X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=b85c7d205e1c7961dd258228ca6263b6d0bffa07;hb=14bad6b2390493bb6ad030c6f3ea7cde4cba1b53;hp=83e4407fbca307d2581b415efbd3964633bf9d8b;hpb=f2cd37c3b51d78aa72b04a85e083d73e9365d9a0;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 83e4407..b85c7d2 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -1,12 +1,34 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 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 jalview.datamodel.*;
-import jalview.analysis.*;
-import jalview.schemes.*;
 import java.awt.*;
 import java.awt.event.*;
+import java.util.Vector;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.schemes.*;
 
-public class APopupMenu extends java.awt.PopupMenu
+public class APopupMenu
+    extends java.awt.PopupMenu implements ActionListener, ItemListener
 {
   Menu groupMenu = new Menu();
   protected MenuItem clustalColour = new MenuItem();
@@ -24,15 +46,15 @@ public class APopupMenu extends java.awt.PopupMenu
   MenuItem noColourmenuItem = new MenuItem();
   protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
 
-
-  AlignmentPanel ap;
-  Menu sequenceMenu = new Menu();
-  MenuItem sequenceName = new MenuItem();
-  Sequence sequence;
+  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();
 
-  public APopupMenu(AlignmentPanel ap, Sequence seq)
+  public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
   {
     ///////////////////////////////////////////////////////////
     // If this is activated from the sequence panel, the user may want to
@@ -41,390 +63,397 @@ public class APopupMenu extends java.awt.PopupMenu
     // If from the IDPanel, we must display the sequence menu
     //////////////////////////////////////////////////////////
 
-    this.ap = ap;
-    sequence = seq;
+    this.ap = apanel;
 
     try
-    {     jbInit();   }
-    catch(Exception e)
-    {    e.printStackTrace();    }
-
+    {
+      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 && links!=null)
+    {
+      Menu linkMenu = new Menu("Link");
+      MenuItem item;
+      String link;
+      for(int i=0; i<links.size(); i++)
+      {
+        link = links.elementAt(i).toString();
+        final String target = link.substring(0, link.indexOf("|"));
+        item = new MenuItem(target);
+        String id = seq.getName();
+        if(id.indexOf("|")>-1)
+             id = id.substring(id.lastIndexOf("|")+1);
+
+        final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))
+               + id +
+               link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
+
+           item.addActionListener(new java.awt.event.ActionListener()
+           {
+               public void actionPerformed(ActionEvent e)
+               {
+                  ap.alignFrame.showURL(url, target);
+               }
+           });
+          linkMenu.add(item);
+      }
+      add(linkMenu);
 
-    if( !ap.av.alignment.getGroups().contains(sg))
-        groupMenu.remove(unGroupMenuItem);
+      item = new MenuItem("Show PDB Structure");
+      item.addActionListener(new java.awt.event.ActionListener()
+           {
+               public void actionPerformed(ActionEvent e)
+               {
+                  addPDB(seq);
+               }
+           });
+
+      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()   ;
+  }
 
-    if(seq==null)
-       remove(sequenceMenu);
+  public void actionPerformed(ActionEvent evt)
+  {
+    if(evt.getSource()==clustalColour)
+      clustalColour_actionPerformed();
+    else if(evt.getSource()==zappoColour)
+      zappoColour_actionPerformed();
+    else if(evt.getSource()==taylorColour)
+      taylorColour_actionPerformed();
+    else if(evt.getSource()==hydrophobicityColour)
+      hydrophobicityColour_actionPerformed();
+    else if(evt.getSource()==helixColour)
+      helixColour_actionPerformed();
+    else if(evt.getSource()==strandColour)
+      strandColour_actionPerformed();
+    else if(evt.getSource()==clustalColour)
+      turnColour_actionPerformed();
+    else if(evt.getSource()==buriedColour)
+      buriedColour_actionPerformed();
+    else if(evt.getSource()==nucleotideMenuItem)
+      nucleotideMenuItem_actionPerformed();
+
+    else if(evt.getSource()==userDefinedColour)
+          userDefinedColour_actionPerformed();
+        else if(evt.getSource()==PIDColour)
+       PIDColour_actionPerformed();
+     else if(evt.getSource()==BLOSUM62Colour)
+      BLOSUM62Colour_actionPerformed();
+    else if(evt.getSource()==noColourmenuItem)
+      noColourmenuItem_actionPerformed();
+    else if(evt.getSource()==conservationMenuItem)
+        conservationMenuItem_itemStateChanged();
+      else if(evt.getSource()==unGroupMenuItem)
+      unGroupMenuItem_actionPerformed();
 
