAME
- physicalEntity entity DATA-SOURCE
  physicalEntity entity SYNONYMS
! unificationXref xref DB-VERSION
  unificationXref utilityClass COMMENT
  unificationXref xref DB
- unificationXref xref ID
  unificationXref xref ID-VERSION
! openControlledVocabulary utilityClass COMMENT
  openControlledVocabulary openControlledVocabulary XREF
  openControlledVocabulary openControlledVocabulary TERM
! transportWithBiochemicalReaction conversion SPONTANEOUS
! transportWithBiochemicalReaction biochemicalReaction DELTA-S
  transportWithBiochemicalReaction conversion RIGHT
  transportWithBiochemicalReaction entity SYNONYMS
! transportWithBiochemicalReaction biochemicalReaction EC-NUMBER
  transportWithBiochemicalReaction biochemicalReaction KEQ
  transportWithBiochemicalReaction entity XREF
- transportWithBiochemicalReaction entity COMMENT
- transportWithBiochemicalReaction biochemicalReaction DELTA-G
  transportWithBiochemicalReaction entity AVAILABILITY
! transportWithBiochemicalReaction entity SHORT-NAME
! transportWithBiochemicalReaction conversion LEFT
  transportWithBiochemicalReaction entity NAME
! transportWithBiochemicalReaction entity DATA-SOURCE
! transportWithBiochemicalReaction biochemicalReaction DELTA-H
! complex entity XREF
! complex complex COMPONENTS
  complex entity COMMENT
! complex entity SHORT-NAME
  complex entity AVAILABILITY
! complex entity NAME
  complex complex ORGANISM
  complex entity DATA-SOURCE
! complex entity SYNONYMS
! rna entity XREF
! rna rna SEQUENCE
  rna entity COMMENT
! rna rna ORGANISM
! rna entity SHORT-NAME
  rna entity AVAILABILITY
- rna entity NAME
- rna entity DATA-SOURCE
  rna entity SYNONYMS
! pathwayStep pathwayStep STEP-INTERACTIONS
  pathwayStep utilityClass COMMENT
  pathwayStep pathwayStep NEXT-STEP
! entity entity XREF
! entity entity COMMENT
! entity entity SHORT-NAME
! entity entity AVAILABILITY
! entity entity NAME
! entity entity DATA-SOURCE
! entity entity SYNONYMS
! interaction entity XREF
  interaction entity COMMENT
! interaction entity SHORT-NAME
  interaction entity AVAILABILITY
- interaction entity NAME
- interaction entity DATA-SOURCE
  interaction entity SYNONYMS
! interaction interaction PARTICIPANTS
! smallMolecule entity XREF
! smallMolecule entity COMMENT
! smallMolecule smallMolecule MOLECULAR-WEIGHT
  smallMolecule smallMolecule STRUCTURE
! smallMolecule entity SHORT-NAME
  smallMolecule entity AVAILABILITY
- smallMolecule entity NAME
- smallMolecule smallMolecule CHEMICAL-FORMULA
- smallMolecule entity DATA-SOURCE
  smallMolecule entity SYNONYMS
! pathway entity XREF
! pathway pathway ORGANISM
  pathway entity COMMENT
! pathway entity SHORT-NAME
  pathway entity AVAILABILITY
- pathway entity NAME
- pathway entity DATA-SOURCE
  pathway entity SYNONYMS
! pathway pathway PATHWAY-COMPONENTS
! utilityClass utilityClass COMMENT
! relationshipXref xref DB-VERSION
  relationshipXref utilityClass COMMENT
! relationshipXref xref DB
! relationshipXref xref ID
  relationshipXref relationshipXref RELATIONSHIP-TYPE
  relationshipXref xref ID-VERSION
! chemicalStructure chemicalStructure STRUCTURE-FORMAT
  chemicalStructure utilityClass COMMENT
  chemicalStructure chemicalStructure STRUCTURE-DATA
--- 1,207 ----
  catalysis entity COMMENT
! catalysis entity XREF
  catalysis entity AVAILABILITY
  catalysis catalysis DIRECTION
  catalysis entity SYNONYMS
  catalysis control CONTROLLED
! catalysis entity DATA-SOURCE
! catalysis entity SHORT-NAME
! catalysis control CONTROLLER
  catalysis catalysis COFACTOR
! catalysis entity NAME
! catalysis control CONTROL-TYPE
! physicalEntityParticipant physicalEntityParticipant CELLULAR-LOCATION
  physicalEntityParticipant utilityClass COMMENT
  physicalEntityParticipant physicalEntityParticipant PHYSICAL-ENTITY
! physicalEntityParticipant physicalEntityParticipant STOICHIOMETRIC-COEFFICIENT
  modulation entity COMMENT
! modulation entity XREF
  modulation entity AVAILABILITY
  modulation entity SYNONYMS
  modulation control CONTROLLED
+ modulation entity DATA-SOURCE
+ modulation entity SHORT-NAME
+ modulation control CONTROLLER
+ modulation entity NAME
  modulation control CONTROL-TYPE
  protein entity COMMENT
! protein entity XREF
  protein entity AVAILABILITY
! protein entity SYNONYMS
  protein protein ORGANISM
  protein entity DATA-SOURCE
! protein entity SHORT-NAME
! protein protein SEQUENCE
! protein entity NAME
! xref utilityClass COMMENT
! xref xref DB-VERSION
! xref xref DB
! xref xref ID-VERSION
! xref xref ID
  dataSource utilityClass COMMENT
  dataSource dataSource NAME
  transport conversion LEFT
  transport conversion RIGHT
+ transport entity COMMENT
+ transport entity XREF
+ transport entity AVAILABILITY
  transport entity SYNONYMS
! transport entity DATA-SOURCE
! transport entity SHORT-NAME
! transport entity NAME
! transport conversion SPONTANEOUS
  complexAssembly conversion LEFT
  complexAssembly conversion RIGHT
+ complexAssembly entity COMMENT
+ complexAssembly entity XREF
+ complexAssembly entity AVAILABILITY
  complexAssembly entity SYNONYMS
! complexAssembly entity DATA-SOURCE
! complexAssembly entity SHORT-NAME
! complexAssembly entity NAME
! complexAssembly conversion SPONTANEOUS
! biochemicalReaction conversion LEFT
  biochemicalReaction conversion RIGHT
  biochemicalReaction entity SYNONYMS
! biochemicalReaction biochemicalReaction DELTA-H
! biochemicalReaction entity SHORT-NAME
! biochemicalReaction entity DATA-SOURCE
! biochemicalReaction conversion SPONTANEOUS
! biochemicalReaction biochemicalReaction DELTA-S
! biochemicalReaction entity COMMENT
  biochemicalReaction biochemicalReaction KEQ
  biochemicalReaction entity XREF
  biochemicalReaction entity AVAILABILITY
! biochemicalReaction biochemicalReaction EC-NUMBER
  biochemicalReaction entity NAME
! biochemicalReaction biochemicalReaction DELTA-G
  control entity COMMENT
! control entity XREF
  control entity AVAILABILITY
  control entity SYNONYMS
  control control CONTROLLED
+ control entity DATA-SOURCE
+ control entity SHORT-NAME
+ control control CONTROLLER
+ control entity NAME
  control control CONTROL-TYPE
! publicationXref utilityClass COMMENT
! publicationXref publicationXref SOURCE
  publicationXref publicationXref URL
  publicationXref xref DB-VERSION
! publicationXref publicationXref TITLE
  publicationXref publicationXref AUTHORS
+ publicationXref xref DB
  publicationXref xref ID-VERSION
! publicationXref publicationXref YEAR
! publicationXref xref ID
  conversion conversion LEFT
  conversion conversion RIGHT
+ conversion entity COMMENT
+ conversion entity XREF
+ conversion entity AVAILABILITY
  conversion entity SYNONYMS
+ conversion entity DATA-SOURCE
+ conversion entity SHORT-NAME
+ conversion entity NAME
+ conversion conversion SPONTANEOUS
+ bioSource utilityClass COMMENT
  bioSource bioSource CELLTYPE
  bioSource bioSource TAXON-XREF
  bioSource bioSource TISSUE
! bioSource bioSource NAME
  physicalEntity entity COMMENT
! physicalEntity entity XREF
  physicalEntity entity AVAILABILITY
  physicalEntity entity SYNONYMS
! physicalEntity entity DATA-SOURCE
! physicalEntity entity SHORT-NAME
! physicalEntity entity NAME
  unificationXref utilityClass COMMENT
+ unificationXref xref DB-VERSION
  unificationXref xref DB
  unificationXref xref ID-VERSION
! unificationXref xref ID
  openControlledVocabulary openControlledVocabulary XREF
+ openControlledVocabulary utilityClass COMMENT
  openControlledVocabulary openControlledVocabulary TERM
! transportWithBiochemicalReaction conversion LEFT
  transportWithBiochemicalReaction conversion RIGHT
  transportWithBiochemicalReaction entity SYNONYMS
! transportWithBiochemicalReaction biochemicalReaction DELTA-H
! transportWithBiochemicalReaction entity SHORT-NAME
! transportWithBiochemicalReaction entity DATA-SOURCE
! transportWithBiochemicalReaction conversion SPONTANEOUS
! transportWithBiochemicalReaction biochemicalReaction DELTA-S
! transportWithBiochemicalReaction entity COMMENT
  transportWithBiochemicalReaction biochemicalReaction KEQ
  transportWithBiochemicalReaction entity XREF
  transportWithBiochemicalReaction entity AVAILABILITY
! transportWithBiochemicalReaction biochemicalReaction EC-NUMBER
  transportWithBiochemicalReaction entity NAME
! transportWithBiochemicalReaction biochemicalReaction DELTA-G
  complex entity COMMENT
! complex entity XREF
  complex entity AVAILABILITY
! complex entity SYNONYMS
  complex complex ORGANISM
  complex entity DATA-SOURCE
! complex entity SHORT-NAME
! complex entity NAME
! complex complex COMPONENTS
! utilityClass utilityClass COMMENT
  rna entity COMMENT
! rna entity XREF
  rna entity AVAILABILITY
  rna entity SYNONYMS
! rna entity DATA-SOURCE
! rna entity SHORT-NAME
! rna rna SEQUENCE
! rna entity NAME
! rna rna ORGANISM
  pathwayStep utilityClass COMMENT
  pathwayStep pathwayStep NEXT-STEP
! pathwayStep pathwayStep STEP-INTERACTIONS
! interaction interaction PARTICIPANTS
  interaction entity COMMENT
! interaction entity XREF
  interaction entity AVAILABILITY
  interaction entity SYNONYMS
! interaction entity DATA-SOURCE
! interaction entity SHORT-NAME
! interaction entity NAME
  smallMolecule smallMolecule STRUCTURE
! smallMolecule smallMolecule MOLECULAR-WEIGHT
! smallMolecule entity COMMENT
! smallMolecule entity XREF
  smallMolecule entity AVAILABILITY
  smallMolecule entity SYNONYMS
! smallMolecule entity DATA-SOURCE
! smallMolecule entity SHORT-NAME
! smallMolecule smallMolecule CHEMICAL-FORMULA
! smallMolecule entity NAME
! pathway pathway PATHWAY-COMPONENTS
  pathway entity COMMENT
! pathway pathway ORGANISM
! pathway entity XREF
  pathway entity AVAILABILITY
  pathway entity SYNONYMS
! pathway entity DATA-SOURCE
! pathway entity SHORT-NAME
! pathway entity NAME
! entity entity COMMENT
! entity entity XREF
! entity entity AVAILABILITY
! entity entity SYNONYMS
! entity entity DATA-SOURCE
! entity entity SHORT-NAME
! entity entity NAME
  relationshipXref utilityClass COMMENT
! relationshipXref xref DB-VERSION
  relationshipXref relationshipXref RELATIONSHIP-TYPE
+ relationshipXref xref DB
  relationshipXref xref ID-VERSION
! relationshipXref xref ID
  chemicalStructure utilityClass COMMENT
  chemicalStructure chemicalStructure STRUCTURE-DATA
+ chemicalStructure chemicalStructure STRUCTURE-FORMAT

