From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 24 Feb 2006 11:47:03 +0000 (+0000)
Subject: Cannot delete residues
X-Git-Tag: Root_VamJalview_2_07b+~90
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8fdfb564d3061e849a26d5a388f333808f0c796a;p=jalview.git

Cannot delete residues
---

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 35ac570..e500422 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -803,24 +803,50 @@ public class AlignFrame
       return;
     }
 
-    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
-                                   HistoryItem.HIDE));
 
     SequenceGroup sg = viewport.getSelectionGroup();
-    boolean allSequences = false;
-    if (sg.sequences.size() == viewport.alignment.getHeight())
+
+
+
+    //Jalview no longer allows deletion of residues.
+    //Check here whether any residues are in selection area
+    if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)
     {
-      allSequences = true;
+      for (int i = 0; i < sg.sequences.size(); i++)
+      {
+        SequenceI seq = sg.getSequenceAt(i);
+        int j = sg.getStartRes();
+        do
+        {
+          if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
+          {
+            JOptionPane.showInternalMessageDialog(
+                Desktop.desktop, "Cannot delete residues from alignment!\n"
+                + "Try hiding columns instead.",
+                "Deletion of residues not permitted",
+                JOptionPane.WARNING_MESSAGE);
+
+            return;
+          }
+          j++;
+        }while(j<=sg.getEndRes());
+      }
     }
 
+
+    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
+                                   HistoryItem.HIDE));
+
+
     for (int i = 0; i < sg.sequences.size(); i++)
     {
       SequenceI seq = sg.getSequenceAt(i);
       int index = viewport.getAlignment().findIndex(seq);
+
       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
 
       // If the cut affects all sequences, remove highlighted columns
-      if (allSequences)
+      if (sg.sequences.size() == viewport.alignment.getHeight())
       {
         viewport.getColumnSelection().removeElements(sg.getStartRes(),
             sg.getEndRes() + 1);
@@ -1194,8 +1220,8 @@ public class AlignFrame
     JInternalFrame frame = new JInternalFrame();
     Finder finder = new Finder(viewport, alignPanel, frame);
     frame.setContentPane(finder);
-    Desktop.addInternalFrame(frame, "Find", 340, 110);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
+    Desktop.addInternalFrame(frame, "Find", 340, 110);
   }
 
   /**
@@ -1329,7 +1355,7 @@ public class AlignFrame
       new SequenceFeatureFetcher(viewport.
                                  alignment,
                                  alignPanel);
-      viewport.showSequenceFeatures(true);
+      viewport.setShowSequenceFeatures(true);
       showSeqFeatures.setSelected(true);
     }
   }
@@ -1347,8 +1373,12 @@ public class AlignFrame
    */
   public void showSeqFeatures_actionPerformed(ActionEvent evt)
   {
-    viewport.showSequenceFeatures(showSeqFeatures.isSelected());
+    viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
     alignPanel.repaint();
+    if (alignPanel.getOverviewPanel() != null)
+    {
+      alignPanel.getOverviewPanel().updateOverviewImage();
+    }
   }
 
   /**
@@ -2627,6 +2657,7 @@ public boolean parseGroupsFile(String file)
     }
 
     viewport.showSequenceFeatures = true;
+    showSeqFeatures.setSelected(true);
     alignPanel.repaint();
     return true;
 }