-/*\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
-\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
- s = new Sequence[av.getSelectionGroup().getSize()];\r
-\r
- for (int i = 0; i < s.length; i++)\r
- {\r
- s[i] = av.getSelectionGroup().getSequenceAt(i);\r
- }\r
- }\r
-\r
- if (s == null)\r
- {\r
- s = new Sequence[av.getAlignment().getHeight()];\r
-\r
- for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
- {\r
- s[i] = av.getAlignment().getSequenceAt(i);\r
- }\r
- }\r
-\r
- //////////////////////This part was done in PCATHread originally. Is it too slow???\r
- pca = new PCA(s);\r
- pca.run();\r
-\r
- // Now find the component coordinates\r
- int ii = 0;\r
-\r
- while ((ii < s.length) && (s[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(s[i], scores[i]);\r
- points.addElement(sp);\r
- }\r
-\r
- rc = new RotatableCanvas(av, points, pca.getM().rows);\r
-\r
- //rc.printPoints();\r
- add(rc, BorderLayout.CENTER);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void run()\r
- {\r
- // do stuff\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 2.9)
+ * Copyright (C) 2015 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.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GPCAPanel;
+import jalview.schemes.ResidueProperties;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.PCAModel;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+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.JCheckBoxMenuItem;
+import javax.swing.JColorChooser;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JRadioButtonMenuItem;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class PCAPanel extends GPCAPanel implements Runnable,
+ IProgressIndicator
+{
+
+ private IProgressIndicator progressBar;
+
+ RotatableCanvas rc;
+
+ AlignmentPanel ap;
+
+ AlignmentViewport av;
+
+ PCAModel pcaModel;
+
+ int top = 0;
+
+ /**
+ * Creates a new PCAPanel object.
+ *
+ * @param av
+ * DOCUMENT ME!
+ * @param s
+ * DOCUMENT ME!
+ */
+ public PCAPanel(AlignmentPanel ap)
+ {
+ this.av = ap.av;
+ this.ap = ap;
+
+ progressBar = new ProgressBar(statusPanel, statusBar);
+
+ boolean sameLength = true;
+ boolean selected = av.getSelectionGroup() != null
+ && av.getSelectionGroup().getSize() > 0;
+ AlignmentView seqstrings = av.getAlignmentView(selected);
+ boolean nucleotide = av.getAlignment().isNucleotide();
+ SequenceI[] seqs;
+ if (!selected)
+ {
+ seqs = av.getAlignment().getSequencesArray();
+ }
+ else
+ {
+ seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
+ }
+ 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,
+ MessageManager.getString("label.pca_sequences_not_aligned"),
+ MessageManager.getString("label.sequences_not_aligned"),
+ JOptionPane.WARNING_MESSAGE);
+
+ return;
+ }
+ pcaModel = new PCAModel(seqstrings, seqs, nucleotide);
+ PaintRefresher.Register(this, av.getSequenceSetId());
+
+ rc = new RotatableCanvas(ap);
+ this.getContentPane().add(rc, BorderLayout.CENTER);
+ Thread worker = new Thread(this);
+ worker.start();
+ }
+
+ @Override
+ protected void scoreMatrix_menuSelected()
+ {
+ scoreMatrixMenu.removeAll();
+ for (final String sm : ResidueProperties.scoreMatrices.keySet())
+ {
+ if (ResidueProperties.getScoreMatrix(sm) != null)
+ {
+ // create an entry for this score matrix for use in PCA
+ JCheckBoxMenuItem jm = new JCheckBoxMenuItem();
+ jm.setText(MessageManager
+ .getStringOrReturn("label.score_model", sm));
+ jm.setSelected(pcaModel.getScore_matrix().equals(sm));
+ if ((ResidueProperties.scoreMatrices.get(sm).isDNA() && ResidueProperties.scoreMatrices
+ .get(sm).isProtein())
+ || pcaModel.isNucleotide() == ResidueProperties.scoreMatrices
+ .get(sm).isDNA())
+ {
+ final PCAPanel us = this;
+ jm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (!pcaModel.getScore_matrix().equals(sm))
+ {
+ pcaModel.setScore_matrix(sm);
