X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=8f1836cfe60b48f1dcd4cc8779106c72a3eda992;hb=d70d7e5bc8da1189f44709b6ec59ea1e23f6f557;hp=1d5eacec0d18ceafc2afdf0f84f50131b49357a1;hpb=3b5ad2b93c9765e2f381ef66dc755184657d7d71;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 1d5eace..8f1836c 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) 2006 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
@@ -26,6 +26,7 @@ import java.util.Vector;
 import jalview.analysis.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
+import jalview.commands.ChangeCaseCommand;
 
 public class APopupMenu
     extends java.awt.PopupMenu implements ActionListener, ItemListener
@@ -58,6 +59,21 @@ public class APopupMenu
   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");
+  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");
+
+  Sequence seq;
+  MenuItem revealAll = new MenuItem();
+  Menu menu1 = new Menu();
+
+  Dialog editNameDialog;
+  Button okDialog = new Button("Accept");
+  Button cancelDialog = new Button("Cancel");;
 
   public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
   {
@@ -69,6 +85,7 @@ public class APopupMenu
     //////////////////////////////////////////////////////////
 
     this.ap = apanel;
+    this.seq = seq;
 
     try
     {
@@ -79,20 +96,34 @@ 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)
+
+    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);
+      }
 
-    if (!ap.av.alignment.getGroups().contains(sg))
+    }
+    else
     {
-      groupMenu.remove(unGroupMenuItem);
+      remove(hideSeqs);
+      remove(groupMenu);
     }
 
-    if (seq != null && links!=null)
+    if (links!=null)
     {
       Menu linkMenu = new Menu("Link");
       MenuItem item;
@@ -102,13 +133,22 @@ 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);
 
            item.addActionListener(new java.awt.event.ActionListener()
            {
@@ -119,21 +159,21 @@ 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)
@@ -163,60 +203,187 @@ public class APopupMenu
       helixColour_actionPerformed();
     else if(source==strandColour)
       strandColour_actionPerformed();
-    else if(source==clustalColour)
+    else if(source==turnColour)
       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)
+    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 == sequenceName)
+      editName();
+    else if (source==okDialog || source==cancelDialog)
+    {
+      editNameDialog.setVisible(false);
+      if(source==cancelDialog)
+        editNameDialog = null;
+    }
+    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==copy)
       ap.alignFrame.copy_actionPerformed();
     else if(source==cut)
       ap.alignFrame.cut_actionPerformed();
-    else if(source==toUpper)
+    else if(source==toUpper || source==toLower || source==toggleCase)
     {
-      SequenceGroup sg = ap.av.getSelectionGroup();
-      if (sg != null)
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    Vector regions = new Vector();
+    if (sg != null)
+    {
+      int start = sg.getStartRes();
+      int end = sg.getEndRes() + 1;
+
+      do
       {
-        for (int g = 0; g < sg.getSize(); g++)
+        if (ap.av.hasHiddenColumns)
         {
-          sg.getSequenceAt(g).changeCase(true, sg.getStartRes(),
-                                         sg.getEndRes() + 1);
+          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;
         }
-        ap.seqPanel.seqCanvas.repaint();
-      }
-    }
-    else if(source==toLower)
-    {
-      SequenceGroup sg = ap.av.getSelectionGroup();
-      if (sg != null)
-      {
-        for (int g = 0; g < sg.getSize(); g++)
+
+        regions.addElement(new int[]
+                           {start, end});
+
+        if (ap.av.hasHiddenColumns)
         {
-          sg.getSequenceAt(g).changeCase(false, sg.getStartRes(),
-                                         sg.getEndRes() + 1);
+          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
+      outputText(evt);
 
   }
 
-  void addPDB(Sequence seq)
+  void outputText(ActionEvent e)
+  {
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
+
+    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(),
+      new Alignment( ap.av.getSelectionAsNewSequence() ),
+        ap.av.showJVSuffix));
+
+  }
+
+  void editName()
+  {
+    TextField id = new TextField(seq.getName(), 40);
+    TextField description = new TextField(seq.getDescription(), 40);
+    Panel panel = new Panel(new BorderLayout());
+    Panel panel2 = new Panel(new BorderLayout());
+    panel2.add(new Label("       Sequence Name "), BorderLayout.WEST);
+    panel2.add(id, BorderLayout.CENTER);
+    panel.add(panel2, BorderLayout.NORTH);
+    panel2 = new Panel(new BorderLayout());
+    panel2.add(new Label("Sequence Description "), BorderLayout.WEST);
+    panel2.add(description, BorderLayout.CENTER);
+    panel.add(panel2, BorderLayout.CENTER);
+
+    panel2 = new Panel(new FlowLayout());
+
+    panel2.add(okDialog);
+    panel2.add(cancelDialog);
+
+    panel.add(panel2, BorderLayout.SOUTH);
+
+    editNameDialog = new Dialog(ap.alignFrame,
+      "Edit Sequence Name / Description",
+      true);
+
+    editNameDialog.add(panel, BorderLayout.NORTH);
+
+    editNameDialog.setBounds(ap.alignFrame.getBounds().x
+                             +(ap.alignFrame.getSize().width-500)/2 ,
+                             ap.alignFrame.getBounds().y
+                             +(ap.alignFrame.getSize().height-120)/2,
+                             500, 120);
+
+    editNameDialog.show();
+
+    if (editNameDialog != null)
+    {
+      seq.setName(id.getText());
+      seq.setDescription(description.getText());
+      ap.repaint();
+    }
+  }
+
+  void addPDB()
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
     cap.setText("Paste your PDB file here.");
@@ -230,7 +397,7 @@ public class APopupMenu
       throws Exception
   {
     groupMenu.setLabel("Group");
-    groupMenu.setLabel("Define");
+    groupMenu.setLabel("Selection");
 
     unGroupMenuItem.setLabel("Remove Group");
     unGroupMenuItem.addActionListener(this);
@@ -243,19 +410,26 @@ 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(editMenu);
+    groupMenu.add(outputmenu);
+    groupMenu.add(menu1);
     colourMenu.add(noColourmenuItem);
     colourMenu.add(clustalColour);
     colourMenu.add(BLOSUM62Colour);
@@ -302,7 +476,6 @@ public class APopupMenu
     BLOSUM62Colour.addActionListener(this);
     conservationMenuItem.setLabel("Conservation");
 
-    add(editMenu);
     editMenu.add(copy);
     copy.addActionListener(this);
     editMenu.add(cut);
@@ -311,6 +484,22 @@ public class APopupMenu
     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);
+    okDialog.addActionListener(this);
+    cancelDialog.addActionListener(this);
 
   }
 
@@ -324,7 +513,8 @@ 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(ap.av.hiddenRepSequences),
+                                     ap.av.alignment.getWidth());
     refresh();
   }
 
@@ -384,7 +574,7 @@ public class APopupMenu
 
     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());
@@ -412,7 +602,7 @@ 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(ap.av.hiddenRepSequences), 0,
                                              ap.av.alignment.getWidth()));
     refresh();
   }
@@ -423,7 +613,7 @@ 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();
@@ -446,7 +636,7 @@ public class APopupMenu
 
       Conservation c = new Conservation("Group",
                                         ResidueProperties.propHash, 3,
-                                        sg.sequences, 0,
+                                        sg.getSequences(ap.av.hiddenRepSequences), 0,
                                         ap.av.alignment.getWidth());
 
       c.calculate();
@@ -503,4 +693,36 @@ 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);
+    }
+
 }