X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=772e67e8b8fccb12aa41810cc8e1af3c81e18e63;hb=6de402db90987d3645f3429d9073c13678d8e980;hp=8c2ecc9f851bbbfde7462e87e131893b067ea6c6;hpb=7c05496d1da22f21ce5ae1a199afb9b16c8777ea;p=jalview.git

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 8c2ecc9..772e67e 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) 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
@@ -18,19 +18,16 @@
  */
 package jalview.gui;
 
-import jalview.analysis.*;
-
-import jalview.datamodel.*;
-
-import jalview.jbgui.*;
+import java.util.*;
 
 import java.awt.*;
 import java.awt.event.*;
-
-import java.util.*;
-import javax.swing.*;
 import java.awt.print.*;
+import javax.swing.*;
 
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.jbgui.*;
 
 /**
  * DOCUMENT ME!
@@ -38,329 +35,450 @@ import java.awt.print.*;
  * @author $author$
  * @version $Revision$
  */
-public class PCAPanel extends GPCAPanel implements Runnable
+public class PCAPanel
+    extends GPCAPanel implements Runnable
 {
-    PCA pca;
-    int top;
-    RotatableCanvas rc;
-    AlignViewport av;
-    String  [] seqstrings;
-    SequenceI  [] seqs;
-
-    /**
-     * Creates a new PCAPanel object.
-     *
-     * @param av DOCUMENT ME!
-     * @param s DOCUMENT ME!
-     */
-    public PCAPanel(AlignViewport av)
+  PCA pca;
+  int top;
+  RotatableCanvas rc;
+  AlignmentPanel ap;
+  AlignViewport av;
+  AlignmentView seqstrings;
+  SequenceI[] seqs;
+
+  /**
+   * Creates a new PCAPanel object.
+   *
+   * @param av DOCUMENT ME!
+   * @param s DOCUMENT ME!
+   */
+  public PCAPanel(AlignmentPanel ap)
+  {
+    this.av = ap.av;
+    this.ap = ap;
+
+    boolean sameLength = true;
+
+    seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);
+    if (av.getSelectionGroup() == null)
     {
-        this.av = av;
+      seqs = av.alignment.getSequencesArray();
+    }
+    else
+    {
+      seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+    }
+    SeqCigar sq[] = seqstrings.getSequences();
+    int length = sq[0].getWidth();
 
-        boolean sameLength = true;
+    for (int i = 0; i < seqs.length; i++)
+    {
+      if (sq[i].getWidth() != length)
+      {
+        sameLength = false;
+        break;
+      }
+    }
 
-        seqstrings = av.getSelectionAsString();
+    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;
+    }
 
-        if (av.getSelectionGroup() == null)
-        {
-          seqs = av.alignment.getSequencesArray();
-        }
-        else
-        {
-          seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
-        }
+    Desktop.addInternalFrame(this, "Principal component analysis",
+                             400, 400);
 
-        int length = seqs[0].getLength();
+    PaintRefresher.Register(this, av.getSequenceSetId());
 
-        for (int i = 0; i < seqs.length; i++)
-        {
-          if (seqs[i].getLength() != length)
-          {
-            sameLength = false;
-            break;
-          }
-        }
+    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();
+  }
 
-        if (!sameLength)
+  /**
+   * DOCUMENT ME!
+   */
+  public void run()
+  {
+    try
+    {
+      pca = new PCA(seqstrings.getSequenceStrings(' '));
+      pca.run();
+
+      // Now find the component coordinates
+      int ii = 0;
+
+      while ( (ii < seqs.length) && (seqs[ii] != null))
+      {
+        ii++;
+      }
+
+      double[][] comps = new double[ii][ii];
+
+      for (int i = 0; i < ii; i++)
+      {
+        if (pca.getEigenvalue(i) > 1e-4)
         {
-          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;
+          comps[i] = pca.component(i);
         }
+      }
 
+      //////////////////
+      xCombobox.setSelectedIndex(0);
+      yCombobox.setSelectedIndex(1);
+      zCombobox.setSelectedIndex(2);
 
-        Desktop.addInternalFrame(this, "Principal component analysis",
-                               400, 400);
+      top = pca.getM().rows - 1;
 
+      Vector points = new Vector();
+      float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
 
-        rc = new RotatableCanvas(av);
-        this.getContentPane().add(rc, BorderLayout.CENTER);
-        Thread worker = new Thread(this);
-        worker.start();
-    }
+      for (int i = 0; i < pca.getM().rows; i++)
+      {
+        SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
+        points.addElement(sp);
+      }
+
+      rc.setPoints(points, pca.getM().rows);
+      rc.repaint();
 
