-/*\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
-\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, SequenceI[] s)\r
- {\r
- this.av = av;\r
-\r
- if ((av.getSelectionGroup() != null) &&\r
- (av.getSelectionGroup().getSize() > 3))\r
- {\r
- seqs = new Sequence[av.getSelectionGroup().getSize()];\r
-\r
- for (int i = 0; i < s.length; i++)\r
- {\r
- seqs[i] = av.getSelectionGroup().getSequenceAt(i);\r
- }\r
- }\r
-\r
- if (s == null)\r
- {\r
- seqs = new Sequence[av.getAlignment().getHeight()];\r
-\r
- for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
- {\r
- seqs[i] = av.getAlignment().getSequenceAt(i);\r
- }\r
- }\r
-\r
-\r
- rc = new RotatableCanvas(av);\r
- add(rc, BorderLayout.CENTER);\r
- Thread worker = new Thread(this);\r
- worker.start();\r
- }\r
-\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void run()\r
- {\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
-\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
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.gui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.awt.print.*;
+import javax.swing.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.jbgui.*;
+
+/**
+ * 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;
+
+ /**
+ * 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)
+ {
+ 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);
+
+ 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 < 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();
+
+ addKeyListener(rc);
+
+ } catch (OutOfMemoryError er)
+ {
+ new OOMWarning("calculating PCA", er);
+
+ }
+
+ }
+
+ /**
+ * 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();
+ try
+ {
+ cap.setText(pca.getDetails());
+ Desktop.addInternalFrame(cap, "PCA details", 500, 500);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("opening PCA details", oom);
+ cap.dispose();
+ }
+ }
+
+ 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[])
+ char gc = '-';
+ try
+ {
+ // we try to get the associated view's gap character
+ // but this may fail if the view was closed...
+ gc = av.getGapCharacter();
+ } catch (Exception ex)
+ {
+ }
+ ;
+ Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(gc);
+
+ if (alAndColsel != null && alAndColsel[0] != null)
+ {
+ // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
+
+ Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
+ Alignment dataset = (av != null && av.getAlignment() != null) ? av
+ .getAlignment().getDataset() : null;
+ 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);
+
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent
+ * )
+ */
+ protected void outputPoints_actionPerformed(ActionEvent e)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ try
+ {
+ cap.setText(getPointsasCsv(false));
+ Desktop.addInternalFrame(cap, "Points for " + getTitle(), 500, 500);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("exporting PCA points", oom);
+ cap.dispose();
+ }
+ }
+
+ private String getPointsasCsv(boolean transformed)
+ {
+ StringBuffer csv = new StringBuffer();
+ csv.append("\"Sequence\"");
+ if (transformed)
+ {
+ csv.append(",");
+ csv.append(xCombobox.getSelectedIndex());
+ csv.append(",");
+ csv.append(yCombobox.getSelectedIndex());
+ csv.append(",");
+ csv.append(zCombobox.getSelectedIndex());
+ }
+ else
+ {
+ for (int d = 1, dmax = pca.component(1).length; d <= dmax; d++)
+ {
+ csv.append("," + d);
+ }
+ }
+ csv.append("\n");
+ for (int s = 0; s < seqs.length; s++)
+ {
+ csv.append("\"" + seqs[s].getName() + "\"");
+ double fl[];
+ if (!transformed)
+ {
+ // output pca in correct order
+ fl = pca.component(s);
+ for (int d = fl.length - 1; d >= 0; d--)
+ {
+ csv.append(",");
+ csv.append(fl[d]);
+ }
+ }
+ else
+ {
+ // output current x,y,z coords for points
+ fl = rc.getPointPosition(s);
+ for (int d = 0; d < fl.length; d++)
+ {
+ csv.append(",");
+ csv.append(fl[d]);
+ }
+ }
+ csv.append("\n");
+ }
+ return csv.toString();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event
+ * .ActionEvent)
+ */
+ protected void outputProjPoints_actionPerformed(ActionEvent e)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ try
+ {
+ cap.setText(getPointsasCsv(true));
+ Desktop.addInternalFrame(cap, "Transformed points for " + getTitle(),
+ 500, 500);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("exporting transformed PCA points", oom);
+ cap.dispose();
+ }
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff