From 3c9136679468c96a6d38f72cb175fb3a4c8dcca9 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Thu, 26 Apr 2018 13:03:52 +0100 Subject: [PATCH] JAL-2962 remove Change Parameters menu from PCA panel --- resources/lang/Messages.properties | 4 +- resources/lang/Messages_es.properties | 4 +- src/jalview/analysis/scoremodels/ScoreModels.java | 4 +- src/jalview/gui/PCAPanel.java | 255 +++++--------------- src/jalview/gui/TreePanel.java | 2 +- src/jalview/jbgui/GPCAPanel.java | 153 +++--------- .../analysis/scoremodels/ScoreModelsTest.java | 10 +- 7 files changed, 103 insertions(+), 329 deletions(-) diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index 3f5aa94..6581504 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -172,10 +172,9 @@ label.principal_component_analysis = Principal Component Analysis label.average_distance_identity = Average Distance Using % Identity label.neighbour_joining_identity = Neighbour Joining Using % Identity label.choose_calculation = Choose Calculation -label.treecalc_title = {0} Using {1} +label.calc_title = {0} Using {1} label.tree_calc_av = Average Distance label.tree_calc_nj = Neighbour Joining -label.select_score_model = Select score model label.score_model_pid = % Identity label.score_model_blosum62 = BLOSUM62 label.score_model_pam250 = PAM 250 @@ -882,7 +881,6 @@ label.error_unsupported_owwner_user_colour_scheme = Unsupported owner for User C label.save_alignment_to_file = Save Alignment to file label.save_features_to_file = Save Features to File label.save_annotation_to_file = Save Annotation to File -label.no_features_on_alignment = No features found on alignment label.save_pdb_file = Save PDB File label.save_text_to_file = Save Text to File label.save_state = Save State diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties index e42d6b8..09be8c9 100644 --- a/resources/lang/Messages_es.properties +++ b/resources/lang/Messages_es.properties @@ -169,10 +169,9 @@ label.principal_component_analysis = An label.average_distance_identity = Distancia Media Usando % de Identidad label.neighbour_joining_identity = Unir vecinos utilizando % de Identidad label.choose_calculation = Elegir el cálculo -label.treecalc_title = {0} utilizando {1} +label.calc_title = {0} utilizando {1} label.tree_calc_av = Distancia media label.tree_calc_nj = Unir vecinos -label.select_score_model = Selecciones modelo de puntuación label.score_model_pid = % Identidad label.score_model_blosum62 = BLOSUM62 label.score_model_pam250 = PAM 250 @@ -808,7 +807,6 @@ label.error_unsupported_owwner_user_colour_scheme = Propietario no soportado par label.save_alignment_to_file = Guardar Alineamiento en fichero label.save_features_to_file = Guardar Características en un fichero label.save_annotation_to_file = Guardar Anotación en un fichero -label.no_features_on_alignment = No se han encontrado características en el alineamiento label.save_pdb_file = Guardar fichero PDB label.save_text_to_file = Guardar Texto en un fichero label.save_state = Guardar estado diff --git a/src/jalview/analysis/scoremodels/ScoreModels.java b/src/jalview/analysis/scoremodels/ScoreModels.java index 7262fb8..3cbd5f1 100644 --- a/src/jalview/analysis/scoremodels/ScoreModels.java +++ b/src/jalview/analysis/scoremodels/ScoreModels.java @@ -66,11 +66,11 @@ public class ScoreModels /* * using LinkedHashMap keeps models ordered as added */ - models = new LinkedHashMap(); + models = new LinkedHashMap<>(); BLOSUM62 = loadScoreMatrix("scoreModel/blosum62.scm"); PAM250 = loadScoreMatrix("scoreModel/pam250.scm"); - registerScoreModel(new PIDModel()); DNA = loadScoreMatrix("scoreModel/dna.scm"); + registerScoreModel(new PIDModel()); registerScoreModel(new FeatureDistanceModel()); } diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index 7ceceee..ec7994f 100644 