X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=fde6bb8c91be72c8caacf5a4fdedefd7d05728ef;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=b26bd740e6b4618bd3dd919b3601be13eb944607;hpb=e5e719a4db6db7d165261151d4638547923fa5d2;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index b26bd74..fde6bb8 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
@@ -19,11 +19,13 @@
 
 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.*;
 
@@ -31,6 +33,7 @@ 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();
@@ -64,9 +67,11 @@ public class APopupMenu
   MenuItem pdb = new MenuItem();
   MenuItem hideSeqs = new MenuItem();
   MenuItem repGroup = new MenuItem();
+  MenuItem sequenceName = new MenuItem("Edit Name/Description");
 
   Sequence seq;
   MenuItem revealAll = new MenuItem();
+  Menu menu1 = new Menu();
 
   public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
   {
@@ -89,19 +94,21 @@ public class APopupMenu
       e.printStackTrace();
     }
 
-    for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size()-2; i++)
+    for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length;
+         i++)
     {
-      MenuItem item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.
-                                     elementAt(
-                                         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(false)>0)
+    if (sg != null && sg.getSize() > 0)
     {
+      editGroupName.setLabel(sg.getName());
       showText.setState(sg.getDisplayText());
       showColourText.setState(sg.getColourText());
       showBoxes.setState(sg.getDisplayBoxes());
@@ -117,12 +124,12 @@ public class APopupMenu
       remove(groupMenu);
     }
 
-    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("|"));
@@ -134,7 +141,9 @@ 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("$SEQUENCE_ID$"))
@@ -142,140 +151,263 @@ public class APopupMenu
               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)
-               {
-                  ap.alignFrame.showURL(url, target);
-               }
-           });
-          linkMenu.add(item);
+        {
+          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);
       }
-      if(seq!=null)
+      if (seq != null)
+      {
         seqMenu.add(linkMenu);
+      }
       else
+      {
         add(linkMenu);
+      }
     }
-    if(seq!=null)
+    if (seq != null)
     {
       seqMenu.setLabel(seq.getName());
       repGroup.setLabel("Represent Group with " + seq.getName());
     }
     else
+    {
       remove(seqMenu);
+    }
 
-    if(!ap.av.hasHiddenRows)
+    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)
+    {
       BLOSUM62Colour_actionPerformed();
+    }
     else if (source == noColourmenuItem)
+    {
       noColourmenuItem_actionPerformed();
+    }
     else if (source == conservationMenuItem)
+    {
       conservationMenuItem_itemStateChanged();
+    }
     else if (source == unGroupMenuItem)
+    {
       unGroupMenuItem_actionPerformed();
+    }
 
-    else if(source == pdb)
+    else if (source == sequenceName)
+    {
+      editName();
+    }
+    else if (source == pdb)
+    {
       addPDB();
-    else if(source == hideSeqs)
+    }
+    else if (source == hideSeqs)
+    {
       hideSequences(false);
-    else if(source == repGroup)
+    }
+    else if (source == repGroup)
+    {
       hideSequences(true);
-    else if(source == revealAll)
+    }
+    else if (source == revealAll)
     {
-        ap.av.showAllHiddenSeqs();
-        ap.repaint();
+      ap.av.showAllHiddenSeqs();
     }
 
-    else if(source==copy)
+    else if (source == editGroupName)
+    {
+      EditNameDialog dialog = new EditNameDialog(
+          getGroup().getName(),
+          getGroup().getDescription(),
+          "       Group Name",
+          "Group Description",
+          ap,
+          "Edit Group Name / Description");
+
+      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 == toUpper || source == toLower || source == toggleCase)
     {
       SequenceGroup sg = ap.av.getSelectionGroup();
+      Vector regions = new Vector();
       if (sg != null)
       {
-        for (int g = 0; g < sg.getSize(true); g++)
+        int start = sg.getStartRes();
+        int end = sg.getEndRes() + 1;
+
+        do
+        {
+          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;
+          }
+        }
+        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
         {
-          if (source == toggleCase)
-           ((SequenceI) sg.getSequences(true).elementAt(g))
-          .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);
-          else
-            ((SequenceI) sg.getSequences(true).elementAt(g))
-                .changeCase(source == toUpper, sg.getStartRes(),
-                                           sg.getEndRes() + 1);
+          description = "To Lower Case";
+          caseChange = ChangeCaseCommand.TO_LOWER;
         }
-        ap.seqPanel.seqCanvas.repaint();
+
+        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
+    {
       outputText(evt);
+    }
 
