X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=0226349aef00c59cbbf260bd5a96cfec91c765c6;hb=a3a196ed2104760ffeeebbca65fc03c361d29b17;hp=a932d66fc4ab8208f50bd23665e12cfd94ff18b8;hpb=6d6d6bc08bca95676a8175c634c03c163fb88684;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index a932d66..0226349 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -1,490 +1,999 @@
-package jalview.appletgui;
-
-import jalview.datamodel.*;
-import jalview.analysis.*;
-import jalview.schemes.*;
-import java.awt.*;
-import java.awt.event.*;
-
-public class APopupMenu extends java.awt.PopupMenu
-{
-  Menu groupMenu = new Menu();
-  protected MenuItem clustalColour = new MenuItem();
-  protected MenuItem zappoColour = new MenuItem();
-  protected MenuItem taylorColour = new MenuItem();
-  protected MenuItem hydrophobicityColour = new MenuItem();
-  protected MenuItem helixColour = new MenuItem();
-  protected MenuItem strandColour = new MenuItem();
-  protected MenuItem turnColour = new MenuItem();
-  protected MenuItem buriedColour = new MenuItem();
-  protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
-  protected MenuItem userDefinedColour = new MenuItem();
-  protected MenuItem PIDColour = new MenuItem();
-  protected MenuItem BLOSUM62Colour = new MenuItem();
-  MenuItem noColourmenuItem = new MenuItem();
-  protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
-
-
-  AlignmentPanel ap;
-  Menu sequenceMenu = new Menu();
-  MenuItem sequenceName = new MenuItem();
-  Sequence sequence;
-  MenuItem unGroupMenuItem = new MenuItem();
-  MenuItem nucleotideMenuItem = new MenuItem();
-  Menu colourMenu = new Menu();
-  CheckboxMenuItem showBoxes = new CheckboxMenuItem();
-  CheckboxMenuItem showText = new CheckboxMenuItem();
-  CheckboxMenuItem showColourText = new CheckboxMenuItem();
-
-  public APopupMenu(AlignmentPanel ap, Sequence seq)
-  {
-    ///////////////////////////////////////////////////////////
-    // If this is activated from the sequence panel, the user may want to
-    // edit or annotate a particular residue. Therefore display the residue menu
-    //
-    // If from the IDPanel, we must display the sequence menu
-    //////////////////////////////////////////////////////////
-
-    this.ap = ap;
-    sequence = seq;
-
-    try
-    {     jbInit();   }
-    catch(Exception e)
-    {    e.printStackTrace();    }
-
-
-    SequenceGroup sg = ap.av.getSelectionGroup();
-    if(sg!=null)
-    {
-      showText.setState(sg.getDisplayText());
-      showColourText.setState(sg.getColourText());
-      showBoxes.setState(sg.getDisplayBoxes());
-    }
-
-    if( !ap.av.alignment.getGroups().contains(sg))
-        groupMenu.remove(unGroupMenuItem);
-
-    if(seq==null)
-       remove(sequenceMenu);
-
-
-  }
-  private void jbInit() throws Exception
-  {
-    groupMenu.setLabel("Group");
-    groupMenu.setLabel("Define");
-
-    sequenceMenu.setLabel("Sequence");
-    sequenceName.setLabel("Edit name");
-    unGroupMenuItem.setLabel("Remove Group");
-    unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        unGroupMenuItem_actionPerformed(e);
-      }
-    });
-
-
-    nucleotideMenuItem.setLabel("Nucleotide");
-    nucleotideMenuItem.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        nucleotideMenuItem_actionPerformed(e);
-      }
-    });
-    conservationMenuItem.addItemListener(new ItemListener()
-    {
-      public void itemStateChanged(ItemEvent itemEvent)
-      {
-        conservationMenuItem_itemStateChanged(itemEvent);
-      }
-    });
-    abovePIDColour.addItemListener(new ItemListener()
-    {
-      public void itemStateChanged(ItemEvent itemEvent)
-      {
-        abovePIDColour_itemStateChanged(itemEvent);
-      }
-    });
-    colourMenu.setLabel("Group Colour");
-    showBoxes.setLabel("Boxes");
-    showBoxes.setState(true);
-    showBoxes.addItemListener(new ItemListener()
-    {
-      public void itemStateChanged(ItemEvent itemEvent)
-      {
-        showBoxes_itemStateChanged(itemEvent);
-      }
-    });
-
-    showText.setLabel("Text");
-    showText.addItemListener(new ItemListener()
-    {
-      public void itemStateChanged(ItemEvent itemEvent)
-      {
-        showText_itemStateChanged(itemEvent);
-      }
-    });
-    showColourText.setLabel("Colour Text");
-    showColourText.addItemListener(new ItemListener()
-    {
-      public void itemStateChanged(ItemEvent itemEvent)
-      {
-        showColourText_itemStateChanged(itemEvent);
-      }
-    });
-
-    add(groupMenu);
-    this.add(sequenceMenu);
-    groupMenu.add(unGroupMenuItem);
-    groupMenu.add(colourMenu);
-    groupMenu.addSeparator();
-    groupMenu.add(showBoxes);
-    groupMenu.add(showText);
-    groupMenu.add(showColourText);
-    sequenceMenu.add(sequenceName);
-    colourMenu.add(noColourmenuItem);
-    colourMenu.add(clustalColour);
-    colourMenu.add(BLOSUM62Colour);
-    colourMenu.add(PIDColour);
-    colourMenu.add(zappoColour);
-    colourMenu.add(taylorColour);
