X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCalculationChooser.java;h=ae92168884495ec933771c24ae68eeeff623110f;hb=4a3def9f59cefe629c9a33d87483283aee085928;hp=8a95594f133d5d431acd9c0b7485783a25704a7f;hpb=968e71fa2914ce20dd8caca18dd7d4651b636af5;p=jalview.git diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java index 8a95594..ae92168 100644 --- a/src/jalview/gui/CalculationChooser.java +++ b/src/jalview/gui/CalculationChooser.java @@ -21,11 +21,15 @@ package jalview.gui; import jalview.analysis.TreeBuilder; +import jalview.analysis.TreeCalculator; +import jalview.analysis.TreeModel; import jalview.analysis.scoremodels.ScoreModels; import jalview.analysis.scoremodels.SimilarityParams; import jalview.api.analysis.ScoreModelI; import jalview.api.analysis.SimilarityParamsI; +import jalview.bin.Cache; import jalview.datamodel.SequenceGroup; +import jalview.ext.archaeopteryx.AptxInit; import jalview.util.MessageManager; import java.awt.BorderLayout; @@ -43,6 +47,7 @@ import java.awt.event.FocusListener; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.beans.PropertyVetoException; +import java.io.IOException; import java.util.ArrayList; import java.util.List; @@ -103,7 +108,12 @@ public class CalculationChooser extends JPanel final ComboBoxTooltipRenderer renderer = new ComboBoxTooltipRenderer(); - List tips = new ArrayList(); + List tips = new ArrayList<>(); + + /* + * the most recently opened PCA results panel + */ + private PCAPanel pcaPanel; /** * Constructor @@ -150,12 +160,15 @@ public class CalculationChooser extends JPanel pca = new JRadioButton( MessageManager.getString("label.principal_component_analysis")); pca.setOpaque(false); + neighbourJoining = new JRadioButton( MessageManager.getString("label.tree_calc_nj")); neighbourJoining.setSelected(true); + neighbourJoining.setOpaque(false); + averageDistance = new JRadioButton( MessageManager.getString("label.tree_calc_av")); - neighbourJoining.setOpaque(false); + averageDistance.setOpaque(false); JPanel calcChoicePanel = new JPanel(new FlowLayout(FlowLayout.LEFT)); calcChoicePanel.setOpaque(false); @@ -164,14 +177,14 @@ public class CalculationChooser extends JPanel JPanel treePanel = new JPanel(new FlowLayout(FlowLayout.LEFT)); treePanel.setOpaque(false); - treePanel.setBorder(BorderFactory.createTitledBorder(MessageManager - .getString("label.tree"))); + JvSwingUtils.createTitledBorder(treePanel, + MessageManager.getString("label.tree"), true); // then copy the inset dimensions for the border-less PCA panel JPanel pcaBorderless = new JPanel(new FlowLayout(FlowLayout.LEFT)); Insets b = treePanel.getBorder().getBorderInsets(treePanel); - pcaBorderless.setBorder(BorderFactory.createEmptyBorder(2, b.left, 2, - b.right)); + pcaBorderless.setBorder( + BorderFactory.createEmptyBorder(2, b.left, 2, b.right)); pcaBorderless.setOpaque(false); pcaBorderless.add(pca, FlowLayout.LEFT); @@ -186,7 +199,7 @@ public class CalculationChooser extends JPanel calcTypes.add(pca); calcTypes.add(neighbourJoining); calcTypes.add(averageDistance); - + ActionListener calcChanged = new ActionListener() { @Override @@ -265,9 +278,9 @@ public class CalculationChooser extends JPanel setMinimumSize(new Dimension(325, height - 10)); String title = MessageManager.getString("label.choose_calculation"); - if (af.getViewport().viewName != null) + if (af.getViewport().getViewName() != null) { - title = title + " (" + af.getViewport().viewName + ")"; + title = title + " (" + af.getViewport().getViewName() + ")"; } Desktop.addInternalFrame(frame, title, width, height, false); @@ -285,6 +298,7 @@ public class CalculationChooser extends JPanel }; }); + validateCalcTypes(); frame.setLayer(JLayeredPane.PALETTE_LAYER); } @@ -335,8 +349,8 @@ public class CalculationChooser extends JPanel */ private boolean checkEnabled(JRadioButton calc, int size, int minsize) { - String ttip = MessageManager.formatMessage( - "label.you_need_at_least_n_sequences", minsize); + String ttip = MessageManager + .formatMessage("label.you_need_at_least_n_sequences", minsize); calc.setEnabled(size >= minsize); if (!calc.isEnabled()) @@ -370,7 +384,7 @@ public class CalculationChooser extends JPanel */ protected JComboBox