X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=e11830ccb0c15d1c290c006cc6d6ac4961294584;hb=012fc200ee0d124003524855ac7cd50be4b7456c;hp=ddb194ea118992260ccfecb85ab00666521c3782;hpb=d6e1bbede5adc04f34c969213ac6a4c6d9e5d34a;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index ddb194e..e11830c 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.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
@@ -77,7 +77,12 @@ public class PopupMenu extends JPopupMenu
   JMenuItem upperCase = new JMenuItem();
   JMenuItem lowerCase = new JMenuItem();
   JMenuItem toggle = new JMenuItem();
+  JMenu pdbMenu = new JMenu();
+  JMenuItem pdbFromFile = new JMenuItem();
+  JMenuItem enterPDB = new JMenuItem();
+  JMenuItem discoverPDB = new JMenuItem();
   JMenu outputMenu = new JMenu();
+  JMenuItem sequenceFeature = new JMenuItem();
 
   /**
      * Creates a new PopupMenu object.
@@ -111,11 +116,10 @@ public class PopupMenu extends JPopupMenu
         colours.add(PIDColour);
         colours.add(BLOSUM62Colour);
 
-        for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)
+        for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
         {
-          JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
-                                         elementAt(
-                                             i));
+          JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );
+
           item.addActionListener(new java.awt.event.ActionListener()
           {
             public void actionPerformed(ActionEvent e)
@@ -140,11 +144,15 @@ public class PopupMenu extends JPopupMenu
 
         if (seq != null)
         {
+          int start = Math.max(sequence.getName().length()-15, 0);
+          sequenceMenu.setText(sequence.getName().substring(start));
+
           JMenuItem menuItem;
           if( seq.getDatasetSequence().getPDBId() != null)
           {
             java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
                 elements();
+
             while (e.hasMoreElements())
             {
               final PDBEntry pdb = (PDBEntry) e.nextElement();
@@ -170,7 +178,7 @@ public class PopupMenu extends JPopupMenu
                   hideSequences(false);
                 }
               });
-          sequenceMenu.add(menuItem);
+          add(menuItem);
 
           if(ap.av.getSelectionGroup() !=null
              && ap.av.getSelectionGroup().getSize(false)>1)
@@ -193,18 +201,17 @@ public class PopupMenu extends JPopupMenu
             if (ap.av.adjustForHiddenSeqs(index) -
                 ap.av.adjustForHiddenSeqs(index - 1) > 1)
             {
-              menuItem = new JMenuItem("Reveal");
+              menuItem = new JMenuItem("Reveal Sequences");
               menuItem.addActionListener(new ActionListener()
               {
                 public void actionPerformed(ActionEvent e)
                 {
                   ap.av.showSequence(index);
-                  ap.repaint();
                   if (ap.overviewPanel != null)
                     ap.overviewPanel.updateOverviewImage();
                 }
               });
-              sequenceMenu.add(menuItem);
+              add(menuItem);
             }
 
             menuItem = new JMenuItem("Reveal All");
@@ -213,16 +220,12 @@ public class PopupMenu extends JPopupMenu
                   public void actionPerformed(ActionEvent e)
                   {
                     ap.av.showAllHiddenSeqs();
-                    ap.repaint();
                     if (ap.overviewPanel != null)
                       ap.overviewPanel.updateOverviewImage();
-                      }
+                    }
                 });
 
-            sequenceMenu.add(menuItem);
-
-
-
+            add(menuItem);
           }
 
 
@@ -304,14 +307,12 @@ public class PopupMenu extends JPopupMenu
         {
             unGroupMenuItem.setVisible(false);
         }
-        else
-        {
-            groupMenu.insertSeparator(3);
-        }
+
 
         if (seq == null)
         {
             sequenceMenu.setVisible(false);
+            pdbMenu.setVisible(false);
         }
 
         if(links != null && links.size()>0)
@@ -350,7 +351,10 @@ public class PopupMenu extends JPopupMenu
 
             linkMenu.add(item);
           }
-          add(linkMenu);
+          if(sequence!=null)
+            sequenceMenu.add(linkMenu);
+          else
+            add(linkMenu);
         }
     }
 