-    public void bgcolour_actionPerformed(ActionEvent e)
+      addKeyListener(rc);
+
+    }
+    catch (OutOfMemoryError er)
     {
-      Color col = JColorChooser.showDialog(this, "Select Background Colour",
-                rc.bgColour);
+      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();
 
-      if(col!=null)
-        rc.bgColour = col;
-      rc.repaint();
     }
 
+  }
 
+  /**
+   * DOCUMENT ME!
+   */
+  void doDimensionChange()
+  {
+    if (top == 0)
+    {
+      return;
+    }
 
+    int dim1 = top - xCombobox.getSelectedIndex();
+    int dim2 = top - yCombobox.getSelectedIndex();
+    int dim3 = top - zCombobox.getSelectedIndex();
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void run()
+    float[][] scores = pca.getComponents(dim1, dim2, dim3, 100);
+
+    for (int i = 0; i < pca.getM().rows; i++)
     {
-      try{
-        pca = new PCA(seqstrings);
-        pca.run();
+      ( (SequencePoint) rc.points.elementAt(i)).coord = scores[i];
+    }
 
-        // Now find the component coordinates
-        int ii = 0;
+    rc.img = null;
+    rc.rotmat.setIdentity();
+    rc.initAxes();
+    rc.paint(rc.getGraphics());
+  }
 
-        while ( (ii < seqs.length) && (seqs[ii] != null))
-        {
-          ii++;
-        }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void xCombobox_actionPerformed(ActionEvent e)
+  {
+    doDimensionChange();
+  }
 
-        double[][] comps = new double[ii][ii];
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void yCombobox_actionPerformed(ActionEvent e)
+  {
+    doDimensionChange();
+  }
 
-        for (int i = 0; i < ii; i++)
-        {
-          if (pca.getEigenvalue(i) > 1e-4)
-          {
-            comps[i] = pca.component(i);
-          }
-        }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void zCombobox_actionPerformed(ActionEvent e)
+  {
+    doDimensionChange();
+  }
 
-        //////////////////
-        xCombobox.setSelectedIndex(0);
-        yCombobox.setSelectedIndex(1);
-        zCombobox.setSelectedIndex(2);
+  public void outputValues_actionPerformed(ActionEvent e)
+  {
+    CutAndPasteTransfer cap = new CutAndPasteTransfer();
+    Desktop.addInternalFrame(cap, "PCA details", 500,
+                             500);
 
-        top = pca.getM().rows - 1;
+    cap.setText(pca.getDetails());
+  }
 
-        Vector points = new Vector();
-        float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
+  public void showLabels_actionPerformed(ActionEvent e)
+  {
+    rc.showLabels(showLabels.getState());
+  }
 
-        for (int i = 0; i < pca.getM().rows; i++)
-        {
-          SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
-          points.addElement(sp);
-        }
+  public void print_actionPerformed(ActionEvent e)
+  {
+    PCAPrinter printer = new PCAPrinter();
+    printer.start();
+  }
 
-        rc.setPoints(points, pca.getM().rows);
-        rc.repaint();
-      }
-     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();
+  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");
 
-    /**
-     * DOCUMENT ME!
+           }
+
+           Desktop.addInternalFrame(cap, "Original Data",
+               400, 400);
      */
-    void doDimensionChange()
-    {
-        if (top == 0)
-        {
-            return;
-        }
+  }
 
-        int dim1 = top - xCombobox.getSelectedIndex();
-        int dim2 = top - yCombobox.getSelectedIndex();
-        int dim3 = top - zCombobox.getSelectedIndex();
+  class PCAPrinter
+      extends Thread implements Printable
+  {
+    public void run()
+    {
+      PrinterJob printJob = PrinterJob.getPrinterJob();
+      PageFormat pf = printJob.pageDialog(printJob.defaultPage());
 
-        float[][] scores = pca.getComponents(dim1, dim2, dim3, 100);
+      printJob.setPrintable(this, pf);
 