Index: Level3Editor.properties
===================================================================
RCS file: /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/io/simpleIO/Level3Editor.properties,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** Level3Editor.properties	15 Aug 2008 15:29:46 -0000	1.4
--- Level3Editor.properties	18 Aug 2008 00:47:15 -0000	1.5
***************
*** 1,501 ****
! Control Interaction interactionType
  Control Entity name
- Control Entity evidence
- Control Entity xref
  Control Entity displayName
  Control Entity comment
! Control Entity dataSource
  Control Control controlled
  Control Entity availability
! Control Control controlType
[...973 lines suppressed...]
  Rna PhysicalEntity cellularLocation
! Rna PhysicalEntity memberPhysicalEntity
! Rna Entity availability
! Rna Entity dataSource
! Rna Entity name
  Rna PhysicalEntity notFeature
  Rna PhysicalEntity boundTo
  Rna Entity displayName
+ Rna Entity xref
+ Rna Rna entityReference
  Rna Entity comment
  Rna PhysicalEntity feature
! Rna Entity standardName
! Rna Entity evidence
! RelationshipXref UtilityClass comment
! RelationshipXref RelationshipXref relationshipType
! RelationshipXref Xref db
! RelationshipXref Xref id
! RelationshipXref Xref dbVersion
! RelationshipXref Xref idVersion

