-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.gui;\r
-\r
-import jalview.analysis.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import jalview.jbgui.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import java.util.*;\r
-import javax.swing.*;\r
-import java.awt.print.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class PCAPanel extends GPCAPanel implements Runnable\r
-{\r
- PCA pca;\r
- int top;\r
- RotatableCanvas rc;\r
- AlignViewport av;\r
- SequenceI [] seqs;\r
-\r
- /**\r
- * Creates a new PCAPanel object.\r
- *\r
- * @param av DOCUMENT ME!\r
- * @param s DOCUMENT ME!\r
- */\r
- public PCAPanel(AlignViewport av)\r
- {\r
- this.av = av;\r
-\r
- boolean sameLength = true;\r
-\r
- if ((av.getSelectionGroup() != null) &&\r
- (av.getSelectionGroup().getSize() > 3))\r
- {\r
- seqs = new Sequence[av.getSelectionGroup().getSize()];\r
- int length = av.getSelectionGroup().getSequenceAt(0).getLength();\r
- for (int i = 0; i < av.getSelectionGroup().getSize(); i++)\r
- {\r
- seqs[i] = av.getSelectionGroup().getSequenceAt(i);\r
- if(seqs[i].getLength()!=length)\r
- {\r
- sameLength = false;\r
- break;\r
- }\r
- }\r
- }\r
- else\r
- {\r
- seqs = new Sequence[av.getAlignment().getHeight()];\r
- int length = av.alignment.getSequenceAt(0).getLength();\r
-\r
- for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
- {\r
- seqs[i] = av.getAlignment().getSequenceAt(i);\r
- if(seqs[i].getLength()!=length)\r
- {\r
- sameLength = false;\r
- break;\r
- }\r
-\r
- }\r
- }\r
-\r
- if (!sameLength)\r
- {\r
- JOptionPane.showMessageDialog(Desktop.desktop,\r
- "The sequences must be aligned before calculating PCA.\n" +\r
- "Try using the Pad function in the edit menu,\n" +\r
- "or one of the multiple sequence alignment web services.",\r
- "Sequences not aligned",\r
- JOptionPane.WARNING_MESSAGE);\r
-\r
- return;\r
- }\r
-\r
-\r
- Desktop.addInternalFrame(this, "Principal component analysis",\r
- 400, 400);\r
-\r
-\r
- rc = new RotatableCanvas(av);\r
- this.getContentPane().add(rc, BorderLayout.CENTER);\r
- Thread worker = new Thread(this);\r
- worker.start();\r
- }\r
-\r
- public void bgcolour_actionPerformed(ActionEvent e)\r
- {\r
- Color col = JColorChooser.showDialog(this, "Select Background Colour",\r
- rc.bgColour);\r
-\r
- if(col!=null)\r
- rc.bgColour = col;\r
- rc.repaint();\r
- }\r
-\r
-\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void run()\r
- {\r
- try{\r
- pca = new PCA(seqs);\r
- pca.run();\r
-\r
- // Now find the component coordinates\r
- int ii = 0;\r
-\r
- while ( (ii < seqs.length) && (seqs[ii] != null))\r
- {\r
- ii++;\r
- }\r
-\r
- double[][] comps = new double[ii][ii];\r
-\r
- for (int i = 0; i < ii; i++)\r
- {\r
- if (pca.getEigenvalue(i) > 1e-4)\r
- {\r
- comps[i] = pca.component(i);\r
- }\r
- }\r
-\r
- //////////////////\r
- xCombobox.setSelectedIndex(0);\r
- yCombobox.setSelectedIndex(1);\r
- zCombobox.setSelectedIndex(2);\r
-\r
- top = pca.getM().rows - 1;\r
-\r
- Vector points = new Vector();\r
- float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);\r
-\r
- for (int i = 0; i < pca.getM().rows; i++)\r
- {\r
- SequencePoint sp = new SequencePoint(seqs[i], scores[i]);\r
- points.addElement(sp);\r
- }\r
-\r
- rc.setPoints(points, pca.getM().rows);\r
- rc.repaint();\r
- seqs = null;\r
- }\r
- catch(OutOfMemoryError er)\r
- { JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "Out of memory calculating PCA!!"\r
- +\r
- "\nSee help files for increasing Java Virtual Machine memory."\r
- , "Out of memory",\r
- JOptionPane.WARNING_MESSAGE);\r
- System.out.println("PCAPanel: "+er);\r
- System.gc();\r
-\r
- }\r
-\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- void doDimensionChange()\r
- {\r
- if (top == 0)\r
- {\r
- return;\r
- }\r
-\r
- int dim1 = top - xCombobox.getSelectedIndex();\r
- int dim2 = top - yCombobox.getSelectedIndex();\r
- int dim3 = top - zCombobox.getSelectedIndex();\r
-\r
- float[][] scores = pca.getComponents(dim1, dim2, dim3, 100);\r
-\r
- for (int i = 0; i < pca.getM().rows; i++)\r
- {\r
- ((SequencePoint) rc.points.elementAt(i)).coord = scores[i];\r
- }\r
-\r
- rc.img = null;\r
- rc.rotmat.setIdentity();\r
- rc.initAxes();\r
- rc.paint(rc.getGraphics());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void xCombobox_actionPerformed(ActionEvent e)\r
- {\r
- doDimensionChange();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void yCombobox_actionPerformed(ActionEvent e)\r
- {\r