-        for (int i = 0; i < pca.getM().rows; i++)
+      if (printJob.printDialog())
+      {
+        try
         {
-            ((SequencePoint) rc.points.elementAt(i)).coord = scores[i];
+          printJob.print();
         }
-
-        rc.img = null;
-        rc.rotmat.setIdentity();
-        rc.initAxes();
-        rc.paint(rc.getGraphics());
+        catch (Exception PrintException)
+        {
+          PrintException.printStackTrace();
+        }
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void xCombobox_actionPerformed(ActionEvent e)
+    public int print(Graphics pg, PageFormat pf, int pi)
+        throws PrinterException
     {
-        doDimensionChange();
-    }
+      pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void yCombobox_actionPerformed(ActionEvent e)
-    {
-        doDimensionChange();
-    }
+      rc.drawBackground(pg, rc.bgColour);
+      rc.drawScene(pg);
+      if (rc.drawAxes == true)
+      {
+        rc.drawAxes(pg);
+      }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void zCombobox_actionPerformed(ActionEvent e)
-    {
-        doDimensionChange();
+      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);
+  }
 
-    public void outputValues_actionPerformed(ActionEvent e)
-    {
-      CutAndPasteTransfer cap = new CutAndPasteTransfer();
-      Desktop.addInternalFrame(cap, "PCA details", 500,
-                500);
+  /**
+   * 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();
 
-      cap.setText(pca.getDetails());
-     }
+    jalview.util.ImageMaker im;
 
-    public void showLabels_actionPerformed(ActionEvent e)
+    if (type == jalview.util.ImageMaker.PNG)
     {
-      rc.showLabels(showLabels.getState());
+      im = new jalview.util.ImageMaker(this,
+                                       jalview.util.ImageMaker.PNG,
+                                       "Make PNG image from PCA",
+                                       width, height,
+                                       null, null);
     }
-
-    public void print_actionPerformed(ActionEvent e)
+    else
     {
-      PCAPrinter printer = new PCAPrinter();
-      printer.start();
+      im = new jalview.util.ImageMaker(this,
+                                       jalview.util.ImageMaker.EPS,
+                                       "Make EPS file from PCA",
+                                       width, height,
+                                       null, this.getTitle());
     }
 
-    public void originalSeqData_actionPerformed(ActionEvent e)
+    if (im.getGraphics() != null)
     {
-      CutAndPasteTransfer cap = new CutAndPasteTransfer();
-      for(int i=0; i<seqs.length; i++)
-          cap.appendText(seqs[i].getName()+"\t"
-                         +seqstrings[i]+"\n");
+      rc.drawBackground(im.getGraphics(), Color.black);
+      rc.drawScene(im.getGraphics());
+      if (rc.drawAxes == true)
+      {
+        rc.drawAxes(im.getGraphics());
+      }
+      im.writeImage();
+    }
+  }
 
-      Desktop.addInternalFrame(cap, "Original Data",
-          400, 400);
+  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);
 
-
-    class PCAPrinter extends Thread implements Printable
+    if ( (viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
     {
-      public void run()
-      {
-        PrinterJob printJob = PrinterJob.getPrinterJob();
-        PageFormat pf = printJob.pageDialog(printJob.defaultPage());
+      viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
+    }
 
-        printJob.setPrintable(this, pf);
+    associateViewsMenu.removeAll();
 
-        if (printJob.printDialog())
-        {
-          try
-          {
-            printJob.print();
-          }
-          catch (Exception PrintException)
-          {
-            PrintException.printStackTrace();
-          }
-        }
-      }
-
-      public int print(Graphics pg, PageFormat pf, int pi)
-          throws PrinterException
+    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()
       {
-        pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
-
-        rc.drawBackground(pg, rc.bgColour);
-        rc.drawScene(pg);
-        if (rc.drawAxes == true)
+        public void actionPerformed(ActionEvent evt)
         {
-          rc.drawAxes(pg);
+          rc.applyToAllViews = false;
+          rc.av = ap.av;
+          rc.ap = ap;
+          PaintRefresher.Register(thisPCAPanel, ap.av.getSequenceSetId());
         }
+      });
 
-        if (pi == 0)
-          return Printable.PAGE_EXISTS;
-        else
-          return Printable.NO_SUCH_PAGE;
-      }
+      associateViewsMenu.add(item);
     }
 
+    final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
 
+    buttonGroup.add(itemf);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void eps_actionPerformed(ActionEvent e)
+    itemf.setSelected(rc.applyToAllViews);
+    itemf.addActionListener(new ActionListener()
     {
-      makePCAImage(jalview.util.ImageMaker.EPS);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void png_actionPerformed(ActionEvent e)
-    {
-       makePCAImage(jalview.util.ImageMaker.PNG);
-    }
+      public void actionPerformed(ActionEvent evt)
+      {
+        rc.applyToAllViews = itemf.isSelected();
+      }
+    });
+    associateViewsMenu.add(itemf);
 
-    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();
-       }
-    }
   }
+
+}