X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=7ceceee81c4ae38fdf4b01cad4ad5fbf9f1bec4f;hb=e34a4c5332c2d4d92651e0adc99ab7c5d262d13b;hp=3b73c5a8b4fb2de8b390dfc4a2ce4d8785bfd6b5;hpb=cee29c9fa89ed1d1df7b3af9f97055d8cd6eb77e;p=jalview.git diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index 3b73c5a..7ceceee 100644 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -24,13 +24,10 @@ import jalview.analysis.scoremodels.ScoreModels; import jalview.analysis.scoremodels.SimilarityParams; import jalview.api.analysis.ScoreModelI; import jalview.api.analysis.SimilarityParamsI; -import jalview.api.analysis.ViewBasedAnalysisI; -import jalview.bin.Cache; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; -import jalview.datamodel.ColumnSelection; -import jalview.datamodel.SeqCigar; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.SequenceI; import jalview.jbgui.GPCAPanel; import jalview.util.MessageManager; @@ -39,6 +36,7 @@ import jalview.viewmodel.PCAModel; import java.awt.BorderLayout; import java.awt.Color; +import java.awt.Dimension; import java.awt.Graphics; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; @@ -61,8 +59,8 @@ 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; @@ -75,8 +73,14 @@ public class PCAPanel extends GPCAPanel implements Runnable, PCAModel pcaModel; + private static final int MIN_WIDTH = 470; + + private static final int MIN_HEIGHT = 250; + int top = 0; + private boolean working; + /** * Creates a new PCAPanel object using default score model and parameters * @@ -84,20 +88,23 @@ public class PCAPanel extends GPCAPanel implements Runnable, */ public PCAPanel(AlignmentPanel alignPanel) { - this(alignPanel, ScoreModels.getInstance().getDefaultModel( - !alignPanel.av.getAlignment().isNucleotide()), + this(alignPanel, + ScoreModels.getInstance() + .getDefaultModel( + !alignPanel.av.getAlignment().isNucleotide()) + .getName(), SimilarityParams.SeqSpace); } /** - * Constructor given sequence data, a similarity (or distance) score model, - * and score calculation parameters + * Constructor given sequence data, a similarity (or distance) score model + * name, and score calculation parameters * * @param alignPanel - * @param scoreModel + * @param modelName * @param params */ - public PCAPanel(AlignmentPanel alignPanel, ScoreModelI scoreModel, + public PCAPanel(AlignmentPanel alignPanel, String modelName, SimilarityParamsI params) { super(); @@ -129,18 +136,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment()); } - // TODO can we allow PCA on unaligned data given choice of - // similarity measure parameters? - if (!checkAligned(seqstrings)) - { - JvOptionPane.showMessageDialog(Desktop.desktop, - MessageManager.getString("label.pca_sequences_not_aligned"), - MessageManager.getString("label.sequences_not_aligned"), - JvOptionPane.WARNING_MESSAGE); - - return; - } - + ScoreModelI scoreModel = ScoreModels.getInstance() + .getScoreModel(modelName, ap); pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel, params); PaintRefresher.Register(this, av.getSequenceSetId()); @@ -152,28 +149,6 @@ public class PCAPanel extends GPCAPanel implements Runnable, } /** - * Answers true if all sequences have the same aligned length, else false - * - * @param seqstrings - * @return - */ - protected boolean checkAligned(AlignmentView seqstrings) - { - SeqCigar sq[] = seqstrings.getSequences(); - int length = sq[0].getWidth(); - boolean sameLength = true; - for (int i = 0; i < sq.length; i++) - { - if (sq[i].getWidth() != length) - { - sameLength = false; - break; - } - } - return sameLength; - } - - /** * Ensure references to potentially very large objects (the PCA matrices) are * nulled when the frame is closed */ @@ -195,10 +170,19 @@ public class PCAPanel extends GPCAPanel implements Runnable, for (final ScoreModelI sm : ScoreModels.getInstance().getModels()) { final String name = sm.getName(); - // create an entry for this score matrix for use in PCA - JCheckBoxMenuItem jm = new