X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=1b9ee91b32cc2e83fe402eec5cc102a7b458918b;hb=e7ed63f1ea56432246a6ed1553f0fe56d26f56ea;hp=9ec2f235de9a0689aaf7ebb69ed7cd16a2257f82;hpb=77dbfda22963c908129cae7947643ad5fce0caad;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 9ec2f23..1b9ee91 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -247,8 +247,7 @@ public class AlignFrame extends GAlignFrame
       viewport.setAlignment( new Alignment(seq) );
       updateEditMenuBar();
       viewport.updateConsensus();
-      alignPanel.RefreshPanels();
-      alignPanel.RefreshPanels();
+      alignPanel.repaint();
   }
 
   public void moveSelectedSequences(boolean up)
@@ -290,7 +289,7 @@ public class AlignFrame extends GAlignFrame
       }
     }
 
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
 
@@ -365,7 +364,7 @@ public class AlignFrame extends GAlignFrame
         viewport.alignment.getWidth();
         viewport.updateConservation();
         viewport.updateConsensus();
-        alignPanel.RefreshPanels();
+        alignPanel.repaint();
       }
 
     }catch(Exception ex){}// could be anything being pasted in here
@@ -408,7 +407,7 @@ public class AlignFrame extends GAlignFrame
      }catch(Exception ex){}
    viewport.updateConservation();
    viewport.updateConsensus();
-     alignPanel.RefreshPanels();
+     alignPanel.repaint();
 
   }
 
@@ -421,8 +420,8 @@ public class AlignFrame extends GAlignFrame
      viewport.setAlignment( new Alignment(seq) );
      updateEditMenuBar();
      viewport.updateConsensus();
-     alignPanel.RefreshPanels();
-     alignPanel.RefreshPanels();
+     alignPanel.repaint();
+     alignPanel.repaint();
   }
 
 
@@ -431,7 +430,7 @@ public class AlignFrame extends GAlignFrame
     viewport.alignment.deleteAllGroups();
     viewport.setSelectionGroup(null);
 
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
 
@@ -489,7 +488,7 @@ public class AlignFrame extends GAlignFrame
           viewport.alignment.deleteGroup(sg);
       }
 
-      alignPanel.RefreshPanels();
+      alignPanel.repaint();
     }
   }
 
@@ -514,7 +513,7 @@ public class AlignFrame extends GAlignFrame
 
 
 
-      alignPanel.RefreshPanels();
+      alignPanel.repaint();
     }
 
   }
@@ -525,7 +524,7 @@ public class AlignFrame extends GAlignFrame
     viewport.getAlignment().removeGaps();
     viewport.updateConservation();
     viewport.updateConsensus();
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
@@ -547,7 +546,7 @@ public class AlignFrame extends GAlignFrame
     }
     viewport.updateConservation();
     viewport.updateConsensus();
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void setGapCharMenuItem_actionPerformed(ActionEvent e)
@@ -561,7 +560,7 @@ public class AlignFrame extends GAlignFrame
     }
     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
     viewport.setGapCharacter(thisChar);
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void findMenuItem_actionPerformed(ActionEvent e)
@@ -580,7 +579,10 @@ public class AlignFrame extends GAlignFrame
     JInternalFrame frame = new JInternalFrame();
     FontChooser fc = new FontChooser( alignPanel, frame );
     frame.setContentPane(fc);
-    Desktop.addInternalFrame(frame, "Change Font", 480,100);
+    Desktop.addInternalFrame(frame, "Change Font", 480,100, false);
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
+    if(alignPanel.getOverviewPanel()!=null)
+      alignPanel.getOverviewPanel().updateOverviewImage();
   }
 
   protected void fullSeqId_actionPerformed(ActionEvent e)
@@ -588,13 +590,13 @@ public class AlignFrame extends GAlignFrame
     viewport.setShowFullId( fullSeqId.isSelected() );
 
     alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
   {
       viewport.setColourText( colourTextMenuItem.isSelected() );
-      alignPanel.RefreshPanels();
+      alignPanel.repaint();
   }
 
   protected void wrapMenuItem_actionPerformed(ActionEvent e)
@@ -604,7 +606,7 @@ public class AlignFrame extends GAlignFrame
     scaleAbove.setVisible( wrapMenuItem.isSelected() );
     scaleLeft.setVisible( wrapMenuItem.isSelected() );
     scaleRight.setVisible( wrapMenuItem.isSelected() );
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   protected void scaleAbove_actionPerformed(ActionEvent e)
@@ -630,20 +632,20 @@ public class AlignFrame extends GAlignFrame
   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void viewTextMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowText( viewTextMenuItem.isSelected() );
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
 
   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void sequenceFeatures_actionPerformed(ActionEvent evt)
@@ -654,7 +656,7 @@ public class AlignFrame extends GAlignFrame
          AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);
          ((Alignment)viewport.alignment).featuresAdded = true;
     }
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
@@ -674,27 +676,20 @@ public class AlignFrame extends GAlignFrame
       return;
 