Index: Level2Editor.properties
===================================================================
RCS file: /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/io/simpleIO/Level2Editor.properties,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** Level2Editor.properties	15 Aug 2008 15:29:46 -0000	1.2
--- Level2Editor.properties	18 Aug 2008 00:47:15 -0000	1.3
***************
*** 1,288 ****
- kPrime utilityClass COMMENT
- kPrime kPrime TEMPERATURE
- kPrime kPrime K-PRIME
  kPrime kPrime PH
  kPrime kPrime PMG
  kPrime kPrime IONIC-STRENGTH
  sequenceInterval utilityClass COMMENT
  sequenceInterval sequenceInterval SEQUENCE-INTERVAL-END
  sequenceInterval sequenceInterval SEQUENCE-INTERVAL-BEGIN
- catalysis interaction EVIDENCE
- catalysis entity SYNONYMS
- catalysis entity XREF
- catalysis entity COMMENT
  catalysis entity NAME
! catalysis entity SHORT-NAME
  catalysis entity AVAILABILITY
  catalysis catalysis DIRECTION
! catalysis control CONTROL-TYPE
! catalysis entity DATA-SOURCE
  catalysis control CONTROLLED
  catalysis control CONTROLLER
  catalysis catalysis COFACTOR
- catalysis physicalInteraction INTERACTION-TYPE
- sequenceFeature utilityClass COMMENT
- sequenceFeature sequenceFeature XREF
  sequenceFeature sequenceFeature FEATURE-LOCATION
- sequenceFeature sequenceFeature NAME
  sequenceFeature sequenceFeature SYNONYMS
  sequenceFeature sequenceFeature FEATURE-TYPE
  sequenceFeature sequenceFeature SHORT-NAME
! physicalEntityParticipant utilityClass COMMENT
! physicalEntityParticipant physicalEntityParticipant CELLULAR-LOCATION
  physicalEntityParticipant physicalEntityParticipant PHYSICAL-ENTITY
  physicalEntityParticipant physicalEntityParticipant STOICHIOMETRIC-COEFFICIENT
! modulation entity SHORT-NAME
  modulation entity NAME
- modulation entity AVAILABILITY
- modulation control CONTROL-TYPE
- modulation entity DATA-SOURCE
- modulation control CONTROLLED
  modulation interaction EVIDENCE
! modulation control CONTROLLER
  modulation entity XREF
  modulation physicalInteraction INTERACTION-TYPE
  modulation entity SYNONYMS
! modulation entity COMMENT
! protein entity SHORT-NAME
  protein entity NAME
- protein entity AVAILABILITY
- protein protein ORGANISM
  protein entity DATA-SOURCE
  protein entity XREF
! protein entity SYNONYMS
! protein entity COMMENT
  protein protein SEQUENCE
! dataSource utilityClass COMMENT
  dataSource dataSource XREF
  dataSource dataSource NAME
! experimentalForm experimentalForm PARTICIPANT
! experimentalForm utilityClass COMMENT
  experimentalForm experimentalForm EXPERIMENTAL-FORM-TYPE
! transport entity SHORT-NAME
  transport entity NAME
! transport entity AVAILABILITY
  transport entity DATA-SOURCE
  transport conversion SPONTANEOUS
- transport interaction EVIDENCE
  transport entity XREF
  transport physicalInteraction INTERACTION-TYPE
- transport entity SYNONYMS
  transport conversion LEFT
! transport conversion RIGHT
! transport entity COMMENT
! complexAssembly entity SHORT-NAME
  complexAssembly entity NAME
! complexAssembly entity AVAILABILITY
  complexAssembly entity DATA-SOURCE
  complexAssembly conversion SPONTANEOUS
- complexAssembly interaction EVIDENCE
  complexAssembly entity XREF
  complexAssembly physicalInteraction INTERACTION-TYPE
- complexAssembly entity SYNONYMS
  complexAssembly conversion LEFT
! complexAssembly conversion RIGHT
! complexAssembly entity COMMENT
! physicalInteraction entity SHORT-NAME
  physicalInteraction entity NAME
- physicalInteraction entity AVAILABILITY
- physicalInteraction entity DATA-SOURCE
  physicalInteraction interaction EVIDENCE
  physicalInteraction interaction PARTICIPANTS
  physicalInteraction entity XREF
  physicalInteraction physicalInteraction INTERACTION-TYPE
  physicalInteraction entity SYNONYMS
! physicalInteraction entity COMMENT
  confidence utilityClass COMMENT
  confidence confidence XREF
! confidence confidence CONFIDENCE-VALUE
! xref xref ID
! xref utilityClass COMMENT
! xref xref DB
! xref xref DB-VERSION
! xref xref ID-VERSION
! dna dna ORGANISM
! dna entity SHORT-NAME
  dna entity NAME
- dna entity AVAILABILITY
  dna dna SEQUENCE
  dna entity DATA-SOURCE
  dna entity XREF
  dna entity SYNONYMS
! dna entity COMMENT
  biochemicalReaction interaction EVIDENCE
! biochemicalReaction entity XREF
  biochemicalReaction entity SYNONYMS
  biochemicalReaction biochemicalReaction EC-NUMBER
- biochemicalReaction entity COMMENT
- biochemicalReaction conversion RIGHT
- biochemicalReaction entity NAME
- biochemicalReaction biochemicalReaction DELTA-S
  biochemicalReaction entity SHORT-NAME
! biochemicalReaction entity AVAILABILITY
  biochemicalReaction biochemicalReaction DELTA-H
  biochemicalReaction biochemicalReaction DELTA-G
- biochemicalReaction entity DATA-SOURCE
- biochemicalReaction conversion SPONTANEOUS
  biochemicalReaction physicalInteraction INTERACTION-TYPE
- biochemicalReaction conversion LEFT
  biochemicalReaction biochemicalReaction KEQ
! control entity SHORT-NAME
  control entity NAME
- control entity AVAILABILITY
- control control CONTROL-TYPE
- control entity DATA-SOURCE
- control control CONTROLLED
  control interaction EVIDENCE
! control control CONTROLLER
  control entity XREF
  control physicalInteraction INTERACTION-TYPE
  control entity SYNONYMS
! control entity COMMENT
! publicationXref xref ID
! publicationXref utilityClass COMMENT
! publicationXref xref DB
! publicationXref publicationXref SOURCE
! publicationXref xref DB-VERSION
  publicationXref xref ID-VERSION
  publicationXref publicationXref YEAR
  publicationXref publicationXref TITLE
- publicationXref publicationXref URL
- publicationXref publicationXref AUTHORS
- evidence utilityClass COMMENT
- evidence evidence EXPERIMENTAL-FORM
  evidence evidence CONFIDENCE
- evidence evidence EVIDENCE-CODE
  evidence evidence XREF
! conversion entity SHORT-NAME
  conversion entity NAME
! conversion entity AVAILABILITY
  conversion entity DATA-SOURCE
  conversion conversion SPONTANEOUS
- conversion interaction EVIDENCE
  conversion entity XREF
  conversion physicalInteraction INTERACTION-TYPE
- conversion entity SYNONYMS
  conversion conversion LEFT
! conversion conversion RIGHT
! conversion entity COMMENT
! bioSource bioSource TAXON-XREF
  bioSource utilityClass COMMENT
- bioSource bioSource NAME
  bioSource bioSource CELLTYPE
! bioSource bioSource TISSUE
! physicalEntity entity SHORT-NAME
  physicalEntity entity NAME
- physicalEntity entity AVAILABILITY
  physicalEntity entity DATA-SOURCE
  physicalEntity entity XREF
  physicalEntity entity SYNONYMS
- physicalEntity entity COMMENT
- sequenceParticipant utilityClass COMMENT
- sequenceParticipant sequenceParticipant SEQUENCE-FEATURE-LIST
- sequenceParticipant physicalEntityParticipant CELLULAR-LOCATION
  sequenceParticipant physicalEntityParticipant PHYSICAL-ENTITY
  sequenceParticipant physicalEntityParticipant STOICHIOMETRIC-COEFFICIENT
! unificationXref xref ID
! unificationXref utilityClass COMMENT
  unificationXref xref DB
  unificationXref xref DB-VERSION
! unificationXref xref ID-VERSION
  openControlledVocabulary utilityClass COMMENT
- openControlledVocabulary openControlledVocabulary XREF
  openControlledVocabulary openControlledVocabulary TERM
  transportWithBiochemicalReaction interaction EVIDENCE
! transportWithBiochemicalReaction entity XREF
  transportWithBiochemicalReaction entity SYNONYMS
  transportWithBiochemicalReaction biochemicalReaction EC-NUMBER
- transportWithBiochemicalReaction entity COMMENT
- transportWithBiochemicalReaction conversion RIGHT
- transportWithBiochemicalReaction entity NAME
- transportWithBiochemicalReaction biochemicalReaction DELTA-S
  transportWithBiochemicalReaction entity SHORT-NAME
! transportWithBiochemicalReaction entity AVAILABILITY
  transportWithBiochemicalReaction biochemicalReaction DELTA-H
  transportWithBiochemicalReaction biochemicalReaction DELTA-G
- transportWithBiochemicalReaction entity DATA-SOURCE
- transportWithBiochemicalReaction conversion SPONTANEOUS
  transportWithBiochemicalReaction physicalInteraction INTERACTION-TYPE
- transportWithBiochemicalReaction conversion LEFT
  transportWithBiochemicalReaction biochemicalReaction KEQ
! complex entity SHORT-NAME
  complex entity NAME
- complex complex COMPONENTS
- complex entity AVAILABILITY
  complex entity DATA-SOURCE
  complex entity XREF
  complex complex ORGANISM
  complex entity SYNONYMS
- complex entity COMMENT
- sequenceLocation utilityClass COMMENT
  externalReferenceUtilityClass utilityClass COMMENT
! deltaGprimeO utilityClass COMMENT
  deltaGprimeO deltaGprimeO PMG
! deltaGprimeO deltaGprimeO DELTA-G-PRIME-O
  deltaGprimeO deltaGprimeO IONIC-STRENGTH
! deltaGprimeO deltaGprimeO PH
  deltaGprimeO deltaGprimeO TEMPERATURE
! sequenceSite utilityClass COMMENT
  sequenceSite sequenceSite POSITION-STATUS
  sequenceSite sequenceSite SEQUENCE-POSITION
! rna entity SHORT-NAME
  rna entity NAME
- rna rna ORGANISM
- rna entity AVAILABILITY
- rna rna SEQUENCE
  rna entity DATA-SOURCE
  rna entity XREF
  rna entity SYNONYMS
- rna entity COMMENT
  pathwayStep utilityClass COMMENT
  pathwayStep pathwayStep NEXT-STEP
  pathwayStep pathwayStep STEP-INTERACTIONS
! entity entity SHORT-NAME
! entity entity NAME
! entity entity AVAILABILITY
! entity entity DATA-SOURCE
! entity entity XREF
! entity entity SYNONYMS
! entity entity COMMENT
! interaction entity SHORT-NAME
  interaction entity NAME
- interaction entity AVAILABILITY
- interaction entity DATA-SOURCE
  interaction interaction EVIDENCE
  interaction interaction PARTICIPANTS
  interaction entity XREF
  interaction entity SYNONYMS
! interaction entity COMMENT
! smallMolecule entity SHORT-NAME
  smallMolecule entity NAME
- smallMolecule smallMolecule CHEMICAL-FORMULA
- smallMolecule smallMolecule MOLECULAR-WEIGHT
- smallMolecule entity AVAILABILITY
  smallMolecule entity DATA-SOURCE
  smallMolecule entity XREF
! smallMolecule entity SYNONYMS
! smallMolecule entity COMMENT
  smallMolecule smallMolecule STRUCTURE
! pathway entity SHORT-NAME
  pathway entity NAME
- pathway pathway EVIDENCE
- pathway entity AVAILABILITY
- pathway pathway ORGANISM
- pathway pathway PATHWAY-COMPONENTS
  pathway entity DATA-SOURCE
  pathway entity XREF
  pathway entity SYNONYMS
! pathway entity COMMENT
! utilityClass utilityClass COMMENT
! relationshipXref xref ID
! relationshipXref utilityClass COMMENT
! relationshipXref xref DB
! relationshipXref xref DB-VERSION
  relationshipXref relationshipXref RELATIONSHIP-TYPE
  relationshipXref xref ID-VERSION
! chemicalStructure utilityClass COMMENT
  chemicalStructure chemicalStructure STRUCTURE-DATA
  chemicalStructure chemicalStructure STRUCTURE-FORMAT
--- 1,288 ----
  kPrime kPrime PH
+ kPrime utilityClass COMMENT
  kPrime kPrime PMG
  kPrime kPrime IONIC-STRENGTH
+ kPrime kPrime TEMPERATURE
+ kPrime kPrime K-PRIME
  sequenceInterval utilityClass COMMENT
  sequenceInterval sequenceInterval SEQUENCE-INTERVAL-END
  sequenceInterval sequenceInterval SEQUENCE-INTERVAL-BEGIN
  catalysis entity NAME
! catalysis entity COMMENT
! catalysis interaction EVIDENCE
! catalysis entity DATA-SOURCE
  catalysis entity AVAILABILITY
  catalysis catalysis DIRECTION
! catalysis entity SYNONYMS
! catalysis entity SHORT-NAME
! catalysis entity XREF
  catalysis control CONTROLLED
+ catalysis physicalInteraction INTERACTION-TYPE
  catalysis control CONTROLLER
+ catalysis control CONTROL-TYPE
  catalysis catalysis COFACTOR
  sequenceFeature sequenceFeature FEATURE-LOCATION
  sequenceFeature sequenceFeature SYNONYMS
  sequenceFeature sequenceFeature FEATURE-TYPE
+ sequenceFeature utilityClass COMMENT
+ sequenceFeature sequenceFeature XREF
  sequenceFeature sequenceFeature SHORT-NAME
! sequenceFeature sequenceFeature NAME
  physicalEntityParticipant physicalEntityParticipant PHYSICAL-ENTITY
  physicalEntityParticipant physicalEntityParticipant STOICHIOMETRIC-COEFFICIENT
! physicalEntityParticipant physicalEntityParticipant CELLULAR-LOCATION
! physicalEntityParticipant utilityClass COMMENT
! modulation entity COMMENT
  modulation entity NAME
  modulation interaction EVIDENCE
! modulation entity DATA-SOURCE
! modulation entity SHORT-NAME
  modulation entity XREF
+ modulation entity AVAILABILITY
+ modulation control CONTROLLED
  modulation physicalInteraction INTERACTION-TYPE
+ modulation control CONTROLLER
  modulation entity SYNONYMS
! modulation control CONTROL-TYPE
! protein entity COMMENT
  protein entity NAME
  protein entity DATA-SOURCE
+ protein entity SHORT-NAME
  protein entity XREF
! protein entity AVAILABILITY
  protein protein SEQUENCE
! protein protein ORGANISM
! protein entity SYNONYMS
  dataSource dataSource XREF
+ dataSource utilityClass COMMENT
  dataSource dataSource NAME
! xref xref ID-VERSION
! xref xref DB
! xref utilityClass COMMENT
! xref xref DB-VERSION
! xref xref ID
  experimentalForm experimentalForm EXPERIMENTAL-FORM-TYPE
! experimentalForm utilityClass COMMENT
! experimentalForm experimentalForm PARTICIPANT
! transport entity COMMENT
  transport entity NAME
! transport interaction EVIDENCE
  transport entity DATA-SOURCE
+ transport entity SHORT-NAME
  transport conversion SPONTANEOUS
  transport entity XREF
+ transport entity AVAILABILITY
+ transport conversion RIGHT
  transport physicalInteraction INTERACTION-TYPE
  transport conversion LEFT
! transport entity SYNONYMS
! complexAssembly entity COMMENT
  complexAssembly entity NAME
! complexAssembly interaction EVIDENCE
  complexAssembly entity DATA-SOURCE
+ complexAssembly entity SHORT-NAME
  complexAssembly conversion SPONTANEOUS
  complexAssembly entity XREF
+ complexAssembly entity AVAILABILITY
+ complexAssembly conversion RIGHT
  complexAssembly physicalInteraction INTERACTION-TYPE
  complexAssembly conversion LEFT
! complexAssembly entity SYNONYMS
! physicalInteraction entity COMMENT
  physicalInteraction entity NAME
  physicalInteraction interaction EVIDENCE
  physicalInteraction interaction PARTICIPANTS
+ physicalInteraction entity DATA-SOURCE
+ physicalInteraction entity SHORT-NAME
  physicalInteraction entity XREF
+ physicalInteraction entity AVAILABILITY
  physicalInteraction physicalInteraction INTERACTION-TYPE
  physicalInteraction entity SYNONYMS
! confidence confidence CONFIDENCE-VALUE
  confidence utilityClass COMMENT
  confidence confidence XREF
! dna entity COMMENT
  dna entity NAME
  dna dna SEQUENCE
  dna entity DATA-SOURCE
+ dna entity SHORT-NAME
  dna entity XREF
+ dna entity AVAILABILITY
+ dna dna ORGANISM
  dna entity SYNONYMS
! biochemicalReaction entity NAME
! biochemicalReaction entity COMMENT
  biochemicalReaction interaction EVIDENCE
! biochemicalReaction entity DATA-SOURCE
! biochemicalReaction conversion SPONTANEOUS
! biochemicalReaction entity AVAILABILITY
! biochemicalReaction conversion LEFT
! biochemicalReaction biochemicalReaction DELTA-S
  biochemicalReaction entity SYNONYMS
  biochemicalReaction biochemicalReaction EC-NUMBER
  biochemicalReaction entity SHORT-NAME
! biochemicalReaction entity XREF
  biochemicalReaction biochemicalReaction DELTA-H
+ biochemicalReaction conversion RIGHT
  biochemicalReaction biochemicalReaction DELTA-G
  biochemicalReaction physicalInteraction INTERACTION-TYPE
  biochemicalReaction biochemicalReaction KEQ
! control entity COMMENT
  control entity NAME
  control interaction EVIDENCE
! control entity DATA-SOURCE
! control entity SHORT-NAME
  control entity XREF
+ control entity AVAILABILITY
+ control control CONTROLLED
  control physicalInteraction INTERACTION-TYPE
+ control control CONTROLLER
  control entity SYNONYMS
! control control CONTROL-TYPE
  publicationXref xref ID-VERSION
+ publicationXref publicationXref SOURCE
+ publicationXref xref DB
+ publicationXref publicationXref AUTHORS
+ publicationXref publicationXref URL
+ publicationXref utilityClass COMMENT
  publicationXref publicationXref YEAR
+ publicationXref xref DB-VERSION
+ publicationXref xref ID
  publicationXref publicationXref TITLE
  evidence evidence CONFIDENCE
  evidence evidence XREF
! evidence evidence EXPERIMENTAL-FORM
! evidence utilityClass COMMENT
! evidence evidence EVIDENCE-CODE
! conversion entity COMMENT
  conversion entity NAME
! conversion interaction EVIDENCE
  conversion entity DATA-SOURCE
+ conversion entity SHORT-NAME
  conversion conversion SPONTANEOUS
  conversion entity XREF
+ conversion entity AVAILABILITY
+ conversion conversion RIGHT
  conversion physicalInteraction INTERACTION-TYPE
  conversion conversion LEFT
! conversion entity SYNONYMS
! bioSource bioSource TISSUE
  bioSource utilityClass COMMENT
  bioSource bioSource CELLTYPE
! bioSource bioSource TAXON-XREF
! bioSource bioSource NAME
! physicalEntity entity COMMENT
  physicalEntity entity NAME
  physicalEntity entity DATA-SOURCE
+ physicalEntity entity SHORT-NAME
  physicalEntity entity XREF
+ physicalEntity entity AVAILABILITY
  physicalEntity entity SYNONYMS
  sequenceParticipant physicalEntityParticipant PHYSICAL-ENTITY
  sequenceParticipant physicalEntityParticipant STOICHIOMETRIC-COEFFICIENT
! sequenceParticipant physicalEntityParticipant CELLULAR-LOCATION
! sequenceParticipant sequenceParticipant SEQUENCE-FEATURE-LIST
! sequenceParticipant utilityClass COMMENT
! unificationXref xref ID-VERSION
  unificationXref xref DB
+ unificationXref utilityClass COMMENT
  unificationXref xref DB-VERSION
! unificationXref xref ID
  openControlledVocabulary utilityClass COMMENT
  openControlledVocabulary openControlledVocabulary TERM
+ openControlledVocabulary openControlledVocabulary XREF
+ transportWithBiochemicalReaction entity NAME
+ transportWithBiochemicalReaction entity COMMENT
  transportWithBiochemicalReaction interaction EVIDENCE
! transportWithBiochemicalReaction entity DATA-SOURCE
! transportWithBiochemicalReaction conversion SPONTANEOUS
! transportWithBiochemicalReaction entity AVAILABILITY
! transportWithBiochemicalReaction conversion LEFT
! transportWithBiochemicalReaction biochemicalReaction DELTA-S
  transportWithBiochemicalReaction entity SYNONYMS
  transportWithBiochemicalReaction biochemicalReaction EC-NUMBER
  transportWithBiochemicalReaction entity SHORT-NAME
! transportWithBiochemicalReaction entity XREF
  transportWithBiochemicalReaction biochemicalReaction DELTA-H
+ transportWithBiochemicalReaction conversion RIGHT
  transportWithBiochemicalReaction biochemicalReaction DELTA-G
  transportWithBiochemicalReaction physicalInteraction INTERACTION-TYPE
  transportWithBiochemicalReaction biochemicalReaction KEQ
! complex entity COMMENT
  complex entity NAME
  complex entity DATA-SOURCE
+ complex entity SHORT-NAME
  complex entity XREF
+ complex entity AVAILABILITY
+ complex complex COMPONENTS
  complex complex ORGANISM
  complex entity SYNONYMS
  externalReferenceUtilityClass utilityClass COMMENT
! utilityClass utilityClass COMMENT
! deltaGprimeO deltaGprimeO PH
  deltaGprimeO deltaGprimeO PMG
! deltaGprimeO utilityClass COMMENT
  deltaGprimeO deltaGprimeO IONIC-STRENGTH
! deltaGprimeO deltaGprimeO DELTA-G-PRIME-O
  deltaGprimeO deltaGprimeO TEMPERATURE
! sequenceLocation utilityClass COMMENT
  sequenceSite sequenceSite POSITION-STATUS
+ sequenceSite utilityClass COMMENT
  sequenceSite sequenceSite SEQUENCE-POSITION
! rna entity COMMENT
  rna entity NAME
  rna entity DATA-SOURCE
+ rna entity SHORT-NAME
  rna entity XREF
+ rna entity AVAILABILITY
+ rna rna SEQUENCE
+ rna rna ORGANISM
  rna entity SYNONYMS
  pathwayStep utilityClass COMMENT
  pathwayStep pathwayStep NEXT-STEP
  pathwayStep pathwayStep STEP-INTERACTIONS
! interaction entity COMMENT
  interaction entity NAME
  interaction interaction EVIDENCE
  interaction interaction PARTICIPANTS
+ interaction entity DATA-SOURCE
+ interaction entity SHORT-NAME
  interaction entity XREF
+ interaction entity AVAILABILITY
  interaction entity SYNONYMS
! smallMolecule entity COMMENT
  smallMolecule entity NAME
  smallMolecule entity DATA-SOURCE
+ smallMolecule entity SHORT-NAME
  smallMolecule entity XREF
! smallMolecule entity AVAILABILITY
  smallMolecule smallMolecule STRUCTURE
! smallMolecule smallMolecule MOLECULAR-WEIGHT
! smallMolecule entity SYNONYMS
! smallMolecule smallMolecule CHEMICAL-FORMULA
! pathway entity COMMENT
  pathway entity NAME
  pathway entity DATA-SOURCE
+ pathway entity SHORT-NAME
  pathway entity XREF
+ pathway entity AVAILABILITY
+ pathway pathway EVIDENCE
+ pathway pathway ORGANISM
  pathway entity SYNONYMS
! pathway pathway PATHWAY-COMPONENTS
! entity entity COMMENT
! entity entity NAME
! entity entity DATA-SOURCE
! entity entity SHORT-NAME
! entity entity XREF
! entity entity AVAILABILITY
! entity entity SYNONYMS
  relationshipXref relationshipXref RELATIONSHIP-TYPE
  relationshipXref xref ID-VERSION
! relationshipXref xref DB
! relationshipXref utilityClass COMMENT
! relationshipXref xref DB-VERSION
! relationshipXref xref ID
  chemicalStructure chemicalStructure STRUCTURE-DATA
+ chemicalStructure utilityClass COMMENT
  chemicalStructure chemicalStructure STRUCTURE-FORMAT

Update of /cvsroot/biopax/Paxtools
In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv7777

Removed Files:
	biopax-level1.owl ont-policy.rdf biopax-level3.owl 
	biopax-level2.owl 
Log Message:
Updates properties and jenaIOHandlerTest

--- biopax-level1.owl DELETED ---

--- biopax-level2.owl DELETED ---

--- ont-policy.rdf DELETED ---

--- biopax-level3.owl DELETED ---

Update of /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/io/jena
In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv7777/src/org/biopax/paxtools/io/jena

Modified Files:
	JenaIOHandler.java 
Log Message:
Updates properties and jenaIOHandlerTest

Index: JenaIOHandler.java
===================================================================
RCS file: /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/io/jena/JenaIOHandler.java,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** JenaIOHandler.java	17 Aug 2008 23:04:07 -0000	1.22
--- JenaIOHandler.java	18 Aug 2008 00:47:15 -0000	1.23
***************
*** 302,324 ****
  		OntProperty ontProperty =
  			((OntProperty) predicate.as(OntProperty.class));
! 		PropertyEditor editor = editorMap.getEditorForProperty(
! 			ontProperty.getLocalName(), bpe.getClass());
! 		if (editor.isMultipleCardinality())
! 		{
! 			NodeIterator nodeIterator =
! 				individual.listPropertyValues(ontProperty);
! 			while (nodeIterator.hasNext())
! 			{
! 				RDFNode propertyValue = (RDFNode) nodeIterator.next();
! 				bindValue(propertyValue, editor, bpe, model);
! 			}
! 		}
! 		else
! 		{
! 			RDFNode propertyValue =
! 				individual.getPropertyValue(ontProperty);
! 			bindValue(propertyValue, editor, bpe, model);
! 		}
! 	}
  
  	private void bindValue(RDFNode propertyValue, PropertyEditor editor,
--- 302,333 ----
  		OntProperty ontProperty =
  			((OntProperty) predicate.as(OntProperty.class));
!         String localName = ontProperty.getLocalName();
!         PropertyEditor editor = editorMap.getEditorForProperty(
!                 localName, bpe.getClass());
!         if(editor != null)
!         {
!             if (editor.isMultipleCardinality())
!             {
!                 NodeIterator nodeIterator =
!                     individual.listPropertyValues(ontProperty);
!                 while (nodeIterator.hasNext())
!                 {
!                     RDFNode propertyValue = (RDFNode) nodeIterator.next();
!                     bindValue(propertyValue, editor, bpe, model);
!                 }
!             }
!             else
!             {
!                 RDFNode propertyValue =
!                     individual.getPropertyValue(ontProperty);
!                 bindValue(propertyValue, editor, bpe, model);
!             }
!         }
!         else
!         {
!             log.error("Could not locate editor!");
!             log.error(predicate + "bpe:" +bpe.getRDFId() +"property:" + localName);
!         }
!     }
  
  	private void bindValue(RDFNode propertyValue, PropertyEditor editor,

Update of /cvsroot/biopax/Paxtools/test/org/biopax/paxtools/io/jena
In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv7777/test/org/biopax/paxtools/io/jena

Modified Files:
	JenaIOHandlerTest.java 
Log Message:
Updates properties and jenaIOHandlerTest

Index: JenaIOHandlerTest.java
===================================================================
RCS file: /cvsroot/biopax/Paxtools/test/org/biopax/paxtools/io/jena/JenaIOHandlerTest.java,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** JenaIOHandlerTest.java	15 Aug 2008 19:25:07 -0000	1.12
--- JenaIOHandlerTest.java	18 Aug 2008 00:47:15 -0000	1.13
***************
*** 16,22 ****
      public void testAllFilesInTestDirectory()
      {
!         JenaIOHandler jenaIOHandler = new JenaIOHandler(null, BioPAXLevel.L2);
  	    jenaIOHandler.treatNilAsNull(true);
!         String pathname = "testfiles";
          File testDir = new File(pathname);
          FilenameFilter filter = new FilenameFilter()
--- 16,34 ----
      public void testAllFilesInTestDirectory()
      {
!         for (BioPAXLevel level : BioPAXLevel.values())
!         {
!             testAllFilesInTestDirectory(level);
!         }
!     }
! 
! 
!     public void testAllFilesInTestDirectory(BioPAXLevel level)
!     {
!         JenaIOHandler jenaIOHandler = new JenaIOHandler(null, level);
!         SimpleExporter simpleExporter = new SimpleExporter(level);
! 
  	    jenaIOHandler.treatNilAsNull(true);
!         String pathname = "testfiles/"+level.name();
!         System.out.println("pathname = " + pathname);
          File testDir = new File(pathname);
          FilenameFilter filter = new FilenameFilter()
***************
*** 33,38 ****
              {
  
!                 readWriteReadTest(pathname, s, jenaIOHandler);
!                 //mergeTest(merged, merger, pathname, s, jenaIOHandler);
              }
              catch (Exception e)
--- 45,49 ----
              {
  
!                 readWriteReadTest(pathname, s, jenaIOHandler,simpleExporter);
              }
              catch (Exception e)
***************
*** 44,47 ****
--- 55,59 ----
          }
      }
+   
      @Test
      public void testMultipleFileReading() throws IOException,
***************
*** 62,66 ****
  
      private void readWriteReadTest(String pathname, String s,
!                                    JenaIOHandler jenaIOHandler)
              throws IllegalAccessException, InvocationTargetException,
                     IOException, ClassNotFoundException
--- 74,78 ----
  
      private void readWriteReadTest(String pathname, String s,
!                                    JenaIOHandler jenaIOHandler, SimpleExporter simpleExporter)
              throws IllegalAccessException, InvocationTargetException,
                     IOException, ClassNotFoundException
***************
*** 69,79 ****
                  new FileInputStream(new File(pathname + "/" + s));
          //jenaIOHandler.setStrict(false);
!         Model level2 =
                  jenaIOHandler.convertFromOWL(in);
     
          FileOutputStream out = new FileOutputStream(pathname + "/out-" + s);
!         SimpleExporter simpleExporter = new SimpleExporter(BioPAXLevel.L2);
!         simpleExporter.convertToOWL(level2,out);
!         //jenaIOHandler.convertToOWL(level2, out);
          in.close();
          out.close();
--- 81,89 ----
                  new FileInputStream(new File(pathname + "/" + s));
          //jenaIOHandler.setStrict(false);
!         Model model =
                  jenaIOHandler.convertFromOWL(in);
     
          FileOutputStream out = new FileOutputStream(pathname + "/out-" + s);
!         simpleExporter.convertToOWL(model,out);
          in.close();
          out.close();
***************
*** 81,85 ****
  	    Model level21 =
                  jenaIOHandler.convertFromOWL(in);
!         assert level2.getObjects().size() == level21.getObjects().size();
  	    in.close();
          
--- 91,95 ----
  	    Model level21 =
                  jenaIOHandler.convertFromOWL(in);
!         assert model.getObjects().size() == level21.getObjects().size();
  	    in.close();

Update of /cvsroot/biopax/Paxtools/test/org/biopax/paxtools/model/level3
In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv7777/test/org/biopax/paxtools/model/level3

Modified Files:
	MockFactory.java 
Log Message:
Updates properties and jenaIOHandlerTest

Index: MockFactory.java
===================================================================
RCS file: /cvsroot/biopax/Paxtools/test/org/biopax/paxtools/model/level3/MockFactory.java,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** MockFactory.java	15 Aug 2008 15:30:43 -0000	1.11
--- MockFactory.java	18 Aug 2008 00:47:15 -0000	1.12
***************
*** 14,19 ****
   * This factory returns decorated objects for testing.
   */
! public class MockFactory implements Level3Factory
! {
  // ------------------------------ FIELDS ------------------------------
  
--- 14,18 ----
   * This factory returns decorated objects for testing.
   */
! public class MockFactory implements Level3Factory {
[...1162 lines suppressed...]
!             throws IllegalAccessException, InvocationTargetException {
          Method[] methods = MockFactory.class.getMethods();
!         for (Method method : methods) {
!             if (method.getName().startsWith("create")) {
                  System.out.println("testing " + method);
                  method.invoke(this);
***************
*** 678,683 ****
  
      public static void main(String[] args)
!             throws InvocationTargetException, IllegalAccessException
!     {
          MockFactory mockFactory = new MockFactory();
          mockFactory.testCreationMethods();
--- 577,581 ----
  
      public static void main(String[] args)
!             throws InvocationTargetException, IllegalAccessException {
          MockFactory mockFactory = new MockFactory();
          mockFactory.testCreationMethods();

Update of /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/impl/level3
In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv31820/src/org/biopax/paxtools/impl/level3

Removed Files:
	DeltaGPrime0Impl.java 
Log Message:
pesky deltaGPrime0Impl deleted

--- DeltaGPrime0Impl.java DELETED ---

Update of /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/proxy/level3
In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv2042/src/org/biopax/paxtools/proxy/level3

Modified Files:
	BioPAXFactoryForPersistence.java 
Log Message:
bug fixes for level 3 support..

Index: BioPAXFactoryForPersistence.java
===================================================================
RCS file: /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/proxy/level3/BioPAXFactoryForPersistence.java,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** BioPAXFactoryForPersistence.java	14 Aug 2008 23:58:01 -0000	1.13
--- BioPAXFactoryForPersistence.java	17 Aug 2008 23:04:08 -0000	1.14
***************
*** 14,21 ****
   * BioPAXFactoryForPersistence
   */
! public class BioPAXFactoryForPersistence implements BioPAXFactory, Level3Factory 
  {
  // BioPAXFactory
! 	
  	public BioPAXLevel getLevel() {
  		return BioPAXLevel.L3;
--- 14,21 ----
   * BioPAXFactoryForPersistence
   */
! public class BioPAXFactoryForPersistence implements BioPAXFactory, Level3Factory
  {
  // BioPAXFactory
! 
  	public BioPAXLevel getLevel() {
  		return BioPAXLevel.L3;
***************
*** 282,285 ****
--- 282,290 ----
       }
  
+     public SequenceModificationVocabulary createSequenceModificationVocabulary() {
+         return new SequenceModificationVocabularyProxy();
+ 
+     }
+ 
      public RelationshipTypeVocabulary createRelationshipTypeVocabulary() {
           return new RelationshipTypeVocabularyProxy();

Update of /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/impl/level3
In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv2042/src/org/biopax/paxtools/impl/level3

Modified Files:
	SimplePhysicalEntityImpl.java Level3FactoryImpl.java 
	NameHelper.java PhysicalEntityImpl.java 
Log Message:
bug fixes for level 3 support..

Index: PhysicalEntityImpl.java
===================================================================
RCS file: /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/impl/level3/PhysicalEntityImpl.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** PhysicalEntityImpl.java	14 Aug 2008 23:58:01 -0000	1.7
--- PhysicalEntityImpl.java	17 Aug 2008 23:04:07 -0000	1.8
***************
*** 4,8 ****
  import org.biopax.paxtools.model.level3.*;
  import org.biopax.paxtools.util.BidirectionalLinkViolationException;
! import org.biopax.paxtools.util.IllegalBioPAXArgumentException;
  
  import java.util.HashSet;
--- 4,9 ----
  import org.biopax.paxtools.model.level3.*;
  import org.biopax.paxtools.util.BidirectionalLinkViolationException;
! import org.apache.commons.logging.Log;
! import org.apache.commons.logging.LogFactory;
  
  import java.util.HashSet;
***************
*** 20,25 ****
  	private Set<EntityFeature> noFeature;
  
  
! 	public PhysicalEntityImpl()
  	{
  		boundTo = new HashSet<PhysicalEntity>();
--- 21,27 ----
  	private Set<EntityFeature> noFeature;
  
+     Log log = LogFactory.getLog(PhysicalEntityImpl.class);
  
!     public PhysicalEntityImpl()
  	{
  		boundTo = new HashSet<PhysicalEntity>();
***************
*** 106,123 ****
  	public void setComponentOf(Complex newComplex)
  	{
! 		if (this.ownerComplex == null ||
! 			!this.ownerComplex.getComponent().contains(this)
! 				&&
! 				(newComplex == null ||
! 					newComplex.getComponent().contains(this)))
! 		{
! 			this.ownerComplex = newComplex;
! 		}
  
! 		else
  		{
! 			throw new BidirectionalLinkViolationException(this, newComplex);
  		}
- 
  	}
  
--- 108,131 ----
  	public void setComponentOf(Complex newComplex)
  	{
! 		if (this.ownerComplex != null)
!         {
!             if(this.ownerComplex== newComplex)
!             {
!                 log.warn("Redundant bidirectional link!");
!             }
  
! 		    else if(this.ownerComplex.getComponent().contains(this))
! 
!             {
!                 throw new BidirectionalLinkViolationException(this, newComplex);
!             }
!         }
!         if
! 
!         		(newComplex == null ||
! 					newComplex.getComponent().contains(this))
  		{
! 			this.ownerComplex = newComplex;
  		}
  	}
  
***************
*** 208,220 ****
  			feature.isNoFeatureOf().contains(this))
  		{
! 			throw new IllegalBioPAXArgumentException(
! 				"Illegal attempt to set the inverse link!");
  
  		}
- 		else
- 		{
  			target.add(this);
- 
- 		}
  	}
  
--- 216,223 ----
  			feature.isNoFeatureOf().contains(this))
  		{
! 			log.warn("Redundant attempt to set the inverse link!");
  
  		}
  			target.add(this);
  	}
  

Index: Level3FactoryImpl.java
===================================================================
RCS file: /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/impl/level3/Level3FactoryImpl.java,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** Level3FactoryImpl.java	14 Aug 2008 23:58:01 -0000	1.13
--- Level3FactoryImpl.java	17 Aug 2008 23:04:07 -0000	1.14
***************
*** 281,284 ****
--- 281,288 ----
      }
  
+     public SequenceModificationVocabulary createSequenceModificationVocabulary() {
+         return new SequenceModificationVocabularyImpl();
+     }
+ 
      public  RelationshipTypeVocabulary createRelationshipTypeVocabulary() {
          return new  RelationshipTypeVocabularyImpl();

Index: NameHelper.java
===================================================================
RCS file: /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/impl/level3/NameHelper.java,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** NameHelper.java	14 Aug 2008 22:31:04 -0000	1.11
--- NameHelper.java	17 Aug 2008 23:04:07 -0000	1.12
***************
*** 114,118 ****
  				!(standardName == null || name.contains(standardName));
  			addDisplayName =
! 				!(displayName.equals(standardName) || displayName == null ||
  					name.contains(displayName));
  		}
--- 114,118 ----
  				!(standardName == null || name.contains(standardName));
  			addDisplayName =
! 				!( displayName == null || displayName.equals(standardName) ||
  					name.contains(displayName));
  		}

Index: SimplePhysicalEntityImpl.java
===================================================================
RCS file: /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/impl/level3/SimplePhysicalEntityImpl.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** SimplePhysicalEntityImpl.java	4 Jun 2008 18:22:58 -0000	1.1
--- SimplePhysicalEntityImpl.java	17 Aug 2008 23:04:07 -0000	1.2
***************
*** 23,28 ****
  	public void setEntityReference(EntityReference entityReference)
  	{
! 		this.entityReference.isEntityReferenceOf().remove(this);
  		this.entityReference = entityReference;
  		this.entityReference.isEntityReferenceOf().add(this);
  	}
--- 23,30 ----
  	public void setEntityReference(EntityReference entityReference)
  	{
! 		if(this.entityReference != null)
!         this.entityReference.isEntityReferenceOf().remove(this);
  		this.entityReference = entityReference;
+         if(this.entityReference != null)
  		this.entityReference.isEntityReferenceOf().add(this);
  	}

Update of /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/io/jena
In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv2042/src/org/biopax/paxtools/io/jena

Modified Files:
	JenaHelper.java JenaIOHandler.java 
Log Message:
bug fixes for level 3 support..

Index: JenaIOHandler.java
===================================================================
RCS file: /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/io/jena/JenaIOHandler.java,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -d -r1.21 -r1.22
*** JenaIOHandler.java	15 Aug 2008 23:19:35 -0000	1.21
--- JenaIOHandler.java	17 Aug 2008 23:04:07 -0000	1.22
***************
*** 54,60 ****
  	 * @see org.biopax.paxtools.controller.ReusedPEPHelper
  	 */
! 	private boolean fixReusedPEPs = true;
  	private ReusedPEPHelper reusedPEPHelper;
! 	private boolean convertingFromLevel1ToLevel2 = true;
  	private boolean treatNilAsNull;
  
--- 54,60 ----
  	 * @see org.biopax.paxtools.controller.ReusedPEPHelper
  	 */
! 	private boolean fixReusedPEPs = false;
  	private ReusedPEPHelper reusedPEPHelper;
! 	private boolean convertingFromLevel1ToLevel2 = false;
  	private boolean treatNilAsNull;
  
***************
*** 105,111 ****
  		this.level = (level == null ? BioPAXLevel.L2 : level);
  
! 		this.factory = (factory != null ? factory : new Level2FactoryImpl());
  
! 		editorMap = new JenaEditorMap(this.level);
  
  	}
--- 105,122 ----
  		this.level = (level == null ? BioPAXLevel.L2 : level);
  
! 		this.factory = (factory != null ? factory : level.getDefaultFactory());
!         //Set defaults
!         if (this.level == BioPAXLevel.L1)
!         {
!             this.convertingFromLevel1ToLevel2 = true;
!             this.fixReusedPEPs = true;
!         }
!         if (this.level == BioPAXLevel.L2)
!         {
!             this.fixReusedPEPs = true;
!         }
  
! 
!         editorMap = new JenaEditorMap(this.level);
  
  	}
***************
*** 146,151 ****
  			FileInputStream in =
  				new FileInputStream(new File(file));
! 			createAndBind(readJenaModel(in), model);
! 			log.trace("read file: " + file);
  		}
  		return model;
--- 157,163 ----
  			FileInputStream in =
  				new FileInputStream(new File(file));
! 			log.debug("start reading file:"+file);
!             createAndBind(readJenaModel(in), model);
! 			log.debug("read file: " + file);
  		}
  		return model;

Index: JenaHelper.java
===================================================================
RCS file: /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/io/jena/JenaHelper.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** JenaHelper.java	15 Aug 2008 23:19:35 -0000	1.1
--- JenaHelper.java	17 Aug 2008 23:04:07 -0000	1.2
***************
*** 18,22 ****
      static
      {
!         OntDocumentManager mgr = new OntDocumentManager("file:ont-policy.rdf;file:org/biopax/paxtools/io/jena/ont-policy.rdf");
  
                  spec = new OntModelSpec(OntModelSpec.OWL_DL_MEM);
--- 18,24 ----
      static
      {
!         String home = JenaHelper.class.getPackage().getName();
!         home.replace(".","/");
!         OntDocumentManager mgr = new OntDocumentManager("file:ont-policy.rdf;file:"+home+"/ont-policy.rdf");
  
                  spec = new OntModelSpec(OntModelSpec.OWL_DL_MEM);

Update of /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/model/level3
In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv2042/src/org/biopax/paxtools/model/level3

Modified Files:
	Level3Factory.java 
Log Message:
bug fixes for level 3 support..

Index: Level3Factory.java
===================================================================
RCS file: /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/model/level3/Level3Factory.java,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** Level3Factory.java	14 Aug 2008 23:58:02 -0000	1.9
--- Level3Factory.java	17 Aug 2008 23:04:07 -0000	1.10
***************
*** 110,113 ****
--- 110,114 ----
  
      public SequenceRegionVocabulary createSequenceRegionVocabulary();
+     public SequenceModificationVocabulary createSequenceModificationVocabulary();
      public RelationshipTypeVocabulary createRelationshipTypeVocabulary();

Update of /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/controller
In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv13714/src/org/biopax/paxtools/controller

Modified Files:
	Integrator.java 
Log Message:
More support for interactive integration.

Index: Integrator.java
===================================================================
RCS file: /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/controller/Integrator.java,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** Integrator.java	25 Jul 2008 16:11:23 -0000	1.11
--- Integrator.java	17 Aug 2008 04:56:20 -0000	1.12
***************
*** 249,266 ****
      }
  
  
      /**
!      * Integrates <em>target</em> and <em>source</em>(s) and returns a
!      * sorted (desc) list of conversion scores.
!      *
!      * @see #setNormalizeModels(boolean)
!      * @see #setOnlyMapping(boolean)
!      * @see #setScoresOver(double)
!      * @see #setSelfRemove(boolean)
!      * @see #setThreshold(Double)
       *
       * @return a sorted list of ConversionScores
       */
!     public List<ConversionScore> integrate() {
          Map<physicalEntityParticipant, Map<physicalEntityParticipant, Double>>
                      pepScoreMatrix = this.pepScoreMatrix;
--- 249,277 ----
      }
  
+     /**
+          * Integrates <em>target</em> and <em>source</em>(s) and returns a
+          * sorted (desc) list of conversion scores.
+          *
+          * @see #setNormalizeModels(boolean)
+          * @see #setOnlyMapping(boolean)
+          * @see #setScoresOver(double)
+          * @see #setSelfRemove(boolean)
+          * @see #setThreshold(Double)
+          *
+          * @return a sorted list of ConversionScores
+          */
+     public List<ConversionScore> integrate() {
+         return integrate(null);
+     }
  
      /**
!      * Does the integration using user-provided scores list.
       *
+      * @see #integrate()
+      * 
+      * @param alternativeScores alternative scores, can be null
       * @return a sorted list of ConversionScores
       */
!     public List<ConversionScore> integrate(List<ConversionScore> alternativeScores) {
          Map<physicalEntityParticipant, Map<physicalEntityParticipant, Double>>
                      pepScoreMatrix = this.pepScoreMatrix;
***************
*** 308,312 ****
          log.info("PEP scores copied.");
  
!         similarConversions = new ArrayList<ConversionScore>(this.similarConversions);
          log.info("Conversion scores copied.");
          /* End of copies */
--- 319,326 ----
          log.info("PEP scores copied.");
  
!         similarConversions = (alternativeScores == null)
!                                 ? new ArrayList<ConversionScore>(this.similarConversions)
!                                 : alternativeScores;
! 
          log.info("Conversion scores copied.");
          /* End of copies */
***************
*** 318,322 ****
          // Sorting is essential for #equalizeEntities. If you are to
          // modify this sort, check there also!
!         log.info("Sorting scores.");
          Collections.sort(similarConversions);
          Collections.reverse(similarConversions);
--- 332,336 ----
          // Sorting is essential for #equalizeEntities. If you are to
          // modify this sort, check there also!
!         log.info("Sorting scores (" + similarConversions.size() + " scores).");
          Collections.sort(similarConversions);
          Collections.reverse(similarConversions);
***************
*** 414,418 ****
              // We are done with conv2
              doNotModifySet.add(conv2);
- 
          }
      }
--- 428,431 ----

Thanks to Brian Turner I had a chance to finally fix this ont-policy 
problem in a reasonable way.

Here is the deal : if you do not put an ont-policy.rdf rdf, paxtools 
will use class-loaded ont-policy at 
/org/biopax/paxtools/io/jena/ont-policy.rdf.
If you want to override its behavior (  probably never) you need to put 
a file called ont-policy.rdf into the home directory. All owl files are 
again class loaded.

Make sure when you compile the project your build enviroment copies .owl 
and .rdf files as resources.

Arman, when you have time can you add this to the documentation?

Cheers,
ED

Update of /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/model
In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv18506/src/org/biopax/paxtools/model

Modified Files:
	BioPAXLevel.java 
Added Files:
	biopax-level3.owl biopax-level1.owl biopax-level2.owl 
Log Message:
Ont-policy and owl file lookup fix- hopefully working this time

--- NEW FILE: biopax-level1.owl ---
<?xml version="1.0"?>
<rdf:RDF
    xmlns="http://www.biopax.org/release/biopax-level1.owl#"
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
    xmlns:owl="http://www.w3.org/2002/07/owl#"
  xml:base="http://www.biopax.org/release/biopax-level1.owl">
  <owl:Ontology rdf:about="">
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >This is version 1.4 of the BioPAX Level 1 ontology.  The goal of the BioPAX group is to develop a common exchange format for biological pathway data.  More information is available at http://www.biopax.org.  This ontology is freely available under the LGPL (http://www.gnu.org/copyleft/lesser.html).</rdfs:comment>
  </owl:Ontology>
  <owl:Class rdf:ID="physicalEntityParticipant">
    <owl:disjointWith>
      <owl:Class rdf:ID="chemicalStructure"/>
    </owl:disjointWith>
    <owl:disjointWith>
      <owl:Class rdf:ID="openControlledVocabulary"/>
    </owl:disjointWith>
    <rdfs:subClassOf>
[...1216 lines suppressed...]
    <rdfs:domain rdf:resource="#biochemicalReaction"/>
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >The unique number assigned to a reaction by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology.

Note that not all biochemical reactions currently have EC numbers assigned to them.</rdfs:comment>
    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
  </owl:DatatypeProperty>
  <owl:DatatypeProperty rdf:ID="DELTA-S">
    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#double"/>
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >For biochemical reactions, this slot refers to the standard transformed entropy change for a reaction written in terms of biochemical reactants (sums of species), delta-S'&lt;sup>o&lt;/sup>.

  delta-G'&lt;sup>o&lt;/sup> = delta-H'&lt;sup>o&lt;/sup> - T delta-S'&lt;sup>o&lt;/sup>

(This definition from EcoCyc)</rdfs:comment>
    <rdfs:domain rdf:resource="#biochemicalReaction"/>
  </owl:DatatypeProperty>
</rdf:RDF>

<!-- Created with Protege (with OWL Plugin 1.3, Build 225.4)  http://protege.stanford.edu -->

--- NEW FILE: biopax-level2.owl ---
<?xml version="1.0"?>
<rdf:RDF
    xmlns="http://www.biopax.org/release/biopax-level2.owl#"
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
    xmlns:owl="http://www.w3.org/2002/07/owl#"
  xml:base="http://www.biopax.org/release/biopax-level2.owl">
  <owl:Ontology rdf:about="">
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >This is version 1.0 of the BioPAX Level 2 ontology.  The goal of the BioPAX group is to develop a common exchange format for biological pathway data.  More information is available at http://www.biopax.org.  This ontology is freely available under the LGPL (http://www.gnu.org/copyleft/lesser.html).</rdfs:comment>
  </owl:Ontology>
  <owl:Class rdf:ID="dataSource">
    <owl:disjointWith>
      <owl:Class rdf:ID="openControlledVocabulary"/>
    </owl:disjointWith>
    <owl:disjointWith>
      <owl:Class rdf:ID="xref"/>
    </owl:disjointWith>
    <owl:disjointWith>
[...2019 lines suppressed...]
    <rdfs:domain rdf:resource="#physicalEntityParticipant"/>
  </owl:DatatypeProperty>
  <owl:DatatypeProperty rdf:about="#K-PRIME">
    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
    <rdfs:domain rdf:resource="#kPrime"/>
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >The apparent equilibrium constant K'. Concentrations in the equilibrium constant equation refer to the total concentrations of  all forms of particular biochemical reactants. For example, in the equilibrium constant equation for the biochemical reaction in which ATP is hydrolyzed to ADP and inorganic phosphate:

K' = [ADP][P&lt;sub>i&lt;/sub>]/[ATP],

The concentration of ATP refers to the total concentration of all of the following species:

[ATP] = [ATP&lt;sup>4-&lt;/sup>] + [HATP&lt;sup>3-&lt;/sup>] + [H&lt;sub>2&lt;/sub>ATP&lt;sup>2-&lt;/sup>] + [MgATP&lt;sup>2-&lt;/sup>] + [MgHATP&lt;sup>-&lt;/sup>] + [Mg&lt;sub>2&lt;/sub>ATP].

The apparent equilibrium constant is formally dimensionless, and can be kept so by inclusion of as many of the terms (1 mol/dm&lt;sup>3&lt;/sup>) in the numerator or denominator as necessary.  It is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log&lt;sub>10&lt;/sub>[Mg&lt;sup>2+&lt;/sup>]).
(Definition from EcoCyc)</rdfs:comment>
  </owl:DatatypeProperty>
</rdf:RDF>

<!-- Created with Protege (with OWL Plugin 1.3, Build 225.4)  http://protege.stanford.edu -->

Index: BioPAXLevel.java
===================================================================
RCS file: /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/model/BioPAXLevel.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** BioPAXLevel.java	15 Aug 2008 19:25:06 -0000	1.7
--- BioPAXLevel.java	15 Aug 2008 23:19:35 -0000	1.8
***************
*** 91,94 ****
--- 91,103 ----
  // -------------------------- OTHER METHODS --------------------------
  
+     /**
+      * This method loads the level file as resource and returns it as
+      * an input stream
+      * @return an input stream from the owl file.
+      */
+     public InputStream getLevelFileAsStream()
+     {
+         return this.getClass().getResourceAsStream(filename);
+     }
  
  // --------------------- ACCESORS and MUTATORS---------------------

--- NEW FILE: biopax-level3.owl ---
<?xml version="1.0"?>
<rdf:RDF
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
    xmlns:xsp="http://www.owl-ontologies.com/2005/08/07/xsp.owl#"
    xmlns="http://www.biopax.org/release/biopax-level3.owl#"
    xmlns:owl="http://www.w3.org/2002/07/owl#"
    xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
    xmlns:swrl="http://www.w3.org/2003/11/swrl#"
    xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
    xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
  xml:base="http://www.biopax.org/release/biopax-level3.owl">
  <owl:Ontology rdf:about="">
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >This is version 0.93 of the BioPAX Level 3 ontology.  The goal of the BioPAX group is to develop a common exchange format for biological pathway data.  More information is available at http://www.biopax.org.  This ontology is freely available under the LGPL (http://www.gnu.org/copyleft/lesser.html).</rdfs:comment>
  </owl:Ontology>
  <owl:Class rdf:ID="Stoichiometry">
    <rdfs:subClassOf>
      <owl:Restriction>
[...1980 lines suppressed...]
    >For biochemical reactions, this property refers to the standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'&lt;sup&gt;o&lt;/sup&gt;.

  delta-G'&lt;sup&gt;o&lt;/sup&gt; = -RT lnK'
and
  delta-G'&lt;sup&gt;o&lt;/sup&gt; = delta-H'&lt;sup&gt;o&lt;/sup&gt; - T delta-S'&lt;sup&gt;o&lt;/sup&gt;

delta-G'&lt;sup&gt;o&lt;/sup&gt; has units of kJ/mol.  Like K', it is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log&lt;sub&gt;10&lt;/sub&gt;[Mg&lt;sup&gt;2+&lt;/sup&gt;]). Therefore, these quantities must be specified, and values for DELTA-G for biochemical reactions are represented as 5-tuples of the form (delta-G'&lt;sup&gt;o&lt;/sup&gt; T I pH pMg).

(This definition from EcoCyc)</rdfs:comment>
    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
    <rdfs:domain rdf:resource="#DeltaG"/>
  </owl:DatatypeProperty>
  <owl:DatatypeProperty rdf:ID="url">
    <rdfs:domain rdf:resource="#PublicationXref"/>
    <rdfs:comment xml:lang="en">The URL at which the publication can be found, if it is available through the Web.</rdfs:comment>
    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
  </owl:DatatypeProperty>
</rdf:RDF>

<!-- Created with Protege (with OWL Plugin 3.4, Build 505)  http://protege.stanford.edu -->

Update of /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/io/jena
In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv18506/src/org/biopax/paxtools/io/jena

Modified Files:
	JenaEditorMap.java JenaIOHandler.java 
Added Files:
	JenaHelper.java ont-policy.rdf 
Log Message:
Ont-policy and owl file lookup fix- hopefully working this time

Index: JenaIOHandler.java
===================================================================
RCS file: /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/io/jena/JenaIOHandler.java,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** JenaIOHandler.java	30 Jul 2008 19:00:31 -0000	1.20
--- JenaIOHandler.java	15 Aug 2008 23:19:35 -0000	1.21
***************
*** 217,225 ****
  	private OntModel readJenaModel(InputStream in)
  	{
- 		OntModel ontModel =
- 			ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM);
  
! 		ontModel.setStrictMode(true);
! 		ontModel.getReader().setProperty("error-mode", "strict");
  		ontModel.read(in, "");
  		ontModel.loadImports();
--- 217,225 ----
  	private OntModel readJenaModel(InputStream in)
  	{
  
!         OntModel ontModel = org.biopax.paxtools.io.jena.JenaHelper.createModel();
! 
! //		ontModel.setStrictMode(true);
! //		ontModel.getReader().setProperty("error-mode", "strict");
  		ontModel.read(in, "");
  		ontModel.loadImports();
***************
*** 227,231 ****
  	}
  
! 	private void createObjects(OntModel ontModel, Model model)
  	{
  		ExtendedIterator extendedIterator = ontModel.listIndividuals();
--- 227,232 ----
  	}
  
! 
!     private void createObjects(OntModel ontModel, Model model)
  	{
  		ExtendedIterator extendedIterator = ontModel.listIndividuals();
***************
*** 376,381 ****
  	private OntModel initializeEmptyOntModel(Model model)
  	{
! 		OntModel ontModel =
! 			ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM);
  		String xmlBase = model.getNameSpacePrefixMap().get("");
  		if (xmlBase == null || xmlBase.equals(""))
--- 377,382 ----
  	private OntModel initializeEmptyOntModel(Model model)
  	{
! 		OntModel ontModel = org.biopax.paxtools.io.jena.JenaHelper.createModel();
! 
  		String xmlBase = model.getNameSpacePrefixMap().get("");
  		if (xmlBase == null || xmlBase.equals(""))

--- NEW FILE: ont-policy.rdf ---
<?xml version='1.0'?>

<!DOCTYPE rdf:RDF [
	<!ENTITY jena    'http://jena.hpl.hp.com/schemas/'>

	<!ENTITY rdf     'http://www.w3.org/1999/02/22-rdf-syntax-ns#'>
	<!ENTITY rdfs    'http://www.w3.org/2000/01/rdf-schema#'>
	<!ENTITY xsd     'http://www.w3.org/2001/XMLSchema#'>
	<!ENTITY base    '&jena;2003/03/ont-manager'>
	<!ENTITY ont     '&base;#'>
	]>

<rdf:RDF
	xmlns:rdf="&rdf;"
	xmlns:rdfs="&rdfs;"
	xmlns="&ont;"
	xml:base="&base;"
	>

	<!--
	 The default set of mappings for locally cached ontologies

	 Author: Ian Dickinson, mailto:ian.dickinson@...
	 CVS:    $Id: ont-policy.rdf,v 1.1 2008/08/15 23:19:35 emekdemir Exp $
 -->

	<DocumentManagerPolicy>
		<!-- policy for controlling the document manager's behaviour -->
		<processImports rdf:datatype="&xsd;boolean">true</processImports>
		<cacheModels rdf:datatype="&xsd;boolean">true</cacheModels>
		<useDeclaredPrefixes rdf:datatype="&xsd;boolean">
			true</useDeclaredPrefixes>
	</DocumentManagerPolicy>


	<OntologySpec>
		<!-- local version of the OWL language ontology (in OWL) -->
		<publicURI rdf:resource="http://www.w3.org/2002/07/owl"/>
		<!-- uncomment the following line to re-direct attempts to http get the file
			<altURL    rdf:resource="file:vocabularies/owl.owl" /-->
		<language rdf:resource="http://www.w3.org/2002/07/owl"/>
		<prefix rdf:datatype="&xsd;string">owl</prefix>
	</OntologySpec>

	<OntologySpec>
		<!-- local version of the RDFS vocabulary -->
		<publicURI rdf:resource="http://www.w3.org/2000/01/rdf-schema"/>
		<!-- uncomment the following line to re-direct attempts to http get the file
			<altURL    rdf:resource="file:vocabularies/rdf-schema.rdf" /-->
		<language rdf:resource="http://www.w3.org/2000/01/rdf-schema"/>
		<prefix rdf:datatype="&xsd;string">rdfs</prefix>

	</OntologySpec>

	<OntologySpec>
		<!-- local version of the RDFS vocabulary -->
		<publicURI rdf:resource="http://www.biopax.org/release/biopax-level1.owl"/>
		<altURL rdf:resource="file:org/biopax/paxtools/model/biopax-level1.owl"/>
		<language rdf:resource="http://www.w3.org/2002/07/owl"/>
		<prefix rdf:datatype="&xsd;string">bp1</prefix>
	</OntologySpec>

	<OntologySpec>
		<!-- local version of the RDFS vocabulary -->
		<publicURI rdf:resource="http://www.biopax.org/release/biopax-level2.owl"/>
		<altURL rdf:resource="file:org/biopax/paxtools/model/biopax-level2.owl"/>
		<language rdf:resource="http://www.w3.org/2002/07/owl"/>
		<prefix rdf:datatype="&xsd;string">bp1</prefix>
	</OntologySpec>

    <OntologySpec>
 		<!-- local version of the RDFS vocabulary -->
 		<publicURI rdf:resource="http://www.biopax.org/release/biopax-level3.owl"/>
 		<altURL rdf:resource="file:org/biopax/paxtools/model/biopax-level3.owl"/>
 		<language rdf:resource="http://www.w3.org/2002/07/owl"/>
 		<prefix rdf:datatype="&xsd;string">bp1</prefix>
 	</OntologySpec>

</rdf:RDF>

--- NEW FILE: JenaHelper.java ---
package org.biopax.paxtools.io.jena;

import com.hp.hpl.jena.ontology.OntDocumentManager;
import com.hp.hpl.jena.ontology.OntModelSpec;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.rdf.model.ModelFactory;

/**
 * Created by IntelliJ IDEA.
 * User: demir
 * Date: Aug 15, 2008
 * Time: 7:11:32 PM
 * To change this template use File | Settings | File Templates.
 */
class JenaHelper
{
    static final OntModelSpec spec;
    static
    {
        OntDocumentManager mgr = new OntDocumentManager("file:ont-policy.rdf;file:org/biopax/paxtools/io/jena/ont-policy.rdf");

                spec = new OntModelSpec(OntModelSpec.OWL_DL_MEM);

                spec.setDocumentManager(mgr);

    }
    static OntModel createModel()
    {
        return ModelFactory.createOntologyModel(spec);
    }
}

Index: JenaEditorMap.java
===================================================================
RCS file: /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/io/jena/JenaEditorMap.java,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** JenaEditorMap.java	15 Aug 2008 19:25:07 -0000	1.15
--- JenaEditorMap.java	15 Aug 2008 23:19:35 -0000	1.16
***************
*** 3,7 ****
  import com.hp.hpl.jena.datatypes.xsd.XSDDatatype;
  import com.hp.hpl.jena.ontology.*;
- import com.hp.hpl.jena.rdf.model.ModelFactory;
  import com.hp.hpl.jena.rdf.model.Resource;
  import com.hp.hpl.jena.util.iterator.ExtendedIterator;
--- 3,6 ----
***************
*** 19,23 ****
  import org.biopax.paxtools.util.IllegalBioPAXArgumentException;
  
! import java.io.*;
  import java.util.HashSet;
  import java.util.Set;
--- 18,24 ----
  import org.biopax.paxtools.util.IllegalBioPAXArgumentException;
  
! import java.io.IOException;
! import java.io.OutputStream;
! import java.io.PrintStream;
  import java.util.HashSet;
  import java.util.Set;
***************
*** 49,62 ****
  
  
          OntModel ontologyDefinition =
!                 ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM);
          //ontologyDefinition.read(this.level.getLevelFileAsStream(), "");
!          InputStream ontStream;
!         try {
!            ontStream = new FileInputStream(this.level.getFilename());
!         } catch (FileNotFoundException e) {
!             throw new RuntimeException(e);
!         }
!         ontologyDefinition.read(ontStream,this.level.getNameSpace());
          preprocessClasses(ontologyDefinition);
          preprocessProperties(ontologyDefinition);
--- 50,59 ----
  
  
+ 
          OntModel ontologyDefinition =
!                 org.biopax.paxtools.io.jena.JenaHelper.createModel();
          //ontologyDefinition.read(this.level.getLevelFileAsStream(), "");
!         ontologyDefinition.read(this.level.getLevelFileAsStream(),
!                                 this.level.getNameSpace());
          preprocessClasses(ontologyDefinition);
          preprocessProperties(ontologyDefinition);

Update of /cvsroot/biopax/Paxtools
In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv26516

Modified Files:
	ont-policy.rdf 
Added Files:
	biopax-level1.owl biopax-level3.owl biopax-level2.owl 
Log Message:
refactored level file handling

--- NEW FILE: biopax-level1.owl ---
<?xml version="1.0"?>
<rdf:RDF
    xmlns="http://www.biopax.org/release/biopax-level1.owl#"
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
    xmlns:owl="http://www.w3.org/2002/07/owl#"
  xml:base="http://www.biopax.org/release/biopax-level1.owl">
  <owl:Ontology rdf:about="">
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >This is version 1.4 of the BioPAX Level 1 ontology.  The goal of the BioPAX group is to develop a common exchange format for biological pathway data.  More information is available at http://www.biopax.org.  This ontology is freely available under the LGPL (http://www.gnu.org/copyleft/lesser.html).</rdfs:comment>
  </owl:Ontology>
  <owl:Class rdf:ID="physicalEntityParticipant">
    <owl:disjointWith>
      <owl:Class rdf:ID="chemicalStructure"/>
    </owl:disjointWith>
    <owl:disjointWith>
      <owl:Class rdf:ID="openControlledVocabulary"/>
    </owl:disjointWith>
    <rdfs:subClassOf>
[...1216 lines suppressed...]
    <rdfs:domain rdf:resource="#biochemicalReaction"/>
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >The unique number assigned to a reaction by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology.

