X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCalculationChooser.java;h=524830670e5cf9528a67b0f7e23add700f7bcdbf;hb=b87512d6e28a2a93ea2f08dcfbee320856c5c8de;hp=7f245b1e33442d210b64b32be725d89d7c1587e5;hpb=ff8e1762f6ca309e3695b7e7dbec4e3262b1dd1c;p=jalview.git diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java index 7f245b1..5248306 100644 --- a/src/jalview/gui/CalculationChooser.java +++ b/src/jalview/gui/CalculationChooser.java @@ -25,6 +25,8 @@ 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; import java.awt.BorderLayout; @@ -47,6 +49,7 @@ import java.util.List; import javax.swing.BorderFactory; import javax.swing.ButtonGroup; +import javax.swing.DefaultComboBoxModel; import javax.swing.JButton; import javax.swing.JCheckBox; import javax.swing.JComboBox; @@ -59,8 +62,13 @@ import javax.swing.event.InternalFrameAdapter; import javax.swing.event.InternalFrameEvent; /** - * A dialog where a user can choose and action Tree or PCA calculation options + * A dialog where a user can choose and action Tree or PCA calculation options. + * + * Allows also for dialog-free static methods openPCAPanel(...) and + * openTreePanel(...) for scripted use. + * */ +@SuppressWarnings("serial") public class CalculationChooser extends JPanel { /* @@ -71,7 +79,11 @@ public class CalculationChooser extends JPanel */ private static boolean treeMatchGaps = true; - private static final Font VERDANA_11PT = new Font("Verdana", 0, 11); + private static Font VERDANA_11PT; + + private static final int MIN_TREE_SELECTION = 3; + + private static final int MIN_PCA_SELECTION = 4; AlignFrame af; @@ -83,7 +95,7 @@ public class CalculationChooser extends JPanel JComboBox modelNames; - JButton ok; + JButton calculate; private JInternalFrame frame; @@ -95,6 +107,46 @@ public class CalculationChooser extends JPanel private JCheckBox shorterSequence; + private static ComboBoxTooltipRenderer renderer; // BH was not static + + List tips = new ArrayList<>(); + + /* + * the most recently opened PCA results panel + */ + private PCAPanel pcaPanel; + + /** + * Open a new Tree panel on the desktop statically. Params are standard (not + * set by Groovy). No dialog is opened. + * + * @param af + * @param treeType + * @param modelName + * @return null if successful; the string + * "label.you_need_at_least_n_sequences" if number of sequences + * selected is inappropriate + */ + public static Object openTreePanel(AlignFrame af, String treeType, + String modelName) + { + return openTreePanel(af, treeType, modelName, null); + } + + /** + * public static method for JalviewJS API to open a PCAPanel without + * necessarily using a dialog. + * + * @param af + * @param modelName + * @return the PCAPanel, or the string "label.you_need_at_least_n_sequences" + * if number of sequences selected is inappropriate + */ + public static Object openPcaPanel(AlignFrame af, String modelName) + { + return openPcaPanel(af, modelName, null); + } + /** * Constructor * @@ -116,7 +168,20 @@ public class CalculationChooser extends JPanel frame = new JInternalFrame(); frame.setContentPane(this); this.setBackground(Color.white); + frame.addFocusListener(new FocusListener() + { + @Override + public void focusLost(FocusEvent e) + { + } + + @Override + public void focusGained(FocusEvent e) + { + validateCalcTypes(); + } + }); /* * Layout consists of 3 or 4 panels: * - first with choice of PCA or tree method NJ or AV @@ -127,11 +192,15 @@ 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); @@ -140,20 +209,19 @@ 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); calcChoicePanel.add(pcaBorderless, FlowLayout.LEFT); - treePanel.add(neighbourJoining); treePanel.add(averageDistance); @@ -163,14 +231,18 @@ public class CalculationChooser extends JPanel calcTypes.add(pca); calcTypes.add(neighbourJoining); calcTypes.add(averageDistance); + + ActionListener calcChanged = new ActionListener() { @Override - public void itemStateChanged(ItemEvent e) + public void actionPerformed(ActionEvent e) { - neighbourJoining.setEnabled(tree.isSelected()); - averageDistance.setEnabled(tree.isSelected()); + validateCalcTypes(); } }; + pca.addActionListener(calcChanged); + neighbourJoining.addActionListener(calcChanged); + averageDistance.addActionListener(calcChanged); /* * score models drop-down - with added tooltips! @@ -196,33 +268,37 @@ public class CalculationChooser extends JPanel paramsPanel.add(includeGappedColumns); paramsPanel.add(shorterSequence); + if (VERDANA_11PT == null) + { + VERDANA_11PT = new Font("Verdana", 0, 11); + } /* * OK / Cancel buttons */ - ok = new JButton(MessageManager.getString("action.calculate")); - ok.setFont(VERDANA_11PT); - ok.addActionListener(new java.awt.event.ActionListener() + calculate = new JButton(MessageManager.getString("action.calculate")); + calculate.setFont(VERDANA_11PT); + calculate.addActionListener(new java.awt.event.ActionListener() { @Override public void actionPerformed(ActionEvent