RepresentGroup count items
[jalview.git] / src / jalview / appletgui / APopupMenu.java
index 1c9b3cd..dca9da4 100755 (executable)
@@ -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
@@ -59,6 +59,14 @@ public class APopupMenu
   MenuItem toUpper = new MenuItem("To Upper Case");\r
   MenuItem toLower = new MenuItem("To Lower Case");\r
   MenuItem toggleCase = new MenuItem("Toggle Case");\r
+  Menu outputmenu = new Menu();\r
+  Menu seqMenu = new Menu();\r
+  MenuItem pdb = new MenuItem();\r
+  MenuItem hideSeqs = new MenuItem();\r
+  MenuItem repGroup = new MenuItem();\r
+\r
+  Sequence seq;\r
+  MenuItem revealAll = new MenuItem();\r
 \r
   public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)\r
   {\r
@@ -70,6 +78,7 @@ public class APopupMenu
     //////////////////////////////////////////////////////////\r
 \r
     this.ap = apanel;\r
+    this.seq = seq;\r
 \r
     try\r
     {\r
@@ -80,9 +89,17 @@ public class APopupMenu
       e.printStackTrace();\r
     }\r
 \r
+    for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)\r
+    {\r
+      MenuItem item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i] );\r
+\r
+      item.addActionListener(this);\r
+      outputmenu.add(item);\r
+    }\r
+\r
     SequenceGroup sg = ap.av.getSelectionGroup();\r
 \r
-    if (sg != null && sg.getSize()>0)\r
+    if (sg != null && sg.getSize(false)>0)\r
     {\r
       showText.setState(sg.getDisplayText());\r
       showColourText.setState(sg.getColourText());\r
@@ -95,8 +112,8 @@ public class APopupMenu
     }\r
     else\r
     {\r
+      remove(hideSeqs);\r
       remove(groupMenu);\r
-      remove(editMenu);\r
     }\r
 \r
     if (links!=null)\r
@@ -126,6 +143,7 @@ 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
@@ -135,22 +153,21 @@ public class APopupMenu
            });\r
           linkMenu.add(item);\r
       }\r
-      add(linkMenu);\r
-\r
       if(seq!=null)\r
-      {\r
-        item = new MenuItem("Show PDB Structure");\r
-        item.addActionListener(new java.awt.event.ActionListener()\r
-        {\r
-          public void actionPerformed(ActionEvent e)\r
-          {\r
-            addPDB(seq);\r
-          }\r
-        });\r
-\r
-        add(item);\r
-      }\r
+        seqMenu.add(linkMenu);\r
+      else\r
+        add(linkMenu);\r
+    }\r
+    if(seq!=null)\r
+    {\r
+      seqMenu.setLabel(seq.getName());\r
+      repGroup.setLabel("Represent Group with " + seq.getName());\r
     }\r
+    else\r
+      remove(seqMenu);\r
+\r
+    if(!ap.av.hasHiddenRows)\r
+      remove(revealAll);\r
   }\r
 \r
   public void itemStateChanged(ItemEvent evt)\r
@@ -180,26 +197,37 @@ 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
     else if(source==nucleotideMenuItem)\r
       nucleotideMenuItem_actionPerformed();\r
 \r
-    else if(source==userDefinedColour)\r
-          userDefinedColour_actionPerformed();\r
-        else if(source==PIDColour)\r
-       PIDColour_actionPerformed();\r
-     else if(source==BLOSUM62Colour)\r
+    else if (source == userDefinedColour)\r
+      userDefinedColour_actionPerformed();\r
+    else if (source == PIDColour)\r
+      PIDColour_actionPerformed();\r
+    else if (source == BLOSUM62Colour)\r
       BLOSUM62Colour_actionPerformed();\r
-    else if(source==noColourmenuItem)\r
+    else if (source == noColourmenuItem)\r
       noColourmenuItem_actionPerformed();\r
-    else if(source==conservationMenuItem)\r
-        conservationMenuItem_itemStateChanged();\r
-      else if(source==unGroupMenuItem)\r
+    else if (source == conservationMenuItem)\r
+      conservationMenuItem_itemStateChanged();\r
+    else if (source == unGroupMenuItem)\r
       unGroupMenuItem_actionPerformed();\r
 \r
+    else if(source == pdb)\r
+      addPDB();\r
+    else if(source == hideSeqs)\r
+      hideSequences(false);\r
+    else if(source == repGroup)\r
+      hideSequences(true);\r
+    else if(source == revealAll)\r
+    {\r
+        ap.av.showAllHiddenSeqs();\r
+    }\r
+\r
     else if(source==copy)\r
       ap.alignFrame.copy_actionPerformed();\r
     else if(source==cut)\r
@@ -209,21 +237,80 @@ public class APopupMenu
       SequenceGroup sg = ap.av.getSelectionGroup();\r
       if (sg != null)\r
       {\r
-        for (int g = 0; g < sg.getSize(); g++)\r
+        for (int g = 0; g < sg.getSize(true); g++)\r
         {\r
-          if (source == toggleCase)\r
-            sg.getSequenceAt(g).toggleCase(sg.getStartRes(), sg.getEndRes() + 1);\r
-          else\r
-            sg.getSequenceAt(g).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
+    else\r
+      outputText(evt);\r
+\r
+  }\r
+\r
+  void outputText(ActionEvent e)\r
+  {\r
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);\r
+    Vector vseqs = new Vector();\r
+\r
+      String [] selection = ap.av.getViewAsString(true);\r
+      SequenceI [] seqs = ap.av.getSelectionAsNewSequence();\r
+      if (selection != null)\r
+      {\r
