RepresentGroup count items
[jalview.git] / src / jalview / appletgui / APopupMenu.java
index 858770a..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
@@ -28,7 +28,7 @@ import jalview.datamodel.*;
 import jalview.schemes.*;\r
 \r
 public class APopupMenu\r
-    extends java.awt.PopupMenu\r
+    extends java.awt.PopupMenu implements ActionListener, ItemListener\r
 {\r
   Menu groupMenu = new Menu();\r
   protected MenuItem clustalColour = new MenuItem();\r
@@ -46,15 +46,29 @@ public class APopupMenu
   MenuItem noColourmenuItem = new MenuItem();\r
   protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
 \r
-  AlignmentPanel ap;\r
+  final AlignmentPanel ap;\r
   MenuItem unGroupMenuItem = new MenuItem();\r
   MenuItem nucleotideMenuItem = new MenuItem();\r
   Menu colourMenu = new Menu();\r
   CheckboxMenuItem showBoxes = new CheckboxMenuItem();\r
   CheckboxMenuItem showText = new CheckboxMenuItem();\r
   CheckboxMenuItem showColourText = new CheckboxMenuItem();\r
-\r
-  public APopupMenu(AlignmentPanel ap, Sequence seq, Vector links)\r
+  Menu editMenu = new Menu("Edit");\r
+  MenuItem copy = new MenuItem("Copy (Jalview Only)");\r
+  MenuItem cut = new MenuItem("Cut (Jalview Only)");\r
+  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
     ///////////////////////////////////////////////////////////\r
     // If this is activated from the sequence panel, the user may want to\r
@@ -63,7 +77,8 @@ public class APopupMenu
     // If from the IDPanel, we must display the sequence menu\r
     //////////////////////////////////////////////////////////\r
 \r
-    this.ap = ap;\r
+    this.ap = apanel;\r
+    this.seq = seq;\r
 \r
     try\r
     {\r
@@ -74,20 +89,34 @@ 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
-    if (sg != null)\r
+\r
+    if (sg != null && sg.getSize(false)>0)\r
     {\r
       showText.setState(sg.getDisplayText());\r
       showColourText.setState(sg.getColourText());\r
       showBoxes.setState(sg.getDisplayBoxes());\r
-    }\r
+      if (!ap.av.alignment.getGroups().contains(sg))\r
+      {\r
+        groupMenu.remove(unGroupMenuItem);\r
+      }\r
 \r
-    if (!ap.av.alignment.getGroups().contains(sg))\r
+    }\r
+    else\r
     {\r
-      groupMenu.remove(unGroupMenuItem);\r
+      remove(hideSeqs);\r
+      remove(groupMenu);\r
     }\r
 \r
-    if (seq != null && links!=null)\r
+    if (links!=null)\r
     {\r
       Menu linkMenu = new Menu("Link");\r
       MenuItem item;\r
@@ -97,92 +126,238 @@ public class APopupMenu
         link = links.elementAt(i).toString();\r
         final String target = link.substring(0, link.indexOf("|"));\r
         item = new MenuItem(target);\r
-        final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))\r
-               + seq.getName() +\r
-               link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
 \r
+        final String url;\r
+\r
+        if (link.indexOf("$SEQUENCE_ID$") > -1)\r
+        {\r
+          String id = seq.getName();\r
+          if (id.indexOf("|") > -1)\r
+            id = id.substring(id.lastIndexOf("|") + 1);\r
+\r
+          url = link.substring(link.indexOf("|") + 1,\r
+                               link.indexOf("$SEQUENCE_ID$"))\r
+              + id +\r
+              link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
+        }\r
+        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
                {\r
-                  jalview.bin.JalviewLite.showURL(url, target);\r
+                  ap.alignFrame.showURL(url, target);\r
                }\r
            });\r
           linkMenu.add(item);\r
       }\r
-      add(linkMenu);\r
+      if(seq!=null)\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
-  private void jbInit()\r
-      throws Exception\r
+  public void itemStateChanged(ItemEvent evt)\r
   {\r
-    groupMenu.setLabel("Group");\r
-    groupMenu.setLabel("Define");\r
+    if(evt.getSource()==abovePIDColour)\r
+      abovePIDColour_itemStateChanged();\r
+    else if(evt.getSource()==showColourText)\r
+      showColourText_itemStateChanged();\r
+    else if(evt.getSource()==showText)\r
+      showText_itemStateChanged();\r
+    else if(evt.getSource()==showBoxes)\r
+       showBoxes_itemStateChanged()   ;\r
+  }\r
 \r
-    unGroupMenuItem.setLabel("Remove Group");\r
-    unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+  public void actionPerformed(ActionEvent evt)\r
+  {\r
+    Object source = evt.getSource();\r
+    if(source==clustalColour)\r
+      clustalColour_actionPerformed();\r
+    else if(source==zappoColour)\r
+      zappoColour_actionPerformed();\r
+    else if(source==taylorColour)\r
+      taylorColour_actionPerformed();\r
+    else if(source==hydrophobicityColour)\r
+      hydrophobicityColour_actionPerformed();\r
+    else if(source==helixColour)\r
+      helixColour_actionPerformed();\r
+    else if(source==strandColour)\r
+      strandColour_actionPerformed();\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
+      BLOSUM62Colour_actionPerformed();\r
+    else if (source == noColourmenuItem)\r
+      noColourmenuItem_actionPerformed();\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
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        unGroupMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
+        ap.av.showAllHiddenSeqs();\r
+    }\r
 \r
-    nucleotideMenuItem.setLabel("Nucleotide");\r
-    nucleotideMenuItem.addActionListener(new ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        nucleotideMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    conservationMenuItem.addItemListener(new ItemListener()\r
+    else if(source==copy)\r
+      ap.alignFrame.copy_actionPerformed();\r
+    else if(source==cut)\r
+      ap.alignFrame.cut_actionPerformed();\r
+    else if(source==toUpper || source==toLower || source==toggleCase)\r
     {\r
-      public void itemStateChanged(ItemEvent itemEvent)\r
+      SequenceGroup sg = ap.av.getSelectionGroup();\r
+      if (sg != null)\r
       {\r
-        conservationMenuItem_itemStateChanged(itemEvent);\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 == 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
-    abovePIDColour.addItemListener(new ItemListener()\r
-    {\r
-      public void itemStateChanged(ItemEvent itemEvent)\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
-        abovePIDColour_itemStateChanged(itemEvent);\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
+\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()\r
+  {\r
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);\r
+    cap.setText("Paste your PDB file here.");\r
+    cap.setPDBImport(seq);\r
+    Frame frame = new Frame();\r
+    frame.add(cap);\r
+    jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);\r
+  }\r
+\r
+  private void jbInit()\r
+      throws Exception\r
+  {\r
+    groupMenu.setLabel("Group");\r
+    groupMenu.setLabel("Selection");\r
+\r
+    unGroupMenuItem.setLabel("Remove Group");\r
+    unGroupMenuItem.addActionListener(this);\r
+\r
+    nucleotideMenuItem.setLabel("Nucleotide");\r
+    nucleotideMenuItem.addActionListener(this);\r
+    conservationMenuItem.addItemListener(this);\r
+    abovePIDColour.addItemListener(this);\r
     colourMenu.setLabel("Group Colour");\r
     showBoxes.setLabel("Boxes");\r
     showBoxes.setState(true);\r
-    showBoxes.addItemListener(new ItemListener()\r
-    {\r
-      public void itemStateChanged(ItemEvent itemEvent)\r
-      {\r
-        showBoxes_itemStateChanged(itemEvent);\r
-      }\r
-    });\r
+    showBoxes.addItemListener(this);\r
 \r
     showText.setLabel("Text");\r
-    showText.addItemListener(new ItemListener()\r
-    {\r
-      public void itemStateChanged(ItemEvent itemEvent)\r
-      {\r
-        showText_itemStateChanged(itemEvent);\r
-      }\r
-    });\r
+    showText.addItemListener(this);\r
     showColourText.setLabel("Colour Text");\r
-    showColourText.addItemListener(new ItemListener()\r
-    {\r
-      public void itemStateChanged(ItemEvent itemEvent)\r
-      {\r
-        showColourText_itemStateChanged(itemEvent);\r
-      }\r
-    });\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
@@ -204,292 +379,204 @@ public class APopupMenu
     colourMenu.add(conservationMenuItem);\r
 \r
     noColourmenuItem.setLabel("None");\r
-    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        noColourmenuItem_actionPerformed(e);\r
-      }\r
-    });\r
+    noColourmenuItem.addActionListener(this);\r
 \r
     clustalColour.setLabel("Clustalx colours");\r
-    clustalColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        clustalColour_actionPerformed(e);\r
-      }\r
-    });\r
+    clustalColour.addActionListener(this);\r
     zappoColour.setLabel("Zappo");\r
-    zappoColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        zappoColour_actionPerformed(e);\r
-      }\r
