-/*\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(false) > 3))\r
- {\r
- seqs = new Sequence[av.getSelectionGroup().getSize(false)];\r
- int length = av.getSelectionGroup().getSequenceAt(0).getLength();\r
- for (int i = 0; i < av.getSelectionGroup().getSize(false); 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GPCAPanel;
+import jalview.math.RotatableMatrix.Axis;
+import jalview.util.ImageMaker;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.PCAModel;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Graphics;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.print.PageFormat;
+import java.awt.print.Printable;
+import java.awt.print.PrinterException;
+import java.awt.print.PrinterJob;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JColorChooser;
+import javax.swing.JMenuItem;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+
+/**
+ * The panel holding the Principal Component Analysis 3-D visualisation
+ */
+public class PCAPanel extends GPCAPanel
+ implements Runnable, IProgressIndicator
+{
+ private static final int MIN_WIDTH = 470;
+
+ private static final int MIN_HEIGHT = 250;
+
+ RotatableCanvas rc;
+
+ AlignmentPanel ap;
+
+ AlignmentViewport av;
+
+ PCAModel pcaModel;
+
+ int top = 0;
+
+ private IProgressIndicator progressBar;
+
+ private boolean working;
+
+ /**
+ * Constructor given sequence data, a similarity (or distance) score model
+ * name, and score calculation parameters
+ *
+ * @param alignPanel
+ * @param modelName
+ * @param params
+ */
+ public PCAPanel(AlignmentPanel alignPanel, String modelName,
+ SimilarityParamsI params)
+ {
+ super();
+ this.av = alignPanel.av;
+ this.ap = alignPanel;
+ boolean nucleotide = av.getAlignment().isNucleotide();
+
+ progressBar = new ProgressBar(statusPanel, statusBar);
+
+ addInternalFrameListener(new InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosed(InternalFrameEvent e)
+ {
+ close_actionPerformed();
+ }
+ });
+
+ boolean selected = av.getSelectionGroup() != null
+ && av.getSelectionGroup().getSize() > 0;
+ AlignmentView seqstrings = av.getAlignmentView(selected);
+ SequenceI[] seqs;
+ if (!selected)
+ {
+ seqs = av.getAlignment().getSequencesArray();
+ }
+ else
+ {
+ seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
+ }
+
+ ScoreModelI scoreModel = ScoreModels.getInstance()
+ .getScoreModel(modelName, ap);
+ pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
+ params);
+ PaintRefresher.Register(this, av.getSequenceSetId());
+
+ rc = new RotatableCanvas(alignPanel);
+ this.getContentPane().add(rc, BorderLayout.CENTER);
+
+ addKeyListener(rc);
+ validate();
+
+ this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
+ }
+
+ /**
+ * Ensure references to potentially very large objects (the PCA matrices) are
+ * nulled when the frame is closed
+ */
+ protected void close_actionPerformed()
+ {
+ pcaModel = null;
+ }
+
+ @Override
+ protected void bgcolour_actionPerformed()
+ {
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_background_colour"),
+ rc.bgColour);
+
+ if (col != null)
+ {
+ rc.bgColour = col;
+ }
+ rc.repaint();
+ }
+
+ /**
+ * Calculates the PCA and displays the results
+ */
+ @Override
+ public void run()
+ {
+ working = true;
+ long progId = System.currentTimeMillis();
+ IProgressIndicator progress = this;
+ String message = MessageManager.getString("label.pca_recalculating");
+ if (getParent() == null)
+ {
+ progress = ap.alignFrame;
+ message = MessageManager.getString("label.pca_calculating");
+ }
+ progress.setProgressBar(message, progId);
+ try
+ {
+ pcaModel.calculate();
+
+ xCombobox.setSelectedIndex(0);
