X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=80f16a39b5af8c2380988b2b69969d5146c1b961;hb=725d3b370f548794f3af6d65d6736f308ae27e28;hp=c1a710508c5e432e088c227d37101a6206167db7;hpb=ac07859006686a2c62bcf57b24742eb610bc46f0;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index c1a7105..80f16a3 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)
@@ -581,6 +580,7 @@ public class AlignFrame extends GAlignFrame
     FontChooser fc = new FontChooser( alignPanel, frame );
     frame.setContentPane(fc);
     Desktop.addInternalFrame(frame, "Change Font", 480,100);
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
   }
 
   protected void fullSeqId_actionPerformed(ActionEvent e)
@@ -588,13 +588,13 @@ 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 +604,7 @@ 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 +630,20 @@ 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 +654,7 @@ 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)
@@ -765,109 +765,141 @@ 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;
-
-        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);
+      threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
 
-          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);
 
     }
     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());
+        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);
 
- //  int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,    "Background");
+          // 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()));
+        }
 
- //  ccs.inc = threshold;
+      }
+    }
 
-   viewport.setGlobalColourScheme(ccs);
 
-  }
-  else
-       viewport.setGlobalColourScheme( cs );
 
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   protected void modifyPID_actionPerformed(ActionEvent e)
   {
-    Desktop.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(), "Background");
+      if(viewport.getAbovePIDThreshold())
+      {
+        SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
+                                   "Background");
+        SliderPanel.showPIDSlider();
+      }
   }
 
   protected void modifyConservation_actionPerformed(ActionEvent e)
   {
-    Desktop.setConservationSliderSource(alignPanel, viewport.globalColourScheme,    "Background");
+    if(viewport.getConservationSelected())
+    {
+      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 )
@@ -875,33 +907,22 @@ if ( viewport.getConservationSelected() )
     else
       changeColour( cs );
 
-    coloursChanging = false;
   }
 
-  boolean coloursChanging = false;
+ // 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;
   }
 
 
@@ -922,7 +943,7 @@ if ( viewport.getConservationSelected() )
 
   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
-    changeColour(new Blosum62ColourScheme(viewport) );
+    changeColour(new Blosum62ColourScheme() );
   }
 
 
@@ -931,14 +952,14 @@ 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)
@@ -946,7 +967,7 @@ if ( viewport.getConservationSelected() )
     addHistoryItem("sort");
     AlignmentSorter.sortByGroup(viewport.getAlignment());
     AlignmentSorter.sortGroups(viewport.getAlignment());
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
@@ -1057,7 +1078,7 @@ if ( viewport.getConservationSelected() )
       {
         addHistoryItem("sort");
         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
-        alignPanel.RefreshPanels();
+        alignPanel.repaint();
       }
     });
 
@@ -1074,126 +1095,64 @@ if ( viewport.getConservationSelected() )
 
   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
   {
-    JInternalFrame frame = new JInternalFrame();
-    ClustalThread ct = new ClustalThread(frame);
-    Thread t = new Thread(ct);
-    t.start();
-    frame.setContentPane(ct);
-     Desktop.addInternalFrame(frame, title, 320, 90);
+     WebserviceInfo info = new WebserviceInfo("Clustal web service",
+     "\"Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"+
+     " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."
+    +" Nucleic Acids Research, submitted, June 1994.",
+     450, 150);
 
+    ClustalThread thread = new ClustalThread(info);
+    thread.start();
   }
 
-  class ClustalThread extends JPanel implements Runnable
-  {
-    Image image;
-    int angle = 0;
-    boolean webServiceRunning = false;
-    JInternalFrame frame;
-    public ClustalThread(JInternalFrame frame)
+    class ClustalThread extends Thread
     {
-      this.frame = frame;
+      WebserviceInfo info;
+      public ClustalThread(WebserviceInfo info)
+      {this.info = info; }
 
-      java.net.URL url = getClass().getResource("/images/logo.gif");
-      if (url != null)
+      public void run()
       {
-        image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
-        MediaTracker mt = new MediaTracker(this);
-        mt.addImage(image, 0);
-        try
+        info.setStatus(WebserviceInfo.STATE_RUNNING);
+        jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
+        Vector sv = viewport.getAlignment().getSequences();
+        SequenceI[] seqs = new SequenceI[sv.size()];
+
+        int i = 0;
+        do
         {
-          mt.waitForID(0);
+          seqs[i] = (SequenceI) sv.elementAt(i);
         }
-        catch (Exception ex)
-        {}
-      }
+        while (++i < sv.size());
 
-      ImageSpinner spinner = new ImageSpinner();
-      spinner.start();
-      webServiceRunning = true;
-    }
-
-    class ImageSpinner extends Thread
-    {
-      public void run()
-      {
-        while(webServiceRunning)
+        SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
+        if (alignment != null)
         {
-          try{
-            Thread.sleep(10);
-            angle+=1;
-            angle %=360;
-            repaint();
-          }
-          catch(Exception ex){}
+          AlignFrame af = new AlignFrame(new Alignment(alignment));
+          Desktop.addInternalFrame(af, title.concat(" - ClustalW Alignment"),
+                                   NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
+          af.clustalColour_actionPerformed(null);
+          af.clustalColour.setSelected(true);
+          info.setStatus(WebserviceInfo.STATE_STOPPED_OK);
+        }
+        else
+        {
+            info.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+            info.appendProgressText("Problem obtaining clustal alignment");
         }
       }
     }
 
-    // JBPNote
-    // Should check to see if the server settings are valid
-    // Need visual-delay indication here.
-    public void run()
-       {
-         jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
-         Vector sv = viewport.getAlignment().getSequences();
-         SequenceI[] seqs = new SequenceI[sv.size()];
-
-         int i = 0;
-         do
-         {
-           seqs[i] = (SequenceI) sv.elementAt(i);
-         }
-         while (++i < sv.size());
-
-         SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
-
-         if (alignment != null)
-         {
-           AlignFrame af = new AlignFrame(new Alignment(alignment));
-           Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
-           af.clustalColour_actionPerformed(null);
-           af.clustalColour.setSelected(true);
-         }
-         else
-           JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",
-                                         JOptionPane.WARNING_MESSAGE);
-
-         webServiceRunning = false;
-         try{
-           frame.setClosed(true);
-         }catch(Exception ex){}
-       }
-
-       public void paintComponent(Graphics g1)
-       {
-         Graphics2D g = (Graphics2D)g1;
-         g.setColor(Color.white);
-         g.fillRect(0,0,getWidth(), getHeight());
-         if(image!=null)
-         {
-
-           g.rotate (Math.toRadians(angle), 28, 28);
-
-           g.drawImage(image,10,10,this);
-           g.rotate (-Math.toRadians(angle), 28, 28 );
-         }
-         g.setFont(new Font("Arial", Font.BOLD, 12));
-         g.setColor(Color.black);
-         g.drawString("Clustal Alignment Web Service running", 60,30);
-       }
-  }
   protected void jpred_actionPerformed(ActionEvent e)
 {
 
-    JInternalFrame frame = new JInternalFrame();
     if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)
     {
       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
       SequenceGroup seqs = viewport.getSelectionGroup();
       if (seqs.getSize() == 1 || !viewport.alignment.isAligned())
       {
-        JPredClient ct = new JPredClient( (SequenceI)
-                                         seqs.getSequenceAt(0));
+        JPredClient ct = new JPredClient( (SequenceI)seqs.getSequenceAt(0));
       }
       else
       {