-    });\r
+    zappoColour.addActionListener(this);\r
     taylorColour.setLabel("Taylor");\r
-    taylorColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        taylorColour_actionPerformed(e);\r
-      }\r
-    });\r
+    taylorColour.addActionListener(this);\r
     hydrophobicityColour.setLabel("Hydrophobicity");\r
-    hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        hydrophobicityColour_actionPerformed(e);\r
-      }\r
-    });\r
+    hydrophobicityColour.addActionListener(this);\r
     helixColour.setLabel("Helix propensity");\r
-    helixColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        helixColour_actionPerformed(e);\r
-      }\r
-    });\r
+    helixColour.addActionListener(this);\r
     strandColour.setLabel("Strand propensity");\r
-    strandColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        strandColour_actionPerformed(e);\r
-      }\r
-    });\r
+    strandColour.addActionListener(this);\r
     turnColour.setLabel("Turn propensity");\r
-    turnColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        turnColour_actionPerformed(e);\r
-      }\r
-    });\r
+    turnColour.addActionListener(this);\r
     buriedColour.setLabel("Buried Index");\r
-    buriedColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        buriedColour_actionPerformed(e);\r
-      }\r
-    });\r
+    buriedColour.addActionListener(this);\r
     abovePIDColour.setLabel("Above % Identity");\r
 \r
     userDefinedColour.setLabel("User Defined");\r
-    userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        userDefinedColour_actionPerformed(e);\r
-      }\r
-    });\r
+    userDefinedColour.addActionListener(this);\r
     PIDColour.setLabel("Percentage Identity");\r
-    PIDColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        PIDColour_actionPerformed(e);\r
-      }\r
-    });\r
+    PIDColour.addActionListener(this);\r
     BLOSUM62Colour.setLabel("BLOSUM62");\r
-    BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        BLOSUM62Colour_actionPerformed(e);\r
-      }\r
-    });\r
+    BLOSUM62Colour.addActionListener(this);\r
     conservationMenuItem.setLabel("Conservation");\r
 \r
+    editMenu.add(copy);\r
+    copy.addActionListener(this);\r
+    editMenu.add(cut);\r
+    cut.addActionListener(this);\r
+    editMenu.add(toUpper);\r
+    toUpper.addActionListener(this);\r
+    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
   void refresh()\r
   {\r
-    SequenceGroup sg = getGroup();\r
-    if(sg!=null)\r
-    {\r
-      SuperGroup superG = ap.av.alignment.getSuperGroup(sg);\r
-\r
-      if (superG != null)\r
-      {\r
-        superG.setSuperGroupProperties(sg);\r
-      }\r
-        }\r
     ap.seqPanel.seqCanvas.repaint();\r
+    if(ap.overviewPanel!=null)\r
+      ap.overviewPanel.updateOverviewImage();\r
   }\r
 \r
-  protected void clustalColour_actionPerformed(ActionEvent e)\r
+  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
-  protected void zappoColour_actionPerformed(ActionEvent e)\r
+  protected void zappoColour_actionPerformed()\r
   {\r
     getGroup().cs = new ZappoColourScheme();\r
     refresh();\r
   }\r
 \r
-  protected void taylorColour_actionPerformed(ActionEvent e)\r
+  protected void taylorColour_actionPerformed()\r
   {\r
     getGroup().cs = new TaylorColourScheme();\r
     refresh();\r
   }\r
 \r
-  protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
+  protected void hydrophobicityColour_actionPerformed()\r
   {\r
     getGroup().cs = new HydrophobicColourScheme();\r
     refresh();\r
   }\r
 \r
-  protected void helixColour_actionPerformed(ActionEvent e)\r
+  protected void helixColour_actionPerformed()\r
   {\r
     getGroup().cs = new HelixColourScheme();\r
     refresh();\r
   }\r
 \r
-  protected void strandColour_actionPerformed(ActionEvent e)\r
+  protected void strandColour_actionPerformed()\r
   {\r
     getGroup().cs = new StrandColourScheme();\r
     refresh();\r
   }\r
 \r
-  protected void turnColour_actionPerformed(ActionEvent e)\r
+  protected void turnColour_actionPerformed()\r
   {\r
     getGroup().cs = new TurnColourScheme();\r
     refresh();\r
   }\r
 \r
-  protected void buriedColour_actionPerformed(ActionEvent e)\r
+  protected void buriedColour_actionPerformed()\r
   {\r
     getGroup().cs = new BuriedColourScheme();\r
     refresh();\r
   }\r
 \r
-  public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