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -21,7 +21,6 @@ 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; @@ -30,6 +29,7 @@ import jalview.datamodel.AlignmentView; import jalview.datamodel.HiddenColumns; import jalview.datamodel.SequenceI; import jalview.jbgui.GPCAPanel; +import jalview.util.ImageMaker; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.PCAModel; @@ -46,7 +46,6 @@ import java.awt.print.PrinterException; import java.awt.print.PrinterJob; import javax.swing.ButtonGroup; -import javax.swing.JCheckBoxMenuItem; import javax.swing.JColorChooser; import javax.swing.JMenuItem; import javax.swing.JRadioButtonMenuItem; @@ -54,17 +53,11 @@ import javax.swing.event.InternalFrameAdapter; import javax.swing.event.InternalFrameEvent; /** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ + * The panel holding the Principal Component Analysis 3-d visualisation */ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator { - - private IProgressIndicator progressBar; - RotatableCanvas rc; AlignmentPanel ap; @@ -73,30 +66,17 @@ public class PCAPanel extends GPCAPanel PCAModel pcaModel; + int top = 0; + private static final int MIN_WIDTH = 470; private static final int MIN_HEIGHT = 250; - int top = 0; + private IProgressIndicator progressBar; private boolean working; /** - * Creates a new PCAPanel object using default score model and parameters - * - * @param alignPanel - */ - 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 * @@ -144,6 +124,10 @@ public class PCAPanel extends GPCAPanel rc = new RotatableCanvas(alignPanel); this.getContentPane().add(rc, BorderLayout.CENTER); + + /* + * perform calculation in a new Thread + */ Thread worker = new Thread(this); worker.start(); } @@ -157,58 +141,8 @@ public class PCAPanel extends GPCAPanel 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 scoreModel_menuSelected() - { - 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) - { - 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() - { - @Override - public void actionPerformed(ActionEvent e) - { - if (!pcaModel.getScoreModelName().equals(name)) - { - ScoreModelI sm2 = ScoreModels.getInstance() - .getScoreModel(name, ap); - pcaModel.setScoreModel(sm2); - Thread worker = new Thread(PCAPanel.this); - worker.start(); - } - } - }); - scoreModelMenu.add(jm); - } - } - } - @Override - public void bgcolour_actionPerformed(ActionEvent e) + protected void bgcolour_actionPerformed() { Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_background_colour"), @@ -222,7 +156,7 @@ public class PCAPanel extends GPCAPanel } /** - * DOCUMENT ME! + * Calculates the PCA and displays the results */ @Override public void run() @@ -239,7 +173,6 @@ public class PCAPanel extends GPCAPanel working = true; try { - calcSettings.setEnabled(false); pcaModel.run(); // //////////////// xCombobox.setSelectedIndex(0); @@ -248,8 +181,6 @@ public class PCAPanel extends GPCAPanel pcaModel.updateRc(rc); // rc.invalidate(); - nuclSetting.setSelected(pcaModel.isNucleotide()); - protSetting.setSelected(!pcaModel.isNucleotide()); top = pcaModel.getTop(); } catch (OutOfMemoryError er) @@ -261,50 +192,26 @@ public class PCAPanel extends GPCAPanel { progress.setProgressBar("", progId); } - calcSettings.setEnabled(true); + repaint(); if (getParent() == null) { addKeyListener(rc); - Desktop.addInternalFrame(this, MessageManager - .getString("label.principal_component_analysis"), 475, 450); + Desktop.addInternalFrame(this, + MessageManager.formatMessage("label.calc_title", "PCA", + pcaModel.getScoreModelName()), + 475, 450); this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); } working = false; } - @Override - protected void nuclSetting_actionPerfomed(ActionEvent arg0) - { - if (!pcaModel.isNucleotide()) - { - pcaModel.setNucleotide(true); - pcaModel.setScoreModel( - ScoreModels.getInstance().getDefaultModel(false)); - Thread worker = new Thread(this); - worker.start(); - } - - } - - @Override - protected void protSetting_actionPerfomed(ActionEvent arg0) - { - - if (pcaModel.isNucleotide()) - { - pcaModel.setNucleotide(false); - pcaModel.setScoreModel( - ScoreModels.getInstance().getDefaultModel(true)); - Thread worker = new Thread(this); - worker.start(); - } - } - /** - * DOCUMENT ME! + * Updates the PCA display after a change of component to use for x, y or z + * axis */ - void doDimensionChange() + @Override + protected void doDimensionChange() { if (top == 0) { @@ -321,44 +228,8 @@ public class PCAPanel extends GPCAPanel rc.paint(rc.getGraphics()); } - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - protected void xCombobox_actionPerformed(ActionEvent e) - { - doDimensionChange(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ @Override - protected void yCombobox_actionPerformed(ActionEvent e) - { - doDimensionChange(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - protected void zCombobox_actionPerformed(ActionEvent e) - { - doDimensionChange(); - } - - @Override - public void outputValues_actionPerformed(ActionEvent e) + protected void outputValues_actionPerformed() { CutAndPasteTransfer cap = new CutAndPasteTransfer(); try @@ -374,20 +245,20 @@ public class PCAPanel extends GPCAPanel } @Override - public void showLabels_actionPerformed(ActionEvent e) + protected void showLabels_actionPerformed() { rc.showLabels(showLabels.getState()); } @Override - public void print_actionPerformed(ActionEvent e) + protected void print_actionPerformed() { PCAPrinter printer = new PCAPrinter(); printer.start(); } @Override - public void originalSeqData_actionPerformed(ActionEvent e) + 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 @@ -412,7 +283,7 @@ public class PCAPanel extends GPCAPanel } catch (Exception ex) { } - ; + Object[] alAndColsel = pcaModel.getSeqtrings() .getAlignmentAndHiddenColumns(gc); @@ -497,7 +368,7 @@ public class PCAPanel extends GPCAPanel rc.drawBackground(pg, rc.bgColour); rc.drawScene(pg); - if (rc.drawAxes == true) + if (rc.drawAxes) { rc.drawAxes(pg); } @@ -514,61 +385,54 @@ public class PCAPanel extends GPCAPanel } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Handler for 'Save as EPS' option */ @Override - public void eps_actionPerformed(ActionEvent e) + protected void eps_actionPerformed() { - makePCAImage(jalview.util.ImageMaker.TYPE.EPS); + makePCAImage(ImageMaker.TYPE.EPS); } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Handler for 'Save as PNG' option */ @Override - public void png_actionPerformed(ActionEvent e) + protected void png_actionPerformed() { - makePCAImage(jalview.util.ImageMaker.TYPE.PNG); + makePCAImage(ImageMaker.TYPE.PNG); } - void makePCAImage(jalview.util.ImageMaker.TYPE type) + void makePCAImage(ImageMaker.TYPE type) { int width = rc.getWidth(); int height = rc.getHeight(); - jalview.util.ImageMaker im; + ImageMaker im; - if (type == jalview.util.ImageMaker.TYPE.PNG) + if (type == ImageMaker.TYPE.PNG) { - im = new jalview.util.ImageMaker(this, - jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from PCA", - width, height, null, null, null, 0, false); + 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) { - im = new jalview.util.ImageMaker(this, - jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from PCA", - width, height, null, this.getTitle(), null, 0, false); + im = new ImageMaker(this, ImageMaker.TYPE.EPS, + "Make EPS file from PCA", width, height, null, + this.getTitle(), null, 0, false); } else { - im = new jalview.util.ImageMaker(this, - jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA", - width, height, null, this.getTitle(), null, 0, false); - + im = new