- doDimensionChange();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void zCombobox_actionPerformed(ActionEvent e)\r
- {\r
- doDimensionChange();\r
- }\r
-\r
-\r
- public void outputValues_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
- Desktop.addInternalFrame(cap, "PCA details", 500,\r
- 500);\r
-\r
- cap.setText(pca.getDetails());\r
- }\r
-\r
- public void showLabels_actionPerformed(ActionEvent e)\r
- {\r
- rc.showLabels(showLabels.getState());\r
- }\r
-\r
- public void print_actionPerformed(ActionEvent e)\r
- {\r
- PCAPrinter printer = new PCAPrinter();\r
- printer.start();\r
- }\r
-\r
-\r
- class PCAPrinter extends Thread implements Printable\r
- {\r
- public void run()\r
- {\r
- PrinterJob printJob = PrinterJob.getPrinterJob();\r
- PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
-\r
- printJob.setPrintable(this, pf);\r
-\r
- if (printJob.printDialog())\r
- {\r
- try\r
- {\r
- printJob.print();\r
- }\r
- catch (Exception PrintException)\r
- {\r
- PrintException.printStackTrace();\r
- }\r
- }\r
- }\r
-\r
- public int print(Graphics pg, PageFormat pf, int pi)\r
- throws PrinterException\r
- {\r
- pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());\r
-\r
- rc.drawBackground(pg, rc.bgColour);\r
- rc.drawScene(pg);\r
- if (rc.drawAxes == true)\r
- {\r
- rc.drawAxes(pg);\r
- }\r
-\r
- if (pi == 0)\r
- return Printable.PAGE_EXISTS;\r
- else\r
- return Printable.NO_SUCH_PAGE;\r
- }\r
- }\r
-\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void eps_actionPerformed(ActionEvent e)\r
- {\r
- makePCAImage(jalview.util.ImageMaker.EPS);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void png_actionPerformed(ActionEvent e)\r
- {\r
- makePCAImage(jalview.util.ImageMaker.PNG);\r
- }\r
-\r
- void makePCAImage(int type)\r
- {\r
- int width = rc.getWidth();\r
- int height = rc.getHeight();\r
-\r
- jalview.util.ImageMaker im;\r
-\r
- if(type == jalview.util.ImageMaker.PNG)\r
- im = new jalview.util.ImageMaker(this,\r
- jalview.util.ImageMaker.PNG,\r
- "Make PNG image from PCA",\r
- width, height,\r
- null, null);\r
- else\r
- im = new jalview.util.ImageMaker(this,\r
- jalview.util.ImageMaker.EPS,\r
- "Make EPS file from PCA",\r
- width, height,\r
- null, this.getTitle());\r
-\r
- if(im.getGraphics()!=null)\r
- {\r
- rc.drawBackground(im.getGraphics(), Color.black);\r
- rc.drawScene(im.getGraphics());\r
- if (rc.drawAxes == true)\r
- {\r
- rc.drawAxes(im.getGraphics());\r
- }\r
- im.writeImage();\r
- }\r
- }\r
- }\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * 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
+ * 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.analysis.*;
+
+import jalview.datamodel.*;
+
+import jalview.jbgui.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import java.util.*;
+import javax.swing.*;
+import java.awt.print.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class PCAPanel extends GPCAPanel implements Runnable
+{
+ PCA pca;
+ int top;
+ RotatableCanvas rc;
+ AlignViewport av;
+ AlignmentView seqstrings;
+ SequenceI [] seqs;
+
+ /**
+ * Creates a new PCAPanel object.
+ *
+ * @param av DOCUMENT ME!
+ * @param s DOCUMENT ME!
+ */
+ public PCAPanel(AlignViewport av)
+ {
+ this.av = av;
+
+ boolean sameLength = true;
+
+ 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();
+
+ for (int i = 0; i < seqs.length; i++)
+ {
+ if (sq[i].getWidth() != length)
+ {
+ sameLength = false;
+ break;
+ }
+ }
+
+ 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;
+ }
+
+
+ Desktop.addInternalFrame(this, "Principal component analysis",
+ 400, 400);
+
+
+ rc = new RotatableCanvas(av);
+ 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 < 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)
+ {
+ comps[i] = pca.component(i);
+ }
+ }
+
+ //////////////////
+ xCombobox.setSelectedIndex(0);
+ yCombobox.setSelectedIndex(1);
+ zCombobox.setSelectedIndex(2);
+
+ top = pca.getM().rows - 1;
+
+ 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.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();
+
+ }
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ void doDimensionChange()
+ {
+ 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];
+ }
+
+ rc.img = null;
+ rc.rotmat.setIdentity();
+ rc.initAxes();
+ 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]);
+
+ //>>>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.NEW_WINDOW_WIDTH,
+ AlignFrame.NEW_WINDOW_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();
+ }
+ }
+ }
git://source.jalview.org / jalview.git / blobdiff