X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=be4a599e748fff68acfd4eb65e4690c85cc7d4b1;hb=19795496c99500c7ea09dcadb39140566478a97b;hp=8f6e49f44740cad34fa0f08a384677204afa3b56;hpb=e13e34f4fce46de357b79344076ebfa7413ad86f;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 8f6e49f..be4a599 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -59,6 +59,14 @@ public class APopupMenu
   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();
+
+  Sequence seq;
+  MenuItem revealAll = new MenuItem();
 
   public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
   {
@@ -70,6 +78,7 @@ public class APopupMenu
     //////////////////////////////////////////////////////////
 
     this.ap = apanel;
+    this.seq = seq;
 
     try
     {
@@ -80,26 +89,35 @@ public class APopupMenu
       e.printStackTrace();
     }
 
+    for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size()-1; i++)
+    {
+      MenuItem item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.
+                                     elementAt(
+                                         i));
+      item.addActionListener(this);
+      outputmenu.add(item);
+    }
+
     SequenceGroup sg = ap.av.getSelectionGroup();
 
-    if (sg != null && sg.getSize()>0)
+    if (sg != null && sg.getSize(false)>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(hideSeqs);
       remove(groupMenu);
-      remove(editMenu);
     }
 
-    if (!ap.av.alignment.getGroups().contains(sg))
-    {
-      groupMenu.remove(unGroupMenuItem);
-    }
-
-    if (seq != null && links!=null)
+    if (links!=null)
     {
       Menu linkMenu = new Menu("Link");
       MenuItem item;
@@ -109,14 +127,24 @@ public class APopupMenu
         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);
+        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);
+
+        System.out.println("add "+url +" "+target);
            item.addActionListener(new java.awt.event.ActionListener()
            {
                public void actionPerformed(ActionEvent e)
@@ -126,21 +154,21 @@ public class APopupMenu
            });
           linkMenu.add(item);
       }
-      add(linkMenu);
-
-      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)
+        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);
   }
 
   public void itemStateChanged(ItemEvent evt)
@@ -177,19 +205,31 @@ public class APopupMenu
     else if(source==nucleotideMenuItem)
       nucleotideMenuItem_actionPerformed();
 
-    else if(source==userDefinedColour)
-          userDefinedColour_actionPerformed();
-        else if(source==PIDColour)
-       PIDColour_actionPerformed();
-     else if(source==BLOSUM62Colour)
+    else if (source == userDefinedColour)
+      userDefinedColour_actionPerformed();
+    else if (source == PIDColour)
+      PIDColour_actionPerformed();
+    else if (source == BLOSUM62Colour)
       BLOSUM62Colour_actionPerformed();
-    else if(source==noColourmenuItem)
+    else if (source == noColourmenuItem)
       noColourmenuItem_actionPerformed();
-    else if(source==conservationMenuItem)
-        conservationMenuItem_itemStateChanged();
-      else if(source==unGroupMenuItem)
+    else if (source == conservationMenuItem)
+      conservationMenuItem_itemStateChanged();
+    else if (source == unGroupMenuItem)
       unGroupMenuItem_actionPerformed();
 
+    else if(source == pdb)
+      addPDB();
+    else if(source == hideSeqs)
+      hideSequences(false);
+    else if(source == repGroup)
+      hideSequences(true);
+    else if(source == revealAll)
+    {
+        ap.av.showAllHiddenSeqs();
+        ap.repaint();
+    }
+
     else if(source==copy)
       ap.alignFrame.copy_actionPerformed();
     else if(source==cut)
@@ -199,21 +239,58 @@ public class APopupMenu
       SequenceGroup sg = ap.av.getSelectionGroup();
       if (sg != null)
       {
-        for (int g = 0; g < sg.getSize(); g++)
+        for (int g = 0; g < sg.getSize(true); g++)
         {
           if (source == toggleCase)
-            sg.getSequenceAt(g).toggleCase(sg.getStartRes(), sg.getEndRes() + 1);
+           ((SequenceI) sg.getSequences(true).elementAt(g))
+          .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);
           else
-            sg.getSequenceAt(g).changeCase(source == toUpper, sg.getStartRes(),
+            ((SequenceI) sg.getSequences(true).elementAt(g))
+                .changeCase(source == toUpper, sg.getStartRes(),
                                            sg.getEndRes() + 1);
         }
         ap.seqPanel.seqCanvas.repaint();
       }
     }
+    else
+      outputText(evt);
 
