X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=dbb014abe4a7740d7aa09023bb14ab78e20ad157;hb=ddbc2166fb6d75ceb356c48b1bf4f951ce042beb;hp=d8e6b06247b2d3a7f357a5efc6ac08151847023a;hpb=3c75c089a56859ec8e7f674d7054e82af41e4b77;p=jalview.git diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index d8e6b06..dbb014a 100644 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -29,7 +29,10 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; import jalview.datamodel.HiddenColumns; import jalview.datamodel.SequenceI; +import jalview.gui.ImageExporter.ImageWriterI; +import jalview.gui.JalviewColourChooser.ColourChooserListener; import jalview.jbgui.GPCAPanel; +import jalview.util.ImageMaker; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.PCAModel; @@ -47,7 +50,6 @@ import java.awt.print.PrinterJob; import javax.swing.ButtonGroup; import javax.swing.JCheckBoxMenuItem; -import javax.swing.JColorChooser; import javax.swing.JMenuItem; import javax.swing.JRadioButtonMenuItem; import javax.swing.event.InternalFrameAdapter; @@ -59,8 +61,8 @@ import javax.swing.event.InternalFrameEvent; * @author $author$ * @version $Revision$ */ -public class PCAPanel extends GPCAPanel implements Runnable, - IProgressIndicator +public class PCAPanel extends GPCAPanel + implements Runnable, IProgressIndicator { private IProgressIndicator progressBar; @@ -79,6 +81,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, int top = 0; + private boolean working; + /** * Creates a new PCAPanel object using default score model and parameters * @@ -86,9 +90,12 @@ public class PCAPanel extends GPCAPanel implements Runnable, */ public PCAPanel(AlignmentPanel alignPanel) { - this(alignPanel, ScoreModels.getInstance() - .getDefaultModel(!alignPanel.av.getAlignment().isNucleotide()) - .getName(), SimilarityParams.SeqSpace); + this(alignPanel, + ScoreModels.getInstance() + .getDefaultModel( + !alignPanel.av.getAlignment().isNucleotide()) + .getName(), + SimilarityParams.SeqSpace); } /** @@ -131,8 +138,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment()); } - ScoreModelI scoreModel = ScoreModels.getInstance().getScoreModel( - modelName, ap); + ScoreModelI scoreModel = ScoreModels.getInstance() + .getScoreModel(modelName, ap); pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel, params); PaintRefresher.Register(this, av.getSequenceSetId()); @@ -189,8 +196,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, { if (!pcaModel.getScoreModelName().equals(name)) { - ScoreModelI sm2 = ScoreModels.getInstance().getScoreModel( - name, ap); + ScoreModelI sm2 = ScoreModels.getInstance() + .getScoreModel(name, ap); pcaModel.setScoreModel(sm2); Thread worker = new Thread(PCAPanel.this); worker.start(); @@ -205,15 +212,18 @@ public class PCAPanel extends GPCAPanel implements Runnable, @Override public void bgcolour_actionPerformed(ActionEvent e) { - Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_background_colour"), - rc.bgColour); - - if (col != null) + String ttl = MessageManager.getString("label.select_background_colour"); + ColourChooserListener listener = new ColourChooserListener() { - rc.bgColour = col; - } - rc.repaint(); + @Override + public void colourSelected(Color c) + { + rc.bgColour = c; + rc.repaint(); + } + }; + JalviewColourChooser.showColourChooser(this, ttl, rc.bgColour, + listener); } /** @@ -231,6 +241,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, message = MessageManager.getString("label.pca_calculating"); } progress.setProgressBar(message, progId); + working = true; try { calcSettings.setEnabled(false); @@ -249,6 +260,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, } catch (OutOfMemoryError er) { new OOMWarning("calculating PCA", er); + working = false; return; } finally { @@ -263,6 +275,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, .getString("label.principal_component_analysis"), 475, 450); this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); } + working = false; } @Override @@ -271,8 +284,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, if (!pcaModel.isNucleotide()) { pcaModel.setNucleotide(true); - pcaModel.setScoreModel(ScoreModels.getInstance().getDefaultModel( - false)); + pcaModel.setScoreModel( + ScoreModels.getInstance().getDefaultModel(false)); Thread worker = new Thread(this); worker.start(); } @@ -286,8 +299,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, if (pcaModel.isNucleotide()) { pcaModel.setNucleotide(false); - pcaModel.setScoreModel(ScoreModels.getInstance() - .getDefaultModel(true)); + pcaModel.setScoreModel( + ScoreModels.getInstance().getDefaultModel(true)); Thread worker = new Thread(this); worker.start(); } @@ -385,8 +398,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, // 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."); + 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 @@ -413,8 +426,9 @@ public class PCAPanel extends GPCAPanel implements Runnable, // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]); AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]); - AlignmentI dataset = (av != null && av.getAlignment() != null) ? av - .getAlignment().getDataset() : null; + AlignmentI dataset = (av != null && av.getAlignment() != null) + ? av.getAlignment().getDataset() + : null; if (dataset != null) { al.setDataset(dataset); @@ -424,8 +438,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, { // make a new frame! AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1], - AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); // >>>This is a fix for the moment, until a better solution is // found!!