Redesign the springsalad-specific user interface

vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/AnnotationsPanel.java

@@ -517,7 +517,6 @@ public JComboBox getJComboBoxURI() {
 				@Override
 				public void actionPerformed(ActionEvent e) {
 					VCMetaDataDataType mdt = (VCMetaDataDataType)jComboBoxURI.getSelectedItem();
-					System.out.println("aici");
 					if(mdt != null && mdt.isSearchable()) {
 						getJButtonSearchRef().setEnabled(true);
 					} else {
@@ -939,7 +938,6 @@ protected void onSelectedObjectsChange(Object[] selectedObjects) {
 			}
 			if(selectedObjects[0] instanceof Identifiable && selectedObjects[0] instanceof Displayable) {
 				selectedObject = (Identifiable)selectedObjects[0];
-				System.out.println("AnnotationsPanel: class: " + selectedObject.getClass().getSimpleName() + ", selected object: " + ((Displayable)selectedObject).getDisplayName());
 			} else {
 				selectedObject = null;
 				System.out.println("Unsupported or null entity");

vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/BioModelEditor.java

@@ -24,6 +24,8 @@
 import javax.swing.JComponent;
 import javax.swing.ListSelectionModel;
 
+import cbit.vcell.mapping.*;
+import cbit.vcell.mapping.gui.*;
 import org.vcell.model.rbm.MolecularType;
 import org.vcell.model.rbm.SpeciesPattern;
 import org.vcell.pathway.BioPaxObject;
@@ -56,20 +58,9 @@
 import cbit.vcell.geometry.CSGObject;
 import cbit.vcell.geometry.GeometryInfo;
 import cbit.vcell.geometry.gui.CSGObjectPropertiesPanel;
-import cbit.vcell.mapping.BioEvent;
-import cbit.vcell.mapping.MathMappingCallbackTaskAdapter;
-import cbit.vcell.mapping.ReactionRuleSpec;
-import cbit.vcell.mapping.ReactionSpec;
-import cbit.vcell.mapping.SimulationContext;
 import cbit.vcell.mapping.SimulationContext.Application;
 import cbit.vcell.mapping.SimulationContext.MathMappingCallback;
 import cbit.vcell.mapping.SimulationContext.NetworkGenerationRequirements;
-import cbit.vcell.mapping.SpeciesContextSpec;
-import cbit.vcell.mapping.gui.DataSymbolsSpecPanel;
-import cbit.vcell.mapping.gui.ReactionRuleSpecPropertiesPanel;
-import cbit.vcell.mapping.gui.SpatialObjectPropertyPanel;
-import cbit.vcell.mapping.gui.SpatialProcessPropertyPanel;
-import cbit.vcell.mapping.gui.SpeciesContextSpecPanel;
 import cbit.vcell.mapping.spatial.SpatialObject;
 import cbit.vcell.mapping.spatial.processes.SpatialProcess;
 import cbit.vcell.model.Model;
@@ -132,6 +123,7 @@ public class BioModelEditor extends DocumentEditor {
 	private ReactionParticipantPropertiesPanel reactionParticipantPropertiesPanel = null;
 	private ApplicationPropertiesPanel applicationPropertiesPanel = null;
 	private SpeciesContextSpecPanel speciesContextSpecPanel = null;
+	private MolecularStructuresPropertiesPanel molecularStructuresPropertiesPanel = null;
 	private KineticsTypeTemplatePanel kineticsTypeTemplatePanel = null;
 	private ReactionRuleSpecPropertiesPanel reactionRuleSpecPropertiesPanel = null;
 	private SimulationSummaryPanel simulationSummaryPanel = null;
@@ -631,6 +623,17 @@ private SpeciesContextSpecPanel getSpeciesContextSpecPanel() {
 	}
 	return speciesContextSpecPanel;
 }
+	private MolecularStructuresPropertiesPanel getMolecularStructuresPropertiesPanel() {
+		if (molecularStructuresPropertiesPanel == null) {
+			try {
+				molecularStructuresPropertiesPanel = new MolecularStructuresPropertiesPanel();
+				molecularStructuresPropertiesPanel.setName("MolecularStructuresPropertiesPanel");
+			} catch (java.lang.Throwable ivjExc) {
+				handleException(ivjExc);
+			}
+		}
+		return molecularStructuresPropertiesPanel;
+	}
 