-    colourMenu.add(hydrophobicityColour);
-    colourMenu.add(helixColour);
-    colourMenu.add(strandColour);
-    colourMenu.add(turnColour);
-    colourMenu.add(buriedColour);
-    colourMenu.add(nucleotideMenuItem);
-    colourMenu.add(userDefinedColour);
-    colourMenu.addSeparator();
-    colourMenu.add(abovePIDColour);
-    colourMenu.add(conservationMenuItem);
-
-    noColourmenuItem.setLabel("None");
-    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        noColourmenuItem_actionPerformed(e);
-      }
-    });
-
-    clustalColour.setLabel("Clustalx colours");
-    clustalColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        clustalColour_actionPerformed(e);
-      }
-    });
-    zappoColour.setLabel("Zappo");
-    zappoColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        zappoColour_actionPerformed(e);
-      }
-    });
-    taylorColour.setLabel("Taylor");
-    taylorColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        taylorColour_actionPerformed(e);
-      }
-    });
-    hydrophobicityColour.setLabel("Hydrophobicity");
-    hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        hydrophobicityColour_actionPerformed(e);
-      }
-    });
-    helixColour.setLabel("Helix propensity");
-    helixColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        helixColour_actionPerformed(e);
-      }
-    });
-    strandColour.setLabel("Strand propensity");
-    strandColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        strandColour_actionPerformed(e);
-      }
-    });
-    turnColour.setLabel("Turn propensity");
-    turnColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        turnColour_actionPerformed(e);
-      }
-    });
-    buriedColour.setLabel("Buried Index");
-    buriedColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        buriedColour_actionPerformed(e);
-      }
-    });
-    abovePIDColour.setLabel("Above % Identity");
-
-    userDefinedColour.setLabel("User Defined");
-    userDefinedColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        userDefinedColour_actionPerformed(e);
-      }
-    });
-    PIDColour.setLabel("Percentage Identity");
-    PIDColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        PIDColour_actionPerformed(e);
-      }
-    });
-    BLOSUM62Colour.setLabel("BLOSUM62");
-    BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        BLOSUM62Colour_actionPerformed(e);
-      }
-    });
-    conservationMenuItem.setLabel("Conservation");
-
-
-  }
-
-  void refresh()
-  {
-    SequenceGroup sg = getGroup();
-    SuperGroup superG = ap.av.alignment.getSuperGroup( sg );
-    if( superG !=null)
-      superG.setSuperGroupProperties( sg );
-
-    ap.seqPanel.seqCanvas.repaint();
-  }
-
-  protected void clustalColour_actionPerformed(ActionEvent e)
-  {
-    SequenceGroup sg = getGroup();
-    sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());
-    refresh();
-  }
-
-  protected void zappoColour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new ZappoColourScheme();
-    refresh();
-  }
-
-  protected void taylorColour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new TaylorColourScheme();
-    refresh();
-  }
-
-
-  protected void hydrophobicityColour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new HydrophobicColourScheme();
-    refresh();
-  }
-
-  protected void helixColour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new HelixColourScheme();
-    refresh();
-  }
-
-  protected void strandColour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new StrandColourScheme();
-    refresh();
-  }
-
-  protected void turnColour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new TurnColourScheme();
-    refresh();
-  }
-
-  protected void buriedColour_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new BuriedColourScheme();
-    refresh();
-  }
-
-  public void nucleotideMenuItem_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = new NucleotideColourScheme();
-    refresh();
-  }
-
-
-
-  protected void abovePIDColour_itemStateChanged(ItemEvent ie)
-  {
-    SequenceGroup sg = getGroup();
-    if (abovePIDColour.getState())
-    {
-      sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-                                               ap.av.alignment.getWidth()));
-      int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
-      if (sg.cs instanceof ResidueColourScheme)
-        ( (ResidueColourScheme)sg. cs).setThreshold(threshold);
-      else if (sg.cs instanceof ScoreColourScheme)
-        ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
-
-      SliderPanel.showPIDSlider();
-
-
-    }
-    else // remove PIDColouring
-    {
-      ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;
-      rcs.setThreshold(0);
-      sg.cs = rcs;
-    }
-
-    refresh();
-
-  }
-
-
-  protected void userDefinedColour_actionPerformed(ActionEvent e)
-  {
-    new UserDefinedColours( ap, getGroup());