+ yCombobox.setSelectedIndex(1);
+ zCombobox.setSelectedIndex(2);
+
+ pcaModel.updateRc(rc);
+ // rc.invalidate();
+ top = pcaModel.getTop();
+
+ } catch (OutOfMemoryError er)
+ {
+ new OOMWarning("calculating PCA", er);
+ working = false;
+ return;
+ } finally
+ {
+ progress.setProgressBar("", progId);
+ }
+
+ repaint();
+ if (getParent() == null)
+ {
+ Desktop.addInternalFrame(this,
+ MessageManager.formatMessage("label.calc_title", "PCA",
+ pcaModel.getScoreModelName()),
+ 475, 450);
+ }
+ working = false;
+ }
+
+ /**
+ * Updates the PCA display after a change of component to use for x, y or z
+ * axis
+ */
+ @Override
+ protected void doDimensionChange()
+ {
+ if (top == 0)
+ {
+ return;
+ }
+
+ int dim1 = top - xCombobox.getSelectedIndex();
+ int dim2 = top - yCombobox.getSelectedIndex();
+ int dim3 = top - zCombobox.getSelectedIndex();
+ pcaModel.updateRcView(dim1, dim2, dim3);
+ rc.resetView();
+ }
+
+ /**
+ * Sets the selected checkbox item index for PCA dimension (1, 2, 3...) for
+ * the given axis (X/Y/Z)
+ *
+ * @param index
+ * @param axis
+ */
+ public void setSelectedDimensionIndex(int index, Axis axis)
+ {
+ switch (axis)
+ {
+ case X:
+ xCombobox.setSelectedIndex(index);
+ break;
+ case Y:
+ yCombobox.setSelectedIndex(index);
+ break;
+ case Z:
+ zCombobox.setSelectedIndex(index);
+ break;
+ default:
+ }
+ }
+
+ @Override
+ protected void outputValues_actionPerformed()
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ try
+ {
+ cap.setText(pcaModel.getDetails());
+ Desktop.addInternalFrame(cap,
+ MessageManager.getString("label.pca_details"), 500, 500);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("opening PCA details", oom);
+ cap.dispose();
+ }
+ }
+
+ @Override
+ protected void showLabels_actionPerformed()
+ {
+ rc.showLabels(showLabels.getState());
+ }
+
+ @Override
+ protected void print_actionPerformed()
+ {
+ PCAPrinter printer = new PCAPrinter();
+ printer.start();
+ }
+
+ /**
+ * If available, shows the data which formed the inputs for the PCA as a new
+ * alignment
+ */
+ @Override
+ public void originalSeqData_actionPerformed()
+ {
+ // JAL-2647 disabled after load from project (until save to project done)
+ if (pcaModel.getInputData() == null)
+ {
+ 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 alignment 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 = pcaModel.getInputData()
+ .getAlignmentAndHiddenColumns(gc);
+
+ if (alAndColsel != null && alAndColsel[0] != null)
+ {
+ // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
+
+ AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
+ AlignmentI 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, (HiddenColumns) 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, MessageManager.formatMessage(
+ "label.original_data_for_params", new String[]
+ { 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
+ {
+ @Override
+ public void run()
+ {
+ PrinterJob printJob = PrinterJob.getPrinterJob();
+ PageFormat defaultPage = printJob.defaultPage();
+ PageFormat pf = printJob.pageDialog(defaultPage);
+
+ if (defaultPage == pf)
+ {
+ /*
+ * user cancelled
+ */
+ return;
+ }
+
+ printJob.setPrintable(this, pf);
+
+ if (printJob.printDialog())
+ {
+ try
+ {
+ printJob.print();
+ } catch (Exception PrintException)
+ {
+ PrintException.printStackTrace();
+ }
+ }
+ }
+
+ @Override
+ public int print(Graphics pg, PageFormat pf, int pi)
+ throws PrinterException
+ {
+ pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
+
+ rc.drawBackground(pg);
+ rc.drawScene(pg);
+ if (rc.drawAxes)
+ {
+ rc.drawAxes(pg);
+ }
+
+ if (pi == 0)
+ {
