From 0cc0607495a69fc52505ae2d306bfbf9137d54aa Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 16 Jun 2005 09:34:31 +0000
Subject: [PATCH] remove gaps applies to selected area

---
 src/jalview/appletgui/AlignFrame.java |   30 +++++++++++++++++++++++++-----
 src/jalview/gui/AlignFrame.java       |   23 +++++++++++++++++++----
 2 files changed, 44 insertions(+), 9 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index b314854..bb4b58a 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -544,16 +544,32 @@ public class AlignFrame
 
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem(new HistoryItem("Remove Gaps",
-                                   viewport.alignment,
+    addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
                                    HistoryItem.HIDE));
+
     SequenceI current;
     int jSize;
-    for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
+
+    Vector seqs=null;
+
+    int start=0, end = viewport.alignment.getWidth();
+
+    if(viewport.getSelectionGroup()!=null)
     {
-      current = viewport.getAlignment().getSequenceAt(i);
+      seqs = viewport.getSelectionGroup().sequences;
+      start = viewport.getSelectionGroup().getStartRes();
+      end = viewport.getSelectionGroup().getEndRes();
+    }
+    else
+      seqs = viewport.alignment.getSequences();
+
+    for (int i = 0; i <seqs.size(); i++)
+    {
+      current = (SequenceI)seqs.elementAt(i);
       jSize = current.getLength();
-      for (int j = 0; j < jSize; j++)
+
+      int j = start;
+      do
       {
         if (jalview.util.Comparison.isGap(current.getCharAt(j)))
         {
@@ -561,13 +577,17 @@ public class AlignFrame
           j--;
           jSize--;
         }
+        j++;
       }
+      while(j < end);
     }
+
     viewport.updateConservation();
     viewport.updateConsensus();
     alignPanel.repaint();
   }
 
+
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
     Finder finder = new Finder(alignPanel);
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 484b8cd..cc7ce48 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -679,13 +679,26 @@ public class AlignFrame
     SequenceI current;
     int jSize;
 
-    for (int i = 0; i < viewport.getAlignment().getSequences().size();
-         i++)
+    Vector seqs=null;
+
+    int start=0, end = viewport.alignment.getWidth();
+
+    if(viewport.getSelectionGroup()!=null)
     {
-      current = viewport.getAlignment().getSequenceAt(i);
+      seqs = viewport.getSelectionGroup().sequences;
+      start = viewport.getSelectionGroup().getStartRes();
+      end = viewport.getSelectionGroup().getEndRes();
+    }
+    else
+      seqs = viewport.alignment.getSequences();
+
+    for (int i = 0; i <seqs.size(); i++)
+    {
+      current = (SequenceI)seqs.elementAt(i);
       jSize = current.getLength();
 
-      for (int j = 0; j < jSize; j++)
+      int j = start;
+      do
       {
         if (jalview.util.Comparison.isGap(current.getCharAt(j)))
         {
@@ -693,7 +706,9 @@ public class AlignFrame
           j--;
           jSize--;
         }
+        j++;
       }
+      while(j < end);
     }
 
     viewport.updateConservation();
-- 
1.7.10.2