-  }
-
-  protected void PIDColour_actionPerformed(ActionEvent e)
-  {
-    SequenceGroup sg = getGroup();
-    sg.cs = new PIDColourScheme();
-    sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-                                               ap.av.alignment.getWidth()));
-    refresh();
-  }
-
-  protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
-  {
-    SequenceGroup sg = getGroup();
-
-    sg.cs = new Blosum62ColourScheme();
-
-    sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-                                               ap.av.alignment.getWidth()));
-
-    refresh();
-  }
-
-
-  protected void noColourmenuItem_actionPerformed(ActionEvent e)
-  {
-    getGroup().cs = null;
-    refresh();
-  }
-
-  protected  void conservationMenuItem_itemStateChanged(ItemEvent ie)
-  {
-    SequenceGroup sg = getGroup();
-
-    if(conservationMenuItem.getState())
-    {
-
-        Conservation c = new Conservation("Group",
-                                          ResidueProperties.propHash, 3,
-                                          sg.sequences, 0,
-                                          ap.av.alignment.getWidth());
-
-        c.calculate();
-        c.verdict(false, ap.av.ConsPercGaps);
-        ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
-
-
-      sg.cs = ccs;
-
-      SliderPanel.setConservationSlider(ap, ccs, sg.getName());
-      SliderPanel.showConservationSlider();
-    }
-    else // remove ConservationColouring
-    {
-        ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
-        sg.cs = ccs.cs;
-    }
-
-     refresh();
-  }
-
-
-  protected void analyze_actionPerformed(ActionEvent e)
-  {
-     CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
-     Frame frame = new Frame();
-     frame.add(cap);
-     jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300);
-     SequenceGroup sg = getGroup();
-     StringBuffer sb = new StringBuffer();
-
-     for(int i=0; i<sg.sequences.size(); i++)
-     {
-       Sequence tmp = (Sequence)sg.sequences.elementAt(i);
-       sb.append(  tmp.getSequence(sg.getStartRes(), sg.getEndRes()+1));
-       sb.append("\n");
-     }
-
-     sb.append("Something amazing will happen soon");
-     cap.setText( sb.toString() );
-
-  }
-
-  SequenceGroup getGroup()
-  {
-    SequenceGroup sg = ap.av.getSelectionGroup();
-
-    // this method won't add a new group if it already exists
-    ap.av.alignment.addGroup(sg);
-
-    return sg;
-  }
-
-  void unGroupMenuItem_actionPerformed(ActionEvent e)
-  {
-     SequenceGroup sg = ap.av.getSelectionGroup();
-     ap.av.alignment.deleteGroup(sg);
-     ap.av.setSelectionGroup(null);
-     ap.repaint();
-  }
-
-
-  public void showColourText_itemStateChanged(ItemEvent itemEvent)
-  {
-    getGroup().setColourText(showColourText.getState());
-    refresh();
-  }
-
-  public void showText_itemStateChanged(ItemEvent itemEvent)
-  {
-    getGroup().setDisplayText(showText.getState());
-    refresh();
-  }
-
-  public void showBoxes_itemStateChanged(ItemEvent itemEvent)
-  {
-    getGroup().setDisplayBoxes(showBoxes.getState());
-    refresh();
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.0.b2)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.appletgui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import jalview.analysis.*;
+import jalview.commands.*;
+import jalview.datamodel.*;
+import jalview.schemes.*;
+import jalview.util.UrlLink;
+import jalview.io.AppletFormatAdapter;
+
+public class APopupMenu extends java.awt.PopupMenu implements
+        ActionListener, ItemListener
+{
+  Menu groupMenu = new Menu();
+
+  MenuItem editGroupName = new MenuItem();
+
+  protected MenuItem clustalColour = new MenuItem();
+
+  protected MenuItem zappoColour = new MenuItem();
+
+  protected MenuItem taylorColour = new MenuItem();
+
+  protected MenuItem hydrophobicityColour = new MenuItem();
+
+  protected MenuItem helixColour = new MenuItem();
+
+  protected MenuItem strandColour = new MenuItem();
+
+  protected MenuItem turnColour = new MenuItem();
+
+  protected MenuItem buriedColour = new MenuItem();
+
+  protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
+
+  protected MenuItem userDefinedColour = new MenuItem();
+
+  protected MenuItem PIDColour = new MenuItem();
+
+  protected MenuItem BLOSUM62Colour = new MenuItem();
+
+  MenuItem noColourmenuItem = new MenuItem();
+
+  protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
+
+  final AlignmentPanel ap;
+
+  MenuItem unGroupMenuItem = new MenuItem();
+
+  MenuItem nucleotideMenuItem = new MenuItem();
+
+  Menu colourMenu = new Menu();
+
+  CheckboxMenuItem showBoxes = new CheckboxMenuItem();
+
+  CheckboxMenuItem showText = new CheckboxMenuItem();
+
+  CheckboxMenuItem showColourText = new CheckboxMenuItem();
+
+  Menu editMenu = new Menu("Edit");
+
+  MenuItem copy = new MenuItem("Copy (Jalview Only)");
+
+  MenuItem cut = new MenuItem("Cut (Jalview Only)");
+
+  MenuItem toUpper = new MenuItem("To Upper Case");
