From 39d42f25edeb526275d178e0259e767e7c29bd78 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 23 Mar 2005 16:27:38 +0000
Subject: [PATCH 1/1] adjustForRemoveLeft / Right added

---
 src/jalview/datamodel/SequenceGroup.java |   37 ++++++++++++++++++++++++++++++
 src/jalview/gui/AlignFrame.java          |   27 ++++++++++++++++++++--
 2 files changed, 62 insertions(+), 2 deletions(-)

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 4c6420c..0cf954b 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -47,6 +47,43 @@ public class SequenceGroup
     endRes = end;
   }
 
+  public boolean adjustForRemoveLeft(int col)
+  {
+    // return value is true if the group still exists
+    if(startRes>=col)
+      startRes = startRes - col;
+    if(endRes>=col)
+    {
+      endRes = endRes - col;
+      if(startRes>endRes)
+        startRes = 0;
+    }
+    else
+    {
+        // must delete this group!!
+        return false;
+    }
+
+    return true;
+  }
+
+  public boolean adjustForRemoveRight(int col)
+  {
+
+    if(startRes>col)
+    {
+      // delete this group
+      return false;
+    }
+
+    if(endRes>=col)
+      endRes = col;
+
+
+    return true;
+  }
+
+
   public String getName()
   {
     return groupName;
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 7071d81..00961d6 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -462,6 +462,18 @@ public class AlignFrame extends GAlignFrame
       int min = colSel.getMin();
       viewport.getAlignment().trimLeft(min);
       colSel.compensateForEdit(0,min);
+
+      if(viewport.getSelectionGroup()!=null)
+        viewport.getSelectionGroup().adjustForRemoveLeft(min);
+
+      Vector groups = viewport.alignment.getGroups();
+      for(int i=0; i<groups.size(); i++)
+      {
+        SequenceGroup sg = (SequenceGroup) groups.get(i);
+        if(!sg.adjustForRemoveLeft(min))
+          viewport.alignment.deleteGroup(sg);
+      }
+
       alignPanel.RefreshPanels();
     }
   }
@@ -473,8 +485,19 @@ public class AlignFrame extends GAlignFrame
     if (colSel.size() > 0)
     {
       int max = colSel.getMax();
-      if(max>1)
-        viewport.getAlignment().trimRight(max);
+      viewport.getAlignment().trimRight(max);
+      if(viewport.getSelectionGroup()!=null)
+        viewport.getSelectionGroup().adjustForRemoveRight(max);
+
+      Vector groups = viewport.alignment.getGroups();
+      for(int i=0; i<groups.size(); i++)
+      {
+        SequenceGroup sg = (SequenceGroup) groups.get(i);
+        if(!sg.adjustForRemoveRight(max))
+          viewport.alignment.deleteGroup(sg);
+      }
+
+
 
       alignPanel.RefreshPanels();
     }
-- 
1.7.10.2