<<< @@ -435,8 +448,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, // msaorder); Desktop.addInternalFrame(af, MessageManager.formatMessage( - "label.original_data_for_params", - new String[] { this.title }), AlignFrame.DEFAULT_WIDTH, + "label.original_data_for_params", new String[] + { this.title }), AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); } } @@ -456,7 +469,16 @@ public class PCAPanel extends GPCAPanel implements Runnable, public void run() { PrinterJob printJob = PrinterJob.getPrinterJob(); - PageFormat pf = printJob.pageDialog(printJob.defaultPage()); + PageFormat defaultPage = printJob.defaultPage(); + PageFormat pf = printJob.pageDialog(defaultPage); + + if (defaultPage == pf) + { + /* + * user cancelled + */ + return; + } printJob.setPrintable(this, pf); @@ -496,67 +518,26 @@ public class PCAPanel extends GPCAPanel implements Runnable, } } - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void eps_actionPerformed(ActionEvent e) - { - makePCAImage(jalview.util.ImageMaker.TYPE.EPS); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void png_actionPerformed(ActionEvent e) - { - makePCAImage(jalview.util.ImageMaker.TYPE.PNG); - } - - void makePCAImage(jalview.util.ImageMaker.TYPE type) + public void makePCAImage(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, null, 0, false); - } - 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(), null, 0, false); - } - else - { - im = new jalview.util.ImageMaker(this, - jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA", - width, height, null, this.getTitle(), null, 0, false); - - } - - if (im.getGraphics() != null) + ImageWriterI writer = new ImageWriterI() { - rc.drawBackground(im.getGraphics(), Color.black); - rc.drawScene(im.getGraphics()); - if (rc.drawAxes == true) + @Override + public void exportImage(Graphics g) throws Exception { - rc.drawAxes(im.getGraphics()); + rc.drawBackground(g, Color.black); + rc.drawScene(g); + if (rc.drawAxes) + { + rc.drawAxes(g); + } } - im.writeImage(); - } + }; + String pca = MessageManager.getString("label.pca"); + ImageExporter exporter = new ImageExporter(writer, null, type, pca); + exporter.doExport(null, this, width, height, pca); } @Override @@ -567,8 +548,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, void buildAssociatedViewMenu() { - AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av - .getSequenceSetId()); + AlignmentPanel[] aps = PaintRefresher + .getAssociatedPanels(av.getSequenceSetId()); if (aps.length == 1 && rc.av == aps[0].av) { associateViewsMenu.setVisible(false); @@ -577,7 +558,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, associateViewsMenu.setVisible(true); - if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem)) + if ((viewMenu + .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem)) { viewMenu.insertSeparator(viewMenu.getItemCount() - 1); } @@ -591,7 +573,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, for (i = 0; i < iSize; i++) { final AlignmentPanel ap = aps[i]; - item = new JRadioButtonMenuItem(ap.av.viewName, ap.av == rc.av); + item = new JRadioButtonMenuItem(ap.av.getViewName(), ap.av == rc.av); buttonGroup.add(item); item.addActionListener(new ActionListener() { @@ -608,7 +590,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, associateViewsMenu.add(item); } - final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views"); + final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem( + "All Views"); buttonGroup.add(itemf); @@ -641,9 +624,9 @@ public class PCAPanel extends GPCAPanel implements Runnable, 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); + Desktop.addInternalFrame(cap, MessageManager + .formatMessage("label.points_for_params", new String[] + { this.getTitle() }), 500, 500); } catch (OutOfMemoryError oom) { new OOMWarning("exporting PCA points", oom); @@ -668,8 +651,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(), zCombobox.getSelectedIndex())); Desktop.addInternalFrame(cap, MessageManager.formatMessage( - "label.transformed_points_for_params", - new String[] { this.getTitle() }), 500, 500); + "label.transformed_points_for_params", new String[] + { this.getTitle() }), 500, 500); } catch (OutOfMemoryError oom) { new OOMWarning("exporting transformed PCA points", oom); @@ -783,4 +766,14 @@ public class PCAPanel extends GPCAPanel implements Runnable, top = t; zCombobox.setSelectedIndex(2); } + + /** + * Answers true if PCA calculation is in progress, else false + * + * @return + */ + public boolean isWorking() + { + return working; + } }