+
+  MenuItem toLower = new MenuItem("To Lower Case");
+
+  MenuItem toggleCase = new MenuItem("Toggle Case");
+
+  Menu outputmenu = new Menu();
+
+  Menu seqMenu = new Menu();
+
+  MenuItem pdb = new MenuItem();
+
+  MenuItem hideSeqs = new MenuItem();
+
+  MenuItem repGroup = new MenuItem();
+
+  MenuItem sequenceName = new MenuItem("Edit Name/Description");
+
+  MenuItem sequenceFeature = new MenuItem("Create Sequence Feature");
+
+  MenuItem editSequence = new MenuItem("Edit Sequence");
+
+  Sequence seq;
+
+  MenuItem revealAll = new MenuItem();
+
+  Menu menu1 = new Menu();
+
+  public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
+  {
+    // /////////////////////////////////////////////////////////
+    // If this is activated from the sequence panel, the user may want to
+    // edit or annotate a particular residue. Therefore display the residue menu
+    //
+    // If from the IDPanel, we must display the sequence menu
+    // ////////////////////////////////////////////////////////
+
+    this.ap = apanel;
+    this.seq = seq;
+
+    try
+    {
+      jbInit();
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+
+    for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
+    {
+      MenuItem item = new MenuItem(
+              jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
+
+      item.addActionListener(this);
+      outputmenu.add(item);
+    }
+
+    SequenceGroup sg = ap.av.getSelectionGroup();
+
+    if (sg != null && sg.getSize() > 0)
+    {
+      editGroupName.setLabel(sg.getName());
+      showText.setState(sg.getDisplayText());
+      showColourText.setState(sg.getColourText());
+      showBoxes.setState(sg.getDisplayBoxes());
+      if (!ap.av.alignment.getGroups().contains(sg))
+      {
+        groupMenu.remove(unGroupMenuItem);
+      }
+
+    }
+    else
+    {
+      remove(hideSeqs);
+      remove(groupMenu);
+    }
+
+    if (links != null && links.size() > 0)
+    {
+      Menu linkMenu = new Menu("Link");
+      String link;
+      for (int i = 0; i < links.size(); i++)
+      {
+        link = links.elementAt(i).toString();
+        UrlLink urlLink = new UrlLink(link);
+        if (!urlLink.isValid())
+        {
+          System.err.println(urlLink.getInvalidMessage());
+          continue;
+        }
+        final String target = urlLink.getTarget(); // link.substring(0,
+                                                    // link.indexOf("|"));
+        final String label = urlLink.getLabel();
+        if (urlLink.isDynamic())
+        {
+
+          // collect matching db-refs
+          DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq
+                  .getDBRef(), new String[]
+          { target });
+          // collect id string too
+          String id = seq.getName();
+          if (dbr != null)
+          {
+            for (int r = 0; r < dbr.length; r++)
+            {
+              if (id != null && dbr[r].getAccessionId().equals(id))
+              {
+                // suppress duplicate link creation for the bare sequence ID
+                // string with this link
+                id = null;
+              }
+              // create Bare ID link for this RUL
+              String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
+                      true);
+              if (urls != null)
+              {
+                for (int u = 0; u < urls.length; u += 2)
+                {
+                  addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
+                }
+              }
+            }
+          }
+          if (id != null)
+          {
+            // create Bare ID link for this RUL
+            String[] urls = urlLink.makeUrls(id, true);
+            if (urls != null)
+            {
+              for (int u = 0; u < urls.length; u += 2)
+              {
+                addshowLink(linkMenu, label, urls[u + 1]);
+              }
+            }
+            // addshowLink(linkMenu, target, url_pref + id + url_suff);
+          }
+        }
+        else
+        {
+          addshowLink(linkMenu, target, urlLink.getUrl_prefix()); // link.substring(link.lastIndexOf("|")+1));
+        }
+        /*
+         * final String url;
+         * 
+         * if (link.indexOf("$SEQUENCE_ID$") > -1) { // Substitute SEQUENCE_ID
+         * string and any matching database reference accessions String url_pref =
+         * link.substring(link.indexOf("|") + 1, link.indexOf("$SEQUENCE_ID$"));
+         * 
+         * String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
+         *  // collect matching db-refs DBRefEntry[] dbr =
+         * jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new
+         * String[]{target}); // collect id string too String id =
+         * seq.getName(); if (id.indexOf("|") > -1) { id =
+         * id.substring(id.lastIndexOf("|") + 1); } if (dbr!=null) { for (int
+         * r=0;r<dbr.length; r++) { if (dbr[r].getAccessionId().equals(id)) { //
