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[jalview.git] / src / jalview / gui / PopupMenu.java

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 3481a31..356e5d5 100755 (executable)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -688,7 +688,7 @@ public class PopupMenu extends JPopupMenu
         if (ap.overviewPanel != null)\r
           ap.overviewPanel.updateOverviewImage();\r
 \r
-        ap.seqPanel.repaint();\r
+        PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
     }\r
 \r
     /**\r
@@ -1126,25 +1126,32 @@ public class PopupMenu extends JPopupMenu
       SequenceGroup sg = ap.av.getSelectionGroup();\r
       if(sg==null || sg.getSize(false)<1)\r
       {\r
-        ap.av.hideSequence(sequence);\r
+        ap.av.hideSequence(new SequenceI[]{sequence});\r
         return;\r
       }\r
 \r
+      int gsize = sg.getSize(false);\r
+      SequenceI [] hseqs;\r
+\r
+      hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ];\r
+\r
         int index = 0;\r
-        while(index < sg.getSize(false))\r
+        while(index < gsize)\r
         {\r
           if(representGroup && sg.getSequenceAt(index)!=sequence)\r
           {\r
             sequence.addHiddenSequence(sg.getSequenceAt(index));\r
-            ap.av.hideSequence(sg.getSequenceAt(index));\r
+            hseqs[index] = sg.getSequenceAt(index);\r
           }\r
           else if(!representGroup)\r
           {\r
-            ap.av.hideSequence(sg.getSequenceAt(index));\r
+            hseqs[index] = sg.getSequenceAt(index);\r
           }\r
           index ++;\r
         }\r
 \r
+        ap.av.hideSequence(hseqs);\r
+\r
         ap.av.setSelectionGroup(null);\r
     }\r
 \r
@@ -1160,45 +1167,58 @@ public class PopupMenu extends JPopupMenu
 \r
   public void upperCase_actionPerformed(ActionEvent e)\r
   {\r
-    SequenceGroup sg = ap.av.getSelectionGroup();\r
-    if(sg==null)\r
-      return;\r
-\r
-    for(int g=0; g<sg.getSize(true); g++)\r
-    {\r
-    ( (SequenceI)sg.getSequences(true).elementAt(g))\r
-        .changeCase(true, sg.getStartRes(), sg.getEndRes()+1);\r
-    }\r
-    ap.repaint();\r
+    changeCase(e.getSource());\r
   }\r
 \r
   public void lowerCase_actionPerformed(ActionEvent e)\r
   {\r
-    SequenceGroup sg = ap.av.getSelectionGroup();\r
-    if(sg==null)\r
-      return;\r
-\r
-    for(int g=0; g<sg.getSize(true); g++)\r
-    {\r
-       ( (SequenceI)sg.getSequences(true).elementAt(g))\r
-           .changeCase(false, sg.getStartRes(), sg.getEndRes()+1);\r
-    }\r
-    ap.repaint();\r
+    changeCase(e.getSource());\r
   }\r
 \r
   public void toggle_actionPerformed(ActionEvent e)\r
   {\r
-    SequenceGroup sg = ap.av.getSelectionGroup();\r
-    if (sg == null)\r
-      return;\r
+    changeCase(e.getSource());\r
+  }\r
 \r
-    for (int g = 0; g < sg.getSize(true); g++)\r
+  void changeCase(Object source)\r
+  {\r
+    SequenceGroup sg = ap.av.getSelectionGroup();\r
+    if (sg != null)\r
     {\r
-      ( (SequenceI)sg.getSequences(true).elementAt(g))\r
-          .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);\r
-    }\r
+      for (int g = 0; g < sg.getSize(true); g++)\r
+      {\r
+        int start = sg.getStartRes();\r
+        int end = sg.getEndRes() + 1;\r
+\r
+        do\r
+        {\r
+          if (ap.av.hasHiddenColumns)\r
+          {\r
+            end = ap.av.colSel.getHiddenBoundaryRight(start);\r
+            if (start == end)\r
+              end = sg.getEndRes() + 1;\r
+            if (end > sg.getEndRes())\r
+              end = sg.getEndRes() + 1;\r
+          }\r
+\r
+          if (source == toggle)\r
+            ( (SequenceI) sg.getSequences(true).elementAt(g))\r
+                .toggleCase(start, end);\r
+          else\r
+            ( (SequenceI) sg.getSequences(true).elementAt(g))\r
+                .changeCase(source == upperCase, start, end);\r
+\r
+          if (ap.av.hasHiddenColumns)\r
+          {\r
+            start = ap.av.colSel.adjustForHiddenColumns(end);\r
+            start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;\r
+          }\r
 \r
-    ap.repaint();\r
+        }\r
+        while (end < sg.getEndRes());\r
+      }\r
+      PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
+    }\r
   }\r
 \r
   public void outputText_actionPerformed(ActionEvent e)\r