     JInternalFrame frame = new JInternalFrame();
-    OverviewPanel overview = alignPanel.getOverviewPanel();
-   try{
-     overview = new OverviewPanel(alignPanel, viewport);
+    OverviewPanel overview = new OverviewPanel(alignPanel);
      frame.setContentPane(overview);
     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
                              frame.getWidth(), frame.getHeight());
     frame.pack();
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
       {
             alignPanel.setOverviewPanel(null);
       };
     });
-    alignPanel.setOverviewPanel( overview );
 
-  }catch(java.lang.OutOfMemoryError ex)
-   {
-     JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"
-                                   +"\nTry reducing the font size.",
-                                   "Out of memory", JOptionPane.WARNING_MESSAGE);
-   }
+    alignPanel.setOverviewPanel( overview );
 
 
   }
@@ -765,106 +760,143 @@ public class AlignFrame extends GAlignFrame
 
   void changeColour(ColourSchemeI cs)
   {
+    int threshold = 0;
 
-    if(viewport.getColourAppliesToAllGroups())
+    if ( viewport.getAbovePIDThreshold() )
     {
-      Vector groups = viewport.alignment.getGroups();
-      for(int i=0; i<groups.size(); i++)
-      {
-        SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
-        sg.cs = cs;
+      threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
 
-        if(abovePIDThreshold.isSelected())
-          abovePIDThreshold_actionPerformed(null);
-        else if( viewport.getConservationSelected() )
-        {
-          Conservation c = new Conservation("Group",
-                                            ResidueProperties.propHash, 3,
-                                            sg.sequences, sg.getStartRes(),
-                                            sg.getEndRes());
-          c.calculate();
-          c.verdict(false, viewport.ConsPercGaps);
-          ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
-          sg.cs = ccs;
-        }
+      if (cs instanceof ResidueColourScheme)
+        ( (ResidueColourScheme) cs).setThreshold(threshold);
+      else if (cs instanceof ScoreColourScheme)
+        ( (ScoreColourScheme) cs).setThreshold(threshold);
 
-      }
+      viewport.setGlobalColourScheme(cs);
     }
+    else if (cs instanceof ResidueColourScheme)
+      ( (ResidueColourScheme) cs).setThreshold(0);
+    else if (cs instanceof ScoreColourScheme)
+      ( (ScoreColourScheme) cs).setThreshold(0);
 
 
-    if ( viewport.getAbovePIDThreshold() )
+
+    if (viewport.getConservationSelected())
     {
- //     int threshold = 0;
-   //   threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");
-      Desktop.hideConservationSlider();
+      ConservationColourScheme ccs = null;
 
- //     if (cs instanceof ResidueColourScheme)
- //       ( (ResidueColourScheme) cs).setThreshold(threshold);
-  //    else if (cs instanceof ScoreColourScheme)
-   //     ( (ScoreColourScheme) cs).setThreshold(threshold);
+      Alignment al = (Alignment) viewport.alignment;
+      Conservation c = new Conservation("All",
+                                        ResidueProperties.propHash, 3,
+                                        al.getSequences(), 0,
+                                        al.getWidth() - 1);
 
-      viewport.setGlobalColourScheme(cs);
+      c.calculate();
+      c.verdict(false, viewport.ConsPercGaps);
+
+      ccs = new ConservationColourScheme(c, cs);
+
+      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+      ccs.setConsensus( viewport.vconsensus );
+      viewport.setGlobalColourScheme(ccs);
+
+      SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
 
     }
     else
-    if (cs instanceof ResidueColourScheme)
-      ( (ResidueColourScheme) cs).setThreshold(0);
-    else if (cs instanceof ScoreColourScheme)
-      ( (ScoreColourScheme) cs).setThreshold(0);
-
+    {
+        // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+        if (cs != null)
+          cs.setConsensus(viewport.vconsensus);
+        viewport.setGlobalColourScheme(cs);
+    }
 
 
+    if(viewport.getColourAppliesToAllGroups())
+    {
+      Vector groups = viewport.alignment.getGroups();
+      for(int i=0; i<groups.size(); i++)
+      {
+        SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
 
-if ( viewport.getConservationSelected() )
- {
-   ConservationColourScheme ccs = null;
+        if (cs instanceof ClustalxColourScheme)
+        {
+          sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
+        }
+        else
+          try
+          {
+            sg.cs = (ColourSchemeI) cs.getClass().newInstance();
+          }
+          catch (Exception ex)
+          {
+            ex.printStackTrace();
+            sg.cs = cs;
+          }
 
-   Alignment al = (Alignment) viewport.alignment;
-   Conservation c = new Conservation("All",
-                                     ResidueProperties.propHash, 3,
-                                     al.getSequences(), 0,
-                                     al.getWidth()-1);
+        if(viewport.getAbovePIDThreshold())
+        {
+          if (sg.cs instanceof ResidueColourScheme)
+            ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
+          else if (sg.cs instanceof ScoreColourScheme)
+            ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
 
-   c.calculate();
-   c.verdict(false, viewport.ConsPercGaps);
+           sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );
+        }
 
