X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=1c9b3cd94091c3bb1a19283843fe2472ba0dfccc;hb=c23f28e21e50f93f6e695bdc86247f2700c35869;hp=42546f956aa5b5a812592f896cdc2a7f3a5a79ef;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 42546f9..1c9b3cd 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -21,13 +21,14 @@ package jalview.appletgui;
 
 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
+    extends java.awt.PopupMenu implements ActionListener, ItemListener
 {
   Menu groupMenu = new Menu();
   protected MenuItem clustalColour = new MenuItem();
@@ -45,18 +46,21 @@ public class APopupMenu
   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)
+  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");
+
+  public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
   {
     ///////////////////////////////////////////////////////////
     // If this is activated from the sequence panel, the user may want to
@@ -65,8 +69,7 @@ public class APopupMenu
     // If from the IDPanel, we must display the sequence menu
     //////////////////////////////////////////////////////////
 
-    this.ap = ap;
-    sequence = seq;
+    this.ap = apanel;
 
     try
     {
@@ -78,101 +81,188 @@ public class APopupMenu
     }
 
     SequenceGroup sg = ap.av.getSelectionGroup();
-    if (sg != null)
+
+    if (sg != null && sg.getSize()>0)
     {
       showText.setState(sg.getDisplayText());
       showColourText.setState(sg.getColourText());
       showBoxes.setState(sg.getDisplayBoxes());
+      if (!ap.av.alignment.getGroups().contains(sg))
+      {
+        groupMenu.remove(unGroupMenuItem);
+      }
+
+    }
+    else
+    {
+      remove(groupMenu);
+      remove(editMenu);
     }
 
-    if (!ap.av.alignment.getGroups().contains(sg))
+    if (links!=null)
     {
-      groupMenu.remove(unGroupMenuItem);
+      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;
+
+        if (link.indexOf("$SEQUENCE_ID$") > -1)
+        {
+          String id = seq.getName();
+          if (id.indexOf("|") > -1)
+            id = id.substring(id.lastIndexOf("|") + 1);
+
+          url = link.substring(link.indexOf("|") + 1,
+                               link.indexOf("$SEQUENCE_ID$"))
+              + id +
+              link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
+        }
+        else
+          url = link.substring(link.lastIndexOf("|")+1);
+
+           item.addActionListener(new java.awt.event.ActionListener()
+           {
+               public void actionPerformed(ActionEvent e)
+               {
+                  ap.alignFrame.showURL(url, target);
+               }
+           });
+          linkMenu.add(item);
+      }
+      add(linkMenu);
+
+      if(seq!=null)
+      {
+        item = new MenuItem("Show PDB Structure");
+        item.addActionListener(new java.awt.event.ActionListener()
+        {
+          public void actionPerformed(ActionEvent e)
+          {
+            addPDB(seq);
+          }
+        });
+
+        add(item);
+      }
     }
+  }
 
-    if (seq == null)
+  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==clustalColour)
+      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==copy)
+      ap.alignFrame.copy_actionPerformed();
+    else if(source==cut)
+      ap.alignFrame.cut_actionPerformed();
+    else if(source==toUpper || source==toLower || source==toggleCase)
     {
-      remove(sequenceMenu);
+      SequenceGroup sg = ap.av.getSelectionGroup();
+      if (sg != null)
+      {
+        for (int g = 0; g < sg.getSize(); g++)
+        {
+          if (source == toggleCase)
+            sg.getSequenceAt(g).toggleCase(sg.getStartRes(), sg.getEndRes() + 1);
+          else
+            sg.getSequenceAt(g).changeCase(source == toUpper, sg.getStartRes(),
+                                           sg.getEndRes() + 1);
+        }
+        ap.seqPanel.seqCanvas.repaint();
+      }
     }
 
