X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=80006c2f5b051e1bdf8f3483c7d847e996a3ddbe;hb=6636e89537d7f51f4a71e616d3bb0f612097d050;hp=b6d43ea2e8e9f9100b99cf2c22c9e7f6621b8516;hpb=ec955aa655d8320258b91eb079bc57f688cd0a07;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index b6d43ea..80006c2 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -1,18 +1,36 @@
+/*
+ * 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
 {
   Menu groupMenu = new Menu();
-  Menu analyze = new Menu();
-  Menu defineMenu = new Menu();
-  Menu groupName = new Menu();
-  Menu groupAnnotation = new Menu();
   protected MenuItem clustalColour = new MenuItem();
   protected MenuItem zappoColour = new MenuItem();
   protected MenuItem taylorColour = new MenuItem();
@@ -28,19 +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();
-  Menu residueMenu = new Menu();
-  MenuItem annotateResidue = new MenuItem();
-
-  Sequence sequence;
   MenuItem unGroupMenuItem = new MenuItem();
-  MenuItem outline = 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 ap, Sequence seq, Vector links)
   {
     ///////////////////////////////////////////////////////////
     // If this is activated from the sequence panel, the user may want to
@@ -50,122 +64,144 @@ public class APopupMenu extends java.awt.PopupMenu
     //////////////////////////////////////////////////////////
 
     this.ap = ap;
-    sequence = seq;
 
     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(seq!=null)
-      residueMenu.setEnabled(false);
-    else
-      sequenceMenu.setEnabled(false);
+    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);
+        final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))
+               + seq.getName() +
+               link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
+
+           item.addActionListener(new java.awt.event.ActionListener()
+           {
+               public void actionPerformed(ActionEvent e)
+               {
+                  jalview.bin.JalviewLite.showURL(url, target);
+               }
+           });
+          linkMenu.add(item);
+      }
+      add(linkMenu);
+    }
   }
-  private void jbInit() throws Exception
+
+  private void jbInit()
+      throws Exception
   {
     groupMenu.setLabel("Group");
-    analyze.setLabel("Analyze");
-    analyze.addActionListener(new java.awt.event.ActionListener()
+    groupMenu.setLabel("Define");
+
+    unGroupMenuItem.setLabel("Remove Group");
+    unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        analyze_actionPerformed(e);
+        unGroupMenuItem_actionPerformed(e);
       }
     });
-    defineMenu.setLabel("Define");
-    groupName.setLabel("Name");
-    groupName.addActionListener(new java.awt.event.ActionListener()
+
+    nucleotideMenuItem.setLabel("Nucleotide");
+    nucleotideMenuItem.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        groupName_actionPerformed(e);
+        nucleotideMenuItem_actionPerformed(e);
       }
     });
-    groupAnnotation.setEnabled(false);
-    groupAnnotation.setLabel("Annotation");
-    groupAnnotation.addActionListener(new java.awt.event.ActionListener()
+    conservationMenuItem.addItemListener(new ItemListener()
     {
-      public void actionPerformed(ActionEvent e)
+      public void itemStateChanged(ItemEvent itemEvent)
       {
-        groupAnnotation_actionPerformed(e);
+        conservationMenuItem_itemStateChanged(itemEvent);
       }
     });
-    sequenceMenu.setLabel("Sequence");
-    sequenceName.setLabel("Edit name");
-    sequenceName.addActionListener(new java.awt.event.ActionListener()
+    abovePIDColour.addItemListener(new ItemListener()
     {
-      public void actionPerformed(ActionEvent e)
+      public void itemStateChanged(ItemEvent itemEvent)
       {
-        sequenceName_actionPerformed(e);
+        abovePIDColour_itemStateChanged(itemEvent);
       }
     });
-    residueMenu.setLabel("Residue");
-    annotateResidue.setEnabled(false);
-    annotateResidue.setActionCommand("annotate residue");
-    annotateResidue.setLabel("annotate residue???");
-    unGroupMenuItem.setLabel("Remove Group");
-    unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+    colourMenu.setLabel("Group Colour");
+    showBoxes.setLabel("Boxes");
+    showBoxes.setState(true);
+    showBoxes.addItemListener(new ItemListener()
     {
-      public void actionPerformed(ActionEvent e)
+      public void itemStateChanged(ItemEvent itemEvent)
       {
-        unGroupMenuItem_actionPerformed(e);
+        showBoxes_itemStateChanged(itemEvent);
       }
     });
 
-    outline.setLabel("Border colour");
-    outline.addActionListener(new java.awt.event.ActionListener()
+    showText.setLabel("Text");
+    showText.addItemListener(new ItemListener()
     {
-      public void actionPerformed(ActionEvent e)
+      public void itemStateChanged(ItemEvent itemEvent)
       {
-        outline_actionPerformed(e);
+        showText_itemStateChanged(itemEvent);
       }
     });
-    nucleotideMenuItem.setLabel("Nucleotide");
-    nucleotideMenuItem.addActionListener(new ActionListener()
+    showColourText.setLabel("Colour Text");
+    showColourText.addItemListener(new ItemListener()
     {
-      public void actionPerformed(ActionEvent e)
+      public void itemStateChanged(ItemEvent itemEvent)
       {
-        nucleotideMenuItem_actionPerformed(e);
+        showColourText_itemStateChanged(itemEvent);
       }
     });
 
     add(groupMenu);
-    this.add(sequenceMenu);
-    this.add(residueMenu);
-    groupMenu.add(defineMenu);
     groupMenu.add(unGroupMenuItem);
+    groupMenu.add(colourMenu);
     groupMenu.addSeparator();
-    groupMenu.add(analyze);
-    defineMenu.add(groupName);
-    defineMenu.add(groupAnnotation);
-    defineMenu.addSeparator();
-    defineMenu.add(outline);
-    defineMenu.addSeparator();
-    defineMenu.add(noColourmenuItem);
-    defineMenu.add(clustalColour);
-    defineMenu.add(BLOSUM62Colour);
-    defineMenu.add(PIDColour);
-
-    defineMenu.add(zappoColour);
-    defineMenu.add(taylorColour);
-    defineMenu.add(hydrophobicityColour);
-    defineMenu.add(helixColour);
-    defineMenu.add(strandColour);
-    defineMenu.add(turnColour);
-    defineMenu.add(buriedColour);
-    defineMenu.add(nucleotideMenuItem);
-
-    defineMenu.add(userDefinedColour);
-
-    defineMenu.addSeparator();
-    defineMenu.add(abovePIDColour);
-    defineMenu.add(conservationMenuItem);
-
-    sequenceMenu.add(sequenceName);
-    residueMenu.add(annotateResidue);
+    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()
@@ -241,13 +277,7 @@ public class APopupMenu extends java.awt.PopupMenu
       }
     });
     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()
     {
@@ -273,26 +303,22 @@ public class APopupMenu extends java.awt.PopupMenu
       }
     });
     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 );
+    if(sg!=null)
+    {
+      SuperGroup superG = ap.av.alignment.getSuperGroup(sg);
 
-    ap.seqPanel.repaint();
+      if (superG != null)
+      {
+        superG.setSuperGroupProperties(sg);
+      }
+        }
+    ap.seqPanel.seqCanvas.repaint();
   }
 
   protected void clustalColour_actionPerformed(ActionEvent e)
@@ -314,7 +340,6 @@ public class APopupMenu extends java.awt.PopupMenu
     refresh();
   }
 
-
   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
   {
     getGroup().cs = new HydrophobicColourScheme();
@@ -351,45 +376,45 @@ public class APopupMenu extends java.awt.PopupMenu
     refresh();
   }
 
-
-
-  protected void abovePIDColour_actionPerformed(ActionEvent e)
+  protected void abovePIDColour_itemStateChanged(ItemEvent ie)
   {
     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)
   {
-    UserDefinedColours chooser = new UserDefinedColours( ap, getGroup());
+    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)
@@ -399,84 +424,65 @@ public class APopupMenu extends java.awt.PopupMenu
     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)
   {
     getGroup().cs = null;
     refresh();
   }
 
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
+  protected void conservationMenuItem_itemStateChanged(ItemEvent ie)
   {
     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());
+      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);
+      c.calculate();
+      c.verdict(false, ap.av.ConsPercGaps);
 
+      sg.cs.setConservation(c);
 
-      sg.cs = ccs;
-
-      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();
-  }
-
-  protected void groupAnnotation_actionPerformed(ActionEvent e)
-  {
-
+    refresh();
   }
 
-  protected void groupName_actionPerformed(ActionEvent e)
+  protected void analyze_actionPerformed(ActionEvent e)
   {
-  /*  SequenceGroup sg = getGroup();
-    String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE);
-    if(reply==null)
-      return;
-
-    sg.setName(reply);
-    groupName.setLabel(reply);*/
-  }
+    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");
+    }
 
-  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() );
+    sb.append("Something amazing will happen soon");
+    cap.setText(sb.toString());
 
   }
 
@@ -485,46 +491,36 @@ public class APopupMenu extends java.awt.PopupMenu
     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 sequenceName_actionPerformed(ActionEvent e)
+  void unGroupMenuItem_actionPerformed(ActionEvent e)
   {
-  /*  String id = sequence.getName();
-    String s = (String)JOptionPane.showInternalInputDialog(
-                ap,
-                "Edit sequence name",
-                "Edit sequence name ("+sequence.getName()+")",
-                JOptionPane.PLAIN_MESSAGE,
-                null,
-                null,
-                id);
-
-    if(s!=null)
-    {
-      sequence.setName(s);
-      ap.repaint();
-    }*/
-
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    ap.av.alignment.deleteGroup(sg);
+    ap.av.setSelectionGroup(null);
+    ap.repaint();
   }
 
-  void unGroupMenuItem_actionPerformed(ActionEvent e)
+  public void showColourText_itemStateChanged(ItemEvent itemEvent)
   {
-     SequenceGroup sg = ap.av.getSelectionGroup();
-     ap.av.alignment.deleteGroup(sg);
-     ap.av.setSelectionGroup(null);
-     ap.repaint();
+    getGroup().setColourText(showColourText.getState());
+    refresh();
   }
 
+  public void showText_itemStateChanged(ItemEvent itemEvent)
+  {
+    getGroup().setDisplayText(showText.getState());
+    refresh();
+  }
 
-  protected void outline_actionPerformed(ActionEvent e)
+  public void showBoxes_itemStateChanged(ItemEvent itemEvent)
   {
-  /*  SequenceGroup sg = getGroup();
-    Color col = JColorChooser.showDialog(this, "Select Outline Colour", Color.BLUE);
-    if(col!=null)
-      sg.setOutlineColour(col);*/
+    getGroup().setDisplayBoxes(showBoxes.getState());
+    refresh();
   }
 
 }