From eb77addf49f8957e88b61f07ce36414c6619a221 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 6 Nov 2006 17:12:55 +0000
Subject: [PATCH 1/1] Only recalc consensus for start to end of group

---
 src/jalview/gui/AlignFrame.java |    9 +++++----
 src/jalview/gui/PopupMenu.java  |   21 ++++++++++++---------
 src/jalview/gui/SeqPanel.java   |    6 +++++-
 3 files changed, 22 insertions(+), 14 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index f82efb5..de3e8fd 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -2073,8 +2073,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
                 viewport.getIgnoreGapsConsensus());
 
          sg.cs.setConsensus(AAFrequency.calculate(
-             sg.getSequences(true), 0,
-             sg.getWidth()));
+             sg.getSequences(true), sg.getStartRes(),
+             sg.getEndRes()+1));
        }
         else
           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
@@ -2084,8 +2084,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         {
           Conservation c = new Conservation("Group",
                                             ResidueProperties.propHash, 3,
-                                            sg.getSequences(true), 0,
-                                            viewport.alignment.getWidth() - 1);
+                                            sg.getSequences(true),
+                                            sg.getStartRes(),
+                                            sg.getEndRes()+1);
           c.calculate();
           c.verdict(false, viewport.ConsPercGaps);
           sg.cs.setConservation(c);
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 0af9df4..5213bad 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -813,9 +813,9 @@ public class PopupMenu extends JPopupMenu
 
         if (abovePIDColour.isSelected())
         {
-            sg.cs.setConsensus(AAFrequency.calculate(
-                    sg.getSequences(true), 0,
-                    ap.av.alignment.getWidth()));
+          sg.cs.setConsensus(AAFrequency.calculate(
+              sg.getSequences(true), sg.getStartRes(),
+              sg.getEndRes() + 1));
 
             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
                     getGroup().getName());
@@ -861,8 +861,9 @@ public class PopupMenu extends JPopupMenu
     {
         SequenceGroup sg = getGroup();
         sg.cs = new PIDColourScheme();
-        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
-                ap.av.alignment.getWidth()));
+        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),
+                                                 sg.getStartRes(),
+                                                 sg.getEndRes() + 1));
         refresh();
     }
 
@@ -877,8 +878,9 @@ public class PopupMenu extends JPopupMenu
 
         sg.cs = new Blosum62ColourScheme();
 
-        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
-                ap.av.alignment.getWidth()));
+        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),
+                                                 sg.getStartRes(),
+                                                 sg.getEndRes() + 1));
 
         refresh();
     }
@@ -909,8 +911,9 @@ public class PopupMenu extends JPopupMenu
         {
             Conservation c = new Conservation("Group",
                     ResidueProperties.propHash, 3,
-                    sg.getSequences(true), 0,
-                    ap.av.alignment.getWidth());
+                    sg.getSequences(true),
+                    sg.getStartRes(),
+                    sg.getEndRes() + 1);
 
             c.calculate();
             c.verdict(false, ap.av.ConsPercGaps);
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index a4c2279..ac93683 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1428,11 +1428,15 @@ public class SeqPanel extends JPanel implements MouseListener,
                 stretchGroup.getWidth());
           }
 
+          if (stretchGroup.cs instanceof Blosum62ColourScheme
+              || stretchGroup.cs instanceof PIDColourScheme
+              || stretchGroup.cs.conservationApplied())
+            stretchGroup.recalcConservation();
+
           if (stretchGroup.cs.conservationApplied())
           {
             SliderPanel.setConservationSlider(ap, stretchGroup.cs,
                                               stretchGroup.getName());
-            stretchGroup.recalcConservation();
           }
           else
           {
-- 
1.7.10.2