-   ccs = new ConservationColourScheme(c, cs);
+        if( viewport.getConservationSelected() )
+        {
+          Conservation c = new Conservation("Group",
+                                            ResidueProperties.propHash, 3,
+                                            sg.sequences, 0, viewport.alignment.getWidth()-1);
+          c.calculate();
+          c.verdict(false, viewport.ConsPercGaps);
+          ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
 
-   viewport.setGlobalColourScheme(ccs);
+          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+          ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
+          sg.cs = ccs;
+        }
+        else
+        {
+          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+          sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
+        }
 
-  }
-  else
-       viewport.setGlobalColourScheme( cs );
+      }
+    }
 
-    alignPanel.RefreshPanels();
+    if(alignPanel.getOverviewPanel()!=null)
+      alignPanel.getOverviewPanel().updateOverviewImage();
+    alignPanel.repaint();
   }
 
   protected void modifyPID_actionPerformed(ActionEvent e)
   {
-    if(viewport.getAbovePIDThreshold())
-    Desktop.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(), "Background");
+      if(viewport.getAbovePIDThreshold())
+      {
+        SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
+                                   "Background");
+        SliderPanel.showPIDSlider();
+      }
   }
 
   protected void modifyConservation_actionPerformed(ActionEvent e)
   {
     if(viewport.getConservationSelected())
-    Desktop.setConservationSliderSource(alignPanel, viewport.globalColourScheme,    "Background");
+    {
+      SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
+                                        "Background");
+      SliderPanel.showConservationSlider();
+    }
   }
 
 
   protected  void conservationMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setConservationSelected(conservationMenuItem.isSelected());
-    if(coloursChanging)
-      return;
-
-    coloursChanging = true;
 
     viewport.setAbovePIDThreshold(false);
     abovePIDThreshold.setSelected(false);
-    Desktop.hidePIDSlider();
-    if(!viewport.getConservationSelected())
-      Desktop.hideConservationSlider();
 
    ColourSchemeI cs = viewport.getGlobalColourScheme();
    if(cs instanceof ConservationColourScheme )
@@ -872,33 +904,24 @@ if ( viewport.getConservationSelected() )
     else
       changeColour( cs );
 
-    coloursChanging = false;
+    modifyConservation_actionPerformed(null);
   }
 
-  boolean coloursChanging = false;
   public void abovePIDThreshold_actionPerformed(ActionEvent e)
   {
-    if(coloursChanging)
-      return;
-
-    coloursChanging = true;
     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
 
     conservationMenuItem.setSelected(false);
     viewport.setConservationSelected(false);
-    Desktop.hideConservationSlider();
-
-    if(!viewport.getAbovePIDThreshold())
-      Desktop.hidePIDSlider();
-
 
     ColourSchemeI cs = viewport.getGlobalColourScheme();
+
     if(cs instanceof ConservationColourScheme )
         changeColour( ((ConservationColourScheme)cs).cs );
     else
         changeColour( cs );
 
-    coloursChanging = false;
+    modifyPID_actionPerformed(null);
   }
 
 
@@ -919,7 +942,7 @@ if ( viewport.getConservationSelected() )
 
   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
-    changeColour(new Blosum62ColourScheme(viewport) );
+    changeColour(new Blosum62ColourScheme() );
   }
 
 
@@ -928,14 +951,14 @@ if ( viewport.getConservationSelected() )
   {
     addHistoryItem("sort");
     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void sortIDMenuItem_actionPerformed(ActionEvent e)
   {
     addHistoryItem("sort");
     AlignmentSorter.sortByID( viewport.getAlignment() );
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
@@ -943,7 +966,7 @@ if ( viewport.getConservationSelected() )
     addHistoryItem("sort");
     AlignmentSorter.sortByGroup(viewport.getAlignment());
     AlignmentSorter.sortGroups(viewport.getAlignment());
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
@@ -1054,7 +1077,7 @@ if ( viewport.getConservationSelected() )
       {
         addHistoryItem("sort");
         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
-        alignPanel.RefreshPanels();
+        alignPanel.repaint();
       }
     });
 
@@ -1165,6 +1188,39 @@ if ( viewport.getConservationSelected() )
 
     }
   }
+  protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
+  {
+    // TODO:resolve which menu item was actually selected
+    // Now, check we have enough sequences
+      if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)
+      {
+        // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+        SequenceGroup seqs = viewport.getSelectionGroup();
+        int sz;
+        SequenceI[] msa = new SequenceI[sz=seqs.getSize()];
+        for (int i = 0; i < sz; i++)
+        {
+          msa[i] = (SequenceI) seqs.getSequenceAt(i);
+        }
+
+        MsaWSClient ct = new jalview.ws.MsaWSClient(msa);
+      }
+      else
+      {
+        Vector seqs = viewport.getAlignment().getSequences();
+
+        if (seqs.size() > 1) {
+          SequenceI[] msa = new SequenceI[seqs.size()];
+          for (int i = 0; i < seqs.size(); i++)
+          {
+            msa[i] = (SequenceI) seqs.elementAt(i);
+          }
+
+          MsaWSClient ct = new MsaWSClient(msa);
+        }
+
+      }
+    }
 
     protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
     // Pick the tree file