ImageMaker(this, ImageMaker.TYPE.SVG, + "Make SVG file from PCA", width, height, null, + this.getTitle(), null, 0, false); } if (im.getGraphics() != null) { rc.drawBackground(im.getGraphics(), Color.black); rc.drawScene(im.getGraphics()); - if (rc.drawAxes == true) + if (rc.drawAxes) { rc.drawAxes(im.getGraphics()); } @@ -577,11 +441,15 @@ public class PCAPanel extends GPCAPanel } @Override - public void viewMenu_menuSelected() + protected void viewMenu_menuSelected() { buildAssociatedViewMenu(); } + /** + * Builds the menu showing the choice of possible views (for the associated + * sequence data) to which the PCA may be linked + */ void buildAssociatedViewMenu() { AlignmentPanel[] aps = PaintRefresher @@ -604,12 +472,12 @@ public class PCAPanel extends GPCAPanel JRadioButtonMenuItem item; ButtonGroup buttonGroup = new ButtonGroup(); - int i, iSize = aps.length; - final PCAPanel thisPCAPanel = this; - for (i = 0; i < iSize; i++) + int iSize = aps.length; + + for (int i = 0; i < iSize; i++) { - final AlignmentPanel ap = aps[i]; - item = new JRadioButtonMenuItem(ap.av.viewName, ap.av == rc.av); + final AlignmentPanel panel = aps[i]; + item = new JRadioButtonMenuItem(panel.av.viewName, panel.av == rc.av); buttonGroup.add(item); item.addActionListener(new ActionListener() { @@ -617,9 +485,10 @@ public class PCAPanel extends GPCAPanel public void actionPerformed(ActionEvent evt) { rc.applyToAllViews = false; - rc.av = ap.av; - rc.ap = ap; - PaintRefresher.Register(thisPCAPanel, ap.av.getSequenceSetId()); + rc.av = panel.av; + rc.ap = panel; + PaintRefresher.Register(PCAPanel.this, + panel.av.getSequenceSetId()); } }); @@ -652,7 +521,7 @@ public class PCAPanel extends GPCAPanel * ) */ @Override - protected void outputPoints_actionPerformed(ActionEvent e) + protected void outputPoints_actionPerformed() { CutAndPasteTransfer cap = new CutAndPasteTransfer(); try @@ -678,7 +547,7 @@ public class PCAPanel extends GPCAPanel * .ActionEvent) */ @Override - protected void outputProjPoints_actionPerformed(ActionEvent e) + protected void outputProjPoints_actionPerformed() { CutAndPasteTransfer cap = new CutAndPasteTransfer(); try @@ -793,7 +662,7 @@ public class PCAPanel extends GPCAPanel } @Override - protected void resetButton_actionPerformed(ActionEvent e) + protected void resetButton_actionPerformed() { int t = top; top = 0; // ugly - prevents dimensionChanged events from being processed diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index 2727db1..e7e4ef8 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -879,7 +879,7 @@ public class TreePanel extends GTreePanel /* * put them together as Using */ - final String ttl = MessageManager.formatMessage("label.treecalc_title", + final String ttl = MessageManager.formatMessage("label.calc_title", treecalcnm, smn); return ttl; } diff --git a/src/jalview/jbgui/GPCAPanel.java b/src/jalview/jbgui/GPCAPanel.java index a183794..bd45bc2 100755 --- a/src/jalview/jbgui/GPCAPanel.java +++ b/src/jalview/jbgui/GPCAPanel.java @@ -46,13 +46,11 @@ public class GPCAPanel extends JInternalFrame { private static final Font VERDANA_12 = new Font("Verdana", 0, 12); - protected JComboBox xCombobox = new JComboBox(); + protected JComboBox xCombobox = new JComboBox<>(); - protected JComboBox yCombobox = new JComboBox(); + protected JComboBox yCombobox = new JComboBox<>(); - protected JComboBox zCombobox = new JComboBox(); - - protected JMenu scoreModelMenu = new JMenu(); + protected JComboBox zCombobox = new JComboBox<>(); protected JMenu viewMenu = new JMenu(); @@ -60,16 +58,13 @@ public class GPCAPanel extends JInternalFrame protected JMenu associateViewsMenu = new JMenu(); - protected JMenu calcSettings = new JMenu(); - - protected JCheckBoxMenuItem nuclSetting = new JCheckBoxMenuItem(); - - protected JCheckBoxMenuItem