X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=d7e0cd78d3c7bea344592aa99589c2570127f426;hb=b69e028fe41a867e72cda2a6d69182ff0c6bd90e;hp=7bda65a597613aeac4e41f4ab5ae531b6f4bb862;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 7bda65a..d7e0cd7 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
@@ -28,6 +28,8 @@ import java.awt.*;
 import java.awt.event.*;
 
 import java.util.*;
+import javax.swing.*;
+import java.awt.print.*;
 
 
 /**
@@ -41,7 +43,10 @@ public class PCAPanel extends GPCAPanel implements Runnable
     PCA pca;
     int top;
     RotatableCanvas rc;
+    AlignmentPanel ap;
     AlignViewport av;
+    AlignmentView seqstrings;
+    SequenceI  [] seqs;
 
     /**
      * Creates a new PCAPanel object.
@@ -49,51 +54,98 @@ public class PCAPanel extends GPCAPanel implements Runnable
      * @param av DOCUMENT ME!
      * @param s DOCUMENT ME!
      */
-    public PCAPanel(AlignViewport av, SequenceI[] s)
+    public PCAPanel(AlignmentPanel ap)
     {
-        this.av = av;
+        this.av = ap.av;
+        this.ap = ap;
 
-        if ((av.getSelectionGroup() != null) &&
-                (av.getSelectionGroup().getSize() > 3))
-        {
-            s = new Sequence[av.getSelectionGroup().getSize()];
+        boolean sameLength = true;
 
-            for (int i = 0; i < s.length; i++)
-            {
-                s[i] = av.getSelectionGroup().getSequenceAt(i);
-            }
+        seqstrings = av.getAlignmentView(av.getSelectionGroup()!=null);
+        if(av.getSelectionGroup()==null)
+        {
+          seqs = av.alignment.getSequencesArray();
         }
+        else
+        {
+          seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+        }
+        SeqCigar sq[]=seqstrings.getSequences();
+        int length = sq[0].getWidth();
 
-        if (s == null)
+        for (int i = 0; i < seqs.length; i++)
         {
-            s = new Sequence[av.getAlignment().getHeight()];
+          if (sq[i].getWidth() != length)
+          {
+            sameLength = false;
+            break;
+          }
+        }
 
-            for (int i = 0; i < av.getAlignment().getHeight(); i++)
-            {
-                s[i] = av.getAlignment().getSequenceAt(i);
-            }
+        if (!sameLength)
+        {
+          JOptionPane.showMessageDialog(Desktop.desktop,
+                                        "The sequences must be aligned before calculating PCA.\n" +
+                                        "Try using the Pad function in the edit menu,\n" +
+                                        "or one of the multiple sequence alignment web services.",
+                                        "Sequences not aligned",
+                                        JOptionPane.WARNING_MESSAGE);
+
+          return;
         }
 
-        //////////////////////This part was done in PCATHread originally. Is it too slow???
-        pca = new PCA(s);
+
+        Desktop.addInternalFrame(this, "Principal component analysis",
+                               400, 400);
+
+
+
+        PaintRefresher.Register(this, av.getSequenceSetId());
+
+        rc = new RotatableCanvas(ap);
+        this.getContentPane().add(rc, BorderLayout.CENTER);
+        Thread worker = new Thread(this);
+        worker.start();
+    }
+
+    public void bgcolour_actionPerformed(ActionEvent e)
+    {
+      Color col = JColorChooser.showDialog(this, "Select Background Colour",
+                rc.bgColour);
+
+      if(col!=null)
+        rc.bgColour = col;
+      rc.repaint();
+    }
+
+
+
+
+    /**
+     * DOCUMENT ME!
+     */
+    public void run()
+    {
+      try{
+        pca = new PCA(seqstrings.getSequenceStrings(' '));
         pca.run();
 
         // Now find the component coordinates
         int ii = 0;
 
-        while ((ii < s.length) && (s[ii] != null))
+        while ( (ii < seqs.length) && (seqs[ii] != null))
         {
-            ii++;
+          ii++;
         }
 
         double[][] comps = new double[ii][ii];
 
         for (int i = 0; i < ii; i++)
         {
-            if (pca.getEigenvalue(i) > 1e-4)
-            {
-                comps[i] = pca.component(i);
-            }
+          if (pca.getEigenvalue(i) > 1e-4)
+          {
+            comps[i] = pca.component(i);
+          }
         }
 
         //////////////////
@@ -108,22 +160,28 @@ public class PCAPanel extends GPCAPanel implements Runnable
 
         for (int i = 0; i < pca.getM().rows; i++)
         {
-            SequencePoint sp = new SequencePoint(s[i], scores[i]);
-            points.addElement(sp);
+          SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
+          points.addElement(sp);
         }
 
-        rc = new RotatableCanvas(av, points, pca.getM().rows);
+        rc.setPoints(points, pca.getM().rows);
+        rc.repaint();
 
-        //rc.printPoints();
-        add(rc, BorderLayout.CENTER);
-    }
+        addKeyListener(rc);
+
+      }
+     catch(OutOfMemoryError er)
+      { JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                              "Out of memory calculating PCA!!"
+                                              +
+                                              "\nSee help files for increasing Java Virtual Machine memory."
+                                              , "Out of memory",
+                                              JOptionPane.WARNING_MESSAGE);
+        System.out.println("PCAPanel: "+er);
+        System.gc();
+
+      }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void run()
-    {
-        // do stuff
     }
 
     /**
@@ -182,4 +240,248 @@ public class PCAPanel extends GPCAPanel implements Runnable
     {
         doDimensionChange();
     }
-}
+
+
+    public void outputValues_actionPerformed(ActionEvent e)
+    {
+      CutAndPasteTransfer cap = new CutAndPasteTransfer();
+      Desktop.addInternalFrame(cap, "PCA details", 500,
+                500);
+
+      cap.setText(pca.getDetails());
+     }
+
+    public void showLabels_actionPerformed(ActionEvent e)
+    {
+      rc.showLabels(showLabels.getState());
+    }
+
+    public void print_actionPerformed(ActionEvent e)
+    {
+      PCAPrinter printer = new PCAPrinter();
+      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
+    {
+      public void run()
+      {
+        PrinterJob printJob = PrinterJob.getPrinterJob();
+        PageFormat pf = printJob.pageDialog(printJob.defaultPage());
+
+        printJob.setPrintable(this, pf);
+
+        if (printJob.printDialog())
+        {
+          try
+          {
+            printJob.print();
+          }
+          catch (Exception PrintException)
+          {
+            PrintException.printStackTrace();
+          }
+        }
+      }
+
+      public int print(Graphics pg, PageFormat pf, int pi)
+          throws PrinterException
+      {
+        pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
+
+        rc.drawBackground(pg, rc.bgColour);
+        rc.drawScene(pg);
+        if (rc.drawAxes == true)
+        {
+          rc.drawAxes(pg);
+        }
+
+        if (pi == 0)
+          return Printable.PAGE_EXISTS;
+        else
+          return Printable.NO_SUCH_PAGE;
+      }
+    }
+
+
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void eps_actionPerformed(ActionEvent e)
+    {
+      makePCAImage(jalview.util.ImageMaker.EPS);
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void png_actionPerformed(ActionEvent e)
+    {
+       makePCAImage(jalview.util.ImageMaker.PNG);
+    }
+
+    void makePCAImage(int type)
+    {
+      int width = rc.getWidth();
+      int height = rc.getHeight();
+
+      jalview.util.ImageMaker im;
+
+      if(type == jalview.util.ImageMaker.PNG)
+        im = new jalview.util.ImageMaker(this,
+                                         jalview.util.ImageMaker.PNG,
+                                         "Make PNG image from PCA",
+                                         width, height,
+                                         null, null);
+        else
+          im = new jalview.util.ImageMaker(this,
+                                 jalview.util.ImageMaker.EPS,
+                                 "Make EPS file from PCA",
+                                 width, height,
+                                 null, this.getTitle());
+
+      if(im.getGraphics()!=null)
+       {
+         rc.drawBackground(im.getGraphics(), Color.black);
+         rc.drawScene(im.getGraphics());
+         if (rc.drawAxes == true)
+         {
+           rc.drawAxes(im.getGraphics());
+         }
+         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");
+
+      buttonGroup.add(itemf);
+
+      itemf.setSelected(rc.applyToAllViews);
+      itemf.addActionListener(new ActionListener()
+      {
+        public void actionPerformed(ActionEvent evt)
+        {
+          rc.applyToAllViews = itemf.isSelected();
+        }
+      });
+      associateViewsMenu.add(itemf);
+
+    }
+
+  }