+         * suppress duplicate link creation for the bare sequence ID string with
+         * this link id = null; } addshowLink(linkMenu,
+         * dbr[r].getSource()+"|"+dbr[r].getAccessionId(), target,
+         * url_pref+dbr[r].getAccessionId()+url_suff); } } if (id!=null) { //
+         * create Bare ID link for this RUL addshowLink(linkMenu, target,
+         * url_pref + id + url_suff); } } else { addshowLink(linkMenu, target,
+         * link.substring(link.lastIndexOf("|")+1)); }
+         */
+      }
+
+      if (seq != null)
+      {
+        seqMenu.add(linkMenu);
+      }
+      else
+      {
+        add(linkMenu);
+      }
+    }
+    if (seq != null)
+    {
+      seqMenu.setLabel(seq.getName());
+      repGroup.setLabel("Represent Group with " + seq.getName());
+    }
+    else
+    {
+      remove(seqMenu);
+    }
+
+    if (!ap.av.hasHiddenRows)
+    {
+      remove(revealAll);
+    }
+  }
+
+  /**
+   * add a show URL menu item to the given linkMenu
+   * 
+   * @param linkMenu
+   * @param target -
+   *                menu label string
+   * @param url -
+   *                url to open
+   */
+  private void addshowLink(Menu linkMenu, final String target,
+          final String url)
+  {
+    addshowLink(linkMenu, target, target, url);
+  }
+
+  /**
+   * add a show URL menu item to the given linkMenu
+   * 
+   * @param linkMenu
+   * @param target -
+   *                URL target window
+   * @param label -
+   *                menu label string
+   * @param url -
+   *                url to open
+   */
+  private void addshowLink(Menu linkMenu, final String target,
+          final String label, final String url)
+  {
+    MenuItem item = new MenuItem(label);
+    item.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        ap.alignFrame.showURL(url, target);
+      }
+    });
+    linkMenu.add(item);
+  }
+
+  public void itemStateChanged(ItemEvent evt)
+  {
+    if (evt.getSource() == abovePIDColour)
+    {
+      abovePIDColour_itemStateChanged();
+    }
+    else if (evt.getSource() == showColourText)
+    {
+      showColourText_itemStateChanged();
+    }
+    else if (evt.getSource() == showText)
+    {
+      showText_itemStateChanged();
+    }
+    else if (evt.getSource() == showBoxes)
+    {
+      showBoxes_itemStateChanged();
+    }
+  }
+
+  public void actionPerformed(ActionEvent evt)
+  {
+    Object source = evt.getSource();
+    if (source == clustalColour)
+    {
+      clustalColour_actionPerformed();
+    }
+    else if (source == zappoColour)
+    {
+      zappoColour_actionPerformed();
+    }
+    else if (source == taylorColour)
+    {
+      taylorColour_actionPerformed();
+    }
+    else if (source == hydrophobicityColour)
+    {
+      hydrophobicityColour_actionPerformed();
+    }
+    else if (source == helixColour)
+    {
+      helixColour_actionPerformed();
+    }
+    else if (source == strandColour)
+    {
+      strandColour_actionPerformed();
+    }
+    else if (source == turnColour)
+    {
+      turnColour_actionPerformed();
+    }
+    else if (source == buriedColour)
+    {
+      buriedColour_actionPerformed();
+    }
+    else if (source == nucleotideMenuItem)
+    {
+      nucleotideMenuItem_actionPerformed();
+    }
+
+    else if (source == userDefinedColour)
+    {
+      userDefinedColour_actionPerformed();
+    }
+    else if (source == PIDColour)
+    {
+      PIDColour_actionPerformed();
+    }
+    else if (source == BLOSUM62Colour)
+    {
+      BLOSUM62Colour_actionPerformed();
+    }
+    else if (source == noColourmenuItem)
+    {
+      noColourmenuItem_actionPerformed();
+    }
+    else if (source == conservationMenuItem)
+    {
+      conservationMenuItem_itemStateChanged();
+    }
+    else if (source == unGroupMenuItem)
+    {
+      unGroupMenuItem_actionPerformed();
+    }
+
+    else if (source == sequenceName)
+    {
+      editName();
+    }
+    else if (source == pdb)
+    {
+      addPDB();
+    }
+    else if (source == hideSeqs)
+    {
+      hideSequences(false);
+    }
+    else if (source == repGroup)
+    {
+      hideSequences(true);
+    }
+    else if (source == revealAll)
+    {
+      ap.av.showAllHiddenSeqs();
+    }
+
+    else if (source == editGroupName)
+    {
+      EditNameDialog dialog = new EditNameDialog(getGroup().getName(),
+              getGroup().getDescription(), "       Group Name",
+              "Group Description", ap.alignFrame,
+              "Edit Group Name / Description", 500, 100, true);
+
+      if (dialog.accept)
+      {
+        getGroup().setName(dialog.getName().replace(' ', '_'));
+        getGroup().setDescription(dialog.getDescription());
+      }
+
+    }
+    else if (source == copy)
+    {
+      ap.alignFrame.copy_actionPerformed();
+    }
+    else if (source == cut)
+    {
+      ap.alignFrame.cut_actionPerformed();
+    }
+    else if (source == editSequence)
+    {
+      SequenceGroup sg = ap.av.getSelectionGroup();
