X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=90cd8e6c88fe35a599c5d7cb477ca7885efc2e76;hb=ae83cc59079dc5374a41402889b6f4192f66e9e2;hp=e680ddeab3fcb15970cd0817878fad8521c221a2;hpb=9c5d69ef1e102b1eac18ec13c362522f40c9000d;p=jalview.git

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index e680dde..90cd8e6 100755
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -43,8 +43,10 @@ public class PCAPanel extends GPCAPanel implements Runnable
     PCA pca;
     int top;
     RotatableCanvas rc;
+    AlignmentPanel ap;
     AlignViewport av;
-    SequenceI [] seqs;
+    AlignmentView seqstrings;
+    SequenceI  [] seqs;
 
     /**
      * Creates a new PCAPanel object.
@@ -52,42 +54,32 @@ public class PCAPanel extends GPCAPanel implements Runnable
      * @param av DOCUMENT ME!
      * @param s DOCUMENT ME!
      */
-    public PCAPanel(AlignViewport av)
+    public PCAPanel(AlignmentPanel ap)
     {
-        this.av = av;
+        this.av = ap.av;
+        this.ap = ap;
 
         boolean sameLength = true;
 
-        if ((av.getSelectionGroup() != null) &&
-                (av.getSelectionGroup().getSize() > 3))
+        seqstrings = av.getAlignmentView(av.getSelectionGroup()!=null);
+        if(av.getSelectionGroup()==null)
         {
-            seqs = new Sequence[av.getSelectionGroup().getSize()];
-            int length = av.getSelectionGroup().getSequenceAt(0).getLength();
-            for (int i = 0; i < av.getSelectionGroup().getSize(); i++)
-            {
-                seqs[i] = av.getSelectionGroup().getSequenceAt(i);
-                if(seqs[i].getLength()!=length)
-                {
-                  sameLength = false;
-                  break;
-                }
-            }
+          seqs = av.alignment.getSequencesArray();
         }
         else
         {
-            seqs = new Sequence[av.getAlignment().getHeight()];
-            int length = av.alignment.getSequenceAt(0).getLength();
-
-            for (int i = 0; i < av.getAlignment().getHeight(); i++)
-            {
-                seqs[i] = av.getAlignment().getSequenceAt(i);
-                if(seqs[i].getLength()!=length)
-               {
-                 sameLength = false;
-                 break;
-               }
+          seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+        }
+        SeqCigar sq[]=seqstrings.getSequences();
+        int length = sq[0].getWidth();
 
-            }
+        for (int i = 0; i < seqs.length; i++)
+        {
+          if (sq[i].getWidth() != length)
+          {
+            sameLength = false;
+            break;
+          }
         }
 
         if (!sameLength)
@@ -107,7 +99,10 @@ public class PCAPanel extends GPCAPanel implements Runnable
                                400, 400);
 
 
-        rc = new RotatableCanvas(av);
+
+        PaintRefresher.Register(this, av.getSequenceSetId());
+
+        rc = new RotatableCanvas(ap);
         this.getContentPane().add(rc, BorderLayout.CENTER);
         Thread worker = new Thread(this);
         worker.start();
@@ -132,7 +127,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
     public void run()
     {
       try{
-        pca = new PCA(seqs);
+        pca = new PCA(seqstrings.getSequenceStrings(' '));
         pca.run();
 
         // Now find the component coordinates
@@ -171,7 +166,9 @@ public class PCAPanel extends GPCAPanel implements Runnable
 
         rc.setPoints(points, pca.getM().rows);
         rc.repaint();
-        seqs = null;
+
+        addKeyListener(rc);
+
       }
      catch(OutOfMemoryError er)
       { JOptionPane.showInternalMessageDialog(Desktop.desktop,
@@ -265,6 +262,67 @@ public class PCAPanel extends GPCAPanel implements Runnable
       printer.start();
     }
 