+ Thread worker = new Thread(us);
+ worker.start();
+ }
+ }
+ });
+ scoreMatrixMenu.add(jm);
+ }
+ }
+ }
+ }
+
+ public void bgcolour_actionPerformed(ActionEvent e)
+ {
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_backgroud_colour"),
+ rc.bgColour);
+
+ if (col != null)
+ {
+ rc.bgColour = col;
+ }
+ rc.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void run()
+ {
+ 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
+ {
+ calcSettings.setEnabled(false);
+ pcaModel.run();
+ // ////////////////
+ xCombobox.setSelectedIndex(0);
+ yCombobox.setSelectedIndex(1);
+ zCombobox.setSelectedIndex(2);
+
+ pcaModel.updateRc(rc);
+ // rc.invalidate();
+ nuclSetting.setSelected(pcaModel.isNucleotide());
+ protSetting.setSelected(!pcaModel.isNucleotide());
+ jvVersionSetting.setSelected(pcaModel.isJvCalcMode());
+ top = pcaModel.getTop();
+
+ } catch (OutOfMemoryError er)
+ {
+ new OOMWarning("calculating PCA", er);
+ return;
+ } finally
+ {
+ progress.setProgressBar("", progId);
+ }
+ calcSettings.setEnabled(true);
+ repaint();
+ if (getParent() == null)
+ {
+ addKeyListener(rc);
+ Desktop.addInternalFrame(this, MessageManager
+ .getString("label.principal_component_analysis"), 475, 450);
+ }
+ }
+
+ @Override
+ protected void nuclSetting_actionPerfomed(ActionEvent arg0)
+ {
+ if (!pcaModel.isNucleotide())
+ {
+ pcaModel.setNucleotide(true);
+ pcaModel.setScore_matrix("DNA");
+ Thread worker = new Thread(this);
+ worker.start();
+ }
+
+ }
+
+ @Override
+ protected void protSetting_actionPerfomed(ActionEvent arg0)
+ {
+
+ if (pcaModel.isNucleotide())
+ {
+ pcaModel.setNucleotide(false);
+ pcaModel.setScore_matrix("BLOSUM62");
+ Thread worker = new Thread(this);
+ worker.start();
+ }
+ }
+
+ @Override
+ protected void jvVersionSetting_actionPerfomed(ActionEvent arg0)
+ {
+ pcaModel.setJvCalcMode(jvVersionSetting.isSelected());
+ Thread worker = new Thread(this);
+ worker.start();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ 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.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(pcaModel.getDetails());
+ Desktop.addInternalFrame(cap,
+ MessageManager.getString("label.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 (pcaModel.getSeqtrings() == 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 = pcaModel.getSeqtrings()
+ .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, 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
+ {
+ 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.TYPE.EPS);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void png_actionPerformed(ActionEvent e)
+ {
+ makePCAImage(jalview.util.ImageMaker.TYPE.PNG);
+ }
+
+ void makePCAImage(jalview.util.ImageMaker.TYPE type)
+ {
+ int width = rc.getWidth();
+ int height = rc.getHeight();
+
+ jalview.util.ImageMaker im;
+
+ if (type == jalview.util.ImageMaker.TYPE.PNG)
+ {
+ im = new jalview.util.ImageMaker(this,
+ jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from PCA",
+ width, height, null, null);
+ }
+ else if (type == jalview.util.ImageMaker.TYPE.EPS)
+ {
+ im = new jalview.util.ImageMaker(this,
+ jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from PCA",
+ width, height, null, this.getTitle());
+ }
+ else
+ {
+ im = new jalview.util.ImageMaker(this,
+ jalview.util.ImageMaker.TYPE.SVG, "Make SVG 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(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)
+ */
+ protected void outputProjPoints_actionPerformed(ActionEvent e)
+ {
+ 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(ActionEvent e)
+ {
+ int t = top;
+ top = 0; // ugly - prevents dimensionChanged events from being processed
+ xCombobox.setSelectedIndex(0);
+ yCombobox.setSelectedIndex(1);
+ top = t;
+ zCombobox.setSelectedIndex(2);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff