Merge pull request #1117 from virtualcell/dan-ss-molecule-edit

Editing or adding a new molecule / species is now properly addressed in existing SS application
virtualcell · Jan 29, 2024 · 28bbcfb · 28bbcfb
2 parents 3ea8f19 + 5ceb8ca
commit 28bbcfb
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Showing 4 changed files with 20 additions and 1 deletion.
diff --git a/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/SpeciesPropertiesPanel.java b/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/SpeciesPropertiesPanel.java
@@ -930,6 +930,7 @@ public void actionPerformed(ActionEvent e) {
 							fieldSpeciesContext.setSpeciesPattern(sp);
 						}
 						fieldSpeciesContext.getSpeciesPattern().addMolecularTypePattern(molecularTypePattern);
+						fieldSpeciesContext.firePropertyChange(SpeciesContext.PROPERTY_NAME_SPECIES_PATTERN_CHANGED, null, fieldSpeciesContext);
 					}
 				});
 			}

diff --git a/vcell-core/src/main/java/cbit/vcell/mapping/ReactionContext.java b/vcell-core/src/main/java/cbit/vcell/mapping/ReactionContext.java
@@ -289,6 +289,9 @@ public void propertyChange(java.beans.PropertyChangeEvent evt) {
 	if (evt.getSource().equals(getModel()) && evt.getPropertyName().equals(RbmModelContainer.PROPERTY_NAME_REACTION_RULE_LIST)){
 		refreshAll();
 	}
+	if(evt.getSource().equals(getModel()) && evt.getPropertyName().equals(Model.PROPERTY_NAME_SPECIES_CONTEXT_SPECIES_PATTERN)) {
+		refreshSpeciesContextSpecsSpeciesPatterns();	// only for springsalad, because we care about the sites (site attributes spec, internal link spec)
+	}
 	if (evt.getSource().equals(getModel()) && evt.getPropertyName().equals(RbmModelContainer.PROPERTY_NAME_MOLECULAR_TYPE_LIST)){
 		;	// do nothing
 	}
@@ -618,6 +621,13 @@ private void refreshSpeciesContextSpecs() throws MappingException {
 		}
 	}
 }
+private void refreshSpeciesContextSpecsSpeciesPatterns() {
+	if(Application.SPRINGSALAD == simContext.getApplicationType()) {
+		for(SpeciesContextSpec scs : fieldSpeciesContextSpecs) {
+			scs.initializeForSpringSaLaD(null);
+		}
+	}
+}
 private void refreshSpeciesContextSpecs(MolecularType mt) {
 	if(Application.SPRINGSALAD == simContext.getApplicationType()) {
 		for(SpeciesContextSpec scs : fieldSpeciesContextSpecs) {

diff --git a/vcell-core/src/main/java/cbit/vcell/model/Model.java b/vcell-core/src/main/java/cbit/vcell/model/Model.java
@@ -83,6 +83,7 @@ public static interface Owner {
     public static final String PROPERTY_NAME_SPECIES_CONTEXTS = "speciesContexts";
     private static final String PROPERTY_NAME_SPECIES = "species";
     public static final String PROPERTY_NAME_MODEL_ENTITY_NAME = "modelEntityName";
+    public static final String PROPERTY_NAME_SPECIES_CONTEXT_SPECIES_PATTERN = "speciesContextSpeciesPattern";
 
     public static final String PROPERTY_NAME_RATERULEVARIABLES = "rateruleVariables";
 
@@ -3302,6 +3303,7 @@ public void propertyChange(java.beans.PropertyChangeEvent evt){
                 fieldDiagrams[i].renameNode((String) evt.getOldValue(), (String) evt.getNewValue());
             }
         }
+
         if(evt.getSource() instanceof ReactionStep && evt.getPropertyName().equals("name")){
             for(int i = 0; i < fieldDiagrams.length; i++){
                 fieldDiagrams[i].renameNode((String) evt.getOldValue(), (String) evt.getNewValue());
@@ -3358,6 +3360,11 @@ public void propertyChange(java.beans.PropertyChangeEvent evt){
             }
         }
 
+        if(evt.getSource() instanceof SpeciesContext && evt.getPropertyName().equals(SpeciesContext.PROPERTY_NAME_SPECIES_PATTERN_CHANGED)) {
+            System.out.println("Model: SpeciesContext test event: " + evt.getPropertyName());
+            firePropertyChange(PROPERTY_NAME_SPECIES_CONTEXT_SPECIES_PATTERN, evt.getOldValue(), evt.getNewValue());
+        }
+
         if((evt.getSource() instanceof ModelParameter ||
                 evt.getSource() instanceof SpeciesContext ||
                 evt.getSource() instanceof StructureSize)

diff --git a/vcell-core/src/main/java/cbit/vcell/model/SpeciesContext.java b/vcell-core/src/main/java/cbit/vcell/model/SpeciesContext.java
@@ -63,7 +63,8 @@ public class SpeciesContext implements Cacheable, Matchable, Relatable, Editable
 
 	private String speciesPatternString = null;
 
-	public static final String PROPERTY_NAME_SPECIES_PATTERN = "speciesPattern";
+	public static final String PROPERTY_NAME_SPECIES_PATTERN = "speciesPattern";	// fired with an empty sp, not very useful
+	public static final String PROPERTY_NAME_SPECIES_PATTERN_CHANGED = "speciesPatternChanged";
 
 	// store SBML unit for speciesContext from SBML species.
 //	private transient VCUnitDefinition sbmlSpeciesUnit = null;
-Original file line number
+Diff line change
@@ Expand Up / @@ -930,6 +930,7 @@ public void actionPerformed(ActionEvent e) { @@
     							fieldSpeciesContext.setSpeciesPattern(sp);
     						}
     						fieldSpeciesContext.getSpeciesPattern().addMolecularTypePattern(molecularTypePattern);
+    						fieldSpeciesContext.firePropertyChange(SpeciesContext.PROPERTY_NAME_SPECIES_PATTERN_CHANGED, null, fieldSpeciesContext);
     					}
     				});
     			}
@@ Expand Down @@