+    public void originalSeqData_actionPerformed(ActionEvent e)
+    {
+      // this was cut'n'pasted from the equivalent TreePanel method - we should make this an abstract function of all jalview analysis windows
+      if (seqstrings==null)
+      {
+        jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
+        return;
+      }
+      // decide if av alignment is sufficiently different to original data to warrant a new window to be created
+      // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
+      // or create a selection box around columns in alignment view
+      // test Alignment(SeqCigar[])
+      Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(av.
+          getGapCharacter());
+
+
+      if (alAndColsel != null && alAndColsel[0]!=null)
+      {
+          // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
+
+          Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
+          Alignment dataset = av.getAlignment().getDataset();
+          if (dataset != null)
+          {
+            al.setDataset(dataset);
+          }
+
+          if (true)
+          {
+              // make a new frame!
+              AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1],
+                                           AlignFrame.DEFAULT_WIDTH,
+                                           AlignFrame.DEFAULT_HEIGHT
+);
+
+              //>>>This is a fix for the moment, until a better solution is found!!<<<
+              // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
+
+              //           af.addSortByOrderMenuItem(ServiceName + " Ordering",
+              //                                     msaorder);
+
+              Desktop.addInternalFrame(af, "Original Data for " + this.title,
+                                       AlignFrame.DEFAULT_WIDTH,
+                                       AlignFrame.DEFAULT_HEIGHT);
+            }
+          }
+          /*      CutAndPasteTransfer cap = new CutAndPasteTransfer();
+                 for (int i = 0; i < seqs.length; i++)
+                 {
+                   cap.appendText(new jalview.util.Format("%-" + 15 + "s").form(
+            seqs[i].getName()));
+                   cap.appendText(" " + seqstrings[i] + "\n");
+
+                 }
+
+                 Desktop.addInternalFrame(cap, "Original Data",
+                     400, 400);
+           */
+    }
+
+
 
     class PCAPrinter extends Thread implements Printable
     {
@@ -360,4 +418,68 @@ public class PCAPanel extends GPCAPanel implements Runnable
          im.writeImage();
        }
     }
+
+
+    public void viewMenu_menuSelected()
+    {
+      buildAssociatedViewMenu();
+    }
+
+
+    void buildAssociatedViewMenu()
+    {
+      AlignmentPanel [] aps = PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
+      if(aps.length==1 && rc.av ==aps[0].av)
+      {
+        associateViewsMenu.setVisible(false);
+        return;
+      }
+
+      associateViewsMenu.setVisible(true);
+
+      if( (viewMenu.getItem(viewMenu.getItemCount()-2) instanceof JMenuItem))
+      {
+        viewMenu.insertSeparator(viewMenu.getItemCount()-1);
+      }
+
+      associateViewsMenu.removeAll();
+
+
+      JRadioButtonMenuItem item;
+      ButtonGroup buttonGroup = new ButtonGroup();
+      int i, iSize = aps.length;
+      final PCAPanel thisPCAPanel = this;
+      for(i=0; i<iSize; i++)
+      {
+          final AlignmentPanel ap = aps[i];
+          item = new JRadioButtonMenuItem(ap.av.viewName, ap.av==rc.av );
+          buttonGroup.add(item);
+          item.addActionListener(new ActionListener()
+              {
+                public void actionPerformed(ActionEvent evt)
+                {
+                  rc.applyToAllViews = false;
+                  rc.av = ap.av;
+                  rc.ap = ap;
+                  PaintRefresher.Register(thisPCAPanel, ap.av.getSequenceSetId());
+                }
+              });
+
+          associateViewsMenu.add(item);
+      }
+
+      final JRadioButtonMenuItem itemf =
+          new JRadioButtonMenuItem("All Views", rc.applyToAllViews);
+      buttonGroup.add(itemf);
+      itemf.addActionListener(new ActionListener()
+      {
+        public void actionPerformed(ActionEvent evt)
+        {
+          rc.applyToAllViews = itemf.isSelected();
+        }
+      });
+      associateViewsMenu.add(itemf);
+
+    }
+
   }