X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=3123184f3b5e95d83aa15c3eb935162627f5502d;hb=b74e294a72e55800143248d8c3938d86dcf02a2f;hp=43bdb2fe78bf0b18037573eba7c04814d6947189;hpb=b08c4a331a047b06a5e57d01961cec991826876d;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 43bdb2f..3123184 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -23,7 +23,7 @@ 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
@@ -32,7 +32,6 @@ public class AlignFrame extends GAlignFrame
   final AlignViewport viewport;
   public AlignFrame(AlignmentI al)
   {
-    super();
     viewport = new AlignViewport(al,true,true,false);
 
     String fontName = jalview.bin.Cache.getProperty("FONT_NAME");
@@ -41,10 +40,20 @@ public class AlignFrame extends GAlignFrame
     if(fontName!=null && fontStyle!=null && fontSize!=null)
       viewport.setFont( new Font(fontName,Integer.parseInt(fontStyle),Integer.parseInt(fontSize)) );
 
+    // add conservation graph to alignment
+    viewport.updateConservation();
+    viewport.updateConsensus();
+
 
     alignPanel = new AlignmentPanel(this, viewport);
+
+    alignPanel.annotationPanel.adjustPanelHeight();
+    alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
+    alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
+
     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
 
+
     addInternalFrameListener(new InternalFrameAdapter()
    {
      public void internalFrameActivated(InternalFrameEvent evt)
@@ -62,22 +71,23 @@ public class AlignFrame extends GAlignFrame
 
   protected void saveAs_actionPerformed(ActionEvent e)
   {
-    String suffix = "";
+    String suffix [] = null;
     if(e.getActionCommand().equals("FASTA"))
-      suffix = "fa";
+      suffix = new String[]{"fa", "fasta"};
     else if(e.getActionCommand().equals("MSF"))
-      suffix = "msf";
+      suffix = new String[]{"msf"};
     else if(e.getActionCommand().equals("CLUSTAL"))
-      suffix = "aln";
+      suffix = new String[]{"aln"};
     else if(e.getActionCommand().equals("BLC"))
-      suffix = "blc";
+      suffix = new String[]{"blc"};
     else if(e.getActionCommand().equals("PIR"))
-      suffix = "pir";
+      suffix = new String[]{"pir"};
     else if(e.getActionCommand().equals("PFAM"))
-      suffix = "pfam";
+      suffix = new String[]{"pfam"};
+
 
     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")
-        , new String[]{suffix}, e.getActionCommand()+" file");
+        , suffix, e.getActionCommand()+" file");
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
     chooser.setToolTipText("Save");
@@ -227,6 +237,8 @@ public class AlignFrame extends GAlignFrame
       seq = (SequenceI[]) history[1];
       viewport.setAlignment( new Alignment(seq) );
       updateEditMenuBar();
+      viewport.updateConsensus();
+      alignPanel.RefreshPanels();
       alignPanel.RefreshPanels();
   }
 
@@ -339,12 +351,14 @@ public class AlignFrame extends GAlignFrame
         int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;
         if (newHeight > 500)
           newHeight = 500;
-        Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);
+        Desktop.addInternalFrame(af, "Copied sequences", 700, 500);
       }
       else
       {
         viewport.setEndSeq(viewport.alignment.getHeight());
         viewport.alignment.getWidth();
+        viewport.updateConservation();
+        viewport.updateConsensus();
         alignPanel.RefreshPanels();
       }
 
@@ -386,6 +400,8 @@ public class AlignFrame extends GAlignFrame
      {
        this.setClosed(true);
      }catch(Exception ex){}
+   viewport.updateConservation();
+   viewport.updateConsensus();
      alignPanel.RefreshPanels();
 
   }
@@ -398,19 +414,12 @@ public class AlignFrame extends GAlignFrame
      SequenceI[] seq = (SequenceI[]) history[1];
      viewport.setAlignment( new Alignment(seq) );
      updateEditMenuBar();
+     viewport.updateConsensus();
+     alignPanel.RefreshPanels();
      alignPanel.RefreshPanels();
   }
 
 
-  public void groupsMenuItem_actionPerformed(ActionEvent e)
-  {
-    GroupEditor geditor = new GroupEditor(viewport, alignPanel);
-    JInternalFrame frame = new JInternalFrame();
-    frame.setContentPane(geditor);
-    Desktop.addInternalFrame(frame, "Group editor", 710, 410);
-    frame.setResizable(false);
-  }
-
   protected void deleteGroups_actionPerformed(ActionEvent e)
   {
     viewport.alignment.deleteAllGroups();
@@ -462,6 +471,18 @@ public class AlignFrame extends GAlignFrame
       int min = colSel.getMin();
       viewport.getAlignment().trimLeft(min);
       colSel.compensateForEdit(0,min);
+
+      if(viewport.getSelectionGroup()!=null)
+        viewport.getSelectionGroup().adjustForRemoveLeft(min);
+
+      Vector groups = viewport.alignment.getGroups();
+      for(int i=0; i<groups.size(); i++)
+      {
+        SequenceGroup sg = (SequenceGroup) groups.get(i);
+        if(!sg.adjustForRemoveLeft(min))
+          viewport.alignment.deleteGroup(sg);
+      }
+
       alignPanel.RefreshPanels();
     }
   }
@@ -473,8 +494,19 @@ public class AlignFrame extends GAlignFrame
     if (colSel.size() > 0)
     {
       int max = colSel.getMax();
-      if(max>1)
-        viewport.getAlignment().trimRight(max);
+      viewport.getAlignment().trimRight(max);
+      if(viewport.getSelectionGroup()!=null)
+        viewport.getSelectionGroup().adjustForRemoveRight(max);
+
+      Vector groups = viewport.alignment.getGroups();
+      for(int i=0; i<groups.size(); i++)
+      {
+        SequenceGroup sg = (SequenceGroup) groups.get(i);
+        if(!sg.adjustForRemoveRight(max))
+          viewport.alignment.deleteGroup(sg);
+      }
+
+
 