   }
 
-  void addPDB(Sequence seq)
+  void outputText(ActionEvent e)
+  {
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
+    Vector vseqs = new Vector();
+
+      String [] selection = ap.av.getViewAsString(true);
+      SequenceI [] seqs = ap.av.getSelectionAsNewSequence();
+      if (selection != null)
+      {
+        for (int i = 0; i < selection.length; i++)
+        {
+          Sequence seq = new Sequence(
+              seqs[i].getName(),
+              selection[i],
+              seqs[i].getStart(), seqs[i].getEnd());
+          seq.setDescription(seqs[i].getDescription());
+          vseqs.addElement( seq );
+      }
+    }
+
+    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(),
+        vseqs,
+        ap.av.showJVSuffix));
+
+  }
+
+  void addPDB()
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
     cap.setText("Paste your PDB file here.");
@@ -227,7 +304,7 @@ public class APopupMenu
       throws Exception
   {
     groupMenu.setLabel("Group");
-    groupMenu.setLabel("Define");
+    groupMenu.setLabel("Selection");
 
     unGroupMenuItem.setLabel("Remove Group");
     unGroupMenuItem.addActionListener(this);
@@ -245,11 +322,22 @@ public class APopupMenu
     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");
 
     add(groupMenu);
+    this.add(seqMenu);
+    this.add(hideSeqs);
+    this.add(revealAll);
+    groupMenu.add(editMenu);
+    groupMenu.add(outputmenu);
+    groupMenu.addSeparator();
     groupMenu.add(unGroupMenuItem);
     groupMenu.add(colourMenu);
-    groupMenu.addSeparator();
     groupMenu.add(showBoxes);
     groupMenu.add(showText);
     groupMenu.add(showColourText);
@@ -299,7 +387,6 @@ public class APopupMenu
     BLOSUM62Colour.addActionListener(this);
     conservationMenuItem.setLabel("Conservation");
 
-    add(editMenu);
     editMenu.add(copy);
     copy.addActionListener(this);
     editMenu.add(cut);
@@ -309,7 +396,13 @@ public class APopupMenu
     editMenu.add(toLower);
     toLower.addActionListener(this);
     editMenu.add(toggleCase);
+    seqMenu.add(pdb);
+    seqMenu.add(repGroup);
     toggleCase.addActionListener(this);
+    pdb.addActionListener(this);
+    hideSeqs.addActionListener(this);
+    repGroup.addActionListener(this);
+    revealAll.addActionListener(this);
 
   }
 
@@ -323,7 +416,7 @@ public class APopupMenu
   protected void clustalColour_actionPerformed()
   {
     SequenceGroup sg = getGroup();
-    sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());
+    sg.cs = new ClustalxColourScheme(sg.getSequences(true), ap.av.alignment.getWidth());
     refresh();
   }
 
@@ -383,7 +476,7 @@ public class APopupMenu
 
     if (abovePIDColour.getState())
     {
-      sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+      sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
                                                ap.av.alignment.getWidth()));
       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
           getGroup().getName());
@@ -411,7 +504,7 @@ public class APopupMenu
   {
     SequenceGroup sg = getGroup();
     sg.cs = new PIDColourScheme();
-    sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
                                              ap.av.alignment.getWidth()));
     refresh();
   }
@@ -422,7 +515,7 @@ public class APopupMenu
 
     sg.cs = new Blosum62ColourScheme();
 
-    sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
                                              ap.av.alignment.getWidth()));
 
     refresh();
@@ -445,7 +538,7 @@ public class APopupMenu
 
       Conservation c = new Conservation("Group",
                                         ResidueProperties.propHash, 3,
-                                        sg.sequences, 0,
+                                        sg.getSequences(true), 0,
                                         ap.av.alignment.getWidth());
 
       c.calculate();
@@ -502,4 +595,33 @@ public class APopupMenu
     refresh();
   }
 
+  void hideSequences(boolean representGroup)
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    if(sg==null || sg.getSize(false)<1)
+    {
+      ap.av.hideSequence(seq);
+      return;
+    }
+
+      int index = 0;
+      while(index < sg.getSize(false))
+      {
+        if(representGroup && sg.getSequenceAt(index)!=seq)
+        {
+          seq.addHiddenSequence(sg.getSequenceAt(index));
+          ap.av.hideSequence(sg.getSequenceAt(index));
+        }
+        else if(!representGroup)
+        {
+          ap.av.hideSequence(sg.getSequenceAt(index));
+        }
+        index ++;
+      }
+
+      ap.av.setSelectionGroup(null);
+      ap.repaint();
+      refresh();
+    }
+
 }