WIP: link length editor

virtualcell · Nov 21, 2024 · 08be444 · 08be444
1 parent 03ba3ce
commit 08be444
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Showing 3 changed files with 38 additions and 5 deletions.
diff --git a/vcell-client/src/main/java/cbit/vcell/mapping/gui/LinkSpecsTableModel.java b/vcell-client/src/main/java/cbit/vcell/mapping/gui/LinkSpecsTableModel.java
@@ -7,10 +7,12 @@
 import cbit.vcell.model.Structure;
 import cbit.vcell.parser.Expression;
 import org.vcell.model.rbm.*;
+import org.vcell.util.Coordinate;
 import org.vcell.util.gui.GuiUtils;
 import org.vcell.util.gui.ScrollTable;
 import org.vcell.util.springsalad.NamedColor;
 
+import javax.swing.*;
 import java.beans.PropertyChangeEvent;
 import java.util.*;
 
@@ -86,13 +88,40 @@ public Object getValueAt(int row, int col) {
     @Override
     public void setValueAt(Object aValue, int row, int col) {
         MolecularInternalLinkSpec mils = getValueAt(row);
+        if(mils == null) {
+            return;
+        }
         ColumnType columnType = columns.get(col);
-        switch (columnType) {
-            case COLUMN_LINK:
+        SpeciesContextSpec scs = getSpeciesContextSpec();
 
+        MolecularComponentPattern mcpOne = mils.getMolecularComponentPatternOne();
+        MolecularComponentPattern mcpTwo = mils. getMolecularComponentPatternTwo();
+        SiteAttributesSpec sasOne = mils. getSite1();
+        SiteAttributesSpec sasTwo = mils. getSite2();
+
+        switch (columnType) {
+            case COLUMN_LINK:   // not editable
                 return;
             case COLUMN_LENGTH:
-
+                if (aValue instanceof String newExpressionString) {
+                    double res = 0.0;
+                    try {
+                        res = Double.parseDouble(newExpressionString);
+                    } catch(NumberFormatException ex) {
+                        JOptionPane.showMessageDialog(null, "Number expected", "Error", JOptionPane.ERROR_MESSAGE);
+                        return;
+                    }
+                    // the link is a derived value, we don't store it - we just show it in the table
+                    // instead, we adjust the x, y, z of the molecules involved
+                    double[] unitVector = mils.unitVector();
+                    double newX = sasOne.getX() + res*unitVector[0];
+                    double newY = sasOne.getY() + res*unitVector[1];
+                    double newZ = sasOne.getZ() + res*unitVector[2];
+                    Coordinate coord = new Coordinate (newX, newY, newZ);
+                    sasTwo.setCoordinate(coord);
+                    refreshData();
+                    scs.firePropertyChange(SpeciesContextSpec.PROPERTY_NAME_LINK_LENGTH, null, mils);
+                }
                 return;
             default:
                 return;
@@ -103,8 +132,9 @@ public boolean isCellEditable(int row, int col) {
         ColumnType columnType = columns.get(col);
         switch (columnType) {
             case COLUMN_LINK:
-            case COLUMN_LENGTH:
                 return false;
+            case COLUMN_LENGTH:
+                return true;
             default:
                 return false;
         }

diff --git a/vcell-client/src/main/java/cbit/vcell/mapping/gui/MolecularStructuresPropertiesPanel.java b/vcell-client/src/main/java/cbit/vcell/mapping/gui/MolecularStructuresPropertiesPanel.java
@@ -65,6 +65,8 @@ public void actionPerformed(java.awt.event.ActionEvent e) {
         public void propertyChange(PropertyChangeEvent evt) {
             if(evt.getSource() instanceof SpeciesContextSpec && evt.getPropertyName().equals(SpeciesContextSpec.PROPERTY_NAME_SITE_ATTRIBUTE)) {
                 updateShape();
+            } else if(evt.getSource() instanceof SpeciesContextSpec && evt.getPropertyName().equals(SpeciesContextSpec.PROPERTY_NAME_LINK_LENGTH)) {
+                updateShape();
             }
         }
     }

diff --git a/vcell-core/src/main/java/cbit/vcell/mapping/SpeciesContextSpec.java b/vcell-core/src/main/java/cbit/vcell/mapping/SpeciesContextSpec.java
@@ -70,7 +70,8 @@ public class SpeciesContextSpec implements Matchable, ScopedSymbolTable, Seriali
     public static final String PARAMETER_NAME_PROXY_PARAMETERS = "proxyParameters";
     private static final String PROPERTY_NAME_WELL_MIXED = "wellMixed";
     private static final String PROPERTY_NAME_FORCECONTINUOUS = "forceContinuous";
-    public static final String PROPERTY_NAME_SITE_ATTRIBUTE = "SiteAttributes";
+    public static final String PROPERTY_NAME_SITE_ATTRIBUTE = "SiteAttributes";     // springsalad
+    public static final String PROPERTY_NAME_LINK_LENGTH = "LinkLength";            // springsalad
     private static final int INITIAL_YZ_SITE_OFFSET = 4;
 
     public static final boolean TrackClusters = true;            // SpringSaLaD specific