protSetting = new JCheckBoxMenuItem(); - protected JLabel statusBar = new JLabel(); protected JPanel statusPanel = new JPanel(); + /** + * Constructor + */ public GPCAPanel() { try @@ -110,7 +105,7 @@ public class GPCAPanel extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - zCombobox_actionPerformed(e); + doDimensionChange(); } }); yCombobox.setFont(VERDANA_12); @@ -119,7 +114,7 @@ public class GPCAPanel extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - yCombobox_actionPerformed(e); + doDimensionChange(); } }); xCombobox.setFont(VERDANA_12); @@ -128,7 +123,7 @@ public class GPCAPanel extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - xCombobox_actionPerformed(e); + doDimensionChange(); } }); JButton resetButton = new JButton(); @@ -139,7 +134,7 @@ public class GPCAPanel extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - resetButton_actionPerformed(e); + resetButton_actionPerformed(); } }); JMenu fileMenu = new JMenu(); @@ -152,7 +147,7 @@ public class GPCAPanel extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - eps_actionPerformed(e); + eps_actionPerformed(); } }); JMenuItem png = new JMenuItem("PNG"); @@ -161,7 +156,7 @@ public class GPCAPanel extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - png_actionPerformed(e); + png_actionPerformed(); } }); JMenuItem outputValues = new JMenuItem(); @@ -171,7 +166,7 @@ public class GPCAPanel extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - outputValues_actionPerformed(e); + outputValues_actionPerformed(); } }); JMenuItem outputPoints = new JMenuItem(); @@ -181,7 +176,7 @@ public class GPCAPanel extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - outputPoints_actionPerformed(e); + outputPoints_actionPerformed(); } }); JMenuItem outputProjPoints = new JMenuItem(); @@ -192,7 +187,7 @@ public class GPCAPanel extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - outputProjPoints_actionPerformed(e); + outputProjPoints_actionPerformed(); } }); JMenuItem print = new JMenuItem(); @@ -202,7 +197,7 @@ public class GPCAPanel extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - print_actionPerformed(e); + print_actionPerformed(); } }); viewMenu.setText(MessageManager.getString("action.view")); @@ -224,33 +219,13 @@ public class GPCAPanel extends JInternalFrame { } }); - scoreModelMenu - .setText(MessageManager.getString("label.select_score_model")); - scoreModelMenu.addMenuListener(new MenuListener() - { - @Override - public void menuSelected(MenuEvent e) - { - scoreModel_menuSelected(); - } - - @Override - public void menuDeselected(MenuEvent e) - { - } - - @Override - public void menuCanceled(MenuEvent e) - { - } - }); showLabels.setText(MessageManager.getString("label.show_labels")); showLabels.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - showLabels_actionPerformed(e); + showLabels_actionPerformed(); } }); JMenuItem bgcolour = new JMenuItem(); @@ -260,7 +235,7 @@ public class GPCAPanel extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - bgcolour_actionPerformed(e); + bgcolour_actionPerformed(); } }); JMenuItem originalSeqData = new JMenuItem(); @@ -270,37 +245,12 @@ public class GPCAPanel extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - originalSeqData_actionPerformed(e); + originalSeqData_actionPerformed(); } }); associateViewsMenu.setText( MessageManager.getString("label.associate_nodes_with")); - calcSettings.setText(MessageManager.getString("action.change_params")); - nuclSetting - .setText(MessageManager.getString("label.nucleotide_matrix")); - protSetting.setText(MessageManager.getString("label.protein_matrix")); - nuclSetting.