X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=3512e4277b988002ce91af4b4098fff52b416854;hb=8dadf27423ca69874dc6a3c9d416974ba5ae767f;hp=2ecdb82dd037fe5d083625c180e7c0f68573b32d;hpb=b04c79d1a830aa7ae7b88b2a5ddd07c9216c826f;p=jalview.git diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index 2ecdb82..3512e42 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; @@ -64,15 +65,15 @@ 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; @@ -120,14 +121,14 @@ 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)); @@ -139,7 +140,13 @@ 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 @@ -147,13 +154,13 @@ public class PCAPanel extends GPCAPanel { Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_background_colour"), - rc.bgColour); + getRotatableCanvas().getBgColour()); if (col != null) { - rc.bgColour = col; + getRotatableCanvas().setBgColour(col); } - rc.repaint(); + getRotatableCanvas().repaint(); } /** @@ -162,6 +169,7 @@ 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 +179,17 @@ 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) { @@ -199,7 +206,7 @@ public class PCAPanel extends GPCAPanel { Desktop.addInternalFrame(this, MessageManager.formatMessage("label.calc_title", "PCA", - pcaModel.getScoreModelName()), + getPcaModel().getScoreModelName()), 475, 450); } working = false; @@ -212,16 +219,16 @@ 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 +261,7 @@ 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 +274,7 @@ public class PCAPanel extends GPCAPanel @Override protected void showLabels_actionPerformed() { - rc.showLabels(showLabels.getState()); + getRotatableCanvas().showLabels(showLabels.getState()); } @Override @@ -277,12 +284,15 @@ public class PCAPanel extends GPCAPanel printer.start(); } + /** + * If available, shows the data which formed the inputs for the PCA as a new + * alignment + */ @Override public void originalSeqData_actionPerformed() { - // 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) + // JAL-2647 disabled after load from project (until save to project done) + if (getPcaModel().getInputData() == null) { Cache.log.info( "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action."); @@ -290,7 +300,7 @@ public class PCAPanel extends GPCAPanel } // 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 + // 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[]) @@ -304,7 +314,7 @@ public class PCAPanel extends GPCAPanel { } - Object[] alAndColsel = pcaModel.getSeqtrings() + Object[] alAndColsel = getPcaModel().getInputData() .getAlignmentAndHiddenColumns(gc); if (alAndColsel != null && alAndColsel[0] != null) @@ -386,11 +396,11 @@ 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) @@ -424,25 +434,24 @@ public class PCAPanel extends GPCAPanel void makePCAImage(ImageMaker.TYPE type) { - int width = rc.getWidth(); - int height = rc.getHeight(); + int width = getRotatableCanvas().getWidth(); + int height = getRotatableCanvas().getHeight(); ImageMaker im; - if (type == ImageMaker.TYPE.PNG) + switch (type) { + case 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) - { + break; + case EPS: im = new ImageMaker(this, ImageMaker.TYPE.EPS, "Make EPS file from PCA", width, height, null, this.getTitle(), null, 0, false); - } - else - { + break; + default: im = new ImageMaker(this, ImageMaker.TYPE.SVG, "Make SVG file from PCA", width, height, null, this.getTitle(), null, 0, false); @@ -450,11 +459,11 @@ public class PCAPanel extends GPCAPanel if (im.getGraphics() != null) { - rc.drawBackground(im.getGraphics(), Color.black); - rc.drawScene(im.getGraphics()); - if (rc.drawAxes) + getRotatableCanvas().drawBackground(im.getGraphics()); + getRotatableCanvas().drawScene(im.getGraphics()); + if (getRotatableCanvas().drawAxes) { - rc.drawAxes(im.getGraphics()); + getRotatableCanvas().drawAxes(im.getGraphics()); } im.writeImage(); } @@ -474,7 +483,7 @@ 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; @@ -497,18 +506,15 @@ 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); } }); @@ -520,13 +526,13 @@ 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); @@ -546,7 +552,7 @@ 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 @@ -572,7 +578,7 @@ 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( @@ -601,11 +607,11 @@ 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; @@ -644,13 +650,13 @@ 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( @@ -684,11 +690,11 @@ 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); } @@ -726,4 +732,69 @@ public class PCAPanel extends GPCAPanel { 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) + { + 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()); + } }