   }
 
   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 );
-      }
-    }
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
 
     Frame frame = new Frame();
     frame.add(cap);
@@ -285,11 +417,29 @@ public class APopupMenu
 
     cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
         e.getActionCommand(),
-        vseqs,
+        new Alignment(ap.av.getSelectionAsNewSequence()),
         ap.av.showJVSuffix));
 
   }
 
+  void editName()
+  {
+    EditNameDialog dialog = new EditNameDialog(
+        seq.getName(),
+        seq.getDescription(),
+        "       Sequence Name",
+        "Sequence Description",
+        ap,
+        "Edit Sequence Name / Description");
+
+    if (dialog.accept)
+    {
+      seq.setName(dialog.getName());
+      seq.setDescription(dialog.getDescription());
+      ap.repaint();
+    }
+  }
+
   void addPDB()
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
@@ -306,6 +456,7 @@ public class APopupMenu
     groupMenu.setLabel("Group");
     groupMenu.setLabel("Selection");
 
+    editGroupName.addActionListener(this);
     unGroupMenuItem.setLabel("Remove Group");
     unGroupMenuItem.addActionListener(this);
 
@@ -317,6 +468,7 @@ public class APopupMenu
     showBoxes.setLabel("Boxes");
     showBoxes.setState(true);
     showBoxes.addItemListener(this);
+    sequenceName.addActionListener(this);
 
     showText.setLabel("Text");
     showText.addItemListener(this);
@@ -328,19 +480,15 @@ public class APopupMenu
     hideSeqs.setLabel("Hide Sequences");
     repGroup.setLabel("Represent Group with");
     revealAll.setLabel("Reveal All");
-
+    menu1.setLabel("Group");
     add(groupMenu);
     this.add(seqMenu);
     this.add(hideSeqs);
     this.add(revealAll);
+    groupMenu.add(editGroupName);
     groupMenu.add(editMenu);
     groupMenu.add(outputmenu);
-    groupMenu.addSeparator();
-    groupMenu.add(unGroupMenuItem);
-    groupMenu.add(colourMenu);
-    groupMenu.add(showBoxes);
-    groupMenu.add(showText);
-    groupMenu.add(showColourText);
+    groupMenu.add(menu1);
     colourMenu.add(noColourmenuItem);
     colourMenu.add(clustalColour);
     colourMenu.add(BLOSUM62Colour);
@@ -396,27 +544,35 @@ public class APopupMenu
     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)
+    if (ap.overviewPanel != null)
+    {
       ap.overviewPanel.updateOverviewImage();
+    }
   }
 
   protected void clustalColour_actionPerformed()
   {
     SequenceGroup sg = getGroup();
-    sg.cs = new ClustalxColourScheme(sg.getSequences(true), ap.av.alignment.getWidth());
+    sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
+                                     ap.av.alignment.getWidth());
     refresh();
   }
 
@@ -471,12 +627,15 @@ 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.getSequences(true), 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());
@@ -504,7 +663,8 @@ public class APopupMenu
   {
     SequenceGroup sg = getGroup();
     sg.cs = new PIDColourScheme();
-    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
+        hiddenRepSequences), 0,
                                              ap.av.alignment.getWidth()));
     refresh();
   }
@@ -515,7 +675,8 @@ public class APopupMenu
 
     sg.cs = new Blosum62ColourScheme();
 
-    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
+        hiddenRepSequences), 0,
                                              ap.av.alignment.getWidth()));
 
     refresh();
@@ -530,15 +691,18 @@ 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.getSequences(true), 0,
+                                        sg.getSequences(ap.av.
+          hiddenRepSequences), 0,
                                         ap.av.alignment.getWidth());
 
       c.calculate();
@@ -557,14 +721,15 @@ 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;
   }
@@ -598,30 +763,34 @@ public class APopupMenu
   void hideSequences(boolean representGroup)
   {
     SequenceGroup sg = ap.av.getSelectionGroup();
-    if(sg==null || sg.getSize(false)<1)
+    if (sg == null || sg.getSize() < 1)
     {
-      ap.av.hideSequence(seq);
+      ap.av.hideSequence(new SequenceI[]
+                         {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.av.setSelectionGroup(null);
-      ap.repaint();
-      refresh();
+    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);
+  }
+
 }