JAL-845 first working linked edit protein -> cDNA

[jalview.git] / src / jalview / gui / SeqPanel.java

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index c10a4a9..2c9b7f6 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -22,6 +22,7 @@ package jalview.gui;
 
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
+import jalview.commands.EditCommand.Edit;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.Sequence;
@@ -34,6 +35,8 @@ import jalview.structure.SelectionListener;
 import jalview.structure.SelectionSource;
 import jalview.structure.SequenceListener;
 import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+import jalview.util.Comparison;
 import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
@@ -281,22 +284,33 @@ public class SeqPanel extends JPanel implements MouseListener,
     return features;
   }
 
+  /**
+   * When all of a sequence of edits are complete, put the resulting edit list
+   * on the history stack (undo list), and reset flags for editing in progress.
+   */
   void endEditing()
   {
-    if (editCommand != null && editCommand.getSize() > 0)
+    try
+    {
+      if (editCommand != null && editCommand.getSize() > 0)
+      {
+        ap.alignFrame.addHistoryItem(editCommand);
+        av.firePropertyChange("alignment", null, av.getAlignment()
+                .getSequences());
+      }
+    } finally
     {
-      ap.alignFrame.addHistoryItem(editCommand);
-      av.firePropertyChange("alignment", null, av.getAlignment()
-              .getSequences());
+      /*
+       * Tidy up come what may...
+       */
+      startseq = -1;
+      lastres = -1;
+      editingSeqs = false;
+      groupEditing = false;
+      keyboardNo1 = null;
+      keyboardNo2 = null;
+      editCommand = null;
     }
-
-    startseq = -1;
-    lastres = -1;
-    editingSeqs = false;
-    groupEditing = false;
-    keyboardNo1 = null;
-    keyboardNo2 = null;
-    editCommand = null;
   }
 
   void setCursorRow()
@@ -649,7 +663,6 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   String lastMessage;
 
-  @Override
   public void mouseOverSequence(SequenceI sequence, int index, int pos)
   {
     String tmp = sequence.hashCode() + " " + index + " " + pos;
@@ -676,6 +689,10 @@ public class SeqPanel extends JPanel implements MouseListener,
   }
 
   @Override
+  public VamsasSource getVamsasSource()
+  {
+    return this.ap == null ? null : this.ap.av;
+  }
   public void updateColours(SequenceI seq, int index)
   {
     System.out.println("update the seqPanel colours");
@@ -962,7 +979,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
     }
 
-    StringBuffer message = new StringBuffer();
+    StringBuilder message = new StringBuilder(64);
     if (groupEditing)
     {
       message.append("Edit group:");
@@ -1187,8 +1204,8 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
         else
         {
-          editCommand.appendEdit(Action.INSERT_GAP, groupSeqs,
-                  startres, startres - lastres, av.getAlignment(), true);
+          appendEdit(Action.INSERT_GAP, groupSeqs, startres, startres
+                  - lastres);
         }
       }
       else
@@ -1203,8 +1220,8 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
         else
         {
-          editCommand.appendEdit(Action.DELETE_GAP, groupSeqs,
-                  startres, lastres - startres, av.getAlignment(), true);
+          appendEdit(Action.DELETE_GAP, groupSeqs, startres, lastres
+                  - startres);
         }
 
       }
@@ -1225,8 +1242,8 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
         else
         {
-          editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[]
-          { seq }, lastres, startres - lastres, av.getAlignment(), true);
+          appendEdit(Action.INSERT_GAP, new SequenceI[]
+          { seq }, lastres, startres - lastres);
         }
       }
       else
@@ -1238,7 +1255,7 @@ public class SeqPanel extends JPanel implements MouseListener,
           {
             for (int j = lastres; j > startres; j--)
             {
-              if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
+              if (!Comparison.isGap(seq.getCharAt(startres)))
               {
                 endEditing();
                 break;
@@ -1253,7 +1270,7 @@ public class SeqPanel extends JPanel implements MouseListener,
             int max = 0;
             for (int m = startres; m < lastres; m++)
             {
-              if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
+              if (!Comparison.isGap(seq.getCharAt(m)))
               {
                 break;
               }
@@ -1262,9 +1279,8 @@ public class SeqPanel extends JPanel implements MouseListener,
 
             if (max > 0)
             {
-              editCommand.appendEdit(Action.DELETE_GAP,
-                      new SequenceI[]
-                      { seq }, startres, max, av.getAlignment(), true);
+              appendEdit(Action.DELETE_GAP, new SequenceI[]
+              { seq }, startres, max);
             }
           }
         }
@@ -1280,8 +1296,8 @@ public class SeqPanel extends JPanel implements MouseListener,
           }
           else
           {
-            editCommand.appendEdit(Action.INSERT_NUC, new SequenceI[]
-            { seq }, lastres, startres - lastres, av.getAlignment(), true);
+            appendEdit(Action.INSERT_NUC, new SequenceI[]
+            { seq }, lastres, startres - lastres);
           }
         }
       }
@@ -1316,22 +1332,37 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
     }
 
-    editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1,
-            av.getAlignment(), true);
+    appendEdit(Action.DELETE_GAP, seq, blankColumn, 1);
+
+    appendEdit(Action.INSERT_GAP, seq, j, 1);
+
+  }
+
+  /**
+   * Helper method to add and perform one edit action.
+   * 
+   * @param action
+   * @param seq
+   * @param pos
+   * @param count
+   */
+  protected void appendEdit(Action action, SequenceI[] seq, int pos,
+          int count)
+  {
 
-    editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1,
-            av.getAlignment(), true);
+    final Edit edit = new EditCommand().new Edit(action, seq, pos, count,
+            av.getAlignment().getGapCharacter());
 
+    editCommand.appendEdit(edit, av.getAlignment(),
+            true, null);
   }
 
   void deleteChar(int j, SequenceI[] seq, int fixedColumn)
   {
 
-    editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1,
-            av.getAlignment(), true);
+    appendEdit(Action.DELETE_GAP, seq, j, 1);
 
-    editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1,
-            av.getAlignment(), true);
+    appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1);
   }
 
   /**