JCheckBoxMenuItem(); - jm.setText(MessageManager.getStringOrReturn("label.score_model_", - name)); + JCheckBoxMenuItem jm = new JCheckBoxMenuItem(name); + + /* + * if the score model doesn't provide a description, try to look one + * up in the text bundle, falling back on its name + */ + String tooltip = sm.getDescription(); + if (tooltip == null) + { + tooltip = MessageManager.getStringOrReturn("label.score_model_", + name); + } + jm.setToolTipText(tooltip); jm.setSelected(pcaModel.getScoreModelName().equals(name)); if ((pcaModel.isNucleotide() && sm.isDNA()) || (!pcaModel.isNucleotide() && sm.isProtein())) @@ -210,7 +194,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, { if (!pcaModel.getScoreModelName().equals(name)) { - ScoreModelI sm2 = configureScoreModel(sm); + ScoreModelI sm2 = ScoreModels.getInstance() + .getScoreModel(name, ap); pcaModel.setScoreModel(sm2); Thread worker = new Thread(PCAPanel.this); worker.start(); @@ -251,6 +236,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, message = MessageManager.getString("label.pca_calculating"); } progress.setProgressBar(message, progId); + working = true; try { calcSettings.setEnabled(false); @@ -264,12 +250,12 @@ public class PCAPanel extends GPCAPanel implements Runnable, // 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); + working = false; return; } finally { @@ -282,7 +268,9 @@ public class PCAPanel extends GPCAPanel implements Runnable, addKeyListener(rc); Desktop.addInternalFrame(this, MessageManager .getString("label.principal_component_analysis"), 475, 450); + this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); } + working = false; } @Override @@ -291,8 +279,8 @@ 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(); } @@ -306,21 +294,13 @@ 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(); } } - @Override - protected void jvVersionSetting_actionPerfomed(ActionEvent arg0) - { - pcaModel.setJvCalcMode(jvVersionSetting.isSelected()); - Thread worker = new Thread(this); - worker.start(); - } - /** * DOCUMENT ME! */ @@ -413,8 +393,8 @@ 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 @@ -434,15 +414,16 @@ public class PCAPanel extends GPCAPanel implements Runnable, } ; Object[] alAndColsel = pcaModel.getSeqtrings() - .getAlignmentAndColumnSelection(gc); + .getAlignmentAndHiddenColumns(gc); if (alAndColsel != null && alAndColsel[0] != null) { // 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); @@ -451,9 +432,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, if (true) { // make a new frame! - AlignFrame af = new AlignFrame(al, - (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); + AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1], + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); // >>>This is a fix for the moment, until a better solution is // found!!<<< @@ -463,8 +443,8 @@ 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); } } @@ -484,7 +464,16 @@ 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); @@ -595,8 +584,8 @@ 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); @@ -605,7 +594,8 @@ 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); } @@ -636,7 +626,8 @@ 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); @@ -669,9 +660,9 @@ 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); @@ -696,8 +687,8 @@ 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); @@ -813,26 +804,12 @@ public class PCAPanel extends GPCAPanel implements Runnable, } /** - * If the score model is one that requires to get state data from the current - * view, allow it to do so + * Answers true if PCA calculation is in progress, else false * - * @param sm * @return */ - protected ScoreModelI configureScoreModel(ScoreModelI sm) + public boolean isWorking() { - if (sm instanceof ViewBasedAnalysisI) - { - try - { - sm = sm.getClass().newInstance(); - ((ViewBasedAnalysisI) sm).configureFromAlignmentView(ap); - } catch (Exception q) - { - Cache.log.error("Couldn't create a scoremodel instance for " - + sm.getName()); - } - } - return sm; + return working; } }