+  }
 
+  void addPDB(Sequence seq)
+  {
+    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
+
+  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);
-      }
-    });
-
+    unGroupMenuItem.addActionListener(this);
 
     nucleotideMenuItem.setLabel("Nucleotide");
-    nucleotideMenuItem.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        nucleotideMenuItem_actionPerformed(e);
-      }
-    });
+    nucleotideMenuItem.addActionListener(this);
+    conservationMenuItem.addItemListener(this);
+    abovePIDColour.addItemListener(this);
+    colourMenu.setLabel("Group Colour");
+    showBoxes.setLabel("Boxes");
+    showBoxes.setState(true);
+    showBoxes.addItemListener(this);
+
+    showText.setLabel("Text");
+    showText.addItemListener(this);
+    showColourText.setLabel("Colour Text");
+    showColourText.addItemListener(this);
 
     add(groupMenu);
-    this.add(sequenceMenu);
     groupMenu.add(unGroupMenuItem);
-    groupMenu.add(noColourmenuItem);
-    groupMenu.add(clustalColour);
-    groupMenu.add(BLOSUM62Colour);
-    groupMenu.add(PIDColour);
-
-    groupMenu.add(zappoColour);
-    groupMenu.add(taylorColour);
-    groupMenu.add(hydrophobicityColour);
-    groupMenu.add(helixColour);
-    groupMenu.add(strandColour);
-    groupMenu.add(turnColour);
-    groupMenu.add(buriedColour);
-    groupMenu.add(nucleotideMenuItem);
-
-    groupMenu.add(userDefinedColour);
-
+    groupMenu.add(colourMenu);
     groupMenu.addSeparator();
-    groupMenu.add(abovePIDColour);
-    groupMenu.add(conservationMenuItem);
-
-    sequenceMenu.add(sequenceName);
+    groupMenu.add(showBoxes);
+    groupMenu.add(showText);
+    groupMenu.add(showColourText);
+    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);
-      }
-    });
+    noColourmenuItem.addActionListener(this);
 
     clustalColour.setLabel("Clustalx colours");
-    clustalColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        clustalColour_actionPerformed(e);
-      }
-    });
+    clustalColour.addActionListener(this);
     zappoColour.setLabel("Zappo");
-    zappoColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        zappoColour_actionPerformed(e);
-      }
-    });
+    zappoColour.addActionListener(this);
     taylorColour.setLabel("Taylor");
-    taylorColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        taylorColour_actionPerformed(e);
-      }
-    });
+    taylorColour.addActionListener(this);
     hydrophobicityColour.setLabel("Hydrophobicity");
-    hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        hydrophobicityColour_actionPerformed(e);
-      }
-    });
+    hydrophobicityColour.addActionListener(this);
     helixColour.setLabel("Helix propensity");
-    helixColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        helixColour_actionPerformed(e);
-      }
-    });
+    helixColour.addActionListener(this);
     strandColour.setLabel("Strand propensity");
-    strandColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        strandColour_actionPerformed(e);
-      }
-    });
+    strandColour.addActionListener(this);
     turnColour.setLabel("Turn propensity");
-    turnColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        turnColour_actionPerformed(e);
-      }
-    });
+    turnColour.addActionListener(this);
     buriedColour.setLabel("Buried Index");
-    buriedColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        buriedColour_actionPerformed(e);
-      }
-    });
+    buriedColour.addActionListener(this);
     abovePIDColour.setLabel("Above % Identity");
-    abovePIDColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        abovePIDColour_actionPerformed(e);
-      }
-    });
+
     userDefinedColour.setLabel("User Defined");
-    userDefinedColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        userDefinedColour_actionPerformed(e);
-      }
-    });
+    userDefinedColour.addActionListener(this);
     PIDColour.setLabel("Percentage Identity");
-    PIDColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        PIDColour_actionPerformed(e);
-      }
-    });
+    PIDColour.addActionListener(this);
     BLOSUM62Colour.setLabel("BLOSUM62");
-    BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        BLOSUM62Colour_actionPerformed(e);
-      }
-    });
+    BLOSUM62Colour.addActionListener(this);
     conservationMenuItem.setLabel("Conservation");
-   conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
-   {
-     public void actionPerformed(ActionEvent e)
-     {
-       conservationMenuItem_actionPerformed(e);
-     }
-   });
-
-
 
   }
 
   void refresh()
   {
-    SequenceGroup sg = getGroup();
-    SuperGroup superG = ap.av.alignment.getSuperGroup( sg );
-    if( superG !=null)
-      superG.setSuperGroupProperties( sg );
-
     ap.seqPanel.seqCanvas.repaint();
+    if(ap.overviewPanel!=null)
+      ap.overviewPanel.updateOverviewImage();
   }
 
-  protected void clustalColour_actionPerformed(ActionEvent e)
+  protected void clustalColour_actionPerformed()
   {
     SequenceGroup sg = getGroup();
     sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());
     refresh();
   }
 
-  protected void zappoColour_actionPerformed(ActionEvent e)
+  protected void zappoColour_actionPerformed()
   {
     getGroup().cs = new ZappoColourScheme();
     refresh();
   }
 