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent arg0) - { - nuclSetting_actionPerfomed(arg0); - } - }); - protSetting.addActionListener(new ActionListener() - { - - @Override - public void actionPerformed(ActionEvent arg0) - { - protSetting_actionPerfomed(arg0); - } - }); - - calcSettings.add(nuclSetting); - calcSettings.add(protSetting); - calcSettings.add(scoreModelMenu); statusPanel.setLayout(new GridLayout()); statusBar.setFont(VERDANA_12); // statusPanel.setBackground(Color.lightGray); @@ -321,7 +271,6 @@ public class GPCAPanel extends JInternalFrame JMenuBar jMenuBar1 = new JMenuBar(); jMenuBar1.add(fileMenu); jMenuBar1.add(viewMenu); - jMenuBar1.add(calcSettings); setJMenuBar(jMenuBar1); fileMenu.add(saveMenu); fileMenu.add(outputValues); @@ -336,91 +285,51 @@ public class GPCAPanel extends JInternalFrame viewMenu.add(associateViewsMenu); } - protected void scoreModel_menuSelected() - { - // TODO Auto-generated method stub - - } - - protected void resetButton_actionPerformed(ActionEvent e) - { - // TODO Auto-generated method stub - - } - - protected void protSetting_actionPerfomed(ActionEvent arg0) - { - // TODO Auto-generated method stub - - } - - protected void nuclSetting_actionPerfomed(ActionEvent arg0) - { - // TODO Auto-generated method stub - - } - - protected void outputPoints_actionPerformed(ActionEvent e) + protected void resetButton_actionPerformed() { - // TODO Auto-generated method stub - } - protected void outputProjPoints_actionPerformed(ActionEvent e) + protected void outputPoints_actionPerformed() { - // TODO Auto-generated method stub - } - protected void xCombobox_actionPerformed(ActionEvent e) + protected void outputProjPoints_actionPerformed() { } - protected void yCombobox_actionPerformed(ActionEvent e) + protected void eps_actionPerformed() { } - protected void zCombobox_actionPerformed(ActionEvent e) + protected void png_actionPerformed() { } - public void eps_actionPerformed(ActionEvent e) + protected void outputValues_actionPerformed() { - } - public void png_actionPerformed(ActionEvent e) + protected void print_actionPerformed() { - } - public void outputValues_actionPerformed(ActionEvent e) + protected void showLabels_actionPerformed() { - } - public void print_actionPerformed(ActionEvent e) + protected void bgcolour_actionPerformed() { - } - public void showLabels_actionPerformed(ActionEvent e) + protected void originalSeqData_actionPerformed() { - } - public void bgcolour_actionPerformed(ActionEvent e) + protected void viewMenu_menuSelected() { - } - public void originalSeqData_actionPerformed(ActionEvent e) + protected void doDimensionChange() { - - } - - public void viewMenu_menuSelected() - { - } } diff --git a/test/jalview/analysis/scoremodels/ScoreModelsTest.java b/test/jalview/analysis/scoremodels/ScoreModelsTest.java index ffcd1a8..5e44d3d 100644 --- a/test/jalview/analysis/scoremodels/ScoreModelsTest.java +++ b/test/jalview/analysis/scoremodels/ScoreModelsTest.java @@ -45,16 +45,16 @@ public class ScoreModelsTest assertTrue(sm instanceof SimilarityScoreModel); assertTrue(sm instanceof PairwiseScoreModelI); assertFalse(sm instanceof DistanceScoreModel); - assertEquals(sm.getName(), "PID"); - assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'C'), 0f); - assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'r'), 1f); + assertEquals(sm.getName(), "DNA"); + assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('c', 'x'), 1f); sm = models.next(); assertTrue(sm instanceof SimilarityScoreModel); assertTrue(sm instanceof PairwiseScoreModelI); assertFalse(sm instanceof DistanceScoreModel); - assertEquals(sm.getName(), "DNA"); - assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('c', 'x'), 1f); + assertEquals(sm.getName(), "PID"); + assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'C'), 0f); + assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'r'), 1f); sm = models.next(); assertFalse(sm instanceof SimilarityScoreModel); -- 1.7.10.2