   }
 
+  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
   {
     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);
-      }
-    });
-    conservationMenuItem.addItemListener(new ItemListener()
-    {
-      public void itemStateChanged(ItemEvent itemEvent)
-      {
-        conservationMenuItem_itemStateChanged(itemEvent);
-      }
-    });
-    abovePIDColour.addItemListener(new ItemListener()
-    {
-      public void itemStateChanged(ItemEvent itemEvent)
-      {
-        abovePIDColour_itemStateChanged(itemEvent);
-      }
-    });
+    nucleotideMenuItem.addActionListener(this);
+    conservationMenuItem.addItemListener(this);
+    abovePIDColour.addItemListener(this);
     colourMenu.setLabel("Group Colour");
     showBoxes.setLabel("Boxes");
     showBoxes.setState(true);
-    showBoxes.addItemListener(new ItemListener()
-    {
-      public void itemStateChanged(ItemEvent itemEvent)
-      {
-        showBoxes_itemStateChanged(itemEvent);
-      }
-    });
+    showBoxes.addItemListener(this);
 
     showText.setLabel("Text");
-    showText.addItemListener(new ItemListener()
-    {
-      public void itemStateChanged(ItemEvent itemEvent)
-      {
-        showText_itemStateChanged(itemEvent);
-      }
-    });
+    showText.addItemListener(this);
     showColourText.setLabel("Colour Text");
-    showColourText.addItemListener(new ItemListener()
-    {
-      public void itemStateChanged(ItemEvent itemEvent)
-      {
-        showColourText_itemStateChanged(itemEvent);
-      }
-    });
+    showColourText.addItemListener(this);
 
     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);
@@ -191,213 +281,143 @@ public class APopupMenu
     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");
 
     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");
 
+    add(editMenu);
+    editMenu.add(copy);
+    copy.addActionListener(this);
+    editMenu.add(cut);
+    cut.addActionListener(this);
+    editMenu.add(toUpper);
+    toUpper.addActionListener(this);
+    editMenu.add(toLower);
+    toLower.addActionListener(this);
+    editMenu.add(toggleCase);
+    toggleCase.addActionListener(this);
+
   }
 
   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_itemStateChanged(ItemEvent ie)
+  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);
-      }
+
+      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()
   {
     new UserDefinedColours(ap, getGroup());
   }
 
-  protected void PIDColour_actionPerformed(ActionEvent e)
+  protected void PIDColour_actionPerformed()
   {
     SequenceGroup sg = getGroup();
     sg.cs = new PIDColourScheme();
@@ -406,7 +426,7 @@ public class APopupMenu
     refresh();
   }
 
-  protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
+  protected void BLOSUM62Colour_actionPerformed()
   {
     SequenceGroup sg = getGroup();
 
@@ -418,15 +438,17 @@ public class APopupMenu
     refresh();
   }
 
-  protected void noColourmenuItem_actionPerformed(ActionEvent e)
+  protected void noColourmenuItem_actionPerformed()
   {
     getGroup().cs = null;
     refresh();
   }
 
-  protected void conservationMenuItem_itemStateChanged(ItemEvent ie)
+  protected void conservationMenuItem_itemStateChanged()
   {
     SequenceGroup sg = getGroup();
+    if(sg.cs==null)
+          return;
 
     if (conservationMenuItem.getState())
     {
@@ -438,54 +460,33 @@ public class APopupMenu
 
       c.calculate();
       c.verdict(false, ap.av.ConsPercGaps);
-      ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
 
-      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();
   }
 
-  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);
@@ -493,19 +494,19 @@ public class APopupMenu
     ap.repaint();
   }
 
-  public void showColourText_itemStateChanged(ItemEvent itemEvent)
+  public void showColourText_itemStateChanged()
   {
     getGroup().setColourText(showColourText.getState());
     refresh();
   }
 
-  public void showText_itemStateChanged(ItemEvent itemEvent)
+  public void showText_itemStateChanged()
   {
     getGroup().setDisplayText(showText.getState());
     refresh();
   }
 
-  public void showBoxes_itemStateChanged(ItemEvent itemEvent)
+  public void showBoxes_itemStateChanged()
   {
     getGroup().setDisplayBoxes(showBoxes.getState());
     refresh();