X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=5eca00fa37c36498535b98db49fd55e76f670e0a;hb=f4b2472c686ae3ca2e19147f468c761b3eef0529;hp=caa2fc2f444dd889f9c96aef856eb5bfa3669da7;hpb=f20566c564e18f418c4ccc29fcf77d0471e49334;p=jalview.git diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index caa2fc2..5eca00f 100644 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -21,6 +21,7 @@ package jalview.gui; import jalview.analysis.scoremodels.ScoreModels; +import jalview.api.AlignViewportI; import jalview.api.analysis.ScoreModelI; import jalview.api.analysis.SimilarityParamsI; import jalview.bin.Cache; @@ -29,10 +30,13 @@ 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.math.RotatableMatrix.Axis; import jalview.util.ImageMaker; import jalview.util.MessageManager; +import jalview.util.Platform; import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.PCAModel; @@ -48,7 +52,6 @@ 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; @@ -64,15 +67,15 @@ public class PCAPanel extends GPCAPanel private static final int MIN_HEIGHT = 250; - RotatableCanvas rc; + private RotatableCanvas rc; AlignmentPanel ap; AlignmentViewport av; - PCAModel pcaModel; + private PCAModel pcaModel; - int top = 0; + private int top = 0; private IProgressIndicator progressBar; @@ -120,17 +123,15 @@ public class PCAPanel extends GPCAPanel ScoreModelI scoreModel = ScoreModels.getInstance() .getScoreModel(modelName, ap); - pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel, - params); + setPcaModel(new PCAModel(seqstrings, seqs, nucleotide, scoreModel, + params)); PaintRefresher.Register(this, av.getSequenceSetId()); - rc = new RotatableCanvas(alignPanel); - this.getContentPane().add(rc, BorderLayout.CENTER); + setRotatableCanvas(new RotatableCanvas(alignPanel)); + this.getContentPane().add(getRotatableCanvas(), BorderLayout.CENTER); - addKeyListener(rc); + addKeyListener(getRotatableCanvas()); validate(); - - this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); } /** @@ -139,21 +140,24 @@ public class PCAPanel extends GPCAPanel */ protected void close_actionPerformed() { - pcaModel = null; + setPcaModel(null); } @Override protected void bgcolour_actionPerformed() { - 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.setBgColour(c); + rc.repaint(); + } + }; + JalviewColourChooser.showColourChooser(this, ttl, rc.getBgColour(), + listener); } /** @@ -162,6 +166,7 @@ public class PCAPanel extends GPCAPanel @Override public void run() { + working = true; long progId = System.currentTimeMillis(); IProgressIndicator progress = this; String message = MessageManager.getString("label.pca_recalculating"); @@ -171,18 +176,17 @@ public class PCAPanel extends GPCAPanel message = MessageManager.getString("label.pca_calculating"); } progress.setProgressBar(message, progId); - working = true; try { - pcaModel.calculate(); + getPcaModel().calculate(); xCombobox.setSelectedIndex(0); yCombobox.setSelectedIndex(1); zCombobox.setSelectedIndex(2); - pcaModel.updateRc(rc); + getPcaModel().updateRc(getRotatableCanvas()); // rc.invalidate(); - top = pcaModel.getTop(); + setTop(getPcaModel().getTop()); } catch (OutOfMemoryError er) { @@ -197,10 +201,8 @@ public class PCAPanel extends GPCAPanel repaint(); if (getParent() == null) { - Desktop.addInternalFrame(this, - MessageManager.formatMessage("label.calc_title", "PCA", - pcaModel.getScoreModelName()), - 475, 450); + addToDesktop(this, getPcaModel().getScoreModelName()); + this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); } working = false; } @@ -212,16 +214,16 @@ public class PCAPanel extends GPCAPanel @Override protected void doDimensionChange() { - if (top == 0) + if (getTop() == 0) { return; } - int dim1 = top - xCombobox.getSelectedIndex(); - int dim2 = top - yCombobox.getSelectedIndex(); - int dim3 = top - zCombobox.getSelectedIndex(); - pcaModel.updateRcView(dim1, dim2, dim3); - rc.resetView(); + int dim1 = getTop() - xCombobox.getSelectedIndex(); + int dim2 = getTop() - yCombobox.getSelectedIndex(); + int dim3 = getTop() - zCombobox.getSelectedIndex(); + getPcaModel().updateRcView(dim1, dim2, dim3); + getRotatableCanvas().resetView(); } /** @@ -254,7 +256,7 @@ public class PCAPanel extends GPCAPanel CutAndPasteTransfer cap = new CutAndPasteTransfer(); try { - cap.setText(pcaModel.getDetails()); + cap.setText(getPcaModel().getDetails()); Desktop.addInternalFrame(cap, MessageManager.getString("label.pca_details"), 500, 500); } catch (OutOfMemoryError oom) @@ -267,7 +269,7 @@ public class PCAPanel extends GPCAPanel @Override protected void showLabels_actionPerformed() { - rc.showLabels(showLabels.getState()); + getRotatableCanvas().showLabels(showLabels.getState()); } @Override @@ -285,7 +287,7 @@ public class PCAPanel extends GPCAPanel public void originalSeqData_actionPerformed() { // JAL-2647 disabled after load from project (until save to project done) - if (pcaModel.getInputData() == null) + if (getPcaModel().getInputData() == null) { Cache.log.info( "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action."); @@ -307,7 +309,7 @@ public class PCAPanel extends GPCAPanel { } - Object[] alAndColsel = pcaModel.getInputData() + Object[] alAndColsel = getPcaModel().getInputData() .getAlignmentAndHiddenColumns(gc); if (alAndColsel != null && alAndColsel[0] != null) @@ -389,11 +391,11 @@ public class PCAPanel extends GPCAPanel { pg.translate((int) pf.getImageableX(), (int) pf.getImageableY()); - rc.drawBackground(pg); - rc.drawScene(pg); - if (rc.drawAxes) + getRotatableCanvas().drawBackground(pg); + getRotatableCanvas().drawScene(pg); + if (getRotatableCanvas().drawAxes) { - rc.drawAxes(pg); + getRotatableCanvas().drawAxes(pg); } if (pi == 0) @@ -407,59 +409,27 @@ public class PCAPanel extends GPCAPanel } } - /** - * 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) + public 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) + int width = getRotatableCanvas().getWidth(); + int height = getRotatableCanvas().getHeight(); + ImageWriterI writer = new ImageWriterI() { - rc.drawBackground(im.getGraphics()); - rc.drawScene(im.getGraphics()); - if (rc.drawAxes) + @Override + public void exportImage(Graphics g) throws Exception { - rc.drawAxes(im.getGraphics()); + RotatableCanvas canvas = getRotatableCanvas(); + canvas.drawBackground(g); + canvas.drawScene(g); + if (canvas.drawAxes) + { + canvas.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 @@ -476,7 +446,7 @@ public class PCAPanel extends GPCAPanel { AlignmentPanel[] aps = PaintRefresher .getAssociatedPanels(av.getSequenceSetId()); - if (aps.length == 1 && rc.av == aps[0].av) + if (aps.length == 1 && getRotatableCanvas().av == aps[0].av) { associateViewsMenu.setVisible(false); return; @@ -499,18 +469,15 @@ public class PCAPanel extends GPCAPanel for (int i = 0; i < iSize; i++) { final AlignmentPanel panel = aps[i]; - item = new JRadioButtonMenuItem(panel.av.viewName, panel.av == rc.av); + item = new JRadioButtonMenuItem(panel.av.getViewName(), + panel.av == getRotatableCanvas().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()); + selectAssociatedView(panel); } }); @@ -522,13 +489,13 @@ public class PCAPanel extends GPCAPanel buttonGroup.add(itemf); - itemf.setSelected(rc.applyToAllViews); + itemf.setSelected(getRotatableCanvas().isApplyToAllViews()); itemf.