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[jalview.git] / src / jalview / appletgui / APopupMenu.java

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index be4a599..e837ec8 100755 (executable)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.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
@@ -67,6 +67,8 @@ public class APopupMenu
 \r
   Sequence seq;\r
   MenuItem revealAll = new MenuItem();\r
+  MenuItem menuItem1 = new MenuItem();\r
+  Menu menu1 = new Menu();\r
 \r
   public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)\r
   {\r
@@ -89,11 +91,10 @@ public class APopupMenu
       e.printStackTrace();\r
     }\r
 \r
-    for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size()-1; i++)\r
+    for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)\r
     {\r
-      MenuItem item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.\r
-                                     elementAt(\r
-                                         i));\r
+      MenuItem item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i] );\r
+\r
       item.addActionListener(this);\r
       outputmenu.add(item);\r
     }\r
@@ -144,7 +145,6 @@ public class APopupMenu
         else\r
           url = link.substring(link.lastIndexOf("|")+1);\r
 \r
-        System.out.println("add "+url +" "+target);\r
            item.addActionListener(new java.awt.event.ActionListener()\r
            {\r
                public void actionPerformed(ActionEvent e)\r
@@ -198,7 +198,7 @@ public class APopupMenu
       helixColour_actionPerformed();\r
     else if(source==strandColour)\r
       strandColour_actionPerformed();\r
-    else if(source==clustalColour)\r
+    else if(source==turnColour)\r
       turnColour_actionPerformed();\r
     else if(source==buriedColour)\r
       buriedColour_actionPerformed();\r
@@ -227,7 +227,6 @@ public class APopupMenu
     else if(source == revealAll)\r
     {\r
         ap.av.showAllHiddenSeqs();\r
-        ap.repaint();\r
     }\r
 \r
     else if(source==copy)\r
@@ -235,22 +234,44 @@ public class APopupMenu
     else if(source==cut)\r
       ap.alignFrame.cut_actionPerformed();\r
     else if(source==toUpper || source==toLower || source==toggleCase)\r
-    {\r
+    {/*\r
       SequenceGroup sg = ap.av.getSelectionGroup();\r
       if (sg != null)\r
       {\r
         for (int g = 0; g < sg.getSize(true); g++)\r
         {\r
-          if (source == toggleCase)\r
-           ((SequenceI) sg.getSequences(true).elementAt(g))\r
-          .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);\r
-          else\r
-            ((SequenceI) sg.getSequences(true).elementAt(g))\r
-                .changeCase(source == toUpper, sg.getStartRes(),\r
-                                           sg.getEndRes() + 1);\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 == toggleCase)\r
+              ( (SequenceI) sg.getSequences(true).elementAt(g))\r
+                  .toggleCase(start, end);\r
+            else\r
+              ( (SequenceI) sg.getSequences(true).elementAt(g))\r
+                  .changeCase(source == toUpper, 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
         ap.seqPanel.seqCanvas.repaint();\r
-      }\r
+      }*/\r
     }\r
     else\r
       outputText(evt);\r
@@ -259,7 +280,7 @@ public class APopupMenu
 \r
   void outputText(ActionEvent e)\r
   {\r
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);\r
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);\r
     Vector vseqs = new Vector();\r
 \r
       String [] selection = ap.av.getViewAsString(true);\r
@@ -328,19 +349,16 @@ public class APopupMenu
     hideSeqs.setLabel("Hide Sequences");\r
     repGroup.setLabel("Represent Group with");\r
     revealAll.setLabel("Reveal All");\r
-\r
+    menuItem1.setLabel("Create Sequence Feature");\r
+    menu1.setLabel("Group");\r
     add(groupMenu);\r
     this.add(seqMenu);\r
     this.add(hideSeqs);\r
     this.add(revealAll);\r
     groupMenu.add(editMenu);\r
     groupMenu.add(outputmenu);\r
-    groupMenu.addSeparator();\r
-    groupMenu.add(unGroupMenuItem);\r
-    groupMenu.add(colourMenu);\r
-    groupMenu.add(showBoxes);\r
-    groupMenu.add(showText);\r
-    groupMenu.add(showColourText);\r
+    groupMenu.add(menuItem1);\r
+    groupMenu.add(menu1);\r
     colourMenu.add(noColourmenuItem);\r
     colourMenu.add(clustalColour);\r
     colourMenu.add(BLOSUM62Colour);\r
@@ -398,6 +416,11 @@ public class APopupMenu
     editMenu.add(toggleCase);\r
     seqMenu.add(pdb);\r
     seqMenu.add(repGroup);\r
+    menu1.add(unGroupMenuItem);\r
+    menu1.add(colourMenu);\r
+    menu1.add(showBoxes);\r
+    menu1.add(showText);\r
+    menu1.add(showColourText);\r
     toggleCase.addActionListener(this);\r
     pdb.addActionListener(this);\r
     hideSeqs.addActionListener(this);\r
@@ -600,28 +623,32 @@ public class APopupMenu
     SequenceGroup sg = ap.av.getSelectionGroup();\r
     if(sg==null || sg.getSize(false)<1)\r
     {\r
-      ap.av.hideSequence(seq);\r
+      ap.av.hideSequence(new SequenceI[]{seq});\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
+      for(int i=0; i<gsize; i++)\r
       {\r
-        if(representGroup && sg.getSequenceAt(index)!=seq)\r
+        if(representGroup && sg.getSequenceAt(i)!=seq)\r
         {\r
-          seq.addHiddenSequence(sg.getSequenceAt(index));\r
-          ap.av.hideSequence(sg.getSequenceAt(index));\r
+          seq.addHiddenSequence(sg.getSequenceAt(i));\r
+          hseqs[index++] = sg.getSequenceAt(i);\r
         }\r
         else if(!representGroup)\r
         {\r
-          ap.av.hideSequence(sg.getSequenceAt(index));\r
+          hseqs[index++] = sg.getSequenceAt(i);\r
         }\r
-        index ++;\r
-      }\r
+        }\r
+\r
+      ap.av.hideSequence(hseqs);\r
 \r
       ap.av.setSelectionGroup(null);\r
-      ap.repaint();\r
-      refresh();\r
     }\r
 \r
 }\r