       alignPanel.RefreshPanels();
     }
@@ -485,6 +517,8 @@ public class AlignFrame extends GAlignFrame
   {
     addHistoryItem("delete gapped columns");
     viewport.getAlignment().removeGaps();
+    viewport.updateConservation();
+    viewport.updateConsensus();
     alignPanel.RefreshPanels();
   }
 
@@ -505,7 +539,8 @@ public class AlignFrame extends GAlignFrame
           jSize--;
         }
     }
-
+    viewport.updateConservation();
+    viewport.updateConsensus();
     alignPanel.RefreshPanels();
   }
 
@@ -535,7 +570,6 @@ public class AlignFrame extends GAlignFrame
 
   public void font_actionPerformed(ActionEvent e)
   {
-   // JOptionPane op = new JOptionPane();
     JInternalFrame frame = new JInternalFrame();
     FontChooser fc = new FontChooser( alignPanel, frame );
     frame.setContentPane(fc);
@@ -560,9 +594,32 @@ 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)
   {
     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
@@ -593,9 +650,15 @@ public class AlignFrame extends GAlignFrame
     alignPanel.RefreshPanels();
   }
 
-  public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
+  public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
   {
-    alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
+    if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())
+    {
+      annotationPanelMenuItem.setSelected(false);
+      return;
+    }
+    viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );
+    alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );
   }
 
   public void overviewMenuItem_actionPerformed(ActionEvent e)
@@ -995,41 +1058,43 @@ if ( viewport.getConservationSelected() )
 
   class ClustalThread extends JPanel implements Runnable
   {
-    Image [] image;
-    int imageIndex = 0;
+    Image image;
+    int angle = 0;
     boolean webServiceRunning = false;
     JInternalFrame frame;
     public ClustalThread(JInternalFrame frame)
     {
       this.frame = frame;
-      image = new Image[9];
-      for(int i=0; i<9; i++)
+
+      java.net.URL url = getClass().getResource("/images/logo.gif");
+      if (url != null)
       {
-        java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");
-        if (url != null)
+        image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+        MediaTracker mt = new MediaTracker(this);
+        mt.addImage(image, 0);
+        try
         {
-          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){}
+          mt.waitForID(0);
         }
+        catch (Exception ex)
+        {}
       }
-      DNATwirler twirler = new DNATwirler();
-      twirler.start();
+
+      ImageSpinner spinner = new ImageSpinner();
+      spinner.start();
       webServiceRunning = true;
     }
 
-    class DNATwirler extends Thread
+    class ImageSpinner extends Thread
     {
       public void run()
       {
         while(webServiceRunning)
         {
           try{
-            Thread.sleep(100);
-            imageIndex++;
-            imageIndex %=9;
+            Thread.sleep(10);
+            angle+=1;
+            angle %=360;
             repaint();
           }
           catch(Exception ex){}
@@ -1073,25 +1138,72 @@ if ( viewport.getConservationSelected() )
          }catch(Exception ex){}
        }
 
-       public void paintComponent(Graphics g)
+       public void paintComponent(Graphics g1)
        {
+         Graphics2D g = (Graphics2D)g1;
          g.setColor(Color.white);
          g.fillRect(0,0,getWidth(), getHeight());
          if(image!=null)
          {
-           g.drawImage(image[imageIndex],10,10,this);
+
+           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", 30,30);
+         g.drawString("Clustal Alignment Web Service running", 60,30);
        }
   }
-  public void jpredMenuItem_actionPerformed(ActionEvent e)
+  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));
+      }
+      else
+      {
+        int sz;
+        SequenceI[] msa = new SequenceI[sz=seqs.getSize()];
+        for (int i = 0; i < sz; i++)
+        {
+          msa[i] = (SequenceI) seqs.getSequenceAt(i);
+        }
+
+        JPredClient ct = new JPredClient(msa);
+      }
+
+    }
+    else
     {
-    //  JInternalFrame frame = new JInternalFrame();
-//      JPredClient ct = new JPredClient((SequenceI)
-    ///                                   viewport.getAlignment().getSequences().elementAt(0));
+      Vector seqs = viewport.getAlignment().getSequences();
+
+      if (seqs.size() == 1 || !viewport.alignment.isAligned())
+      {
+        JPredClient ct = new JPredClient( (SequenceI)
+                                         seqs.elementAt(0));
+      }
+      else
+      {
+        SequenceI[] msa = new SequenceI[seqs.size()];
+        for (int i = 0; i < seqs.size(); i++)
+        {
+          msa[i] = (SequenceI) seqs.elementAt(i);
+        }
+
+        JPredClient ct = new JPredClient(msa);
+      }
+
     }
+  }
 
     protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
     // Pick the tree file