+ return Printable.PAGE_EXISTS;
+ }
+ else
+ {
+ return Printable.NO_SUCH_PAGE;
+ }
+ }
+ }
+
+ /**
+ * Handler for 'Save as EPS' option
+ */
+ @Override
+ protected void eps_actionPerformed()
+ {
+ makePCAImage(ImageMaker.TYPE.EPS);
+ }
+
+ /**
+ * Handler for 'Save as PNG' option
+ */
+ @Override
+ protected void png_actionPerformed()
+ {
+ makePCAImage(ImageMaker.TYPE.PNG);
+ }
+
+ void makePCAImage(ImageMaker.TYPE type)
+ {
+ int width = rc.getWidth();
+ int height = rc.getHeight();
+
+ ImageMaker im;
+
+ switch (type)
+ {
+ case PNG:
+ im = new ImageMaker(this, ImageMaker.TYPE.PNG,
+ "Make PNG image from PCA", width, height, null, null, null, 0,
+ false);
+ break;
+ case EPS:
+ im = new ImageMaker(this, ImageMaker.TYPE.EPS,
+ "Make EPS file from PCA", width, height, null,
+ this.getTitle(), null, 0, false);
+ break;
+ default:
+ im = new ImageMaker(this, ImageMaker.TYPE.SVG,
+ "Make SVG file from PCA", width, height, null,
+ this.getTitle(), null, 0, false);
+ }
+
+ if (im.getGraphics() != null)
+ {
+ rc.drawBackground(im.getGraphics());
+ rc.drawScene(im.getGraphics());
+ if (rc.drawAxes)
+ {
+ rc.drawAxes(im.getGraphics());
+ }
+ im.writeImage();
+ }
+ }
+
+ @Override
+ protected void viewMenu_menuSelected()
+ {
+ buildAssociatedViewMenu();
+ }
+
+ /**
+ * Builds the menu showing the choice of possible views (for the associated
+ * sequence data) to which the PCA may be linked
+ */
+ 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 iSize = aps.length;
+
+ for (int i = 0; i < iSize; i++)
+ {
+ final AlignmentPanel ap = aps[i];
+ item = new JRadioButtonMenuItem(ap.av.getViewName(), ap.av == rc.av);
+ buttonGroup.add(item);
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent evt)
+ {
+ rc.applyToAllViews = false;
+ rc.av = panel.av;
+ rc.ap = panel;
+ PaintRefresher.Register(PCAPanel.this,
+ panel.av.getSequenceSetId());
+ }
+ });
+
+ associateViewsMenu.add(item);
+ }
+
+ final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
+ "All Views");
+
+ buttonGroup.add(itemf);
+
+ itemf.setSelected(rc.applyToAllViews);
+ itemf.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent evt)
+ {
+ rc.applyToAllViews = itemf.isSelected();
+ }
+ });
+ associateViewsMenu.add(itemf);
+
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent
+ * )
+ */
+ @Override
+ protected void outputPoints_actionPerformed()
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ try
+ {
+ cap.setText(pcaModel.getPointsasCsv(false,
+ xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
+ zCombobox.getSelectedIndex()));
+ Desktop.addInternalFrame(cap, MessageManager
+ .formatMessage("label.points_for_params", new String[]
+ { this.getTitle() }), 500, 500);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("exporting PCA points", oom);
+ cap.dispose();
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event
+ * .ActionEvent)
+ */
+ @Override
+ protected void outputProjPoints_actionPerformed()
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ try
+ {
+ cap.setText(pcaModel.getPointsasCsv(true,
+ xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
+ zCombobox.getSelectedIndex()));
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.transformed_points_for_params", new String[]
+ { this.getTitle() }), 500, 500);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("exporting transformed PCA points", oom);
+ cap.dispose();
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
+ */
+ @Override
+ public void setProgressBar(String message, long id)
+ {
+ progressBar.setProgressBar(message, id);
+ // if (progressBars == null)
+ // {