+  public void nucleotideMenuItem_actionPerformed()\r
   {\r
     getGroup().cs = new NucleotideColourScheme();\r
     refresh();\r
   }\r
 \r
-  protected void abovePIDColour_itemStateChanged(ItemEvent ie)\r
+  protected void abovePIDColour_itemStateChanged()\r
   {\r
     SequenceGroup sg = getGroup();\r
+    if(sg.cs==null)\r
+          return;\r
+\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
-      if (sg.cs instanceof ResidueColourScheme)\r
-      {\r
-        ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
-      }\r
-      else if (sg.cs instanceof ScoreColourScheme)\r
-      {\r
-        ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
-      }\r
+\r
+      sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
 \r
       SliderPanel.showPIDSlider();\r
 \r
     }\r
     else // remove PIDColouring\r
     {\r
-      ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;\r
-      rcs.setThreshold(0);\r
-      sg.cs = rcs;\r
+      sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
     }\r
 \r
     refresh();\r
 \r
   }\r
 \r
-  protected void userDefinedColour_actionPerformed(ActionEvent e)\r
+  protected void userDefinedColour_actionPerformed()\r
   {\r
     new UserDefinedColours(ap, getGroup());\r
   }\r
 \r
-  protected void PIDColour_actionPerformed(ActionEvent e)\r
+  protected void PIDColour_actionPerformed()\r
   {\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
 \r
-  protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
+  protected void BLOSUM62Colour_actionPerformed()\r
   {\r
     SequenceGroup sg = getGroup();\r
 \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
   }\r
 \r
-  protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
+  protected void noColourmenuItem_actionPerformed()\r
   {\r
     getGroup().cs = null;\r
     refresh();\r
   }\r
 \r
-  protected void conservationMenuItem_itemStateChanged(ItemEvent ie)\r
+  protected void conservationMenuItem_itemStateChanged()\r
   {\r
     SequenceGroup sg = getGroup();\r
+    if(sg.cs==null)\r
+          return;\r
 \r
     if (conservationMenuItem.getState())\r
     {\r
 \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
       c.verdict(false, ap.av.ConsPercGaps);\r
-      ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 \r
-      sg.cs = ccs;\r
+      sg.cs.setConservation(c);\r
 \r
-      SliderPanel.setConservationSlider(ap, ccs, sg.getName());\r
+      SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
       SliderPanel.showConservationSlider();\r
     }\r
     else // remove ConservationColouring\r
     {\r
-      ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;\r
-      sg.cs = ccs.cs;\r
+      sg.cs.setConservation(null);\r
     }\r
 \r
     refresh();\r
   }\r
 \r
-  protected void analyze_actionPerformed(ActionEvent e)\r
-  {\r
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
-    Frame frame = new Frame();\r
-    frame.add(cap);\r
-    jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300);\r
-    SequenceGroup sg = getGroup();\r
-    StringBuffer sb = new StringBuffer();\r
-\r
-    for (int i = 0; i < sg.sequences.size(); i++)\r
-    {\r
-      Sequence tmp = (Sequence) sg.sequences.elementAt(i);\r
-      sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
-      sb.append("\n");\r
-    }\r
-\r
-    sb.append("Something amazing will happen soon");\r
-    cap.setText(sb.toString());\r
-\r
-  }\r
 \r
   SequenceGroup getGroup()\r
   {\r
@@ -502,7 +589,7 @@ public class APopupMenu
     return sg;\r
   }\r
 \r
-  void unGroupMenuItem_actionPerformed(ActionEvent e)\r
+  void unGroupMenuItem_actionPerformed()\r
   {\r
     SequenceGroup sg = ap.av.getSelectionGroup();\r
     ap.av.alignment.deleteGroup(sg);\r
@@ -510,22 +597,55 @@ public class APopupMenu
     ap.repaint();\r
   }\r
 \r
-  public void showColourText_itemStateChanged(ItemEvent itemEvent)\r
+  public void showColourText_itemStateChanged()\r
   {\r
     getGroup().setColourText(showColourText.getState());\r
     refresh();\r
   }\r
 \r
-  public void showText_itemStateChanged(ItemEvent itemEvent)\r
+  public void showText_itemStateChanged()\r
   {\r
     getGroup().setDisplayText(showText.getState());\r
     refresh();\r
   }\r
 \r
-  public void showBoxes_itemStateChanged(ItemEvent itemEvent)\r
+  public void showBoxes_itemStateChanged()\r
   {\r
     getGroup().setDisplayBoxes(showBoxes.getState());\r
     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