buildModelOptionsList() { - final JComboBox scoreModelsCombo = new JComboBox(); + final JComboBox scoreModelsCombo = new JComboBox<>(); scoreModelsCombo.setRenderer(renderer); /* @@ -383,7 +397,8 @@ public class CalculationChooser extends JPanel @Override public void mouseEntered(MouseEvent e) { - scoreModelsCombo.setToolTipText(tips.get(scoreModelsCombo.getSelectedIndex())); + scoreModelsCombo.setToolTipText( + tips.get(scoreModelsCombo.getSelectedIndex())); } @Override @@ -412,39 +427,41 @@ public class CalculationChooser extends JPanel { Object curSel = comboBox.getSelectedItem(); toolTips.clear(); - DefaultComboBoxModel model = new DefaultComboBoxModel(); + DefaultComboBoxModel model = new DefaultComboBoxModel<>(); + /* + * select the score models applicable to the alignment type + */ + boolean nucleotide = af.getViewport().getAlignment().isNucleotide(); + List models = getApplicableScoreModels(nucleotide, + pca.isSelected()); /* * now we can actually add entries to the combobox, * remembering their descriptions for tooltips */ - ScoreModels scoreModels = ScoreModels.getInstance(); boolean selectedIsPresent = false; - for (ScoreModelI sm : scoreModels.getModels()) + for (ScoreModelI sm : models) { - boolean nucleotide = af.getViewport().getAlignment().isNucleotide(); - if (sm.isDNA() && nucleotide || sm.isProtein() && !nucleotide) + if (curSel != null && sm.getName().equals(curSel)) + { + selectedIsPresent = true; + curSel = sm.getName(); + } + model.addElement(sm.getName()); + + /* + * tooltip is description if provided, else text lookup with + * fallback on the model name + */ + String tooltip = sm.getDescription(); + if (tooltip == null) { - if (curSel != null && sm.getName().equals(curSel)) - { - selectedIsPresent = true; - curSel = sm.getName(); - } - model.addElement(sm.getName()); - - /* - * tooltip is description if provided, else text lookup with - * fallback on the model name - */ - String tooltip = sm.getDescription(); - if (tooltip == null) - { - tooltip = MessageManager.getStringOrReturn("label.score_model_", - sm.getName()); - } - toolTips.add(tooltip); + tooltip = MessageManager.getStringOrReturn("label.score_model_", + sm.getName()); } + toolTips.add(tooltip); } + if (selectedIsPresent) { model.setSelectedItem(curSel); @@ -454,57 +471,145 @@ public class CalculationChooser extends JPanel } /** + * Builds a list of score models which are applicable for the alignment and + * calculation type (peptide or generic models for protein, nucleotide or + * generic models for nucleotide). + *

+ * As a special case, includes BLOSUM62 as an extra option for nucleotide PCA. + * This is for backwards compatibility with Jalview prior to 2.8 when BLOSUM62 + * was the only score matrix supported. This is included if property + * BLOSUM62_PCA_FOR_NUCLEOTIDE is set to true in the Jalview properties file. + * + * @param nucleotide + * @param forPca + * @return + */ + protected static List getApplicableScoreModels( + boolean nucleotide, boolean forPca) + { + List filtered = new ArrayList<>(); + + ScoreModels scoreModels = ScoreModels.getInstance(); + for (ScoreModelI sm : scoreModels.getModels()) + { + if (!nucleotide && sm.isProtein() || nucleotide && sm.isDNA()) + { + filtered.add(sm); + } + } + + /* + * special case: add BLOSUM62 as last option for nucleotide PCA, + * for backwards compatibility with Jalview < 2.8 (JAL-2962) + */ + if (nucleotide && forPca + && Cache.getDefault("BLOSUM62_PCA_FOR_NUCLEOTIDE", false)) + { + filtered.add(scoreModels.getBlosum62()); + } + + return filtered; + } + + /** * Open and calculate the selected tree or PCA on 'OK' + * + * @throws IOException */ protected void calculate_actionPerformed() { boolean doPCA = pca.isSelected(); - String modelName = modelNames.getSelectedItem().toString(); + String substitutionMatrix = modelNames.getSelectedItem().toString(); SimilarityParamsI params = getSimilarityParameters(doPCA); if (doPCA) { - openPcaPanel(modelName, params); + openPcaPanel(substitutionMatrix, params); } else { - openTreePanel(modelName, params); + try + { + createTree(substitutionMatrix, params); + } catch (IOException e) + { + // TODO Auto-generated catch block + e.printStackTrace(); + } + + + + + + } // closeFrame(); } + protected void createTree(String substitutionMatrix, + SimilarityParamsI params) throws IOException + { + String treeAlgo = determineTreeAlgo(); + TreeCalculator treeCalculator = new TreeCalculator(treeAlgo, + substitutionMatrix, params); + TreeBuilder calculatedTree = treeCalculator.makeTree(af.getViewport()); + + // AptxInit.createInstanceFromCalculation(calculatedTree); + + TreeModel tree = new TreeModel(calculatedTree); + jalview.io.NewickFile newick = new jalview.io.NewickFile( + tree.getTopNode()); + String output = newick.print(tree.hasBootstrap(), tree.hasDistances(), + tree.hasRootDistance()); + AptxInit.createInstanceFromNhx(af.getTitle(), output, + af.getViewport()); + // openTreePanel(tree, treeAlgo, substitutionMatrix); + } + + + protected String determineTreeAlgo() // to be modified & expanded + { + String treeAlgorithm = neighbourJoining.isSelected() + ? TreeBuilder.NEIGHBOUR_JOINING + : TreeBuilder.AVERAGE_DISTANCE; + + return treeAlgorithm; + + } + + protected void checkEnoughSequences(AlignViewport viewport) + { + SequenceGroup sg = viewport.getSelectionGroup(); + if (sg != null && sg.getSize() < MIN_TREE_SELECTION) + { + JvOptionPane.showMessageDialog(Desktop.desktop, + MessageManager.formatMessage( + "label.you_need_at_least_n_sequences", + MIN_TREE_SELECTION), + MessageManager.getString("label.not_enough_sequences"), + JvOptionPane.WARNING_MESSAGE); + return; + } + } + /** * Open a new Tree panel on the desktop * - * @param modelName + * @param tree * @param params + * @param treeAlgo */ - protected void openTreePanel(String modelName, SimilarityParamsI params) + protected void openTreePanel(TreeModel tree, String treeAlgo, + String substitutionMatrix) { /* * gui validation shouldn't allow insufficient sequences here, but leave * this check in in case this method gets exposed programmatically in future */ - AlignViewport viewport = af.getViewport(); - SequenceGroup sg = viewport.getSelectionGroup(); - if (sg != null && sg.getSize() < MIN_TREE_SELECTION) - { - JvOptionPane - .showMessageDialog( - Desktop.desktop, - MessageManager - .formatMessage("label.you_need_at_least_n_sequences", - MIN_TREE_SELECTION), - MessageManager - .getString("label.not_enough_sequences"), - JvOptionPane.WARNING_MESSAGE); - return; - } + checkEnoughSequences(af.getViewport()); - String treeType = neighbourJoining.isSelected() ? TreeBuilder.NEIGHBOUR_JOINING - : TreeBuilder.AVERAGE_DISTANCE; - af.newTreePanel(treeType, modelName, params); + af.newTreePanel(tree, treeAlgo, substitutionMatrix); } /** @@ -522,18 +627,26 @@ public class CalculationChooser extends JPanel * this check in in case this method gets exposed programmatically in future */ if (((viewport.getSelectionGroup() != null) - && (viewport.getSelectionGroup().getSize() < MIN_PCA_SELECTION) && (viewport - .getSelectionGroup().getSize() > 0)) + && (viewport.getSelectionGroup().getSize() < MIN_PCA_SELECTION) + && (viewport.getSelectionGroup().getSize() > 0)) || (viewport.getAlignment().getHeight() < MIN_PCA_SELECTION)) { - JvOptionPane.showInternalMessageDialog(this, MessageManager - .formatMessage("label.you_need_at_least_n_sequences", - MIN_PCA_SELECTION), MessageManager - .getString("label.sequence_selection_insufficient"), + JvOptionPane.showInternalMessageDialog(this, + MessageManager.formatMessage( + "label.you_need_at_least_n_sequences", + MIN_PCA_SELECTION), + MessageManager + .getString("label.sequence_selection_insufficient"), JvOptionPane.WARNING_MESSAGE); return; } - new PCAPanel(af.alignPanel, modelName, params); + + /* + * construct the panel and kick off its calculation thread + */ + pcaPanel = new PCAPanel(af.alignPanel, modelName, params); + new Thread(pcaPanel).start(); + } /** @@ -575,7 +688,8 @@ public class CalculationChooser extends JPanel */ boolean matchGap = doPCA ? false : treeMatchGaps; - return new SimilarityParams(includeGapGap, matchGap, includeGapResidue, matchOnShortestLength); + return new SimilarityParams(includeGapGap, matchGap, includeGapResidue, + matchOnShortestLength); } /** @@ -590,4 +704,9 @@ public class CalculationChooser extends JPanel { } } + + public PCAPanel getPcaPanel() + { + return pcaPanel; + } }