+
+      if (sg != null)
+      {
+        if (seq == null)
+          seq = (Sequence) sg.getSequenceAt(0);
+
+        EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString(
+                sg.getStartRes(), sg.getEndRes() + 1), null,
+                "Edit Sequence ", null,
+
+                ap.alignFrame, "Edit Sequence", 500, 100, true);
+
+        if (dialog.accept)
+        {
+          EditCommand editCommand = new EditCommand("Edit Sequences",
+                  EditCommand.REPLACE, dialog.getName().replace(' ',
+                          ap.av.getGapCharacter()), sg
+                          .getSequencesAsArray(ap.av.hiddenRepSequences),
+                  sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
+
+          ap.alignFrame.addHistoryItem(editCommand);
+
+          ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+                  .getSequences());
+        }
+      }
+    }
+    else if (source == toUpper || source == toLower || source == toggleCase)
+    {
+      SequenceGroup sg = ap.av.getSelectionGroup();
+      Vector regions = new Vector();
+      if (sg != null)
+      {
+        int start = sg.getStartRes();
+        int end = sg.getEndRes() + 1;
+
+        do
+        {
+          if (ap.av.hasHiddenColumns)
+          {
+            if (start == 0)
+            {
+              start = ap.av.colSel.adjustForHiddenColumns(start);
+            }
+
+            end = ap.av.colSel.getHiddenBoundaryRight(start);
+            if (start == end)
+            {
+              end = sg.getEndRes() + 1;
+            }
+            if (end > sg.getEndRes())
+            {
+              end = sg.getEndRes() + 1;
+            }
+          }
+
+          regions.addElement(new int[]
+          { start, end });
+
+          if (ap.av.hasHiddenColumns)
+          {
+            start = ap.av.colSel.adjustForHiddenColumns(end);
+            start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
+          }
+        } while (end < sg.getEndRes());
+
+        int[][] startEnd = new int[regions.size()][2];
+        for (int i = 0; i < regions.size(); i++)
+        {
+          startEnd[i] = (int[]) regions.elementAt(i);
+        }
+
+        String description;
+        int caseChange;
+
+        if (source == toggleCase)
+        {
+          description = "Toggle Case";
+          caseChange = ChangeCaseCommand.TOGGLE_CASE;
+        }
+        else if (source == toUpper)
+        {
+          description = "To Upper Case";
+          caseChange = ChangeCaseCommand.TO_UPPER;
+        }
+        else
+        {
+          description = "To Lower Case";
+          caseChange = ChangeCaseCommand.TO_LOWER;
+        }
+
+        ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
+                sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
+                caseChange);
+
+        ap.alignFrame.addHistoryItem(caseCommand);
+
+        ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+                .getSequences());
+
+      }
+    }
+    else if (source == sequenceFeature)
+    {
+      SequenceGroup sg = ap.av.getSelectionGroup();
+      if (sg == null)
+      {
+        return;
+      }
+      int rsize=0,gSize = sg.getSize();
+      SequenceI[] rseqs,seqs = new SequenceI[gSize];
+      SequenceFeature[] tfeatures,features = new SequenceFeature[gSize];
+      
+      for (int i = 0; i < gSize; i++)
+      {
+        int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
+        int end = sg.findEndRes(sg.getSequenceAt(i));
+        if (start<=end)
+        {
+          seqs[rsize] = sg.getSequenceAt(i);
+          features[rsize] = new SequenceFeature(null, null, null, start, end,
+                "Jalview");
+          rsize++;
+        }
+      }
+      rseqs = new SequenceI[rsize];
+      tfeatures = new SequenceFeature[rsize];
+      System.arraycopy(seqs,0,rseqs, 0, rsize);
+      System.arraycopy(features, 0, tfeatures, 0, rsize);
+      features = tfeatures;
+      seqs = rseqs;
+
+      if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+              features, true, ap))
+      {
+        ap.alignFrame.sequenceFeatures.setState(true);
+        ap.av.showSequenceFeatures(true);
+        ap.highlightSearchResults(null);
+      }
+    }
+    else
+    {
+      outputText(evt);
+    }
+
+  }
+
+  void outputText(ActionEvent e)
+  {
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
+
+    Frame frame = new Frame();
+    frame.add(cap);
+    jalview.bin.JalviewLite.addFrame(frame, "Selection output - "
+            + e.getActionCommand(), 600, 500);
+
+    cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(e
+            .getActionCommand(), new Alignment(ap.av
+            .getSelectionAsNewSequence()), ap.av.showJVSuffix));
+
+  }
+
+  void editName()
+  {
+    EditNameDialog dialog = new EditNameDialog(seq.getName(), seq
+            .getDescription(), "       Sequence Name",
+            "Sequence Description", ap.alignFrame,