 private void initialize() {
 	try {
@@ -681,6 +684,7 @@ private void initialize() {
 		getReactionRulePropertiesPanel().setSelectionManager(selectionManager);
 		getReactionPropertiesPanel().setSelectionManager(selectionManager);
 		getSpeciesContextSpecPanel().setSelectionManager(selectionManager);
+		getMolecularStructuresPropertiesPanel().setSelectionManager(selectionManager);
 		getReactionRuleSpecPropertiesPanel().setSelectionManager(selectionManager);
 		getSpatialObjectPropertyPanel().setSelectionManager(selectionManager);
 		getSpatialProcessPropertyPanel().setSelectionManager(selectionManager);
@@ -769,7 +773,19 @@ protected void setRightBottomPanelOnSelection(Object[] selections) {
 			bShowInDatabaseProperties = true;
 			bottomComponent = geometryMetaDataPanel;
 		} else if (singleSelection instanceof SpeciesContextSpec) {
-			bottomComponent = getSpeciesContextSpecPanel();
+			SpeciesContextSpec scs = (SpeciesContextSpec)singleSelection;
+			switch(scs.provenance) {
+				case LangevinSpecs:
+					bottomComponent = getMolecularStructuresPropertiesPanel();
+					break;
+				case LangevinInitialConditions:	// TODO: we'll have here a simplified SpeciesContextSpecPanel
+					bottomComponent = getSpeciesContextSpecPanel();
+					break;
+				case GeneralInitialConditions:
+				default:
+					bottomComponent = getSpeciesContextSpecPanel();
+					break;
+			}
 		} else if (singleSelection instanceof ReactionSpec) {
 			bottomComponent = getKineticsTypeTemplatePanel();
 		} else if (singleSelection instanceof ReactionRuleSpec) {		// 
@@ -1006,7 +1022,6 @@ private BioModelEditorApplicationsPanel getBioModelEditorApplicationsPanel() {
 /**
  * Sets the bioModel property (cbit.vcell.biomodel.BioModel) value.
  * @param bioModel The new value for the property.
- * @see #getBioModel
  */
 public void setBioModel(BioModel bioModel) {
 	if (this.bioModel == bioModel) {
@@ -1016,6 +1031,7 @@ public void setBioModel(BioModel bioModel) {
 	bioModelEditorModelPanel.setBioModel(bioModel);
 	getBioModelEditorApplicationsPanel().setBioModel(bioModel);
 	getSpeciesContextSpecPanel().setBioModel(bioModel);
+	getMolecularStructuresPropertiesPanel().setBioModel(bioModel);
 	getReactionRuleSpecPropertiesPanel().setBioModel(bioModel);
 	getScriptingPanel().setBioModel(bioModel);	
 	getBioModelEditorPathwayPanel().setBioModel(bioModel);
@@ -1041,7 +1057,7 @@ public void setBioModel(BioModel bioModel) {
 /**
  * Insert the method's description here.
  * Creation date: (5/7/2004 5:40:13 PM)
- * @param newBioModelWindowManager cbit.vcell.client.desktop.BioModelWindowManager
+ * @param bioModelWindowManager cbit.vcell.client.desktop.BioModelWindowManager
  */
 public void setBioModelWindowManager(BioModelWindowManager bioModelWindowManager) {
 	if (this.bioModelWindowManager == bioModelWindowManager) {

