X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=6d3f073abfd2d5341407a02e30f777b9cac19894;hb=1a56a24b084eadd78387eabf71dc7114e356bd00;hp=5a98d55dafc0813b395c79c3798339ec22c32d4e;hpb=821c04574cbf7c2d5ba5e80b9319ca7304317d58;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 5a98d55..6d3f073 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
@@ -21,11 +21,9 @@ package jalview.gui;
 import MCview.*;
 
 import jalview.analysis.*;
-
 import jalview.datamodel.*;
-
-
 import jalview.schemes.*;
+import jalview.commands.ChangeCaseCommand;
 
 import java.awt.*;
 import java.awt.event.*;
@@ -81,7 +79,8 @@ public class PopupMenu extends JPopupMenu
   JMenuItem pdbFromFile = new JMenuItem();
   JMenuItem enterPDB = new JMenuItem();
   JMenuItem discoverPDB = new JMenuItem();
-  JMenuItem jMenuItem1 = new JMenuItem();
+  JMenu outputMenu = new JMenu();
+  JMenuItem sequenceFeature = new JMenuItem();
 
   /**
      * Creates a new PopupMenu object.
@@ -115,11 +114,10 @@ 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)
@@ -128,7 +126,8 @@ public class PopupMenu extends JPopupMenu
             }
           });
 
-    }
+          outputMenu.add(item);
+        }
 
 
         try
@@ -143,8 +142,7 @@ public class PopupMenu extends JPopupMenu
 
         if (seq != null)
         {
-          int start = Math.max(sequence.getName().length()-15, 0);
-          sequenceMenu.setText(sequence.getName().substring(start));
+          sequenceMenu.setText(sequence.getName());
 
           JMenuItem menuItem;
           if( seq.getDatasetSequence().getPDBId() != null)
@@ -206,7 +204,6 @@ public class PopupMenu extends JPopupMenu
                 public void actionPerformed(ActionEvent e)
                 {
                   ap.av.showSequence(index);
-                  ap.repaint();
                   if (ap.overviewPanel != null)
                     ap.overviewPanel.updateOverviewImage();
                 }
@@ -220,10 +217,9 @@ public class PopupMenu extends JPopupMenu
                   public void actionPerformed(ActionEvent e)
                   {
                     ap.av.showAllHiddenSeqs();
-                    ap.repaint();
                     if (ap.overviewPanel != null)
                       ap.overviewPanel.updateOverviewImage();
-                      }
+                    }
                 });
 
             add(menuItem);
@@ -352,7 +348,10 @@ public class PopupMenu extends JPopupMenu
 
             linkMenu.add(item);
           }
-          sequenceMenu.add(linkMenu);
+          if(sequence!=null)
+            sequenceMenu.add(linkMenu);
+          else
+            add(linkMenu);
         }
     }
 
@@ -450,7 +449,7 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        upperCase_actionPerformed(e);
+        changeCase(e);
       }
     });
     copy.setText("Copy");
@@ -466,7 +465,7 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        lowerCase_actionPerformed(e);
+        changeCase(e);
       }
     });
     toggle.setText("Toggle Case");
@@ -474,7 +473,7 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        toggle_actionPerformed(e);
+        changeCase(e);
       }
     });
     pdbMenu.setText("Associate Structure with Sequence");
@@ -502,21 +501,31 @@ public class PopupMenu extends JPopupMenu
         discoverPDB_actionPerformed(e);
       }
     });
-    jMenuItem1.setText("Output to Textbox...");
+    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);
     groupMenu.add(editMenu);
-    groupMenu.add(jMenuItem1);
+    groupMenu.add(outputMenu);
+    groupMenu.addSeparator();
+    groupMenu.add(sequenceFeature);
     groupMenu.addSeparator();
     groupMenu.add(groupName);
     groupMenu.add(unGroupMenuItem);
-        groupMenu.add(colourMenu);
+    groupMenu.add(colourMenu);
     groupMenu.add(showBoxes);
-        groupMenu.add(showText);
-        groupMenu.add(showColourText);
+    groupMenu.add(showText);
+    groupMenu.add(showColourText);
     groupMenu.add(outline);
-        sequenceMenu.add(sequenceName);
+    sequenceMenu.add(sequenceName);
     sequenceMenu.add(pdbMenu);
     colourMenu.add(noColourmenuItem);
         colourMenu.add(clustalColour);
@@ -687,7 +696,7 @@ public class PopupMenu extends JPopupMenu
         if (ap.overviewPanel != null)
           ap.overviewPanel.updateOverviewImage();
 
-        ap.seqPanel.repaint();
+        PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
     }
 
     /**
@@ -804,9 +813,9 @@ public class PopupMenu extends JPopupMenu
 
         if (abovePIDColour.isSelected())
         {
-            sg.cs.setConsensus(AAFrequency.calculate(
-                    sg.getSequences(true), 0,
-                    ap.av.alignment.getWidth()));
+          sg.cs.setConsensus(AAFrequency.calculate(
+              sg.getSequences(true), sg.getStartRes(),
+              sg.getEndRes() + 1));
 
             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
                     getGroup().getName());
@@ -841,6 +850,7 @@ public class PopupMenu extends JPopupMenu
 
          sg.cs = udc;
        }
+       refresh();
      }
     /**
      * DOCUMENT ME!
@@ -851,8 +861,9 @@ public class PopupMenu extends JPopupMenu
     {
         SequenceGroup sg = getGroup();
         sg.cs = new PIDColourScheme();
-        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
-                ap.av.alignment.getWidth()));
+        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),
+                                                 sg.getStartRes(),
+                                                 sg.getEndRes() + 1));
         refresh();
     }
 
