From 9ca1d7a3776d77e402c3899184ae041d56f72ca6 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 10 Oct 2006 11:15:58 +0000
Subject: [PATCH] Only getGroups once if groupEditingcvs update

---
 src/jalview/appletgui/SeqPanel.java |   36 ++++++++++++++++++-----------------
 src/jalview/gui/SeqPanel.java       |   32 ++++++++++++++++---------------
 2 files changed, 36 insertions(+), 32 deletions(-)

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 97f3703..7e5a207 100755
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -814,8 +814,15 @@ public class SeqPanel
       }
 
 
+
       if (groupEditing)
       {
+        Vector vseqs = sg.getSequences(true);
+        int g, groupSize = vseqs.size();
+        SequenceI[] groupSeqs = new SequenceI[groupSize];
+        for (g = 0; g < groupSeqs.length; g++)
+          groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
+
         // drag to right
         if (insertGap)
         {
@@ -839,13 +846,13 @@ public class SeqPanel
                fixedRight--)
           {
             blank = true;
-            for (int s = 0; s < sg.getSize(true); s++)
+
+            for (g = 0; g < groupSize; g++)
             {
-              seq = (SequenceI)sg.getSequences(true).elementAt(s);
               for (int j = 0; j < startres - lastres; j++)
               {
                 if (!jalview.util.Comparison.isGap(
-                    seq.getCharAt(fixedRight - j)))
+                    groupSeqs[g].getCharAt(fixedRight - j)))
                 {
                   blank = false;
                   break;
@@ -894,19 +901,17 @@ public class SeqPanel
           /// Are we able to delete?
           // ie are all columns blank?
 
-          for (int s = 0; s < sg.getSize(true); s++)
+          for (g = 0; g < groupSize; g++)
           {
-            seq = (SequenceI)sg.getSequences(true).elementAt(s);
-
             for (int j = startres; j < lastres; j++)
             {
-              if (seq.getSequence().length() <= j)
+              if (groupSeqs[g].getLength() <= j)
               {
                 continue;
               }
 
               if (!jalview.util.Comparison.isGap(
-                  seq.getSequence().charAt(j)))
+                  groupSeqs[g].getCharAt(j)))
               {
                 // Not a gap, block edit not valid
                 endEditing();
@@ -917,10 +922,8 @@ public class SeqPanel
         }
 
 
-        for (int i = 0; i < sg.getSize(true); i++)
+        for (g = 0; g < groupSize; g++)
         {
-          seq = (SequenceI) sg.getSequences(true).elementAt(i);
-
           if (insertGap)
           {
             // dragging to the right
@@ -928,10 +931,10 @@ public class SeqPanel
             {
               if (fixedColumns && fixedRight != -1)
               {
-                insertChar(j, seq, fixedRight);
+                insertChar(j, groupSeqs[g], fixedRight);
               }
               else
-                insertChar(j, seq);
+                insertChar(j, groupSeqs[g]);
             }
           }
           else
@@ -941,17 +944,16 @@ public class SeqPanel
             {
               if (fixedColumns && fixedRight != -1)
               {
-                deleteChar(startres, seq, fixedRight);
+                deleteChar(startres, groupSeqs[g], fixedRight);
               }
               else
               {
-                deleteChar(startres, seq);
+                deleteChar(startres, groupSeqs[g]);
               }
             }
           }
         }
-      }
-      else /////Editing a single sequence///////////
+      }      else /////Editing a single sequence///////////
       {
         if (insertGap)
         {
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 4b7a388..5782797 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -835,6 +835,12 @@ public class SeqPanel extends JPanel implements MouseListener,
 
         if (groupEditing)
         {
+          Vector vseqs = sg.getSequences(true);
+          int g, groupSize = vseqs.size();
+          SequenceI[] groupSeqs = new SequenceI[groupSize];
+          for (g = 0; g < groupSeqs.length; g++)
+            groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
+
           // drag to right
           if (insertGap)
           {
@@ -858,13 +864,13 @@ public class SeqPanel extends JPanel implements MouseListener,
                  fixedRight--)
             {
               blank = true;
-              for (int s = 0; s < sg.getSize(true); s++)
+
+              for (g = 0; g < groupSize; g++)
               {
-                seq = (SequenceI)sg.getSequences(true).elementAt(s);
                 for (int j = 0; j < startres - lastres; j++)
                 {
                   if (!jalview.util.Comparison.isGap(
-                      seq.getCharAt(fixedRight - j)))
+                      groupSeqs[g].getCharAt(fixedRight - j)))
                   {
                     blank = false;
                     break;
@@ -913,19 +919,17 @@ public class SeqPanel extends JPanel implements MouseListener,
             /// Are we able to delete?
             // ie are all columns blank?
 
-            for (int s = 0; s < sg.getSize(true); s++)
+            for (g = 0; g < groupSize; g++)
             {
-              seq = (SequenceI)sg.getSequences(true).elementAt(s);
-
               for (int j = startres; j < lastres; j++)
               {
-                if (seq.getSequence().length() <= j)
+                if (groupSeqs[g].getLength() <= j)
                 {
                   continue;
                 }
 
                 if (!jalview.util.Comparison.isGap(
-                    seq.getSequence().charAt(j)))
+                    groupSeqs[g].getCharAt(j)))
                 {
                   // Not a gap, block edit not valid
                   endEditing();
@@ -936,10 +940,8 @@ public class SeqPanel extends JPanel implements MouseListener,
           }
 
 
-          for (int i = 0; i < sg.getSize(true); i++)
+          for (g = 0; g < groupSize; g++)
           {
-            seq = (SequenceI) sg.getSequences(true).elementAt(i);
-
             if (insertGap)
             {
               // dragging to the right
@@ -947,10 +949,10 @@ public class SeqPanel extends JPanel implements MouseListener,
               {
                 if (fixedColumns && fixedRight != -1)
                 {
-                  insertChar(j, seq, fixedRight);
+                  insertChar(j, groupSeqs[g], fixedRight);
                 }
                 else
-                  insertChar(j, seq);
+                  insertChar(j, groupSeqs[g]);
               }
             }
             else
@@ -960,11 +962,11 @@ public class SeqPanel extends JPanel implements MouseListener,
               {
                 if (fixedColumns && fixedRight != -1)
                 {
-                  deleteChar(startres, seq, fixedRight);
+                  deleteChar(startres, groupSeqs[g], fixedRight);
                 }
                 else
                 {
-                  deleteChar(startres, seq);
+                  deleteChar(startres, groupSeqs[g]);
                 }
               }
             }
-- 
1.7.10.2