X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=803f323d480811fd8f53bea6cf75af3e5de1b38e;hb=83f6c6309e9705037a0853a26da74821c9d4fd12;hp=0d4e3e1203f641356ff28e07ddb8117d17040993;hpb=6f707193c7997803f7e7ae9d17359e6e32b4a7e4;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 0d4e3e1..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) 2006 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
@@ -19,14 +19,16 @@
 
 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.commands.ChangeCaseCommand;
+import jalview.io.AppletFormatAdapter;
 
 public class APopupMenu
     extends java.awt.PopupMenu implements ActionListener, ItemListener
@@ -67,6 +69,8 @@ public class APopupMenu
   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();
@@ -93,9 +97,11 @@ public class APopupMenu
       e.printStackTrace();
     }
 
-    for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
+    for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length;
+         i++)
     {
-      MenuItem item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i] );
+      MenuItem item = new MenuItem(jalview.io.AppletFormatAdapter.
+                                   WRITEABLE_FORMATS[i]);
 
       item.addActionListener(this);
       outputmenu.add(item);
@@ -103,7 +109,7 @@ public class APopupMenu
 
     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());
@@ -121,12 +127,12 @@ 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("|"));
@@ -138,7 +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("$SEQUENCE_ID$"))
@@ -146,190 +154,322 @@ 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);
+        {
+          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==turnColour)
+    }
+    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 == sequenceName)
+    else if (source == sequenceName)
+    {
       editName();
-    else if(source == pdb)
+    }
+    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.av.showAllHiddenSeqs();
     }
 
-    else if(source==editGroupName)
+    else if (source == editGroupName)
     {
       EditNameDialog dialog = new EditNameDialog(
           getGroup().getName(),
           getGroup().getDescription(),
           "       Group Name",
           "Group Description",
-          ap,
-          "Edit Group Name / 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)
+    else if (source == copy)
+    {
       ap.alignFrame.copy_actionPerformed();
-    else if(source==cut)
-      ap.alignFrame.cut_actionPerformed();
-    else if(source==toUpper || source==toLower || source==toggleCase)
+    }
+    else if (source == cut)
     {
-    SequenceGroup sg = ap.av.getSelectionGroup();
-    Vector regions = new Vector();
-    if (sg != null)
+      ap.alignFrame.cut_actionPerformed();
+    }
+    else if(source == editSequence)
     {
-      int start = sg.getStartRes();
-      int end = sg.getEndRes() + 1;
+      SequenceGroup sg = ap.av.getSelectionGroup();
 
-      do
+      if(sg!=null)
       {
-        if (ap.av.hasHiddenColumns)
+        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)
         {
-          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;
+          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)
+      {
+        int start = sg.getStartRes();
+        int end = sg.getEndRes() + 1;
 
-        regions.addElement(new int[]
-                           {start, end});
+        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());
 
-        if (ap.av.hasHiddenColumns)
+        int[][] startEnd = new int[regions.size()][2];
+        for (int i = 0; i < regions.size(); i++)
         {
-          start = ap.av.colSel.adjustForHiddenColumns(end);
-          start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
+          startEnd[i] = (int[]) regions.elementAt(i);
         }
-      }
-      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;
+        }
 
-      String description;
-      int caseChange;
+        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());
 
-      if(source==toggleCase)
-      {
-        description = "Toggle Case";
-        caseChange = ChangeCaseCommand.TOGGLE_CASE;
-      }
-      else if(source==toUpper)
-      {
-        description = "To Upper Case";
-        caseChange = ChangeCaseCommand.TO_UPPER;
       }
-      else
+    }
+    else if(source == sequenceFeature)
+    {
+      SequenceGroup sg = ap.av.getSelectionGroup();
+      if (sg == null)
       {
-        description = "To Lower Case";
-        caseChange = ChangeCaseCommand.TO_LOWER;
+        return;
       }
 
