X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=9ed81abb1cb5984c3603944798777a07342f4f66;hb=e9f4df7b610b6bbe64a1447641b8dffdfc3a78c6;hp=3481a3103dd6cecc052a2a7198940f8e55ffe637;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 3481a31..9ed81ab 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -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.*;
@@ -82,6 +80,9 @@ public class PopupMenu extends JPopupMenu
   JMenuItem enterPDB = new JMenuItem();
   JMenuItem discoverPDB = new JMenuItem();
   JMenu outputMenu = new JMenu();
+  JMenuItem sequenceFeature = new JMenuItem();
+  JMenuItem textColour = new JMenuItem();
+  JMenu jMenu1 = new JMenu();
 
   /**
      * Creates a new PopupMenu object.
@@ -143,8 +144,7 @@ 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)
@@ -180,7 +180,7 @@ public class PopupMenu extends JPopupMenu
           add(menuItem);
 
           if(ap.av.getSelectionGroup() !=null
-             && ap.av.getSelectionGroup().getSize(false)>1)
+             && ap.av.getSelectionGroup().getSize()>1)
           {
             menuItem = new JMenuItem("Represent Group with " + seq.getName());
             menuItem.addActionListener(new java.awt.event.ActionListener()
@@ -451,7 +451,7 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        upperCase_actionPerformed(e);
+        changeCase(e);
       }
     });
     copy.setText("Copy");
@@ -467,7 +467,7 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        lowerCase_actionPerformed(e);
+        changeCase(e);
       }
     });
     toggle.setText("Toggle Case");
@@ -475,7 +475,7 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        toggle_actionPerformed(e);
+        changeCase(e);
       }
     });
     pdbMenu.setText("Associate Structure with Sequence");
@@ -504,21 +504,33 @@ public class PopupMenu extends JPopupMenu
       }
     });
     outputMenu.setText("Output to Textbox...");
+    sequenceFeature.setText("Create Sequence Feature");
+    sequenceFeature.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        sequenceFeature_actionPerformed(e);
+      }
+    });
+    textColour.setText("Text Colour");
+    textColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        textColour_actionPerformed(e);
+      }
+    });
+    jMenu1.setText("Group");
     add(groupMenu);
 
     add(sequenceMenu);
     groupMenu.add(editMenu);
     groupMenu.add(outputMenu);
-    groupMenu.addSeparator();
-    groupMenu.add(groupName);
-    groupMenu.add(unGroupMenuItem);
-        groupMenu.add(colourMenu);
-    groupMenu.add(showBoxes);
-        groupMenu.add(showText);
-        groupMenu.add(showColourText);
-    groupMenu.add(outline);
-        sequenceMenu.add(sequenceName);
+    groupMenu.add(sequenceFeature);
+    groupMenu.add(jMenu1);
+    sequenceMenu.add(sequenceName);
     sequenceMenu.add(pdbMenu);
+    colourMenu.add(textColour);
     colourMenu.add(noColourmenuItem);
         colourMenu.add(clustalColour);
         colourMenu.add(BLOSUM62Colour);
@@ -565,6 +577,13 @@ public class PopupMenu extends JPopupMenu
     pdbMenu.add(pdbFromFile);
     pdbMenu.add(enterPDB);
     pdbMenu.add(discoverPDB);
+    jMenu1.add(groupName);
+    jMenu1.add(unGroupMenuItem);
+    jMenu1.add(colourMenu);
+    jMenu1.add(showBoxes);
+    jMenu1.add(showText);
+    jMenu1.add(showColourText);
+    jMenu1.add(outline);
     noColourmenuItem.setText("None");
         noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
             {
@@ -688,7 +707,7 @@ public class PopupMenu extends JPopupMenu
         if (ap.overviewPanel != null)
           ap.overviewPanel.updateOverviewImage();
 
-        ap.seqPanel.repaint();
+        PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
     }
 
