From 1db5f61912957e4b380e5d321074421d21e20aa8 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 1 Dec 2004 17:06:15 +0000
Subject: [PATCH] Char to string comparison

---
 src/jalview/gui/SeqPanel.java |   46 ++++++++++++++++++++++-------------------
 1 file changed, 25 insertions(+), 21 deletions(-)

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 3df1dac..1714a31 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -24,6 +24,9 @@ public class SeqPanel extends JPanel
   public    boolean editFlag;
   protected AlignViewport av;
 
+  // if character is inserted or deleted, we will need to recalculate the conservation
+  int seqEditOccurred = -1;
+
   public SeqPanel(AlignViewport av, AlignmentPanel p) {
     this.av         = av;
 
@@ -56,15 +59,19 @@ public class SeqPanel extends JPanel
   public void doMouseReleased(MouseEvent evt) {
 
     int x = evt.getX();
-      int res = (int)(x/av.getCharWidth()) + av.getStartRes();
+    int res = (int)(x/av.getCharWidth()) + av.getStartRes();
 
-      endres = res;
+    endres = res;
 
       // This is to detect edits - we're at the end of an edit if mouse is up
-      editFlag = false;
-      startseq = -1;
-      startres = -1;
-      lastres  = -1;
+    editFlag = false;
+    startseq = -1;
+    startres = -1;
+    lastres  = -1;
+    if(seqEditOccurred>-1)
+      updateConservation(seqEditOccurred);
+
+    seqEditOccurred = -1;
 
     parent.RefreshPanels();
     repaint();
@@ -177,8 +184,8 @@ public class SeqPanel extends JPanel
               {
 		if (!flag)
                 {
-		  if (!s.getSequence().substring(j,j+1).equals(av.getAlignment().getGapCharacter()) &&
-		      !s.getSequence().substring(j,j+1).equals(" "))
+		  if (s.getSequence().charAt(j)!=av.getAlignment().getGapCharacter() &&
+		      s.getSequence().charAt(j)==' ')
                   {
 		    res = j+1;
 		    flag = true;
@@ -266,28 +273,28 @@ public class SeqPanel extends JPanel
 
   public void insertChar(int j, int seq)
   {
-    av.getAlignment().getSequenceAt(seq).insertCharAt(j, av.getGapCharacter().charAt(0));
-    updateConservation(seq);
+    av.getAlignment().getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
+    seqEditOccurred=seq;
   }
 
-  public void deleteChar(int j, int res, int sno)
+  public void deleteChar(int j, int res, int seq)
   {
 
-    if (av.getAlignment().getSequenceAt(sno).getSequence().substring(j,j+1).equals(".") ||
-        av.getAlignment().getSequenceAt(sno).getSequence().substring(j,j+1).equals("-") ||
-        av.getAlignment().getSequenceAt(sno).getSequence().substring(j,j+1).equals(" ") )
+    if (av.getAlignment().getSequenceAt(seq).getSequence().charAt(j)=='.' ||
+        av.getAlignment().getSequenceAt(seq).getSequence().charAt(j)=='-' ||
+        av.getAlignment().getSequenceAt(seq).getSequence().charAt(j)==' ' )
     {
-        av.getAlignment().getSequenceAt(sno).deleteCharAt(j);
+        av.getAlignment().getSequenceAt(seq).deleteCharAt(j);
     }
-    updateConservation(sno);
+
     av.getAlignment().getWidth();
     repaint();
+    seqEditOccurred=seq;
   }
 
 
   void updateConservation(int i)
   {
-
     Alignment al = (Alignment) av.getAlignment();
     SequenceGroup sg = av.alignment.findGroup( al.getSequenceAt(i));
     if(sg==null || !(sg.cs instanceof ConservationColourScheme))
@@ -308,6 +315,7 @@ public class SeqPanel extends JPanel
 
   public void setColourScheme(ColourSchemeI cs, boolean showConservation)
   {
+    seqCanvas.paintFlag = true;
     if (av.getSelection().size() == 0)
     {
       seqCanvas.cs = cs;
@@ -378,11 +386,7 @@ public class SeqPanel extends JPanel
       ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
       sg.cs = ccs.cs;
     }
-
-
-
    }
-   seqCanvas.paintFlag = true;
    repaint();
   }
 
-- 
1.7.10.2