-      ChangeCaseCommand caseCommand = new ChangeCaseCommand(
-          description, sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd, caseChange
-          );
-
-      ap.alignFrame.addHistoryItem(caseCommand);
+      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");
+      }
 
-      ap.av.firePropertyChange("alignment", null,
-                                ap.av.getAlignment().getSequences());
-
-    }
+      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);
+    }
 
   }
 
@@ -345,7 +485,7 @@ public class APopupMenu
 
     cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
         e.getActionCommand(),
-      new Alignment( ap.av.getSelectionAsNewSequence() ),
+        new Alignment(ap.av.getSelectionAsNewSequence()),
         ap.av.showJVSuffix));
 
   }
@@ -355,27 +495,49 @@ public class APopupMenu
     EditNameDialog dialog = new EditNameDialog(
         seq.getName(),
         seq.getDescription(),
-        "       Sequence Name ",
-        "Sequence Description ",
-        ap,
-        "Edit Sequence Name / Description");
+        "       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.repaint();
+      ap.paintAlignment(false);
     }
   }
 
   void addPDB()
   {
-    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);
+    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()
@@ -383,6 +545,7 @@ public class APopupMenu
   {
     groupMenu.setLabel("Group");
     groupMenu.setLabel("Selection");
+    sequenceFeature.addActionListener(this);
 
     editGroupName.addActionListener(this);
     unGroupMenuItem.setLabel("Remove Group");
@@ -416,7 +579,9 @@ public class APopupMenu
     groupMenu.add(editGroupName);
     groupMenu.add(editMenu);
     groupMenu.add(outputmenu);
+    groupMenu.add(sequenceFeature);
     groupMenu.add(menu1);
+
     colourMenu.add(noColourmenuItem);
     colourMenu.add(clustalColour);
     colourMenu.add(BLOSUM62Colour);
@@ -467,6 +632,10 @@ public class APopupMenu
     copy.addActionListener(this);
     editMenu.add(cut);
     cut.addActionListener(this);
+
+    editMenu.add(editSequence);
+    editSequence.addActionListener(this);
+
     editMenu.add(toUpper);
     toUpper.addActionListener(this);
     editMenu.add(toLower);
@@ -489,9 +658,7 @@ public class APopupMenu
 
   void refresh()
   {
-    ap.seqPanel.seqCanvas.repaint();
-    if(ap.overviewPanel!=null)
-      ap.overviewPanel.updateOverviewImage();
+    ap.paintAlignment(true);
   }
 
   protected void clustalColour_actionPerformed()
@@ -553,12 +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.getSequences(ap.av.hiddenRepSequences), 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());
@@ -586,7 +756,8 @@ public class APopupMenu
   {
     SequenceGroup sg = getGroup();
     sg.cs = new PIDColourScheme();
-    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0,
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
+        hiddenRepSequences), 0,
                                              ap.av.alignment.getWidth()));
     refresh();
   }
@@ -597,7 +768,8 @@ public class APopupMenu
 
     sg.cs = new Blosum62ColourScheme();
 
-    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0,
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
+        hiddenRepSequences), 0,
                                              ap.av.alignment.getWidth()));
 
     refresh();
@@ -612,15 +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.getSequences(ap.av.hiddenRepSequences), 0,
+                                        sg.getSequences(ap.av.
+          hiddenRepSequences), 0,
                                         ap.av.alignment.getWidth());
 
       c.calculate();
@@ -639,14 +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;
   }
@@ -656,7 +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()
@@ -680,9 +856,10 @@ public class APopupMenu
   void hideSequences(boolean representGroup)
   {
     SequenceGroup sg = ap.av.getSelectionGroup();
-    if(sg==null || sg.getSize()<1)
+    if (sg == null || sg.getSize() < 1)
     {
-      ap.av.hideSequence(new SequenceI[]{seq});
+      ap.av.hideSequence(new SequenceI[]
+                         {seq});
       return;
     }
 
@@ -707,6 +884,6 @@ public class APopupMenu
     }
 
     ap.av.hideSequence(hseqs);
-    }
+  }
 
 }