From 816f6d685d041b982810be8129129b02a440417c Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 12 Sep 2005 17:00:39 +0000
Subject: [PATCH] Remove gaps in regions, not char by char

---
 src/jalview/appletgui/AlignFrame.java |   44 ++++++++++++++++++++++++++-------
 src/jalview/gui/AlignFrame.java       |   38 ++++++++++++++++++++++------
 2 files changed, 66 insertions(+), 16 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index ccf2bd2..14a341d 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -623,30 +623,56 @@ public class AlignFrame
     {
       seqs = viewport.getSelectionGroup().sequences;
       start = viewport.getSelectionGroup().getStartRes();
-      end = viewport.getSelectionGroup().getEndRes();
+      end = viewport.getSelectionGroup().getEndRes()+1;
     }
     else
       seqs = viewport.alignment.getSequences();
 
-    for (int i = 0; i <seqs.size(); i++)
+    for (int i = 0; i < seqs.size(); i++)
     {
-      current = (SequenceI)seqs.elementAt(i);
+      current = (SequenceI) seqs.elementAt(i);
       jSize = current.getLength();
 
+      // Removing a range is much quicker than removing gaps
+      // one by one for long sequences
       int j = start;
+      int rangeStart=-1, rangeEnd=-1;
+
       do
       {
         if (jalview.util.Comparison.isGap(current.getCharAt(j)))
         {
-          current.deleteCharAt(j);
-          j--;
-          jSize--;
+          if(rangeStart==-1)
+           {
+             rangeStart = j;
+             rangeEnd = j+1;
+           }
+           else
+           {
+             rangeEnd++;
+           }
+           j++;
         }
-        j++;
+        else
+        {
+          if(rangeStart>-1)
+          {
+            current.deleteChars(rangeStart, rangeEnd);
+            j-=rangeEnd-rangeStart;
+            jSize-=rangeEnd-rangeStart;
+            rangeStart = -1;
+            rangeEnd = -1;
+          }
+          else
+            j++;
+        }
+      }
+      while (j < end && j < jSize);
+      if(rangeStart>-1)
+      {
+       current.deleteChars(rangeStart, rangeEnd);
       }
-      while(j < end && j < jSize) ;
     }
-
     viewport.setStartRes(seq.findIndex(startRes)-1);
     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 8e3dfc8..e82356c 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -744,7 +744,6 @@ public class AlignFrame
    */
   protected void delete_actionPerformed(ActionEvent e)
   {
-    boolean seqsdeleted = false;
 
     if (viewport.getSelectionGroup() == null)
     {
@@ -776,7 +775,6 @@ public class AlignFrame
 
       if (seq.getSequence().length() < 1)
       {
-        seqsdeleted = true;
         viewport.getAlignment().deleteSequence(seq);
       }
       else
@@ -1005,7 +1003,7 @@ public class AlignFrame
     {
       seqs = viewport.getSelectionGroup().sequences;
       start = viewport.getSelectionGroup().getStartRes();
-      end = viewport.getSelectionGroup().getEndRes();
+      end = viewport.getSelectionGroup().getEndRes()+1;
     }
     else
     {
@@ -1017,19 +1015,45 @@ public class AlignFrame
       current = (SequenceI) seqs.elementAt(i);
       jSize = current.getLength();
 
+      // Removing a range is much quicker than removing gaps
+      // one by one for long sequences
       int j = start;
+      int rangeStart=-1, rangeEnd=-1;
 
       do
       {
         if (jalview.util.Comparison.isGap(current.getCharAt(j)))
         {
-          current.deleteCharAt(j);
-          j--;
-          jSize--;
+          if(rangeStart==-1)
+           {
+             rangeStart = j;
+             rangeEnd = j+1;
+           }
+           else
+           {
+             rangeEnd++;
+           }
+           j++;
+        }
+        else
+        {
+          if(rangeStart>-1)
+          {
+            current.deleteChars(rangeStart, rangeEnd);
+            j-=rangeEnd-rangeStart;
+            jSize-=rangeEnd-rangeStart;
+            rangeStart = -1;
+            rangeEnd = -1;
+          }
+          else
+            j++;
         }
-        j++;
       }
       while (j < end && j < jSize);
+      if(rangeStart>-1)
+      {
+       current.deleteChars(rangeStart, rangeEnd);
+      }
     }
 
     viewport.setStartRes(seq.findIndex(startRes)-1);
-- 
1.7.10.2