+            "Edit Sequence Name / Description", 500, 100, true);
+
+    if (dialog.accept)
+    {
+      seq.setName(dialog.getName());
+      seq.setDescription(dialog.getDescription());
+      ap.paintAlignment(false);
+    }
+  }
+
+  void addPDB()
+  {
+    if (seq.getPDBId() != null)
+    {
+      PDBEntry entry = (PDBEntry) seq.getPDBId().firstElement();
+
+      if (ap.av.applet.jmolAvailable)
+        new jalview.appletgui.AppletJmol(entry, new Sequence[]
+        { seq }, null, ap, AppletFormatAdapter.URL);
+      else
+        new MCview.AppletPDBViewer(entry, new Sequence[]
+        { seq }, null, ap, AppletFormatAdapter.URL);
+
+    }
+    else
+    {
+      CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
+      cap.setText("Paste your PDB file here.");
+      cap.setPDBImport(seq);
+      Frame frame = new Frame();
+      frame.add(cap);
+      jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);
+    }
+  }
+
+  private void jbInit() throws Exception
+  {
+    groupMenu.setLabel("Group");
+    groupMenu.setLabel("Selection");
+    sequenceFeature.addActionListener(this);
+
+    editGroupName.addActionListener(this);
+    unGroupMenuItem.setLabel("Remove Group");
+    unGroupMenuItem.addActionListener(this);
+
+    nucleotideMenuItem.setLabel("Nucleotide");
+    nucleotideMenuItem.addActionListener(this);
+    conservationMenuItem.addItemListener(this);
+    abovePIDColour.addItemListener(this);
+    colourMenu.setLabel("Group Colour");
+    showBoxes.setLabel("Boxes");
+    showBoxes.setState(true);
+    showBoxes.addItemListener(this);
+    sequenceName.addActionListener(this);
+
+    showText.setLabel("Text");
+    showText.addItemListener(this);
+    showColourText.setLabel("Colour Text");
+    showColourText.addItemListener(this);
+    outputmenu.setLabel("Output to Textbox...");
+    seqMenu.setLabel("Sequence");
+    pdb.setLabel("View PDB Structure");
+    hideSeqs.setLabel("Hide Sequences");
+    repGroup.setLabel("Represent Group with");
+    revealAll.setLabel("Reveal All");
+    menu1.setLabel("Group");
+    add(groupMenu);
+    this.add(seqMenu);
+    this.add(hideSeqs);
+    this.add(revealAll);
+    groupMenu.add(editGroupName);
+    groupMenu.add(editMenu);
+    groupMenu.add(outputmenu);
+    groupMenu.add(sequenceFeature);
+    groupMenu.add(menu1);
+
+    colourMenu.add(noColourmenuItem);
+    colourMenu.add(clustalColour);
+    colourMenu.add(BLOSUM62Colour);
+    colourMenu.add(PIDColour);
+    colourMenu.add(zappoColour);
+    colourMenu.add(taylorColour);
+    colourMenu.add(hydrophobicityColour);
+    colourMenu.add(helixColour);
+    colourMenu.add(strandColour);
+    colourMenu.add(turnColour);
+    colourMenu.add(buriedColour);
+    colourMenu.add(nucleotideMenuItem);
+    colourMenu.add(userDefinedColour);
+    colourMenu.addSeparator();
+    colourMenu.add(abovePIDColour);
+    colourMenu.add(conservationMenuItem);
+
+    noColourmenuItem.setLabel("None");
+    noColourmenuItem.addActionListener(this);
+
+    clustalColour.setLabel("Clustalx colours");
+    clustalColour.addActionListener(this);
+    zappoColour.setLabel("Zappo");
+    zappoColour.addActionListener(this);
+    taylorColour.setLabel("Taylor");
+    taylorColour.addActionListener(this);
+    hydrophobicityColour.setLabel("Hydrophobicity");
+    hydrophobicityColour.addActionListener(this);
+    helixColour.setLabel("Helix propensity");
+    helixColour.addActionListener(this);
+    strandColour.setLabel("Strand propensity");
+    strandColour.addActionListener(this);
+    turnColour.setLabel("Turn propensity");
+    turnColour.addActionListener(this);
+    buriedColour.setLabel("Buried Index");
+    buriedColour.addActionListener(this);
+    abovePIDColour.setLabel("Above % Identity");
+
+    userDefinedColour.setLabel("User Defined");
+    userDefinedColour.addActionListener(this);
+    PIDColour.setLabel("Percentage Identity");
+    PIDColour.addActionListener(this);
+    BLOSUM62Colour.setLabel("BLOSUM62");
+    BLOSUM62Colour.addActionListener(this);
+    conservationMenuItem.setLabel("Conservation");
+
+    editMenu.add(copy);
+    copy.addActionListener(this);
+    editMenu.add(cut);
+    cut.addActionListener(this);
+
+    editMenu.add(editSequence);
+    editSequence.addActionListener(this);
+
+    editMenu.add(toUpper);
+    toUpper.addActionListener(this);
+    editMenu.add(toLower);
+    toLower.addActionListener(this);
+    editMenu.add(toggleCase);
+    seqMenu.add(sequenceName);
+    seqMenu.add(pdb);
+    seqMenu.add(repGroup);
+    menu1.add(unGroupMenuItem);
+    menu1.add(colourMenu);
+    menu1.add(showBoxes);
+    menu1.add(showText);
+    menu1.add(showColourText);
+    toggleCase.addActionListener(this);
+    pdb.addActionListener(this);
+    hideSeqs.addActionListener(this);
+    repGroup.addActionListener(this);
+    revealAll.addActionListener(this);
+  }
+
+  void refresh()
+  {
+    ap.paintAlignment(true);
+  }
+
