X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=803f323d480811fd8f53bea6cf75af3e5de1b38e;hb=feaa53e0e6dea15a236b99097347df52c21db896;hp=1c9b3cd94091c3bb1a19283843fe2472ba0dfccc;hpb=f441357783f32298b738d32d5c87000ac0e33768;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 1c9b3cd..803f323 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 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
@@ -19,18 +19,22 @@
 
 package jalview.appletgui;
 
+import java.util.*;
+
 import java.awt.*;
 import java.awt.event.*;
-import java.util.Vector;
 
 import jalview.analysis.*;
+import jalview.commands.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
+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();
@@ -59,6 +63,18 @@ 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();
+  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)
   {
@@ -70,6 +86,7 @@ public class APopupMenu
     //////////////////////////////////////////////////////////
 
     this.ap = apanel;
+    this.seq = seq;
 
     try
     {
@@ -80,10 +97,21 @@ public class APopupMenu
       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)
+    if (sg != null && sg.getSize() > 0)
     {
+      editGroupName.setLabel(sg.getName());
       showText.setState(sg.getDisplayText());
       showColourText.setState(sg.getColourText());
       showBoxes.setState(sg.getDisplayBoxes());
@@ -95,16 +123,16 @@ public class APopupMenu
     }
     else
     {
+      remove(hideSeqs);
       remove(groupMenu);
-      remove(editMenu);
     }
 
-    if (links!=null)
+    if (links != null)
     {
       Menu linkMenu = new Menu("Link");
       MenuItem item;
       String link;
-      for(int i=0; i<links.size(); i++)
+      for (int i = 0; i < links.size(); i++)
       {
         link = links.elementAt(i).toString();
         final String target = link.substring(0, link.indexOf("|"));
@@ -116,7 +144,9 @@ public class APopupMenu
         {
           String id = seq.getName();
           if (id.indexOf("|") > -1)
+          {
             id = id.substring(id.lastIndexOf("|") + 1);
+          }
 
           url = link.substring(link.indexOf("|") + 1,
                                link.indexOf("$SEQUENCE_ID$"))
@@ -124,121 +154,400 @@ public class APopupMenu
               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);
+        {
+          url = link.substring(link.lastIndexOf("|") + 1);
+        }
 
-      if(seq!=null)
-      {
-        item = new MenuItem("Show PDB Structure");
         item.addActionListener(new java.awt.event.ActionListener()
         {
           public void actionPerformed(ActionEvent e)
           {
-            addPDB(seq);
+            ap.alignFrame.showURL(url, target);
           }
         });
-
-        add(item);
+        linkMenu.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)
   {
-    if(evt.getSource()==abovePIDColour)
+    if (evt.getSource() == abovePIDColour)
+    {
       abovePIDColour_itemStateChanged();
-    else if(evt.getSource()==showColourText)
+    }
+    else if (evt.getSource() == showColourText)
+    {
       showColourText_itemStateChanged();
-    else if(evt.getSource()==showText)
+    }
+    else if (evt.getSource() == showText)
+    {
       showText_itemStateChanged();
-    else if(evt.getSource()==showBoxes)
-       showBoxes_itemStateChanged()   ;
+    }
+    else if (evt.getSource() == showBoxes)
+    {
+      showBoxes_itemStateChanged();
+    }
   }
 
   public void actionPerformed(ActionEvent evt)
   {
     Object source = evt.getSource();
-    if(source==clustalColour)
+    if (source == clustalColour)
+    {
       clustalColour_actionPerformed();
-    else if(source==zappoColour)
+    }
+    else if (source == zappoColour)
+    {
       zappoColour_actionPerformed();
-    else if(source==taylorColour)
+    }
+    else if (source == taylorColour)
+    {
       taylorColour_actionPerformed();
-    else if(source==hydrophobicityColour)
+    }
+    else if (source == hydrophobicityColour)
+    {
       hydrophobicityColour_actionPerformed();
-    else if(source==helixColour)
+    }
+    else if (source == helixColour)
+    {
       helixColour_actionPerformed();
-    else if(source==strandColour)
+    }
+    else if (source == strandColour)
+    {
       strandColour_actionPerformed();
-    else if(source==clustalColour)
+    }
+    else if (source == turnColour)
+    {
       turnColour_actionPerformed();
-    else if(source==buriedColour)
+    }
+    else if (source == buriedColour)
+    {
       buriedColour_actionPerformed();
-    else if(source==nucleotideMenuItem)
+    }
+    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==copy)
+    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)
+    }
+    else if (source == cut)
+    {
       ap.alignFrame.cut_actionPerformed();
-    else if(source==toUpper || source==toLower || source==toggleCase)
+    }
+    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)
       {
-        for (int g = 0; g < sg.getSize(); g++)
+        int start = sg.getStartRes();
+        int end = sg.getEndRes() + 1;
+
+        do
         {
-          if (source == toggleCase)
-            sg.getSequenceAt(g).toggleCase(sg.getStartRes(), sg.getEndRes() + 1);
-          else
-            sg.getSequenceAt(g).changeCase(source == toUpper, sg.getStartRes(),
-                                           sg.getEndRes() + 1);
+          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;
+          }
         }
-        ap.seqPanel.seqCanvas.repaint();
+        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 gSize = sg.getSize();
+      SequenceI[] seqs = new SequenceI[gSize];
+      SequenceFeature[] features = new SequenceFeature[gSize];
+
+      for (int i = 0; i < gSize; i++)
+      {
+        seqs[i] = sg.getSequenceAt(i);
+        int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
+        int end = sg.findEndRes(sg.getSequenceAt(i));
+        features[i] = new SequenceFeature(null, null, null, start, end,
+                                          "Jalview");
+      }
+
+      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 addPDB(Sequence seq)
+  void outputText(ActionEvent e)
   {
     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);
+    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("Define");
+    groupMenu.setLabel("Selection");
+    sequenceFeature.addActionListener(this);
 
