Only recalc consensus for start to end of group

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index f82efb5..de3e8fd 100755 (executable)
--- 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 (executable)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -813,9 +813,9 @@ public class PopupMenu extends JPopupMenu
 \r
         if (abovePIDColour.isSelected())\r
         {\r
-            sg.cs.setConsensus(AAFrequency.calculate(\r
-                    sg.getSequences(true), 0,\r
-                    ap.av.alignment.getWidth()));\r
+          sg.cs.setConsensus(AAFrequency.calculate(\r
+              sg.getSequences(true), sg.getStartRes(),\r
+              sg.getEndRes() + 1));\r
 \r
             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
                     getGroup().getName());\r
@@ -861,8 +861,9 @@ public class PopupMenu extends JPopupMenu
     {\r
         SequenceGroup sg = getGroup();\r
         sg.cs = new PIDColourScheme();\r
-        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
-                ap.av.alignment.getWidth()));\r
+        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),\r
+                                                 sg.getStartRes(),\r
+                                                 sg.getEndRes() + 1));\r
         refresh();\r
     }\r
 \r
@@ -877,8 +878,9 @@ public class PopupMenu extends JPopupMenu
 \r
         sg.cs = new Blosum62ColourScheme();\r
 \r
-        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
-                ap.av.alignment.getWidth()));\r
+        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),\r
+                                                 sg.getStartRes(),\r
+                                                 sg.getEndRes() + 1));\r
 \r
         refresh();\r
     }\r
@@ -909,8 +911,9 @@ public class PopupMenu extends JPopupMenu
         {\r
             Conservation c = new Conservation("Group",\r
                     ResidueProperties.propHash, 3,\r
-                    sg.getSequences(true), 0,\r
-                    ap.av.alignment.getWidth());\r
+                    sg.getSequences(true),\r
+                    sg.getStartRes(),\r
+                    sg.getEndRes() + 1);\r
 \r
             c.calculate();\r
             c.verdict(false, ap.av.ConsPercGaps);\r

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index a4c2279..ac93683 100755 (executable)
--- 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());\r
           }\r
 \r
+          if (stretchGroup.cs instanceof Blosum62ColourScheme\r
+              || stretchGroup.cs instanceof PIDColourScheme\r
+              || stretchGroup.cs.conservationApplied())\r
+            stretchGroup.recalcConservation();\r
+\r
           if (stretchGroup.cs.conservationApplied())\r
           {\r
             SliderPanel.setConservationSlider(ap, stretchGroup.cs,\r
                                               stretchGroup.getName());\r
-            stretchGroup.recalcConservation();\r
           }\r
           else\r
           {\r