Reset ClustalX after removing gaps

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index fae50d9..80e8438 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -599,6 +599,7 @@ public class AlignFrame
     viewport.getAlignment().removeGaps();\r
     viewport.updateConservation();\r
     viewport.updateConsensus();\r
+    resetAllClustalSchemes();\r
     alignPanel.repaint();\r
   }\r
 \r
@@ -644,11 +645,34 @@ public class AlignFrame
       while(j < end && j < jSize) ;\r
     }\r
 \r
+    resetAllClustalSchemes();\r
     viewport.updateConservation();\r
     viewport.updateConsensus();\r
     alignPanel.repaint();\r
   }\r
 \r
+  void resetAllClustalSchemes()\r
+  {\r
+    if(viewport.getGlobalColourScheme()!=null\r
+       && viewport.getGlobalColourScheme() instanceof ClustalxColourScheme)\r
+    {\r
+      ((ClustalxColourScheme)viewport.getGlobalColourScheme()).\r
+          resetClustalX(viewport.alignment.getSequences(),\r
+                        viewport.alignment.getWidth());\r
+    }\r
+\r
+    int s, sSize = viewport.alignment.getGroups().size();\r
+    for(s=0; s<sSize; s++)\r
+    {\r
+      SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
+      if(sg.cs instanceof ClustalxColourScheme)\r
+      {\r
+        ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());\r
+      }\r
+    }\r
+  }\r
+\r
+\r
 \r
   public void findMenuItem_actionPerformed(ActionEvent e)\r
   {\r

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 9a5863f..ee7676c 100755 (executable)
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -535,9 +535,9 @@ public class SeqPanel
 \r
         if (cs instanceof ClustalxColourScheme)\r
         {\r
-          ClustalxColourScheme cxs = (ClustalxColourScheme) cs;\r
-          cxs.resetClustalX(av.alignment.getSequences(),\r
-                            av.alignment.getWidth());\r
+          ((ClustalxColourScheme)cs).\r
+              resetClustalX(av.alignment.getSequences(),\r
+                                av.alignment.getWidth());\r
           cs.setConservation(c);\r
           av.setGlobalColourScheme(cs);\r
         }\r

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index bdcea36..084ad7d 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -961,6 +961,7 @@ public class AlignFrame
                                    viewport.alignment, HistoryItem.HIDE));\r
 \r
     viewport.getAlignment().removeGaps();\r
+    resetAllClustalSchemes();\r
     viewport.updateConservation();\r
     viewport.updateConsensus();\r
     alignPanel.repaint();\r
@@ -1017,11 +1018,34 @@ public class AlignFrame
       while (j < end && j < jSize);\r
     }\r
 \r
+    resetAllClustalSchemes();\r
+\r
     viewport.updateConservation();\r
     viewport.updateConsensus();\r
     alignPanel.repaint();\r
   }\r
 \r
+  void resetAllClustalSchemes()\r
+  {\r
+    if(viewport.getGlobalColourScheme()!=null\r
+       && viewport.getGlobalColourScheme() instanceof ClustalxColourScheme)\r
+    {\r
+      ((ClustalxColourScheme)viewport.getGlobalColourScheme()).\r
+          resetClustalX(viewport.alignment.getSequences(),\r
+                        viewport.alignment.getWidth());\r
+    }\r
+\r
+    int s, sSize = viewport.alignment.getGroups().size();\r
+    for(s=0; s<sSize; s++)\r
+    {\r
+      SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
+      if(sg.cs instanceof ClustalxColourScheme)\r
+      {\r
+        ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());\r
+      }\r
+    }\r
+  }\r
+\r
   /**\r
    * DOCUMENT ME!\r
    *\r

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 444b6bb..de1a533 100755 (executable)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -650,9 +650,10 @@ public class SeqPanel extends JPanel
 \r
             if (cs instanceof ClustalxColourScheme)\r
             {\r
-              ClustalxColourScheme cxs = (ClustalxColourScheme) cs;\r
-              cxs.resetClustalX(av.alignment.getSequences(),\r
+              ((ClustalxColourScheme)cs).\r
+                  resetClustalX(av.alignment.getSequences(),\r
                                 av.alignment.getWidth());\r
+\r
               cs.setConservation(c);\r
               av.setGlobalColourScheme(cs);\r
             }\r