X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=d8e6b06247b2d3a7f357a5efc6ac08151847023a;hb=ad48d68e5790a0fa55e947b9ab9bb4eb5ca716ca;hp=3f0c37f04988ad1a1811c501121044499190c887;hpb=7f5ab7d1f58d870622968e0e6a430f33403b8e4f;p=jalview.git diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index 3f0c37f..d8e6b06 100644 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -21,14 +21,13 @@ package jalview.gui; import jalview.analysis.scoremodels.ScoreModels; +import jalview.analysis.scoremodels.SimilarityParams; import jalview.api.analysis.ScoreModelI; -import jalview.api.analysis.ViewBasedAnalysisI; -import jalview.bin.Cache; +import jalview.api.analysis.SimilarityParamsI; 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; @@ -37,6 +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; @@ -73,29 +73,54 @@ 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; /** - * Creates a new PCAPanel object. + * Creates a new PCAPanel object using default score model and parameters * - * @param av - * DOCUMENT ME! - * @param s - * DOCUMENT ME! + * @param alignPanel */ - public PCAPanel(AlignmentPanel ap) + public PCAPanel(AlignmentPanel alignPanel) + { + this(alignPanel, ScoreModels.getInstance() + .getDefaultModel(!alignPanel.av.getAlignment().isNucleotide()) + .getName(), SimilarityParams.SeqSpace); + } + + /** + * Constructor given sequence data, a similarity (or distance) score model + * name, and score calculation parameters + * + * @param alignPanel + * @param modelName + * @param params + */ + public PCAPanel(AlignmentPanel alignPanel, String modelName, + SimilarityParamsI params) { super(); - this.av = ap.av; - this.ap = ap; + this.av = alignPanel.av; + this.ap = alignPanel; + boolean nucleotide = av.getAlignment().isNucleotide(); progressBar = new ProgressBar(statusPanel, statusBar); - boolean sameLength = true; + addInternalFrameListener(new InternalFrameAdapter() + { + @Override + public void internalFrameClosed(InternalFrameEvent e) + { + close_actionPerformed(); + } + }); + boolean selected = av.getSelectionGroup() != null && av.getSelectionGroup().getSize() > 0; AlignmentView seqstrings = av.getAlignmentView(selected); - boolean nucleotide = av.getAlignment().isNucleotide(); SequenceI[] seqs; if (!selected) { @@ -105,41 +130,14 @@ public class PCAPanel extends GPCAPanel implements Runnable, { seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment()); } - SeqCigar sq[] = seqstrings.getSequences(); - int length = sq[0].getWidth(); - for (int i = 0; i < seqs.length; i++) - { - if (sq[i].getWidth() != length) - { - sameLength = false; - break; - } - } - - if (!sameLength) - { - JvOptionPane.showMessageDialog(Desktop.desktop, - MessageManager.getString("label.pca_sequences_not_aligned"), - MessageManager.getString("label.sequences_not_aligned"), - JvOptionPane.WARNING_MESSAGE); - - return; - } - - addInternalFrameListener(new InternalFrameAdapter() - { - @Override - public void internalFrameClosed(InternalFrameEvent e) - { - close_actionPerformed(); - } - }); - - pcaModel = new PCAModel(seqstrings, seqs, nucleotide); + ScoreModelI scoreModel = ScoreModels.getInstance().getScoreModel( + modelName, ap); + pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel, + params); PaintRefresher.Register(this, av.getSequenceSetId()); - rc = new RotatableCanvas(ap); + rc = new RotatableCanvas(alignPanel); this.getContentPane().add(rc, BorderLayout.CENTER); Thread worker = new Thread(this); worker.start(); @@ -167,10 +165,19 @@ 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())) @@ -182,7 +189,8 @@ 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(); @@ -236,7 +244,6 @@ 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) @@ -254,6 +261,7 @@ 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)); } } @@ -285,14 +293,6 @@ public class PCAPanel extends GPCAPanel implements Runnable, } } - @Override - protected void jvVersionSetting_actionPerfomed(ActionEvent arg0) - { - pcaModel.setJvCalcMode(jvVersionSetting.isSelected()); - Thread worker = new Thread(this); - worker.start(); - } - /** * DOCUMENT ME! */ @@ -406,7 +406,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, } ; Object[] alAndColsel = pcaModel.getSeqtrings() - .getAlignmentAndColumnSelection(gc); + .getAlignmentAndHiddenColumns(gc); if (alAndColsel != null && alAndColsel[0] != null) { @@ -423,8 +423,8 @@ 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 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 @@ -783,28 +783,4 @@ public class PCAPanel extends GPCAPanel implements Runnable, top = t; zCombobox.setSelectedIndex(2); } - - /** - * If the score model is one that requires to get state data from the current - * view, allow it to do so - * - * @param sm - * @return - */ - protected ScoreModelI configureScoreModel(ScoreModelI sm) - { - 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; - } }