X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=b00a584baa6de294244da59889262f0905eb39fc;hb=6d5aff5f7ace98b6416c7e9dc2a8fdc6ad194902;hp=7b67e810d9618ddfcebc292e1c5a8f0d6c02b187;hpb=1a204eb6f91465df533751cd6e592ddd11dcce5d;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 7b67e81..b00a584 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -23,15 +23,24 @@ import java.awt.print.*;
 import javax.swing.*;
 import javax.swing.event.*;
 import java.util.*;
-import  java.awt.datatransfer.*;
+import java.awt.datatransfer.*;
 
 
 public class AlignFrame extends GAlignFrame
 {
   final AlignmentPanel alignPanel;
   final AlignViewport viewport;
+  public static final int NEW_WINDOW_WIDTH = 700;
+  public static final int NEW_WINDOW_HEIGHT = 500;
+
   public AlignFrame(AlignmentI al)
   {
+    try{
+      String ip = java.net.InetAddress.getLocalHost().getHostAddress();
+      if( !ip.startsWith("10."))
+        alignMenu.setVisible(false);
+    }
+    catch(java.net.UnknownHostException e){}
     viewport = new AlignViewport(al,true,true,false);
 
     String fontName = jalview.bin.Cache.getProperty("FONT_NAME");
@@ -348,10 +357,7 @@ public class AlignFrame extends GAlignFrame
         SequenceI[] newSeqs = new SequenceI[seqs.size()];
         seqs.toArray(newSeqs);
         AlignFrame af = new AlignFrame(new Alignment(newSeqs));
-        int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;
-        if (newHeight > 500)
-          newHeight = 500;
-        Desktop.addInternalFrame(af, "Copied sequences", 700, 500);
+        Desktop.addInternalFrame(af, "Copied sequences", NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
       }
       else
       {
@@ -560,10 +566,11 @@ public class AlignFrame extends GAlignFrame
 
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
-      JInternalFrame frame = new JInternalFrame();
-      Finder finder = new Finder(viewport, alignPanel, frame);
-      frame.setContentPane(finder);
-     Desktop.addInternalFrame(frame, "Find", 340,110);
+    JInternalFrame frame = new JInternalFrame();
+    Finder finder = new Finder(viewport, alignPanel, frame);
+    frame.setContentPane(finder);
+    Desktop.addInternalFrame(frame, "Find", 340,110, false);
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
 
   }
 
@@ -574,6 +581,7 @@ 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)
@@ -594,8 +602,31 @@ public class AlignFrame extends GAlignFrame
   {
     viewport.setWrapAlignment( wrapMenuItem.isSelected() );
     alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
+    scaleAbove.setVisible( wrapMenuItem.isSelected() );
+    scaleLeft.setVisible( wrapMenuItem.isSelected() );
+    scaleRight.setVisible( wrapMenuItem.isSelected() );
+    alignPanel.RefreshPanels();
   }
 
+  protected void scaleAbove_actionPerformed(ActionEvent e)
+  {
+    viewport.setScaleAboveWrapped(scaleAbove.isSelected());
+    alignPanel.repaint();
+  }
+
+  protected void scaleLeft_actionPerformed(ActionEvent e)
+  {
+    viewport.setScaleLeftWrapped(scaleLeft.isSelected());
+    alignPanel.repaint();
+  }
+
+  protected void scaleRight_actionPerformed(ActionEvent e)
+  {
+    viewport.setScaleRightWrapped(scaleRight.isSelected());
+    alignPanel.repaint();
+  }
+
+
 
   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
   {
@@ -735,39 +766,11 @@ 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, 100);
-          ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
-
-          sg.cs = ccs;
-        }
-
-      }
-    }
-
-
-    if ( viewport.getAbovePIDThreshold())
-    {
-      int threshold = 0;
-      threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");
-      Desktop.hideConservationSlider();
+      threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
 
       if (cs instanceof ResidueColourScheme)
         ( (ResidueColourScheme) cs).setThreshold(threshold);
@@ -775,60 +778,118 @@ public class AlignFrame extends GAlignFrame
         ( (ScoreColourScheme) cs).setThreshold(threshold);
 
       viewport.setGlobalColourScheme(cs);
-
     }
-    else
-    if (cs instanceof ResidueColourScheme)
+    else if (cs instanceof ResidueColourScheme)
       ( (ResidueColourScheme) cs).setThreshold(0);
     else if (cs instanceof ScoreColourScheme)
       ( (ScoreColourScheme) cs).setThreshold(0);
 
 
 
+    if (viewport.getConservationSelected())
+    {
+      ConservationColourScheme ccs = null;
 
-if ( viewport.getConservationSelected() )
- {
-   ConservationColourScheme ccs = null;
+      Alignment al = (Alignment) viewport.alignment;
+      Conservation c = new Conservation("All",
+                                        ResidueProperties.propHash, 3,
+                                        al.getSequences(), 0,
+                                        al.getWidth() - 1);
 
-   Alignment al = (Alignment) viewport.alignment;
-   Conservation c = new Conservation("All",
-                                     ResidueProperties.propHash, 3,
-                                     al.getSequences(), 0,
-                                     al.getWidth());
+      c.calculate();
+      c.verdict(false, viewport.ConsPercGaps);
 
-   c.calculate();
-   c.verdict(false, 100);
+      ccs = new ConservationColourScheme(c, cs);
 
-   ccs = new ConservationColourScheme(c, cs);
+      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+      ccs.setConsensus( viewport.vconsensus );
+      viewport.setGlobalColourScheme(ccs);
 
-   int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,
-       "Background");
+    }
+    else
+    {
+        // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+      cs.setConsensus( viewport.vconsensus );
+      viewport.setGlobalColourScheme(cs);
+    }
 
