X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=772e67e8b8fccb12aa41810cc8e1af3c81e18e63;hb=e9217775986fbca85770d7fe5b3763b6920b0c3f;hp=d0b3bbca7501c30aed5537e60a0d0247d5801ff4;hpb=8f2acf658e855209c6db6b68d5cc0779733c3d7e;p=jalview.git

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index d0b3bbc..772e67e 100755
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -1,101 +1,204 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.gui;
 
-import jalview.datamodel.*;
-import jalview.analysis.PCA;
-import jalview.jbgui.*;
+import java.util.*;
+
 import java.awt.*;
 import java.awt.event.*;
-import java.util.*;
+import java.awt.print.*;
+import javax.swing.*;
 
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.jbgui.*;
 
-public class PCAPanel extends GPCAPanel implements Runnable
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class PCAPanel
+    extends GPCAPanel implements Runnable
 {
   PCA pca;
   int top;
   RotatableCanvas rc;
+  AlignmentPanel ap;
   AlignViewport av;
+  AlignmentView seqstrings;
+  SequenceI[] seqs;
 
-  public void run()
+  /**
+   * Creates a new PCAPanel object.
+   *
+   * @param av DOCUMENT ME!
+   * @param s DOCUMENT ME!
+   */
+  public PCAPanel(AlignmentPanel ap)
   {
-    // do stuff
-  }
+    this.av = ap.av;
+    this.ap = ap;
 
-  public PCAPanel(AlignViewport av, SequenceI[] s) {
+    boolean sameLength = true;
 
-    this.av = av;
-    if(av.getSelectionGroup()!=null && av.getSelectionGroup().getSize()>3)
+    seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);
+    if (av.getSelectionGroup() == null)
     {
-      s = new Sequence[av.getSelectionGroup().getSize()];
-      for(int i=0; i<s.length; i++)
-        s[i] = av.getSelectionGroup().getSequenceAt(i);
+      seqs = av.alignment.getSequencesArray();
     }
+    else
+    {
+      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(s==null)
+    if (!sameLength)
     {
-      s = new Sequence[av.getAlignment().getHeight()];
-      for (int i = 0; i < av.getAlignment().getHeight(); i++)
-        s[i] = av.getAlignment().getSequenceAt(i);
-     }
+      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);
-    pca.run();
+    Desktop.addInternalFrame(this, "Principal component analysis",
+                             400, 400);
 
-    // Now find the component coordinates
-    int ii=0;
-    while (ii < s.length && s[ii] != null)
+    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)
     {
-      ii++;
+      rc.bgColour = col;
     }
+    rc.repaint();
+  }
 
-    double[][] comps = new double[ii][ii];
-
-    for (int i=0; i < ii; i++ )
+  /**
+   * DOCUMENT ME!
+   */
+  public void run()
+  {
+    try
     {
-      if (pca.getEigenvalue(i) > 1e-4)
+      pca = new PCA(seqstrings.getSequenceStrings(' '));
+      pca.run();
+
+      // Now find the component coordinates
+      int ii = 0;
+
+      while ( (ii < seqs.length) && (seqs[ii] != null))
       {
-        comps[i]  = pca.component(i);
+        ii++;
       }
-    }
 
-    //////////////////
+      double[][] comps = new double[ii][ii];
 
-    xCombobox.setSelectedIndex(0);
-    yCombobox.setSelectedIndex(1);
-    zCombobox.setSelectedIndex(2);
+      for (int i = 0; i < ii; i++)
+      {
+        if (pca.getEigenvalue(i) > 1e-4)
+        {
+          comps[i] = pca.component(i);
+        }
+      }
 
-    top = pca.getM().rows-1;
+      //////////////////
+      xCombobox.setSelectedIndex(0);
+      yCombobox.setSelectedIndex(1);
+      zCombobox.setSelectedIndex(2);
 
-    Vector points = new Vector();
-    float[][] scores = pca.getComponents(top-1,top-2,top-3,100);
+      top = pca.getM().rows - 1;
 
-    for (int i =0; i < pca.getM().rows; i++ )
-    {
-      SequencePoint sp = new SequencePoint(s[i],scores[i]);
-      points.addElement(sp);
-    }
+      Vector points = new Vector();
+      float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
+
+      for (int i = 0; i < pca.getM().rows; i++)
+      {
+        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();
+      addKeyListener(rc);
 
-    add(rc, BorderLayout.CENTER);
-  }
+    }
+    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!
+   */
   void doDimensionChange()
   {
-    if(top==0)
+    if (top == 0)
+    {
       return;
+    }
 
     int dim1 = top - xCombobox.getSelectedIndex();
     int dim2 = top - yCombobox.getSelectedIndex();
     int dim3 = top - zCombobox.getSelectedIndex();
 
-    float[][] scores  = pca.getComponents(dim1,dim2,dim3,100);
-    for (int i=0; i < pca.getM().rows; i++) {
-      ((SequencePoint)rc.points.elementAt(i)).coord = scores[i];
+    float[][] scores = pca.getComponents(dim1, dim2, dim3, 100);
+
+    for (int i = 0; i < pca.getM().rows; i++)
+    {
+      ( (SequencePoint) rc.points.elementAt(i)).coord = scores[i];
     }
 
     rc.img = null;
@@ -104,19 +207,278 @@ public class PCAPanel extends GPCAPanel implements Runnable
     rc.paint(rc.getGraphics());
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void xCombobox_actionPerformed(ActionEvent e)
   {
     doDimensionChange();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void yCombobox_actionPerformed(ActionEvent e)
   {
     doDimensionChange();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void zCombobox_actionPerformed(ActionEvent e)
   {
     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);
+
+  }
+
 }