X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCalculationChooser.java;h=daab62b94524d0acca9ba5d9e7aa1f3d30aa0283;hb=95600b03ceeaf7162219dfa9b0a6bed432228b60;hp=6f5510ce3d2b62008950019404eed332cc799163;hpb=620d3204a1b556ba249595be908fbc190cf7e1cf;p=jalview.git diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java index 6f5510c..daab62b 100644 --- a/src/jalview/gui/CalculationChooser.java +++ b/src/jalview/gui/CalculationChooser.java @@ -20,13 +20,6 @@ */ package jalview.gui; -import jalview.analysis.TreeBuilder; -import jalview.analysis.scoremodels.ScoreModels; -import jalview.analysis.scoremodels.SimilarityParams; -import jalview.api.analysis.ScoreModelI; -import jalview.api.analysis.SimilarityParamsI; -import jalview.util.MessageManager; - import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; @@ -59,6 +52,16 @@ import javax.swing.JRadioButton; import javax.swing.event.InternalFrameAdapter; import javax.swing.event.InternalFrameEvent; +import jalview.analysis.TreeBuilder; +import jalview.analysis.scoremodels.ScoreMatrix; +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.util.MessageManager; + /** * A dialog where a user can choose and action Tree or PCA calculation options */ @@ -74,12 +77,17 @@ public class CalculationChooser extends JPanel private static final Font VERDANA_11PT = new Font("Verdana", 0, 11); + + private static final int MIN_PAIRWISE_SELECTION = 2; + private static final int MIN_TREE_SELECTION = 3; private static final int MIN_PCA_SELECTION = 4; AlignFrame af; + JRadioButton pairwise; + JRadioButton pca; JRadioButton neighbourJoining; @@ -102,7 +110,12 @@ 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 @@ -123,6 +136,7 @@ public class CalculationChooser extends JPanel { setLayout(new BorderLayout()); frame = new JInternalFrame(); + frame.setFrameIcon(null); frame.setContentPane(this); this.setBackground(Color.white); frame.addFocusListener(new FocusListener() @@ -149,12 +163,18 @@ 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); + + pairwise = new JRadioButton(MessageManager.getString("label.pairwise_alignment")); + pairwise.setOpaque(false); JPanel calcChoicePanel = new JPanel(new FlowLayout(FlowLayout.LEFT)); calcChoicePanel.setOpaque(false); @@ -163,14 +183,14 @@ 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); @@ -180,12 +200,14 @@ public class CalculationChooser extends JPanel treePanel.add(averageDistance); calcChoicePanel.add(treePanel); + calcChoicePanel.add(pairwise,FlowLayout.CENTER); ButtonGroup calcTypes = new ButtonGroup(); calcTypes.add(pca); calcTypes.add(neighbourJoining); calcTypes.add(averageDistance); - + calcTypes.add(pairwise); + ActionListener calcChanged = new ActionListener() { @Override @@ -197,7 +219,7 @@ public class CalculationChooser extends JPanel pca.addActionListener(calcChanged); neighbourJoining.addActionListener(calcChanged); averageDistance.addActionListener(calcChanged); - + pairwise.addActionListener(calcChanged); /* * score models drop-down - with added tooltips! */ @@ -264,14 +286,12 @@ 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); + Desktop.addInternalFrame(frame, title, width, height, false); calcChoicePanel.doLayout(); revalidate(); /* @@ -286,6 +306,7 @@ public class CalculationChooser extends JPanel }; }); + validateCalcTypes(); frame.setLayer(JLayeredPane.PALETTE_LAYER); } @@ -309,8 +330,10 @@ public class CalculationChooser extends JPanel MIN_TREE_SELECTION); boolean checkAverageDistance = checkEnabled(averageDistance, size, MIN_TREE_SELECTION); + boolean checkPairwise = checkEnabled(pairwise, size, + MIN_PAIRWISE_SELECTION); - if (checkPca || checkNeighbourJoining || checkAverageDistance) + if (checkPca || checkNeighbourJoining || checkAverageDistance || checkPairwise) { calculate.setToolTipText(null); calculate.setEnabled(true); @@ -336,8 +359,8 @@ 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()) @@ -371,7 +394,7 @@ public class CalculationChooser extends JPanel */ protected JComboBox buildModelOptionsList() { - final JComboBox scoreModelsCombo = new JComboBox(); + final JComboBox scoreModelsCombo = new JComboBox<>(); scoreModelsCombo.setRenderer(renderer); /* @@ -384,7 +407,8 @@ public class CalculationChooser extends JPanel @Override public void mouseEntered(MouseEvent e) { - scoreModelsCombo.setToolTipText(tips.get(scoreModelsCombo.getSelectedIndex())); + scoreModelsCombo.setToolTipText( + tips.get(scoreModelsCombo.getSelectedIndex())); } @Override @@ -413,39 +437,42 @@ 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)) { - 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); + 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); } + if (selectedIsPresent) { model.setSelectedItem(curSel); @@ -455,6 +482,47 @@ 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' */ protected void calculate_actionPerformed() @@ -466,15 +534,33 @@ public class CalculationChooser extends JPanel if (doPCA) { openPcaPanel(modelName, params); - } - else + } else { + if (pairwise.isSelected()) + { + openPairwisePanel(modelName,params); + } else { openTreePanel(modelName, params); - } + }} // closeFrame(); } + private void openPairwisePanel(String modelName, SimilarityParamsI params) + { + ScoreModelI sm = ScoreModels.getInstance().getScoreModel(modelName, af.alignPanel); + if (sm==null || !(sm instanceof ScoreMatrix)) + { + return; + } + JInternalFrame frame = new JInternalFrame(); + frame.setFrameIcon(null); + frame.setContentPane(new PairwiseAlignPanel(af.getViewport(),(ScoreMatrix)sm)); + Desktop.addInternalFrame(frame, + MessageManager.getString("action.pairwise_alignment"), 600, + 500); + } + /** * Open a new Tree panel on the desktop * @@ -488,21 +574,20 @@ public class CalculationChooser extends JPanel * this check in in case this method gets exposed programmatically in future */ AlignViewport viewport = af.getViewport(); - if (viewport.getSelectionGroup().getSize() < MIN_TREE_SELECTION) + 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", + 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); + MessageManager.getString("label.not_enough_sequences"), + JvOptionPane.WARNING_MESSAGE); return; } - String treeType = neighbourJoining.isSelected() ? TreeBuilder.NEIGHBOUR_JOINING + String treeType = neighbourJoining.isSelected() + ? TreeBuilder.NEIGHBOUR_JOINING : TreeBuilder.AVERAGE_DISTANCE; af.newTreePanel(treeType, modelName, params); } @@ -522,19 +607,28 @@ 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 +669,8 @@ 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 +685,9 @@ public class CalculationChooser extends JPanel { } } + + public PCAPanel getPcaPanel() + { + return pcaPanel; + } }