-   ccs.inc = threshold;
 
-   viewport.setGlobalColourScheme(ccs);
+    if(viewport.getColourAppliesToAllGroups())
+    {
+      Vector groups = viewport.alignment.getGroups();
+      for(int i=0; i<groups.size(); i++)
+      {
+        SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
+
+
+        try{
+          sg.cs = (ColourSchemeI)cs.getClass().newInstance();
+        }catch(Exception ex){}
+
+        if(viewport.getAbovePIDThreshold())
+        {
+          if (sg.cs instanceof ResidueColourScheme)
+            ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
+          else if (sg.cs instanceof ScoreColourScheme)
+            ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
+
+           sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );
+        }
+
+        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);
+
+          // 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();
   }
 
+  protected void modifyPID_actionPerformed(ActionEvent e)
+  {
+      if(viewport.getAbovePIDThreshold())
+      {
+        SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
+                                   "Background");
+        SliderPanel.showPIDSlider();
+      }
+  }
+
+  protected void modifyConservation_actionPerformed(ActionEvent e)
+  {
+    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 )
@@ -836,33 +897,22 @@ 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;
   }
 
 
@@ -872,10 +922,7 @@ if ( viewport.getConservationSelected() )
     JInternalFrame frame = new JInternalFrame();
     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
     frame.setContentPane(chooser);
-    Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
-    frame.setResizable(false);
-    frame.setIconifiable(false);
-    frame.setMaximizable(false);
+    Desktop.addInternalFrame(frame,"User defined colours", 450,540, false );
   }
 
   public void PIDColour_actionPerformed(ActionEvent e)
@@ -886,7 +933,7 @@ if ( viewport.getConservationSelected() )
 
   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
-    changeColour(new Blosum62ColourScheme(viewport) );
+    changeColour(new Blosum62ColourScheme() );
   }
 
 
@@ -913,24 +960,12 @@ if ( viewport.getConservationSelected() )
     alignPanel.RefreshPanels();
   }
 
-  public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem("sort");
-    if(viewport.getCurrentTree()==null)
-      return;
-
-    AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
-    alignPanel.RefreshPanels();
-  }
-
   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
   {
     RedundancyPanel sp = new RedundancyPanel(alignPanel);
     JInternalFrame frame = new JInternalFrame();
     frame.setContentPane(sp);
-    Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);
-    frame.setMaximizable(false);
-    frame.setResizable(false);
+    Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);
 
   }
 
@@ -1004,140 +1039,110 @@ if ( viewport.getConservationSelected() )
       return;
     }
 
-    TreePanel tp=null;
-   if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() > 3)
-   {
-     tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences,type, pwType,
+    final TreePanel tp;
+    if (viewport.getSelectionGroup() != null &&
+        viewport.getSelectionGroup().getSize() > 3)
+    {
+      tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
+                         pwType,
                          0, viewport.alignment.getWidth());
-   }
-   else
-   {
-     tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
-                         type, pwType,  0, viewport.alignment.getWidth());
-   }
+    }
+    else
+    {
+      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
+                         type, pwType, 0, viewport.alignment.getWidth());
+    }
+
+   addTreeMenuItem(tp, title);
 
    Desktop.addInternalFrame(tp, title, 600, 500);
   }
 
+  void addTreeMenuItem(final TreePanel treePanel, String title)
+  {
+    final JMenuItem item = new JMenuItem(title);
+    sortByTreeMenu.add(item);
+    item.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addHistoryItem("sort");
+        AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
+        alignPanel.RefreshPanels();
+      }
+    });
 
+    treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+    {
+      public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
+      {
+        sortByTreeMenu.remove(item);
+      };
+    });
+
+  }
 
 
   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, 300, 80);
+     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 imageIndex = 0;
-    boolean webServiceRunning = false;
-    JInternalFrame frame;
-    public ClustalThread(JInternalFrame frame)
+    class ClustalThread extends Thread
     {
-      this.frame = frame;
-      image = new Image[9];
-      for(int i=0; i<9; i++)
+      WebserviceInfo info;
+      public ClustalThread(WebserviceInfo info)
+      {this.info = info; }
+
+      public void run()
       {
-        java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");
-        if (url != null)
+        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
         {
-          image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);
-          MediaTracker mt = new MediaTracker(this);
-          mt.addImage(image[i], i);
-          try{mt.waitForID(i);}
-          catch(Exception ex){}
+          seqs[i] = (SequenceI) sv.elementAt(i);
         }
-      }
-      DNATwirler twirler = new DNATwirler();
-      twirler.start();
-      webServiceRunning = true;
-    }
+        while (++i < sv.size());
 
-    class DNATwirler extends Thread
-    {
-      public void run()
-      {
-        while(webServiceRunning)
+        SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
+        if (alignment != null)
         {
-          try{
-            Thread.sleep(100);
-            imageIndex++;
-            imageIndex %=9;
-            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));
-          af.clustalColour.setSelected(true);
-          af.clustalColour_actionPerformed(null);
-           Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),
-                                    700, 500); // JBPNote - is there a new window geom. property ?
-         }
-         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 g)
-       {
-         g.setColor(Color.white);
-         g.fillRect(0,0,getWidth(), getHeight());
-         if(image!=null)
-         {
-           g.drawImage(image[imageIndex],10,10,this);
-         }
-         g.setFont(new Font("Arial", Font.BOLD, 12));
-         g.setColor(Color.black);
-         g.drawString("Clustal Alignment Web Service running", 30,30);
-       }
-  }
   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
       {
@@ -1199,6 +1204,7 @@ if ( viewport.getConservationSelected() )
           tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
                              fin, "FromFile", choice);
           Desktop.addInternalFrame(tp, title, 600, 500);
+          addTreeMenuItem(tp, title);
         }
       }
       catch (Exception ex)