@@ -363,7 +367,7 @@ public class PopupMenu extends JPopupMenu
     private void jbInit() throws Exception
     {
         groupMenu.setText("Group");
-        groupMenu.setText("Group");
+        groupMenu.setText("Selection");
         groupName.setText("Name");
         groupName.addActionListener(new java.awt.event.ActionListener()
             {
@@ -475,23 +479,58 @@ public class PopupMenu extends JPopupMenu
         toggle_actionPerformed(e);
       }
     });
+    pdbMenu.setText("Associate Structure with Sequence");
+    pdbFromFile.setText("From File");
+    pdbFromFile.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        pdbFromFile_actionPerformed(e);
+      }
+    });
+    enterPDB.setText("Enter PDB Id");
+    enterPDB.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        enterPDB_actionPerformed(e);
+      }
+    });
+    discoverPDB.setText("Discover PDB ids");
+    discoverPDB.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        discoverPDB_actionPerformed(e);
+      }
+    });
     outputMenu.setText("Output to Textbox...");
+    sequenceFeature.setText("Create Sequence Feature");
+    sequenceFeature.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        sequenceFeature_actionPerformed(e);
+      }
+    });
     add(groupMenu);
-        add(sequenceMenu);
-    this.add(editMenu);
-    this.add(outputMenu);
+
+    add(sequenceMenu);
+    groupMenu.add(editMenu);
+    groupMenu.add(outputMenu);
+    groupMenu.addSeparator();
+    groupMenu.add(sequenceFeature);
+    groupMenu.addSeparator();
     groupMenu.add(groupName);
-        groupMenu.addSeparator();
-        groupMenu.add(unGroupMenuItem);
+    groupMenu.add(unGroupMenuItem);
         groupMenu.add(colourMenu);
-        groupMenu.addSeparator();
-        groupMenu.add(showBoxes);
+    groupMenu.add(showBoxes);
         groupMenu.add(showText);
         groupMenu.add(showColourText);
-        groupMenu.addSeparator();
-        groupMenu.add(outline);
+    groupMenu.add(outline);
         sequenceMenu.add(sequenceName);
-        colourMenu.add(noColourmenuItem);
+    sequenceMenu.add(pdbMenu);
+    colourMenu.add(noColourmenuItem);
         colourMenu.add(clustalColour);
         colourMenu.add(BLOSUM62Colour);
         colourMenu.add(PIDColour);
@@ -534,6 +573,9 @@ public class PopupMenu extends JPopupMenu
     editMenu.add(upperCase);
     editMenu.add(lowerCase);
     editMenu.add(toggle);
+    pdbMenu.add(pdbFromFile);
+    pdbMenu.add(enterPDB);
+    pdbMenu.add(discoverPDB);
     noColourmenuItem.setText("None");
         noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
             {
@@ -657,7 +699,7 @@ public class PopupMenu extends JPopupMenu
         if (ap.overviewPanel != null)
           ap.overviewPanel.updateOverviewImage();
 
-        ap.seqPanel.repaint();
+        PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
     }
 
     /**
@@ -811,6 +853,7 @@ public class PopupMenu extends JPopupMenu
 
          sg.cs = udc;
        }
+       refresh();
      }
     /**
      * DOCUMENT ME!
@@ -1095,27 +1138,32 @@ public class PopupMenu extends JPopupMenu
       SequenceGroup sg = ap.av.getSelectionGroup();
       if(sg==null || sg.getSize(false)<1)
       {
-        ap.av.hideSequence(sequence);
+        ap.av.hideSequence(new SequenceI[]{sequence});
         return;
       }
 
+      int gsize = sg.getSize(false);
+      SequenceI [] hseqs;
+
+      hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ];
+
         int index = 0;
-        while(index < sg.getSize(false))
+        for(int i=0; i<gsize; i++)
         {
-          if(representGroup && sg.getSequenceAt(index)!=sequence)
+          if(representGroup && sg.getSequenceAt(i)!=sequence)
           {
-            sequence.addHiddenSequence(sg.getSequenceAt(index));
-            ap.av.hideSequence(sg.getSequenceAt(index));
+            sequence.addHiddenSequence(sg.getSequenceAt(i));
+            hseqs[index++] = sg.getSequenceAt(i);
           }
           else if(!representGroup)
           {
-            ap.av.hideSequence(sg.getSequenceAt(index));
+            hseqs[index++] = sg.getSequenceAt(i);
           }
-          index ++;
         }
 
+        ap.av.hideSequence(hseqs);
+
         ap.av.setSelectionGroup(null);
-        refresh();
     }
 
   public void copy_actionPerformed(ActionEvent e)
@@ -1130,45 +1178,58 @@ public class PopupMenu extends JPopupMenu
 
   public void upperCase_actionPerformed(ActionEvent e)
   {
-    SequenceGroup sg = ap.av.getSelectionGroup();
-    if(sg==null)
-      return;
-
-    for(int g=0; g<sg.getSize(true); g++)
-    {
-    ( (SequenceI)sg.getSequences(true).elementAt(g))
-        .changeCase(true, sg.getStartRes(), sg.getEndRes()+1);
-    }
-    ap.repaint();
+    changeCase(e.getSource());
   }
 
   public void lowerCase_actionPerformed(ActionEvent e)
   {
-    SequenceGroup sg = ap.av.getSelectionGroup();
-    if(sg==null)
-      return;
-
-    for(int g=0; g<sg.getSize(true); g++)
-    {
-       ( (SequenceI)sg.getSequences(true).elementAt(g))
-           .changeCase(false, sg.getStartRes(), sg.getEndRes()+1);
-    }
-    ap.repaint();
+    changeCase(e.getSource());
   }
 
   public void toggle_actionPerformed(ActionEvent e)
   {
-    SequenceGroup sg = ap.av.getSelectionGroup();
-    if (sg == null)
-      return;
+    changeCase(e.getSource());
+  }
 