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { - rc.applyToAllViews = itemf.isSelected(); + getRotatableCanvas().setApplyToAllViews(itemf.isSelected()); } }); associateViewsMenu.add(itemf); @@ -548,7 +515,7 @@ public class PCAPanel extends GPCAPanel CutAndPasteTransfer cap = new CutAndPasteTransfer(); try { - cap.setText(pcaModel.getPointsasCsv(false, + cap.setText(getPcaModel().getPointsasCsv(false, xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(), zCombobox.getSelectedIndex())); Desktop.addInternalFrame(cap, MessageManager @@ -574,7 +541,7 @@ public class PCAPanel extends GPCAPanel CutAndPasteTransfer cap = new CutAndPasteTransfer(); try { - cap.setText(pcaModel.getPointsasCsv(true, + cap.setText(getPcaModel().getPointsasCsv(true, xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(), zCombobox.getSelectedIndex())); Desktop.addInternalFrame(cap, MessageManager.formatMessage( @@ -603,11 +570,11 @@ public class PCAPanel extends GPCAPanel // } // // JPanel progressPanel; - // Long lId = new Long(id); + // Long lId = Long.valueOf(id); // GridLayout layout = (GridLayout) statusPanel.getLayout(); // if (progressBars.get(lId) != null) // { - // progressPanel = (JPanel) progressBars.get(new Long(id)); + // progressPanel = (JPanel) progressBars.get(Long.valueOf(id)); // statusPanel.remove(progressPanel); // progressBars.remove(lId); // progressPanel = null; @@ -646,13 +613,13 @@ public class PCAPanel extends GPCAPanel final IProgressIndicatorHandler handler) { progressBar.registerHandler(id, handler); - // if (progressBarHandlers == null || !progressBars.contains(new Long(id))) + // if (progressBarHandlers == null || !progressBars.contains(Long.valueOf(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)); + // progressBarHandlers.put(Long.valueOf(id), handler); + // final JPanel progressPanel = (JPanel) progressBars.get(Long.valueOf(id)); // if (handler.canCancel()) // { // JButton cancel = new JButton( @@ -686,11 +653,11 @@ public class PCAPanel extends GPCAPanel @Override protected void resetButton_actionPerformed() { - int t = top; - top = 0; // ugly - prevents dimensionChanged events from being processed + int t = getTop(); + setTop(0); // ugly - prevents dimensionChanged events from being processed xCombobox.setSelectedIndex(0); yCombobox.setSelectedIndex(1); - top = t; + setTop(t); zCombobox.setSelectedIndex(2); } @@ -738,7 +705,67 @@ public class PCAPanel extends GPCAPanel */ public void setInputData(AlignmentView data) { - pcaModel.setInputData(data); + getPcaModel().setInputData(data); originalSeqData.setVisible(data != null); } + + public AlignViewportI getAlignViewport() + { + return av; + } + + public PCAModel getPcaModel() + { + return pcaModel; + } + + public void setPcaModel(PCAModel pcaModel) + { + this.pcaModel = pcaModel; + } + + public RotatableCanvas getRotatableCanvas() + { + return rc; + } + + public void setRotatableCanvas(RotatableCanvas rc) + { + this.rc = rc; + } + + public int getTop() + { + return top; + } + + public void setTop(int top) + { + this.top = top; + } + + /** + * set the associated view for this PCA. + * + * @param panel + */ + public void selectAssociatedView(AlignmentPanel panel) + { + getRotatableCanvas().setApplyToAllViews(false); + + ap = panel; + av = panel.av; + + getRotatableCanvas().av = panel.av; + getRotatableCanvas().ap = panel; + PaintRefresher.Register(PCAPanel.this, panel.av.getSequenceSetId()); + } + + public static void addToDesktop(PCAPanel panel, String modelName) + { + Dimension dim = Platform.getDimIfEmbedded(panel, 475, 450); + Desktop.addInternalFrame(panel, MessageManager.formatMessage( + "label.calc_title", "PCA", modelName), dim.width, + dim.height); + } }