+ // progressBars = new Hashtable();
+ // progressBarHandlers = new Hashtable();
+ // }
+ //
+ // JPanel progressPanel;
+ // Long lId = new Long(id);
+ // GridLayout layout = (GridLayout) statusPanel.getLayout();
+ // if (progressBars.get(lId) != null)
+ // {
+ // progressPanel = (JPanel) progressBars.get(new Long(id));
+ // statusPanel.remove(progressPanel);
+ // progressBars.remove(lId);
+ // progressPanel = null;
+ // if (message != null)
+ // {
+ // statusBar.setText(message);
+ // }
+ // if (progressBarHandlers.contains(lId))
+ // {
+ // progressBarHandlers.remove(lId);
+ // }
+ // layout.setRows(layout.getRows() - 1);
+ // }
+ // else
+ // {
+ // progressPanel = new JPanel(new BorderLayout(10, 5));
+ //
+ // JProgressBar progressBar = new JProgressBar();
+ // progressBar.setIndeterminate(true);
+ //
+ // progressPanel.add(new JLabel(message), BorderLayout.WEST);
+ // progressPanel.add(progressBar, BorderLayout.CENTER);
+ //
+ // layout.setRows(layout.getRows() + 1);
+ // statusPanel.add(progressPanel);
+ //
+ // progressBars.put(lId, progressPanel);
+ // }
+ // // update GUI
+ // // setMenusForViewport();
+ // validate();
+ }
+
+ @Override
+ public void registerHandler(final long id,
+ final IProgressIndicatorHandler handler)
+ {
+ progressBar.registerHandler(id, handler);
+ // if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
+ // {
+ // throw new
+ // Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
+ // }
+ // progressBarHandlers.put(new Long(id), handler);
+ // final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
+ // if (handler.canCancel())
+ // {
+ // JButton cancel = new JButton(
+ // MessageManager.getString("action.cancel"));
+ // final IProgressIndicator us = this;
+ // cancel.addActionListener(new ActionListener()
+ // {
+ //
+ // @Override
+ // public void actionPerformed(ActionEvent e)
+ // {
+ // handler.cancelActivity(id);
+ // us.setProgressBar(MessageManager.formatMessage("label.cancelled_params",
+ // new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
+ // }
+ // });
+ // progressPanel.add(cancel, BorderLayout.EAST);
+ // }
+ }
+
+ /**
+ *
+ * @return true if any progress bars are still active
+ */
+ @Override
+ public boolean operationInProgress()
+ {
+ return progressBar.operationInProgress();
+ }
+
+ @Override
+ protected void resetButton_actionPerformed()
+ {
+ int t = top;
+ top = 0; // ugly - prevents dimensionChanged events from being processed
+ xCombobox.setSelectedIndex(0);
+ yCombobox.setSelectedIndex(1);
+ top = t;
+ zCombobox.setSelectedIndex(2);
+ }
+
+ /**
+ * Answers true if PCA calculation is in progress, else false
+ *
+ * @return
+ */
+ public boolean isWorking()
+ {
+ return working;
+ }
+
+ /**
+ * Answers the selected checkbox item index for PCA dimension for the X, Y or
+ * Z axis of the display
+ *
+ * @param axis
+ * @return
+ */
+ public int getSelectedDimensionIndex(Axis axis)
+ {
+ switch (axis)
+ {
+ case X:
+ return xCombobox.getSelectedIndex();
+ case Y:
+ return yCombobox.getSelectedIndex();
+ default:
+ return zCombobox.getSelectedIndex();
+ }
+ }
+
+ public void setShowLabels(boolean show)
+ {
+ showLabels.setSelected(show);
+ }
+
+ /**
+ * Sets the input data used to calculate the PCA. This is provided for
+ * 'restore from project', which does not currently support this (AL-2647), so
+ * sets the value to null, and hides the menu option for "Input Data...". J
+ *
+ * @param data
+ */
+ public void setInputData(AlignmentView data)
+ {
+ pcaModel.setInputData(data);
+ originalSeqData.setVisible(data != null);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff