X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCalculationChooser.java;h=4e22a74485798aee2955faca65b64f61e9c802e4;hb=ef7125ccaa49531e0f0930955af7a1710f6c4372;hp=a9f396634a63e9746e8ce405380ada7ec38b087e;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java index a9f3966..4e22a74 100644 --- a/src/jalview/gui/CalculationChooser.java +++ b/src/jalview/gui/CalculationChooser.java @@ -20,14 +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.datamodel.SequenceGroup; -import jalview.util.MessageManager; - import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; @@ -60,6 +52,17 @@ import javax.swing.JRadioButton; import javax.swing.event.InternalFrameAdapter; import javax.swing.event.InternalFrameEvent; +import jalview.analysis.AlignmentUtils; +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.bin.Cache; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.SequenceGroup; +import jalview.util.MessageManager; + /** * A dialog where a user can choose and action Tree or PCA calculation options */ @@ -78,6 +81,21 @@ public class CalculationChooser extends JPanel private static final int MIN_TREE_SELECTION = 3; private static final int MIN_PCA_SELECTION = 4; + + private String secondaryStructureModelName; + + private void getSecondaryStructureModelName() { + + ScoreModels scoreModels = ScoreModels.getInstance(); + for (ScoreModelI sm : scoreModels.getModels()) + { + if (sm.isSecondaryStructure()) + { + secondaryStructureModelName = sm.getName(); + } + } + + } AlignFrame af; @@ -88,6 +106,8 @@ public class CalculationChooser extends JPanel JRadioButton averageDistance; JComboBox modelNames; + + JComboBox ssSourceDropdown; JButton calculate; @@ -103,7 +123,12 @@ 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 @@ -115,6 +140,7 @@ public class CalculationChooser extends JPanel this.af = alignFrame; init(); af.alignPanel.setCalculationDialog(this); + } /** @@ -122,8 +148,10 @@ public class CalculationChooser extends JPanel */ void init() { + getSecondaryStructureModelName(); setLayout(new BorderLayout()); frame = new JInternalFrame(); + frame.setFrameIcon(null); frame.setContentPane(this); this.setBackground(Color.white); frame.addFocusListener(new FocusListener() @@ -150,12 +178,15 @@ 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); @@ -164,8 +195,8 @@ 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)); @@ -198,16 +229,37 @@ public class CalculationChooser extends JPanel pca.addActionListener(calcChanged); neighbourJoining.addActionListener(calcChanged); averageDistance.addActionListener(calcChanged); + + + //to do + ssSourceDropdown = buildSSSourcesOptionsList(); + ssSourceDropdown.setVisible(false); // Initially hide the dropdown /* * score models drop-down - with added tooltips! */ modelNames = buildModelOptionsList(); + + // Step 3: Show or Hide Dropdown Based on Selection + modelNames.addActionListener(new ActionListener() { + @Override + public void actionPerformed(ActionEvent e) { + String selectedModel = modelNames.getSelectedItem().toString(); + + if (selectedModel.equals(secondaryStructureModelName)) { + ssSourceDropdown.setVisible(true); + } else { + ssSourceDropdown.setVisible(false); + } + } + }); + JPanel scoreModelPanel = new JPanel(new FlowLayout(FlowLayout.CENTER)); scoreModelPanel.setOpaque(false); scoreModelPanel.add(modelNames); - + scoreModelPanel.add(ssSourceDropdown); + /* * score model parameters */ @@ -222,7 +274,7 @@ public class CalculationChooser extends JPanel paramsPanel.add(matchGaps); paramsPanel.add(includeGappedColumns); paramsPanel.add(shorterSequence); - + /* * OK / Cancel buttons */ @@ -260,14 +312,14 @@ public class CalculationChooser extends JPanel } this.add(actionPanel, BorderLayout.SOUTH); - int width = 350; + int width = 365; int height = includeParams ? 420 : 240; 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 +337,7 @@ public class CalculationChooser extends JPanel }; }); + validateCalcTypes(); frame.setLayer(JLayeredPane.PALETTE_LAYER); } @@ -370,7 +423,7 @@ public class CalculationChooser extends JPanel */ protected JComboBox buildModelOptionsList() { - final JComboBox scoreModelsCombo = new JComboBox(); + final JComboBox scoreModelsCombo = new JComboBox<>(); scoreModelsCombo.setRenderer(renderer); /* @@ -407,53 +460,146 @@ public class CalculationChooser extends JPanel return scoreModelsCombo; } + + private JComboBox buildSSSourcesOptionsList() + { + final JComboBox comboBox = new JComboBox<>(); + Object curSel = comboBox.getSelectedItem(); + DefaultComboBoxModel sourcesModel = new DefaultComboBoxModel<>(); + + List ssSources = getApplicableSecondaryStructureSources(); + + boolean selectedIsPresent = false; + for (String source : ssSources) + { + if (curSel != null && source.equals(curSel)) + { + selectedIsPresent = true; + curSel = source; + } + sourcesModel.addElement(source); + + } + + if (selectedIsPresent) + { + sourcesModel.setSelectedItem(curSel); + } + comboBox.setModel(sourcesModel); + + return comboBox; + } + + private void updateScoreModels(JComboBox comboBox, List toolTips) { 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(); + AlignmentAnnotation[] alignmentAnnotations = af.getViewport().getAlignment().getAlignmentAnnotation(); + + boolean ssPresent = AlignmentUtils.isSecondaryStructurePresent(alignmentAnnotations); + + List models = getApplicableScoreModels(nucleotide, pca.isSelected(), + ssPresent); /* * 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); } // finally, update the model comboBox.setModel(model); + + } + + /** + * 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, boolean ssPresent) + { + List filtered = new ArrayList<>(); + + ScoreModels scoreModels = ScoreModels.getInstance(); + for (ScoreModelI sm : scoreModels.getModels()) + { + if (!nucleotide && sm.isProtein() || nucleotide && sm.isDNA() + || ssPresent && sm.isSecondaryStructure()) + { + 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; } + + protected List getApplicableSecondaryStructureSources() + { + AlignmentAnnotation[] annotations = af.getViewport().getAlignment().getAlignmentAnnotation(); + + List ssSources = AlignmentUtils.getSecondaryStructureSources(annotations); + //List ssSources = AlignmentUtils.extractSSSourceInAlignmentAnnotation(annotations); + + + return ssSources; + } + /** * Open and calculate the selected tree or PCA on 'OK' */ @@ -461,8 +607,16 @@ public class CalculationChooser extends JPanel { boolean doPCA = pca.isSelected(); String modelName = modelNames.getSelectedItem().toString(); - SimilarityParamsI params = getSimilarityParameters(doPCA); - + String ssSource = ""; + Object selectedItem = ssSourceDropdown.getSelectedItem(); + if (selectedItem != null) { + ssSource = selectedItem.toString(); + } + SimilarityParams params = getSimilarityParameters(doPCA); + if(ssSource.length()>0) + { + params.setSecondaryStructureSource(ssSource); + } if (doPCA) { openPcaPanel(modelName, params); @@ -534,7 +688,13 @@ public class CalculationChooser extends JPanel 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(); + } /** @@ -557,7 +717,7 @@ public class CalculationChooser extends JPanel * @param doPCA * @return */ - protected SimilarityParamsI getSimilarityParameters(boolean doPCA) + protected SimilarityParams getSimilarityParameters(boolean doPCA) { // commented out: parameter choices read from gui widgets // SimilarityParamsI params = new SimilarityParams( @@ -592,4 +752,9 @@ public class CalculationChooser extends JPanel { } } + + public PCAPanel getPcaPanel() + { + return pcaPanel; + } }