-  protected void taylorColour_actionPerformed(ActionEvent e)
+  protected void taylorColour_actionPerformed()
   {
     getGroup().cs = new TaylorColourScheme();
     refresh();
   }
 
-
-  protected void hydrophobicityColour_actionPerformed(ActionEvent e)
+  protected void hydrophobicityColour_actionPerformed()
   {
     getGroup().cs = new HydrophobicColourScheme();
     refresh();
   }
 
-  protected void helixColour_actionPerformed(ActionEvent e)
+  protected void helixColour_actionPerformed()
   {
     getGroup().cs = new HelixColourScheme();
     refresh();
   }
 
-  protected void strandColour_actionPerformed(ActionEvent e)
+  protected void strandColour_actionPerformed()
   {
     getGroup().cs = new StrandColourScheme();
     refresh();
   }
 
-  protected void turnColour_actionPerformed(ActionEvent e)
+  protected void turnColour_actionPerformed()
   {
     getGroup().cs = new TurnColourScheme();
     refresh();
   }
 
-  protected void buriedColour_actionPerformed(ActionEvent e)
+  protected void buriedColour_actionPerformed()
   {
     getGroup().cs = new BuriedColourScheme();
     refresh();
   }
 
-  public void nucleotideMenuItem_actionPerformed(ActionEvent e)
+  public void nucleotideMenuItem_actionPerformed()
   {
     getGroup().cs = new NucleotideColourScheme();
     refresh();
   }
 
-
-
-  protected void abovePIDColour_actionPerformed(ActionEvent e)
+  protected void abovePIDColour_itemStateChanged()
   {
     SequenceGroup sg = getGroup();
+    if(sg.cs==null)
+          return;
+
     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);
+      int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
+          getGroup().getName());
 
-      SliderPanel.showPIDSlider();
+      sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
 
+      SliderPanel.showPIDSlider();
 
     }
     else // remove PIDColouring
     {
-      ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;
-      rcs.setThreshold(0);
-      sg.cs = rcs;
+      sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
     }
 
     refresh();
 
   }
 
-
-  protected void userDefinedColour_actionPerformed(ActionEvent e)
+  protected void userDefinedColour_actionPerformed()
   {
-    UserDefinedColours chooser = new UserDefinedColours( ap, getGroup());
+    new UserDefinedColours(ap, getGroup());
   }
 
-  protected void PIDColour_actionPerformed(ActionEvent e)
+  protected void PIDColour_actionPerformed()
   {
-
+    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)
+  protected void BLOSUM62Colour_actionPerformed()
   {
     SequenceGroup sg = getGroup();
 
     sg.cs = new Blosum62ColourScheme();
 
     sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-                                               ap.av.alignment.getWidth()));
+                                             ap.av.alignment.getWidth()));
 
     refresh();
   }
 
-
-  protected void noColourmenuItem_actionPerformed(ActionEvent e)
+  protected void noColourmenuItem_actionPerformed()
   {
     getGroup().cs = null;
     refresh();
   }
 
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
+  protected void conservationMenuItem_itemStateChanged()
   {
     SequenceGroup sg = getGroup();
+    if(sg.cs==null)
+          return;
 
-    if(conservationMenuItem.getState())
+    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);
+      Conservation c = new Conservation("Group",
+                                        ResidueProperties.propHash, 3,
+                                        sg.sequences, 0,
+                                        ap.av.alignment.getWidth());
 
+      c.calculate();
+      c.verdict(false, ap.av.ConsPercGaps);
 
-      sg.cs = ccs;
+      sg.cs.setConservation(c);
 
-      SliderPanel.setConservationSlider(ap, ccs, sg.getName());
+      SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
       SliderPanel.showConservationSlider();
     }
     else // remove ConservationColouring
     {
-        ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
-        sg.cs = ccs.cs;
+      sg.cs.setConservation(null);
     }
 
-     refresh();
+    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);
+    if(sg!=null)
+      ap.av.alignment.addGroup(sg);
 
     return sg;
   }
 
-  void unGroupMenuItem_actionPerformed(ActionEvent e)
+  void unGroupMenuItem_actionPerformed()
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    ap.av.alignment.deleteGroup(sg);
+    ap.av.setSelectionGroup(null);
+    ap.repaint();
+  }
+
+  public void showColourText_itemStateChanged()
+  {
+    getGroup().setColourText(showColourText.getState());
+    refresh();
+  }
+
+  public void showText_itemStateChanged()
   {
-     SequenceGroup sg = ap.av.getSelectionGroup();
-     ap.av.alignment.deleteGroup(sg);
-     ap.av.setSelectionGroup(null);
-     ap.repaint();
+    getGroup().setDisplayText(showText.getState());
+    refresh();
   }
 
+  public void showBoxes_itemStateChanged()
+  {
+    getGroup().setDisplayBoxes(showBoxes.getState());
+    refresh();
+  }
 
 }