+  protected void clustalColour_actionPerformed()
+  {
+    SequenceGroup sg = getGroup();
+    sg.cs = new ClustalxColourScheme(sg
+            .getSequences(ap.av.hiddenRepSequences), ap.av.alignment
+            .getWidth());
+    refresh();
+  }
+
+  protected void zappoColour_actionPerformed()
+  {
+    getGroup().cs = new ZappoColourScheme();
+    refresh();
+  }
+
+  protected void taylorColour_actionPerformed()
+  {
+    getGroup().cs = new TaylorColourScheme();
+    refresh();
+  }
+
+  protected void hydrophobicityColour_actionPerformed()
+  {
+    getGroup().cs = new HydrophobicColourScheme();
+    refresh();
+  }
+
+  protected void helixColour_actionPerformed()
+  {
+    getGroup().cs = new HelixColourScheme();
+    refresh();
+  }
+
+  protected void strandColour_actionPerformed()
+  {
+    getGroup().cs = new StrandColourScheme();
+    refresh();
+  }
+
+  protected void turnColour_actionPerformed()
+  {
+    getGroup().cs = new TurnColourScheme();
+    refresh();
+  }
+
+  protected void buriedColour_actionPerformed()
+  {
+    getGroup().cs = new BuriedColourScheme();
+    refresh();
+  }
+
+  public void nucleotideMenuItem_actionPerformed()
+  {
+    getGroup().cs = new NucleotideColourScheme();
+    refresh();
+  }
+
+  protected void abovePIDColour_itemStateChanged()
+  {
+    SequenceGroup sg = getGroup();
+    if (sg.cs == null)
+    {
+      return;
+    }
+
+    if (abovePIDColour.getState())
+    {
+      sg.cs.setConsensus(AAFrequency.calculate(sg
+              .getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment
+              .getWidth()));
+      int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
+              .getName());
+
+      sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
+
+      SliderPanel.showPIDSlider();
+
+    }
+    else
+    // remove PIDColouring
+    {
+      sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+    }
+
+    refresh();
+
+  }
+
+  protected void userDefinedColour_actionPerformed()
+  {
+    new UserDefinedColours(ap, getGroup());
+  }
+
+  protected void PIDColour_actionPerformed()
+  {
+    SequenceGroup sg = getGroup();
+    sg.cs = new PIDColourScheme();
+    sg.cs.setConsensus(AAFrequency.calculate(sg
+            .getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment
+            .getWidth()));
+    refresh();
+  }
+
+  protected void BLOSUM62Colour_actionPerformed()
+  {
+    SequenceGroup sg = getGroup();
+
+    sg.cs = new Blosum62ColourScheme();
+
+    sg.cs.setConsensus(AAFrequency.calculate(sg
+            .getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment
+            .getWidth()));
+
+    refresh();
+  }
+
+  protected void noColourmenuItem_actionPerformed()
+  {
+    getGroup().cs = null;
+    refresh();
+  }
+
+  protected void conservationMenuItem_itemStateChanged()
+  {
+    SequenceGroup sg = getGroup();
+    if (sg.cs == null)
+    {
+      return;
+    }
+
+    if (conservationMenuItem.getState())
+    {
+
+      Conservation c = new Conservation("Group",
+              ResidueProperties.propHash, 3, sg
+                      .getSequences(ap.av.hiddenRepSequences), 0,
+              ap.av.alignment.getWidth());
+
+      c.calculate();
+      c.verdict(false, ap.av.ConsPercGaps);
+
+      sg.cs.setConservation(c);
+
+      SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
+      SliderPanel.showConservationSlider();
+    }
+    else
+    // remove ConservationColouring
+    {
+      sg.cs.setConservation(null);
+    }
+
+    refresh();
+  }
+
+  SequenceGroup getGroup()
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+
+    // this method won't add a new group if it already exists
+    if (sg != null)
+    {
+      ap.av.alignment.addGroup(sg);
+    }
+
+    return sg;
+  }
+
+  void unGroupMenuItem_actionPerformed()
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    ap.av.alignment.deleteGroup(sg);
+    ap.av.setSelectionGroup(null);
+    ap.paintAlignment(true);
+  }
+
+  public void showColourText_itemStateChanged()
+  {
+    getGroup().setColourText(showColourText.getState());
+    refresh();
+  }
+
+  public void showText_itemStateChanged()
+  {
+    getGroup().setDisplayText(showText.getState());
+    refresh();
+  }
+
+  public void showBoxes_itemStateChanged()
+  {
+    getGroup().setDisplayBoxes(showBoxes.getState());
+    refresh();
+  }
+
+  void hideSequences(boolean representGroup)
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    if (sg == null || sg.getSize() < 1)
+    {
+      ap.av.hideSequence(new SequenceI[]
+      { seq });
+      return;
+    }
+
+    ap.av.setSelectionGroup(null);
+
+    if (representGroup)
+    {
+      ap.av.hideRepSequences(seq, sg);
+
+      return;
+    }
+
+    int gsize = sg.getSize();
+    SequenceI[] hseqs;
+
+    hseqs = new SequenceI[gsize];
+
+    int index = 0;
+    for (int i = 0; i < gsize; i++)
+    {
+      hseqs[index++] = sg.getSequenceAt(i);
+    }
+
+    ap.av.hideSequence(hseqs);
+  }
+
+}