     /**
@@ -699,7 +718,7 @@ public class PopupMenu extends JPopupMenu
     protected void clustalColour_actionPerformed(ActionEvent e)
     {
         SequenceGroup sg = getGroup();
-        sg.cs = new ClustalxColourScheme(sg.getSequences(true),
+        sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
                 ap.av.alignment.getWidth());
         refresh();
     }
@@ -805,9 +824,9 @@ 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(ap.av.hiddenRepSequences), sg.getStartRes(),
+              sg.getEndRes() + 1));
 
             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
                     getGroup().getName());
@@ -842,6 +861,7 @@ public class PopupMenu extends JPopupMenu
 
          sg.cs = udc;
        }
+       refresh();
      }
     /**
      * DOCUMENT ME!
@@ -852,8 +872,9 @@ 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(ap.av.hiddenRepSequences),
+                                                 sg.getStartRes(),
+                                                 sg.getEndRes() + 1));
         refresh();
     }
 
@@ -868,8 +889,9 @@ 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(ap.av.hiddenRepSequences),
+                                                 sg.getStartRes(),
+                                                 sg.getEndRes() + 1));
 
         refresh();
     }
@@ -900,8 +922,9 @@ public class PopupMenu extends JPopupMenu
         {
             Conservation c = new Conservation("Group",
                     ResidueProperties.propHash, 3,
-                    sg.getSequences(true), 0,
-                    ap.av.alignment.getWidth());
+                    sg.getSequences(ap.av.hiddenRepSequences),
+                    sg.getStartRes(),
+                    sg.getEndRes() + 1);
 
             c.calculate();
             c.verdict(false, ap.av.ConsPercGaps);
@@ -940,31 +963,6 @@ public class PopupMenu extends JPopupMenu
         groupName.setText(reply);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void analyze_actionPerformed(ActionEvent e)
-    {
-        CutAndPasteTransfer cap = new CutAndPasteTransfer();
-        JInternalFrame frame = new JInternalFrame();
-        frame.setContentPane(cap);
-        Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
-
-        SequenceGroup sg = getGroup();
-        StringBuffer sb = new StringBuffer();
-
-        for (int i = 0; i < sg.getSize(false); i++)
-        {
-            Sequence tmp = (Sequence) sg.getSequences(false).elementAt(i);
-            sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
-            sb.append("\n");
-        }
-
-        sb.append("Something amazing will happen soon");
-        cap.setText(sb.toString());
-    }
 
     /**
      * DOCUMENT ME!
@@ -1028,13 +1026,15 @@ 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());
+
     }
 
     /**
@@ -1124,28 +1124,33 @@ public class PopupMenu extends JPopupMenu
     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(sequence);
+        ap.av.hideSequence(new SequenceI[]{sequence});
         return;
       }
 
-        int index = 0;
-        while(index < sg.getSize(false))
-        {
-          if(representGroup && sg.getSequenceAt(index)!=sequence)
-          {
-            sequence.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);
+      if (representGroup)
+      {
+        ap.av.hideRepSequences(sequence, 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);
     }
 
   public void copy_actionPerformed(ActionEvent e)
@@ -1158,52 +1163,85 @@ 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());
+
+      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==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(ap.av.hiddenRepSequences),
+          startEnd, caseChange
+          );
+
+      ap.alignFrame.addHistoryItem(caseCommand);
 
-    for (int g = 0; g < sg.getSize(true); g++)
-    {
-      ( (SequenceI)sg.getSequences(true).elementAt(g))
-          .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);
-    }
 
-    ap.repaint();
+      ap.av.firePropertyChange("alignment", null,
+                                ap.av.getAlignment().getSequences());
+
+    }
   }
 
   public void outputText_actionPerformed(ActionEvent e)
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
+    cap.setForInput(null);
     Desktop.addInternalFrame(cap,
                              "Alignment output - " + e.getActionCommand(), 600,
                              500);
@@ -1290,4 +1328,38 @@ 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();
+    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);
+    }
+  }
+
+  public void textColour_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = getGroup();
+    if (sg != null)
+      new TextColourChooser().chooseColour(ap, sg);
+  }
 }