@@ -867,8 +878,9 @@ public class PopupMenu extends JPopupMenu
 
         sg.cs = new Blosum62ColourScheme();
 
-        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
-                ap.av.alignment.getWidth()));
+        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),
+                                                 sg.getStartRes(),
+                                                 sg.getEndRes() + 1));
 
         refresh();
     }
@@ -899,8 +911,9 @@ public class PopupMenu extends JPopupMenu
         {
             Conservation c = new Conservation("Group",
                     ResidueProperties.propHash, 3,
-                    sg.getSequences(true), 0,
-                    ap.av.alignment.getWidth());
+                    sg.getSequences(true),
+                    sg.getStartRes(),
+                    sg.getEndRes() + 1);
 
             c.calculate();
             c.verdict(false, ap.av.ConsPercGaps);
@@ -1027,13 +1040,15 @@ public class PopupMenu extends JPopupMenu
             }
 
             s = s.replace(' ', '_');
-            sequence.getDatasetSequence().setName(s);
             sequence.setName(s);
             ap.repaint();
         }
 
-        sequence.getDatasetSequence().setDescription(description.getText());
         sequence.setDescription(description.getText());
+
+        ap.av.firePropertyChange("alignment", null,
+                                  ap.av.getAlignment().getSequences());
+
     }
 
     /**
@@ -1125,28 +1140,32 @@ 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);
-        ap.repaint();
-        refresh();
     }
 
   public void copy_actionPerformed(ActionEvent e)
@@ -1159,47 +1178,78 @@ public class PopupMenu extends JPopupMenu
     ap.alignFrame.cut_actionPerformed(null);
   }
 
-  public void upperCase_actionPerformed(ActionEvent e)
+  void changeCase(ActionEvent e)
   {
+    Object source = e.getSource();
     SequenceGroup sg = ap.av.getSelectionGroup();
-    if(sg==null)
-      return;
-
-    for(int g=0; g<sg.getSize(true); g++)
+    Vector regions = new Vector();
+    if (sg != null)
     {
-    ( (SequenceI)sg.getSequences(true).elementAt(g))
-        .changeCase(true, sg.getStartRes(), sg.getEndRes()+1);
-    }
-    ap.repaint();
-  }
+      int start = sg.getStartRes();
+      int end = sg.getEndRes() + 1;
 
-  public void lowerCase_actionPerformed(ActionEvent e)
-  {
-    SequenceGroup sg = ap.av.getSelectionGroup();
-    if(sg==null)
-      return;
+      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;
+        }
 
-    for(int g=0; g<sg.getSize(true); g++)
-    {
-       ( (SequenceI)sg.getSequences(true).elementAt(g))
-           .changeCase(false, sg.getStartRes(), sg.getEndRes()+1);
-    }
-    ap.repaint();
-  }
+        regions.addElement(new int[]
+                           {start, end});
 
-  public void toggle_actionPerformed(ActionEvent e)
-  {
-    SequenceGroup sg = ap.av.getSelectionGroup();
-    if (sg == null)
-      return;
+        if (ap.av.hasHiddenColumns)
+        {
+          start = ap.av.colSel.adjustForHiddenColumns(end);
+          start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
+        }
+      }
+      while (end < sg.getEndRes());
 
-    for (int g = 0; g < sg.getSize(true); g++)
-    {
-      ( (SequenceI)sg.getSequences(true).elementAt(g))
-          .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);
-    }
+      int[][] startEnd = new int[regions.size()][2];
+      for (int i = 0; i < regions.size(); i++)
+      {
+        startEnd[i] = (int[]) regions.elementAt(i);
+      }
 
-    ap.repaint();
+
+      String description;
+      int caseChange;
+
+      if(source==toggle)
+      {
+        description = "Toggle Case";
+        caseChange = ChangeCaseCommand.TOGGLE_CASE;
+      }
+      else if(source==upperCase)
+      {
+        description = "To Upper Case";
+        caseChange = ChangeCaseCommand.TO_UPPER;
+      }
+      else
+      {
+        description = "To Lower Case";
+        caseChange = ChangeCaseCommand.TO_LOWER;
+      }
+
+      ChangeCaseCommand caseCommand = new ChangeCaseCommand(
+          description, sg.getSequencesAsArray(true), startEnd, caseChange
+          );
+
+      ap.alignFrame.addHistoryItem(caseCommand);
+
+
+      ap.av.firePropertyChange("alignment", null,
+                                ap.av.getAlignment().getSequences());
+
+    }
   }
 
   public void outputText_actionPerformed(ActionEvent e)
@@ -1274,18 +1324,6 @@ public class PopupMenu extends JPopupMenu
 
   public void enterPDB_actionPerformed(ActionEvent e)
   {
-    int size = (ap.av.getSelectionGroup() == null ? 0 :
-                ap.av.getSelectionGroup().getSize(false));
-
-    if (size == 0 || size > 1)
-    {
-      JOptionPane.showInternalMessageDialog(
-          Desktop.desktop,
-          "Select a single sequence to specify a PDB id for first",
-          "Select Single Selected", JOptionPane.WARNING_MESSAGE);
-      return;
-    }
-
     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
         "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
 
@@ -1293,7 +1331,7 @@ public class PopupMenu extends JPopupMenu
     {
       PDBEntry entry = new PDBEntry();
       entry.setId(id);
-      ap.av.getSelectionGroup().getSequenceAt(0).getDatasetSequence()
+      sequence.getDatasetSequence()
           .addPDBId(entry);
     }
   }
@@ -1303,4 +1341,31 @@ public class PopupMenu extends JPopupMenu
     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);
+    }
+  }
 }