-    for (int g = 0; g < sg.getSize(true); g++)
+  void changeCase(Object source)
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    if (sg != null)
     {
-      ( (SequenceI)sg.getSequences(true).elementAt(g))
-          .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);
-    }
+      for (int g = 0; g < sg.getSize(true); g++)
+      {
+        int start = sg.getStartRes();
+        int end = sg.getEndRes() + 1;
 
-    ap.repaint();
+        do
+        {
+          if (ap.av.hasHiddenColumns)
+          {
+            end = ap.av.colSel.getHiddenBoundaryRight(start);
+            if (start == end)
+              end = sg.getEndRes() + 1;
+            if (end > sg.getEndRes())
+              end = sg.getEndRes() + 1;
+          }
+
+          if (source == toggle)
+            ( (SequenceI) sg.getSequences(true).elementAt(g))
+                .toggleCase(start, end);
+          else
+            ( (SequenceI) sg.getSequences(true).elementAt(g))
+                .changeCase(source == upperCase, start, end);
+
+          if (ap.av.hasHiddenColumns)
+          {
+            start = ap.av.colSel.adjustForHiddenColumns(end);
+            start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
+          }
+
+        }
+        while (end < sg.getEndRes());
+      }
+      PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
+    }
   }
 
   public void outputText_actionPerformed(ActionEvent e)
@@ -1183,7 +1244,7 @@ public class PopupMenu extends JPopupMenu
     if(ap.av.hasHiddenColumns)
     {
       System.out.println("PROMPT USER HERE");
-      omitHidden = ap.av.getSelectionAsString();
+      omitHidden = ap.av.getViewAsString(true);
     }
 
     cap.setText(new FormatAdapter().formatSequences(
@@ -1191,4 +1252,100 @@ public class PopupMenu extends JPopupMenu
         ap.av.getSelectionAsNewSequence(),
         omitHidden));
   }
+
+
+  public void pdbFromFile_actionPerformed(ActionEvent e)
+  {
+     jalview.io.JalviewFileChooser chooser
+         = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
+         getProperty(
+             "LAST_DIRECTORY"));
+     chooser.setFileView(new jalview.io.JalviewFileView());
+     chooser.setDialogTitle("Select a PDB file");
+     chooser.setToolTipText("Load a PDB file");
+
+     int value = chooser.showOpenDialog(null);
+
+     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+     {
+       PDBEntry entry = new PDBEntry();
+       String choice = chooser.getSelectedFile().getPath();
+       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+       try
+       {
+         MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
+                                       jalview.io.AppletFormatAdapter.FILE);
+
+         if (pdbfile.id == null)
+         {
+           String reply = JOptionPane.showInternalInputDialog(
+               Desktop.desktop,
+               "Couldn't find a PDB id in the file supplied."
+               + "Please enter an Id to identify this structure.",
+               "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
+           if (reply == null)
+             return;
+
+           entry.setId(reply);
+         }
+         else
+           entry.setId(pdbfile.id);
+       }
+       catch (java.io.IOException ex)
+       {
+         ex.printStackTrace();
+       }
+
+       entry.setFile(choice);
+       sequence.getDatasetSequence().addPDBId(entry);
+     }
+
+  }
+
+  public void enterPDB_actionPerformed(ActionEvent e)
+  {
+    String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
+        "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
+
+    if (id != null && id.length() > 0)
+    {
+      PDBEntry entry = new PDBEntry();
+      entry.setId(id);
+      sequence.getDatasetSequence()
+          .addPDBId(entry);
+    }
+  }
+
+  public void discoverPDB_actionPerformed(ActionEvent e)
+  {
+    new jalview.io.DBRefFetcher(
+             ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);
+  }
+
+  public void sequenceFeature_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    if(sg==null)
+      return;
+
+    int gSize= sg.getSize(false);
+    SequenceI [] seqs = new SequenceI[gSize];
+    SequenceFeature [] features = new SequenceFeature[gSize];
+
+    for (int i = 0; i < gSize; i++)
+    {
+      seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
+      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()
+        .createNewFeatures(seqs, features))
+    {
+      ap.alignFrame.showSeqFeatures.setSelected(true);
+      ap.av.setShowSequenceFeatures(true);
+      ap.highlightSearchResults(null);
+    }
+  }
 }