+        for (int i = 0; i < selection.length; i++)\r
+        {\r
+          Sequence seq = new Sequence(\r
+              seqs[i].getName(),\r
+              selection[i],\r
+              seqs[i].getStart(), seqs[i].getEnd());\r
+          seq.setDescription(seqs[i].getDescription());\r
+          vseqs.addElement( seq );\r
+      }\r
+    }\r
+\r
+    Frame frame = new Frame();\r
+    frame.add(cap);\r
+    jalview.bin.JalviewLite.addFrame(frame,\r
+                                     "Selection output - " + e.getActionCommand(),\r
+                                     600, 500);\r
+\r
+    cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(\r
+        e.getActionCommand(),\r
+        vseqs,\r
+        ap.av.showJVSuffix));\r
 \r
   }\r
 \r
-  void addPDB(Sequence seq)\r
+  void addPDB()\r
   {\r
     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);\r
     cap.setText("Paste your PDB file here.");\r
@@ -237,7 +324,7 @@ public class APopupMenu
       throws Exception\r
   {\r
     groupMenu.setLabel("Group");\r
-    groupMenu.setLabel("Define");\r
+    groupMenu.setLabel("Selection");\r
 \r
     unGroupMenuItem.setLabel("Remove Group");\r
     unGroupMenuItem.addActionListener(this);\r
@@ -255,11 +342,22 @@ public class APopupMenu
     showText.addItemListener(this);\r
     showColourText.setLabel("Colour Text");\r
     showColourText.addItemListener(this);\r
+    outputmenu.setLabel("Output to Textbox...");\r
+    seqMenu.setLabel("Sequence");\r
+    pdb.setLabel("View PDB Structure");\r
+    hideSeqs.setLabel("Hide Sequences");\r
+    repGroup.setLabel("Represent Group with");\r
+    revealAll.setLabel("Reveal All");\r
 \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.addSeparator();\r
     groupMenu.add(showBoxes);\r
     groupMenu.add(showText);\r
     groupMenu.add(showColourText);\r
@@ -309,7 +407,6 @@ public class APopupMenu
     BLOSUM62Colour.addActionListener(this);\r
     conservationMenuItem.setLabel("Conservation");\r
 \r
-    add(editMenu);\r
     editMenu.add(copy);\r
     copy.addActionListener(this);\r
     editMenu.add(cut);\r
@@ -319,7 +416,13 @@ public class APopupMenu
     editMenu.add(toLower);\r
     toLower.addActionListener(this);\r
     editMenu.add(toggleCase);\r
+    seqMenu.add(pdb);\r
+    seqMenu.add(repGroup);\r
     toggleCase.addActionListener(this);\r
+    pdb.addActionListener(this);\r
+    hideSeqs.addActionListener(this);\r
+    repGroup.addActionListener(this);\r
+    revealAll.addActionListener(this);\r
 \r
   }\r
 \r
@@ -333,7 +436,7 @@ public class APopupMenu
   protected void clustalColour_actionPerformed()\r
   {\r
     SequenceGroup sg = getGroup();\r
-    sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());\r
+    sg.cs = new ClustalxColourScheme(sg.getSequences(true), ap.av.alignment.getWidth());\r
     refresh();\r
   }\r
 \r
@@ -393,7 +496,7 @@ public class APopupMenu
 \r
     if (abovePIDColour.getState())\r
     {\r
-      sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+      sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
                                                ap.av.alignment.getWidth()));\r
       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
           getGroup().getName());\r
@@ -421,7 +524,7 @@ public class APopupMenu
   {\r
     SequenceGroup sg = getGroup();\r
     sg.cs = new PIDColourScheme();\r
-    sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
                                              ap.av.alignment.getWidth()));\r
     refresh();\r
   }\r
@@ -432,7 +535,7 @@ public class APopupMenu
 \r
     sg.cs = new Blosum62ColourScheme();\r
 \r
-    sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
                                              ap.av.alignment.getWidth()));\r
 \r
     refresh();\r
@@ -455,7 +558,7 @@ public class APopupMenu
 \r
       Conservation c = new Conservation("Group",\r
                                         ResidueProperties.propHash, 3,\r
-                                        sg.sequences, 0,\r
+                                        sg.getSequences(true), 0,\r
                                         ap.av.alignment.getWidth());\r
 \r
       c.calculate();\r
@@ -512,4 +615,37 @@ public class APopupMenu
     refresh();\r
   }\r
 \r
+  void hideSequences(boolean representGroup)\r
+  {\r
+    SequenceGroup sg = ap.av.getSelectionGroup();\r
+    if(sg==null || sg.getSize(false)<1)\r
+    {\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
+      for(int i=0; i<gsize; i++)\r
+      {\r
+        if(representGroup && sg.getSequenceAt(i)!=seq)\r
+        {\r
+          seq.addHiddenSequence(sg.getSequenceAt(i));\r
+          hseqs[index++] = sg.getSequenceAt(i);\r
+        }\r
+        else if(!representGroup)\r
+        {\r
+          hseqs[index++] = sg.getSequenceAt(index);\r
+        }\r
+        }\r
+\r
+      ap.av.hideSequence(hseqs);\r
+\r
+      ap.av.setSelectionGroup(null);\r
+    }\r
+\r
 }\r