Multiple Views

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 9764f4a..356e5d5 100755 (executable)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -115,11 +115,10 @@ public class PopupMenu extends JPopupMenu
         colours.add(PIDColour);\r
         colours.add(BLOSUM62Colour);\r
 \r
-        for (int i = 0; i < jalview.io.FormatAdapter.formats.size()-2; i++)\r
+        for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)\r
         {\r
-          JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
-                                         elementAt(\r
-                                             i));\r
+          JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );\r
+\r
           item.addActionListener(new java.awt.event.ActionListener()\r
           {\r
             public void actionPerformed(ActionEvent e)\r
@@ -207,7 +206,6 @@ public class PopupMenu extends JPopupMenu
                 public void actionPerformed(ActionEvent e)\r
                 {\r
                   ap.av.showSequence(index);\r
-                  ap.repaint();\r
                   if (ap.overviewPanel != null)\r
                     ap.overviewPanel.updateOverviewImage();\r
                 }\r
@@ -221,10 +219,9 @@ public class PopupMenu extends JPopupMenu
                   public void actionPerformed(ActionEvent e)\r
                   {\r
                     ap.av.showAllHiddenSeqs();\r
-                    ap.repaint();\r
                     if (ap.overviewPanel != null)\r
                       ap.overviewPanel.updateOverviewImage();\r
-                      }\r
+                    }\r
                 });\r
 \r
             add(menuItem);\r
@@ -691,7 +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
@@ -1129,28 +1126,33 @@ 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
-        ap.repaint();\r
-        refresh();\r
     }\r
 \r
   public void copy_actionPerformed(ActionEvent e)\r
@@ -1165,45 +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
-    ap.repaint();\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
+        }\r
+        while (end < sg.getEndRes());\r
+      }\r
+      PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
+    }\r
   }\r
 \r
   public void outputText_actionPerformed(ActionEvent e)\r