X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=d8e6b06247b2d3a7f357a5efc6ac08151847023a;hp=aa01bf5ace2be431b9b9fc3d4d5889d93cdc2ec6;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hpb=8677e6e34e291edc58c1da2fc9c958473754143f diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index aa01bf5..d8e6b06 100644 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -20,20 +20,23 @@ */ package jalview.gui; +import jalview.analysis.scoremodels.ScoreModels; +import jalview.analysis.scoremodels.SimilarityParams; +import jalview.api.analysis.ScoreModelI; +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.schemes.ResidueProperties; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; 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; @@ -70,29 +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) { @@ -102,41 +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(); @@ -151,40 +152,52 @@ public class PCAPanel extends GPCAPanel implements Runnable, pcaModel = null; } + /** + * Repopulate the options and actions under the score model menu when it is + * selected. Options will depend on whether 'nucleotide' or 'peptide' + * modelling is selected (and also possibly on whether any additional score + * models have been added). + */ @Override - protected void scoreMatrix_menuSelected() + protected void scoreModel_menuSelected() { - scoreMatrixMenu.removeAll(); - for (final String sm : ResidueProperties.scoreMatrices.keySet()) - { - if (ResidueProperties.getScoreMatrix(sm) != null) + scoreModelMenu.removeAll(); + for (final ScoreModelI sm : ScoreModels.getInstance().getModels()) + { + final String name = sm.getName(); + 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) { - // create an entry for this score matrix for use in PCA - JCheckBoxMenuItem jm = new JCheckBoxMenuItem(); - jm.setText(MessageManager.getStringOrReturn("label.score_model_", - sm)); - jm.setSelected(pcaModel.getScore_matrix().equals(sm)); - if ((ResidueProperties.scoreMatrices.get(sm).isDNA() && ResidueProperties.scoreMatrices - .get(sm).isProtein()) - || pcaModel.isNucleotide() == ResidueProperties.scoreMatrices - .get(sm).isDNA()) + 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())) + { + jm.addActionListener(new ActionListener() { - final PCAPanel us = this; - jm.addActionListener(new ActionListener() + @Override + public void actionPerformed(ActionEvent e) { - @Override - public void actionPerformed(ActionEvent e) + if (!pcaModel.getScoreModelName().equals(name)) { - if (!pcaModel.getScore_matrix().equals(sm)) - { - pcaModel.setScore_matrix(sm); - Thread worker = new Thread(us); - worker.start(); - } + ScoreModelI sm2 = ScoreModels.getInstance().getScoreModel( + name, ap); + pcaModel.setScoreModel(sm2); + Thread worker = new Thread(PCAPanel.this); + worker.start(); } - }); - scoreMatrixMenu.add(jm); - } + } + }); + scoreModelMenu.add(jm); } } } @@ -193,7 +206,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, public void bgcolour_actionPerformed(ActionEvent e) { Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_backgroud_colour"), + MessageManager.getString("label.select_background_colour"), rc.bgColour); if (col != null) @@ -231,7 +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) @@ -249,6 +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)); } } @@ -258,7 +271,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, if (!pcaModel.isNucleotide()) { pcaModel.setNucleotide(true); - pcaModel.setScore_matrix("DNA"); + pcaModel.setScoreModel(ScoreModels.getInstance().getDefaultModel( + false)); Thread worker = new Thread(this); worker.start(); } @@ -272,20 +286,13 @@ public class PCAPanel extends GPCAPanel implements Runnable, if (pcaModel.isNucleotide()) { pcaModel.setNucleotide(false); - pcaModel.setScore_matrix("BLOSUM62"); + 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! */ @@ -399,7 +406,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, } ; Object[] alAndColsel = pcaModel.getSeqtrings() - .getAlignmentAndColumnSelection(gc); + .getAlignmentAndHiddenColumns(gc); if (alAndColsel != null && alAndColsel[0] != null) { @@ -416,8 +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