X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=211c3706ef49da66f20ec0ff5f2b6e8b6cabfcfe;hb=051cab343aed415a342a787e10ebd075f05243f6;hp=f0ba274a31a167f88984db02892f135a6d30cb14;hpb=88e9d982ef43c740e3f29b34156f4f57836a84e3;p=jalview.git diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index f0ba274..211c370 100644 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -20,22 +20,6 @@ */ 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; @@ -48,12 +32,31 @@ 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; +import jalview.analysis.scoremodels.ScoreModels; +import jalview.api.AlignViewportI; +import jalview.api.analysis.ScoreModelI; +import jalview.api.analysis.SimilarityParamsI; +import jalview.bin.Console; +import jalview.datamodel.Alignment; +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.io.exceptions.ImageOutputException; +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; + /** * The panel holding the Principal Component Analysis 3-D visualisation */ @@ -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; @@ -90,6 +93,7 @@ public class PCAPanel extends GPCAPanel SimilarityParamsI params) { super(); + this.setFrameIcon(null); this.av = alignPanel.av; this.ap = alignPanel; boolean nucleotide = av.getAlignment().isNucleotide(); @@ -120,17 +124,15 @@ 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 +141,30 @@ public class PCAPanel extends GPCAPanel */ protected void close_actionPerformed() { - pcaModel = null; + setPcaModel(null); + if (this.rc != null) + { + this.rc.sequencePoints = null; + this.rc.setAxisEndPoints(null); + this.rc = 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 +173,7 @@ 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 +183,17 @@ 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) { @@ -199,8 +210,9 @@ public class PCAPanel extends GPCAPanel { Desktop.addInternalFrame(this, MessageManager.formatMessage("label.calc_title", "PCA", - pcaModel.getScoreModelName()), + getPcaModel().getScoreModelName()), 475, 450); + this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); } working = false; } @@ -212,16 +224,16 @@ 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 +266,7 @@ 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 +279,7 @@ public class PCAPanel extends GPCAPanel @Override protected void showLabels_actionPerformed() { - rc.showLabels(showLabels.getState()); + getRotatableCanvas().showLabels(showLabels.getState()); } @Override @@ -285,9 +297,9 @@ 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( + Console.info( "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action."); return; } @@ -307,7 +319,7 @@ public class PCAPanel extends GPCAPanel { } - Object[] alAndColsel = pcaModel.getInputData() + Object[] alAndColsel = getPcaModel().getInputData() .getAlignmentAndHiddenColumns(gc); if (alAndColsel != null && alAndColsel[0] != null) @@ -389,11 +401,11 @@ public class PCAPanel extends GPCAPanel { pg.translate((int) pf.getImageableX(), (int) pf.getImageableY()); - rc.drawBackground(pg, rc.bgColour); - 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 +419,30 @@ 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; - - if (type == ImageMaker.TYPE.PNG) - { - im = new ImageMaker(this, 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 ImageMaker(this, ImageMaker.TYPE.EPS, - "Make EPS file from PCA", width, height, null, - this.getTitle(), null, 0, false); - } - else + int width = getRotatableCanvas().getWidth(); + int height = getRotatableCanvas().getHeight(); + ImageWriterI writer = new ImageWriterI() { - 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(), Color.black); - 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); + try { + exporter.doExport(null, this, width, height, pca); + } catch (ImageOutputException ioex) { + Console.error("Unexpected error whilst writing "+type.toString(),ioex); } } @@ -477,7 +460,7 @@ 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; @@ -500,18 +483,15 @@ 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); } }); @@ -523,13 +503,13 @@ 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); @@ -549,7 +529,7 @@ 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 @@ -575,7 +555,7 @@ 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( @@ -604,11 +584,11 @@ 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; @@ -647,13 +627,14 @@ 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( @@ -687,11 +668,11 @@ 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); } @@ -739,7 +720,59 @@ 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()); + } }