+    editGroupName.addActionListener(this);
     unGroupMenuItem.setLabel("Remove Group");
     unGroupMenuItem.addActionListener(this);
 
@@ -250,19 +559,29 @@ public class APopupMenu
     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);
-    groupMenu.add(unGroupMenuItem);
-    groupMenu.add(colourMenu);
-    groupMenu.addSeparator();
-    groupMenu.add(showBoxes);
-    groupMenu.add(showText);
-    groupMenu.add(showColourText);
+    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);
@@ -309,31 +628,44 @@ public class APopupMenu
     BLOSUM62Colour.addActionListener(this);
     conservationMenuItem.setLabel("Conservation");
 
-    add(editMenu);
     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.seqPanel.seqCanvas.repaint();
-    if(ap.overviewPanel!=null)
-      ap.overviewPanel.updateOverviewImage();
+    ap.paintAlignment(true);
   }
 
   protected void clustalColour_actionPerformed()
   {
     SequenceGroup sg = getGroup();
-    sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());
+    sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
+                                     ap.av.alignment.getWidth());
     refresh();
   }
 
@@ -388,12 +720,15 @@ public class APopupMenu
   protected void abovePIDColour_itemStateChanged()
   {
     SequenceGroup sg = getGroup();
-    if(sg.cs==null)
-          return;
+    if (sg.cs == null)
+    {
+      return;
+    }
 
     if (abovePIDColour.getState())
     {
-      sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+      sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
+          hiddenRepSequences), 0,
                                                ap.av.alignment.getWidth()));
       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
           getGroup().getName());
@@ -421,7 +756,8 @@ 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(ap.av.
+        hiddenRepSequences), 0,
                                              ap.av.alignment.getWidth()));
     refresh();
   }
@@ -432,7 +768,8 @@ public class APopupMenu
 
     sg.cs = new Blosum62ColourScheme();
 
-    sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
+        hiddenRepSequences), 0,
                                              ap.av.alignment.getWidth()));
 
     refresh();
@@ -447,15 +784,18 @@ public class APopupMenu
   protected void conservationMenuItem_itemStateChanged()
   {
     SequenceGroup sg = getGroup();
-    if(sg.cs==null)
-          return;
+    if (sg.cs == null)
+    {
+      return;
+    }
 
     if (conservationMenuItem.getState())
     {
 
       Conservation c = new Conservation("Group",
                                         ResidueProperties.propHash, 3,
-                                        sg.sequences, 0,
+                                        sg.getSequences(ap.av.
+          hiddenRepSequences), 0,
                                         ap.av.alignment.getWidth());
 
       c.calculate();
@@ -474,14 +814,15 @@ public class APopupMenu
     refresh();
   }
 
-
   SequenceGroup getGroup()
   {
     SequenceGroup sg = ap.av.getSelectionGroup();
 
     // this method won't add a new group if it already exists
-    if(sg!=null)
+    if (sg != null)
+    {
       ap.av.alignment.addGroup(sg);
+    }
 
     return sg;
   }
@@ -491,7 +832,7 @@ public class APopupMenu
     SequenceGroup sg = ap.av.getSelectionGroup();
     ap.av.alignment.deleteGroup(sg);
     ap.av.setSelectionGroup(null);
-    ap.repaint();
+    ap.paintAlignment(true);
   }
 
   public void showColourText_itemStateChanged()
@@ -512,4 +853,37 @@ public class APopupMenu
     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);
+  }
+
 }