vcell-client/src/main/java/cbit/vcell/graph/gui/SsldLargeShapePanel.java

@@ -0,0 +1,77 @@
+package cbit.vcell.graph.gui;
+
+import javax.swing.*;
+
+public class SsldLargeShapePanel extends JPanel {
+
+//    private boolean showDifferencesOnly = false;
+//    private boolean bShowMoleculeColor = false;
+//    private boolean bShowNonTrivialOnly = false;
+
+
+    // zooming the shape, 0 means normal size, a negative number means smaller shape
+    private static final int SmallestZoomFactor = -7;			// -7 is the smallest where the shapes scale decently well
+    private static final int DefaultZoomFactor = 0;
+    private static final int LargestZoomFactor = 0;
+    private int zoomFactor = DefaultZoomFactor;
+
+    // by default the shapes are editable and their border and text is black / gray, aso
+    // otherwise they are a shade of brown, very much alike the DefaultScrollTableCellRenderer.uneditableForeground
+    private boolean editable = true;
+
+
+
+//    public void setShowMoleculeColor(boolean bShowMoleculeColor) {
+//        this.bShowMoleculeColor = bShowMoleculeColor;
+//    }
+//    public void setShowNonTrivialOnly(boolean bShowNonTrivialOnly) {
+//        this.bShowNonTrivialOnly = bShowNonTrivialOnly;
+//    }
+
+
+    public boolean zoomLarger() {	// returns false when upper limit was reached
+        zoomFactor++;
+        if(zoomFactor >= LargestZoomFactor) {
+            zoomFactor = LargestZoomFactor;
+            System.out.println("MAX. Factor is " + zoomFactor);
+            return false;
+        } else {
+            System.out.println("Up. Factor is " + zoomFactor);
+            return true;
+        }
+    }
+    public void setZoomFactor(int newZoomFactor) {
+        if(newZoomFactor > LargestZoomFactor || newZoomFactor < SmallestZoomFactor) {
+            throw new RuntimeException("Large Shape Panel zoom factor is out of bounds");
+        }
+        zoomFactor = newZoomFactor;
+    }
+    public boolean zoomSmaller() {	// returns false when lower limit was reached
+        zoomFactor--;
+        if(zoomFactor <= SmallestZoomFactor) {
+            zoomFactor = SmallestZoomFactor;
+            System.out.println("MIN. Factor is " + zoomFactor);
+            return false;
+        } else {
+            System.out.println("Down. Factor is " + zoomFactor);
+            return true;
+        }
+    }
+    public boolean isLargestZoomFactor() {
+        return zoomFactor >= LargestZoomFactor ? true : false;
+    }
+    public boolean isSmallestZoomFactor() {
+        return zoomFactor <= SmallestZoomFactor ? true : false;
+    }
+    public int getZoomFactor() {
+        return zoomFactor;
+    }
+
+    public void setEditable(boolean editable) {
+        this.editable = editable;
+    }
+    public boolean isEditable() {
+        return editable;
+    }
+
+}

vcell-client/src/main/java/cbit/vcell/mapping/gui/InitialConditionsPanel.java

@@ -15,6 +15,7 @@
 import java.awt.Component;
 import java.awt.FlowLayout;
 import java.awt.Graphics;
+import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.Vector;
 
@@ -157,8 +158,15 @@ public void valueChanged(javax.swing.event.ListSelectionEvent e) {
             if (e.getValueIsAdjusting()) {
                 return;
             }
-            if (e.getSource() == getScrollPaneTable().getSelectionModel())
-                setSelectedObjectsFromTable(getScrollPaneTable(), tableModel);
+            if (e.getSource() == getScrollPaneTable().getSelectionModel()) {
+
+                int row = getScrollPaneTable().getSelectedRow();
+                SpeciesContextSpec scsSelected = tableModel.getValueAt(row);
+
+                ArrayList<Object> selectedObjects = new ArrayList<Object>();
+                selectedObjects.add(scsSelected);
+                selectionManager.setSelectedObjects(selectedObjects.toArray());
+            }
         }
 
         ;
@@ -440,7 +448,7 @@ private JSortTable getScrollPaneTable() {
             try {
                 table = new JSortTable();
                 table.setName("spceciesContextSpecsTable");
-                tableModel = new SpeciesContextSpecsTableModel(table);
+                tableModel = new SpeciesContextSpecsTableModel(table, this);
                 table.setModel(tableModel);
                 table.setScrollTableActionManager(new InternalScrollTableActionManager(table));
                 table.setAutoResizeMode(JTable.AUTO_RESIZE_SUBSEQUENT_COLUMNS);