Note that not all biochemical reactions currently have EC numbers assigned to them.</rdfs:comment>
    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
  </owl:DatatypeProperty>
  <owl:DatatypeProperty rdf:ID="DELTA-S">
    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#double"/>
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >For biochemical reactions, this slot refers to the standard transformed entropy change for a reaction written in terms of biochemical reactants (sums of species), delta-S'&lt;sup>o&lt;/sup>.

  delta-G'&lt;sup>o&lt;/sup> = delta-H'&lt;sup>o&lt;/sup> - T delta-S'&lt;sup>o&lt;/sup>

(This definition from EcoCyc)</rdfs:comment>
    <rdfs:domain rdf:resource="#biochemicalReaction"/>
  </owl:DatatypeProperty>
</rdf:RDF>

<!-- Created with Protege (with OWL Plugin 1.3, Build 225.4)  http://protege.stanford.edu -->

--- NEW FILE: biopax-level2.owl ---
<?xml version="1.0"?>
<rdf:RDF
    xmlns="http://www.biopax.org/release/biopax-level2.owl#"
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
    xmlns:owl="http://www.w3.org/2002/07/owl#"
  xml:base="http://www.biopax.org/release/biopax-level2.owl">
  <owl:Ontology rdf:about="">
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >This is version 1.0 of the BioPAX Level 2 ontology.  The goal of the BioPAX group is to develop a common exchange format for biological pathway data.  More information is available at http://www.biopax.org.  This ontology is freely available under the LGPL (http://www.gnu.org/copyleft/lesser.html).</rdfs:comment>
  </owl:Ontology>
  <owl:Class rdf:ID="dataSource">
    <owl:disjointWith>
      <owl:Class rdf:ID="openControlledVocabulary"/>
    </owl:disjointWith>
    <owl:disjointWith>
      <owl:Class rdf:ID="xref"/>
    </owl:disjointWith>
    <owl:disjointWith>
[...2019 lines suppressed...]
    <rdfs:domain rdf:resource="#physicalEntityParticipant"/>
  </owl:DatatypeProperty>
  <owl:DatatypeProperty rdf:about="#K-PRIME">
    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
    <rdfs:domain rdf:resource="#kPrime"/>
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >The apparent equilibrium constant K'. Concentrations in the equilibrium constant equation refer to the total concentrations of  all forms of particular biochemical reactants. For example, in the equilibrium constant equation for the biochemical reaction in which ATP is hydrolyzed to ADP and inorganic phosphate:

K' = [ADP][P&lt;sub>i&lt;/sub>]/[ATP],

The concentration of ATP refers to the total concentration of all of the following species:

[ATP] = [ATP&lt;sup>4-&lt;/sup>] + [HATP&lt;sup>3-&lt;/sup>] + [H&lt;sub>2&lt;/sub>ATP&lt;sup>2-&lt;/sup>] + [MgATP&lt;sup>2-&lt;/sup>] + [MgHATP&lt;sup>-&lt;/sup>] + [Mg&lt;sub>2&lt;/sub>ATP].

The apparent equilibrium constant is formally dimensionless, and can be kept so by inclusion of as many of the terms (1 mol/dm&lt;sup>3&lt;/sup>) in the numerator or denominator as necessary.  It is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log&lt;sub>10&lt;/sub>[Mg&lt;sup>2+&lt;/sup>]).
(Definition from EcoCyc)</rdfs:comment>
  </owl:DatatypeProperty>
</rdf:RDF>

<!-- Created with Protege (with OWL Plugin 1.3, Build 225.4)  http://protege.stanford.edu -->

Index: ont-policy.rdf
===================================================================
RCS file: /cvsroot/biopax/Paxtools/ont-policy.rdf,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** ont-policy.rdf	15 Aug 2008 15:31:00 -0000	1.7
--- ont-policy.rdf	15 Aug 2008 19:25:07 -0000	1.8
***************
*** 55,71 ****
  	<OntologySpec>
  		<!-- local version of the RDFS vocabulary -->
! 		<publicURI rdf:resource="http://www.biopax.org/release/biopax-level2.owl"/>
! 		<altURL rdf:resource="file:src/org/biopax/paxtools/model/biopax-level2.owl"/>
  		<language rdf:resource="http://www.w3.org/2002/07/owl"/>
  		<prefix rdf:datatype="&xsd;string">bp1</prefix>
  	</OntologySpec>
  
! 		<OntologySpec>
  		<!-- local version of the RDFS vocabulary -->
  		<publicURI rdf:resource="http://www.biopax.org/release/biopax-level2.owl"/>
! 		<altURL rdf:resource="file:src/org/biopax/paxtools/model/biopax-level2.owl"/>
  		<language rdf:resource="http://www.w3.org/2002/07/owl"/>
  		<prefix rdf:datatype="&xsd;string">bp1</prefix>
  	</OntologySpec>
  
  </rdf:RDF>
--- 55,79 ----
  	<OntologySpec>
  		<!-- local version of the RDFS vocabulary -->
! 		<publicURI rdf:resource="http://www.biopax.org/release/biopax-level1.owl"/>
! 		<altURL rdf:resource="file:biopax-level1.owl"/>
  		<language rdf:resource="http://www.w3.org/2002/07/owl"/>
  		<prefix rdf:datatype="&xsd;string">bp1</prefix>
  	</OntologySpec>
  
! 	<OntologySpec>
  		<!-- local version of the RDFS vocabulary -->
  		<publicURI rdf:resource="http://www.biopax.org/release/biopax-level2.owl"/>
! 		<altURL rdf:resource="file:biopax-level2.owl"/>
  		<language rdf:resource="http://www.w3.org/2002/07/owl"/>
  		<prefix rdf:datatype="&xsd;string">bp1</prefix>
  	</OntologySpec>
  
+     <OntologySpec>
+  		<!-- local version of the RDFS vocabulary -->
+  		<publicURI rdf:resource="http://www.biopax.org/release/biopax-level3.owl"/>
+  		<altURL rdf:resource="file:biopax-level3.owl"/>
+  		<language rdf:resource="http://www.w3.org/2002/07/owl"/>
+  		<prefix rdf:datatype="&xsd;string">bp1</prefix>
+  	</OntologySpec>
+ 
  </rdf:RDF>

--- NEW FILE: biopax-level3.owl ---
<?xml version="1.0"?>
<rdf:RDF
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
    xmlns:xsp="http://www.owl-ontologies.com/2005/08/07/xsp.owl#"
    xmlns="http://www.biopax.org/release/biopax-level3.owl#"
    xmlns:owl="http://www.w3.org/2002/07/owl#"
    xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
    xmlns:swrl="http://www.w3.org/2003/11/swrl#"
    xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
    xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
  xml:base="http://www.biopax.org/release/biopax-level3.owl">
  <owl:Ontology rdf:about="">
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >This is version 0.93 of the BioPAX Level 3 ontology.  The goal of the BioPAX group is to develop a common exchange format for biological pathway data.  More information is available at http://www.biopax.org.  This ontology is freely available under the LGPL (http://www.gnu.org/copyleft/lesser.html).</rdfs:comment>
  </owl:Ontology>
  <owl:Class rdf:ID="Stoichiometry">
    <rdfs:subClassOf>
      <owl:Restriction>
[...1980 lines suppressed...]
    >For biochemical reactions, this property refers to the standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'&lt;sup&gt;o&lt;/sup&gt;.

  delta-G'&lt;sup&gt;o&lt;/sup&gt; = -RT lnK'
and
  delta-G'&lt;sup&gt;o&lt;/sup&gt; = delta-H'&lt;sup&gt;o&lt;/sup&gt; - T delta-S'&lt;sup&gt;o&lt;/sup&gt;

delta-G'&lt;sup&gt;o&lt;/sup&gt; has units of kJ/mol.  Like K', it is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log&lt;sub&gt;10&lt;/sub&gt;[Mg&lt;sup&gt;2+&lt;/sup&gt;]). Therefore, these quantities must be specified, and values for DELTA-G for biochemical reactions are represented as 5-tuples of the form (delta-G'&lt;sup&gt;o&lt;/sup&gt; T I pH pMg).

(This definition from EcoCyc)</rdfs:comment>
    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
    <rdfs:domain rdf:resource="#DeltaG"/>
  </owl:DatatypeProperty>
  <owl:DatatypeProperty rdf:ID="url">
    <rdfs:domain rdf:resource="#PublicationXref"/>
    <rdfs:comment xml:lang="en">The URL at which the publication can be found, if it is available through the Web.</rdfs:comment>
    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
  </owl:DatatypeProperty>
</rdf:RDF>

<!-- Created with Protege (with OWL Plugin 3.4, Build 505)  http://protege.stanford.edu -->

Update of /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/io/jena
In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv26516/src/org/biopax/paxtools/io/jena

Modified Files:
	JenaEditorMap.java 
Log Message:
refactored level file handling

Index: JenaEditorMap.java
===================================================================
RCS file: /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/io/jena/JenaEditorMap.java,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** JenaEditorMap.java	10 Mar 2008 22:36:34 -0000	1.14
--- JenaEditorMap.java	15 Aug 2008 19:25:07 -0000	1.15
***************
*** 19,25 ****
  import org.biopax.paxtools.util.IllegalBioPAXArgumentException;
  
! import java.io.IOException;
! import java.io.OutputStream;
! import java.io.PrintStream;
  import java.util.HashSet;
  import java.util.Set;
--- 19,23 ----
  import org.biopax.paxtools.util.IllegalBioPAXArgumentException;
  
! import java.io.*;
  import java.util.HashSet;
  import java.util.Set;
***************
*** 54,59 ****
                  ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM);
          //ontologyDefinition.read(this.level.getLevelFileAsStream(), "");
!         ontologyDefinition.read(this.level.getLevelFileAsStream(),
!                                 this.level.getNameSpace());
          preprocessClasses(ontologyDefinition);
          preprocessProperties(ontologyDefinition);
--- 52,62 ----
                  ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM);
          //ontologyDefinition.read(this.level.getLevelFileAsStream(), "");
!          InputStream ontStream;
!         try {
!            ontStream = new FileInputStream(this.level.getFilename());
!         } catch (FileNotFoundException e) {
!             throw new RuntimeException(e);
!         }
!         ontologyDefinition.read(ontStream,this.level.getNameSpace());
          preprocessClasses(ontologyDefinition);
          preprocessProperties(ontologyDefinition);

Update of /cvsroot/biopax/Paxtools/test/org/biopax/paxtools/io/jena
In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv26516/test/org/biopax/paxtools/io/jena

Modified Files:
	JenaIOHandlerTest.java 
Log Message:
refactored level file handling

Index: JenaIOHandlerTest.java
===================================================================
RCS file: /cvsroot/biopax/Paxtools/test/org/biopax/paxtools/io/jena/JenaIOHandlerTest.java,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** JenaIOHandlerTest.java	11 Aug 2008 17:25:05 -0000	1.11
--- JenaIOHandlerTest.java	15 Aug 2008 19:25:07 -0000	1.12
***************
*** 24,28 ****
              public boolean accept(File dir, String name)
              {
!                 return (name.endsWith("sample.owl"));
              }
          };
--- 24,28 ----
              public boolean accept(File dir, String name)
              {
!                 return (name.endsWith(".owl"));
              }
          };

Update of /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/model
In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv26516/src/org/biopax/paxtools/model

Modified Files:
	BioPAXLevel.java 
Removed Files:
	biopax-level3.owl biopax-level1.owl biopax-level2.owl 
Log Message:
refactored level file handling

--- biopax-level1.owl DELETED ---

--- biopax-level2.owl DELETED ---

Index: BioPAXLevel.java
===================================================================
RCS file: /cvsroot/biopax/Paxtools/src/org/biopax/paxtools/model/BioPAXLevel.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** BioPAXLevel.java	12 Mar 2008 16:51:18 -0000	1.6
--- BioPAXLevel.java	15 Aug 2008 19:25:06 -0000	1.7
***************
*** 91,103 ****
  // -------------------------- OTHER METHODS --------------------------
  
-     /**
-      * This method loads the level file as resource and returns it as
-      * an input stream
-      * @return an input stream from the owl file.
-      */
-     public InputStream getLevelFileAsStream()
-     {
-         return this.getClass().getResourceAsStream(filename);
-     }
  
  // --------------------- ACCESORS and MUTATORS---------------------
--- 91,94 ----

--- biopax-level3.owl DELETED ---