X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=f861a7c1cba3229922092a33d05568e313fc7148;hb=2467c106c4be8b70f244a160739be63efc6b58ea;hp=482dff37d946c67bb10c44b79cadfc281a7edad6;hpb=8a62c90cab2506fc5c52126fa5ddb84af917befc;p=jalview.git diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index 482dff3..f861a7c 100644 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -24,12 +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.HiddenColumns; import jalview.datamodel.SequenceI; import jalview.jbgui.GPCAPanel; import jalview.util.MessageManager; @@ -38,6 +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; @@ -60,8 +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; @@ -74,6 +73,10 @@ 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; /** @@ -83,20 +86,23 @@ 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(); @@ -128,6 +134,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment()); } + ScoreModelI scoreModel = ScoreModels.getInstance() + .getScoreModel(modelName, ap); pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel, params); PaintRefresher.Register(this, av.getSequenceSetId()); @@ -184,7 +192,8 @@ 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(); @@ -255,6 +264,7 @@ 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)); } } @@ -264,8 +274,8 @@ 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(); } @@ -279,8 +289,8 @@ 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(); } @@ -378,8 +388,8 @@ 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 @@ -399,15 +409,16 @@ 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); @@ -416,9 +427,8 @@ 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!!<<< @@ -428,8 +438,8 @@ 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); } } @@ -560,8 +570,8 @@ 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); @@ -570,7 +580,8 @@ 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); } @@ -601,7 +612,8 @@ 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); @@ -634,9 +646,9 @@ 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); @@ -661,8 +673,8 @@ 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); @@ -776,28 +788,4 @@ 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; - } }