e) { - ok_actionPerformed(); + calculate_actionPerformed(); } }); - JButton cancel = new JButton(MessageManager.getString("action.close")); - cancel.setFont(VERDANA_11PT); - cancel.addActionListener(new java.awt.event.ActionListener() + JButton close = new JButton(MessageManager.getString("action.close")); + close.setFont(VERDANA_11PT); + close.addActionListener(new java.awt.event.ActionListener() { @Override public void actionPerformed(ActionEvent e) { - cancel_actionPerformed(e); + close_actionPerformed(); } }); JPanel actionPanel = new JPanel(); actionPanel.setOpaque(false); - actionPanel.add(ok); - actionPanel.add(cancel); + actionPanel.add(calculate); + actionPanel.add(close); boolean includeParams = false; this.add(calcChoicePanel, BorderLayout.CENTER); @@ -238,14 +314,12 @@ 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(); /* @@ -260,10 +334,85 @@ public class CalculationChooser extends JPanel }; }); + validateCalcTypes(); frame.setLayer(JLayeredPane.PALETTE_LAYER); } /** + * enable calculations applicable for the current alignment or selection. + */ + protected void validateCalcTypes() + { + int size = af.getViewport().getAlignment().getHeight(); + if (af.getViewport().getSelectionGroup() != null) + { + size = af.getViewport().getSelectionGroup().getSize(); + } + + /* + * disable calc options for which there is insufficient input data + * return value of true means enabled and selected + */ + boolean checkPca = checkEnabled(pca, size, MIN_PCA_SELECTION); + boolean checkNeighbourJoining = checkEnabled(neighbourJoining, size, + MIN_TREE_SELECTION); + boolean checkAverageDistance = checkEnabled(averageDistance, size, + MIN_TREE_SELECTION); + + if (checkPca || checkNeighbourJoining || checkAverageDistance) + { + calculate.setToolTipText(null); + calculate.setEnabled(true); + } + else + { + calculate.setEnabled(false); + } + updateScoreModels(modelNames, tips); + } + + /** + * Check the input and disable a calculation's radio button if necessary. A + * tooltip is shown for disabled calculations. + * + * @param calc + * - radio button for the calculation being validated + * @param size + * - size of input to calculation + * @param minsize + * - minimum size for calculation + * @return true if size >= minsize and calc.isSelected + */ + private boolean checkEnabled(JRadioButton calc, int size, int minsize) + { + String ttip = MessageManager + .formatMessage("label.you_need_at_least_n_sequences", minsize); + + calc.setEnabled(size >= minsize); + if (!calc.isEnabled()) + { + calc.setToolTipText(ttip); + } + else + { + calc.setToolTipText(null); + } + if (calc.isSelected()) + { + modelNames.setEnabled(calc.isEnabled()); + if (calc.isEnabled()) + { + return true; + } + else + { + calculate.setToolTipText(ttip); + } + } + return false; + } + + /** * A rather elaborate helper method (blame Swing, not me) that builds a * drop-down list of score models (by name) with descriptions as tooltips. * There is also a tooltip shown for the currently selected item when hovering @@ -271,73 +420,143 @@ public class CalculationChooser extends JPanel */ protected JComboBox buildModelOptionsList() { - final JComboBox comboBox = new JComboBox(); - ComboBoxTooltipRenderer renderer = new ComboBoxTooltipRenderer(); - comboBox.setRenderer(renderer); - final List tips = new ArrayList(); + JComboBox scoreModelsCombo = new JComboBox<>(); + if (renderer == null) + { + renderer = new ComboBoxTooltipRenderer(); + } + scoreModelsCombo.setRenderer(renderer); /* * show tooltip on mouse over the combobox * note the listener has to be on the components that make up * the combobox, doesn't work if just on the combobox */ - MouseAdapter mouseListener = new MouseAdapter() + final MouseAdapter mouseListener = new MouseAdapter() { @Override public void mouseEntered(MouseEvent e) { - comboBox.setToolTipText(tips.get(comboBox.getSelectedIndex())); + scoreModelsCombo.setToolTipText( + tips.get(scoreModelsCombo.getSelectedIndex())); } @Override public void mouseExited(MouseEvent e) { - comboBox.setToolTipText(null); + scoreModelsCombo.setToolTipText(null); } }; - for (Component c : comboBox.getComponents()) + for (Component c : scoreModelsCombo.getComponents()) { c.addMouseListener(mouseListener); } + updateScoreModels(scoreModelsCombo, tips); + + /* + * set the list of tooltips on the combobox's renderer + */ + renderer.setTooltips(tips); + + return scoreModelsCombo; + } + + private void updateScoreModels(JComboBox comboBox, + List toolTips) + { + Object curSel = comboBox.getSelectedItem(); + toolTips.clear(); + 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(); - for (ScoreModelI sm : scoreModels.getModels()) + boolean selectedIsPresent = false; + for (ScoreModelI sm : models) { - boolean nucleotide = af.getViewport().getAlignment().isNucleotide(); - if (sm.isDNA() && nucleotide || sm.isProtein() && !nucleotide) + if (curSel != null && sm.getName().equals(curSel)) { - comboBox.addItem(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()); - } - tips.add(tooltip); + selectedIsPresent = true; + curSel = sm.getName(); } + model.addElement(sm.getName()); /* - * set the list of tooltips on the combobox's renderer + * tooltip is description if provided, else text lookup with + * fallback on the model name */ - renderer.setTooltips(tips); + String tooltip = sm.getDescription(); + if (tooltip == null) + { + tooltip = MessageManager.getStringOrReturn("label.score_model_", + sm.getName()); + } + toolTips.add(tooltip); } - return comboBox; + 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) + { + 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(Preferences.BLOSUM62_PCA_FOR_NUCLEOTIDE, + false)) + { + filtered.add(scoreModels.getBlosum62()); + } + + return filtered; } /** * Open and calculate the selected tree or PCA on 'OK' */ - protected void ok_actionPerformed() + protected void calculate_actionPerformed() { boolean doPCA = pca.isSelected(); String modelName = modelNames.getSelectedItem().toString(); @@ -363,9 +582,20 @@ public class CalculationChooser extends JPanel */ protected void openTreePanel(String modelName, SimilarityParamsI params) { - String treeType = neighbourJoining.isSelected() ? TreeBuilder.NEIGHBOUR_JOINING - : TreeBuilder.AVERAGE_DISTANCE; - af.newTreePanel(treeType, modelName, params); + Object ret = openTreePanel(af, + neighbourJoining.isSelected() ? TreeBuilder.NEIGHBOUR_JOINING + : TreeBuilder.AVERAGE_DISTANCE, + modelName, params); + if (ret instanceof String) + { + JvOptionPane.showMessageDialog(this, // was opening on Desktop? + MessageManager.formatMessage( + (String) ret, + MIN_TREE_SELECTION), + MessageManager.getString("label.not_enough_sequences"), + JvOptionPane.WARNING_MESSAGE); + + } } /** @@ -376,23 +606,99 @@ public class CalculationChooser extends JPanel */ protected void openPcaPanel(String modelName, SimilarityParamsI params) { + Object ret = openPcaPanel(af, modelName, params); + if (ret instanceof String) + { + JvOptionPane.showInternalMessageDialog(this, + MessageManager.formatMessage( + (String) ret, + MIN_PCA_SELECTION), + MessageManager + .getString("label.sequence_selection_insufficient"), + JvOptionPane.WARNING_MESSAGE); + } + else + { + // only used for test suite + pcaPanel = (PCAPanel) ret; + } + + } + + /** + * Open a new Tree panel on the desktop statically + * + * @param af + * @param treeType + * @param modelName + * @param params + * @return null, or the string "label.you_need_at_least_n_sequences" if number + * of sequences selected is inappropriate + */ + public static Object openTreePanel(AlignFrame af, String treeType, + String modelName, SimilarityParamsI params) + { + + /* + * 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) + { + return "label.you_need_at_least_n_sequences"; + } + + if (params == null) + { + params = getSimilarityParameters(false); + } + + af.newTreePanel(treeType, modelName, params); + return null; + } + + /** + * public static method for JalviewJS API + * + * @param af + * @param modelName + * @param params + * @return the PCAPanel, or null if number of sequences selected is + * inappropriate + */ + public static Object openPcaPanel(AlignFrame af, String modelName, + SimilarityParamsI params) + { + AlignViewport viewport = af.getViewport(); + + /* + * gui validation shouldn't allow insufficient sequences here, but leave + * this check in in case this method gets exposed programmatically in future + * + * + */ if (((viewport.getSelectionGroup() != null) - && (viewport.getSelectionGroup().getSize() < 4) && (viewport - .getSelectionGroup().getSize() > 0)) - || (viewport.getAlignment().getHeight() < 4)) - { - JvOptionPane - .showInternalMessageDialog( - this, - MessageManager - .getString("label.principal_component_analysis_must_take_least_four_input_sequences"), - MessageManager - .getString("label.sequence_selection_insufficient"), - JvOptionPane.WARNING_MESSAGE); - return; + && (viewport.getSelectionGroup().getSize() < MIN_PCA_SELECTION) + && (viewport.getSelectionGroup().getSize() > 0)) + || (viewport.getAlignment().getHeight() < MIN_PCA_SELECTION)) + { + return "label.you_need_at_least_n_sequences"; } - new PCAPanel(af.alignPanel, modelName, params); + + if (params == null) + { + params = getSimilarityParameters(true); + } + + /* + * construct the panel and kick off its calculation thread + */ + PCAPanel pcap = new PCAPanel(af.alignPanel, modelName, params); + new Thread(pcap).start(); + return pcap; } /** @@ -408,6 +714,7 @@ public class CalculationChooser extends JPanel } } + /** * Returns a data bean holding parameters for similarity (or distance) model * calculation @@ -415,7 +722,8 @@ public class CalculationChooser extends JPanel * @param doPCA * @return */ - protected SimilarityParamsI getSimilarityParameters(boolean doPCA) + public static SimilarityParamsI getSimilarityParameters( + boolean doPCA) { // commented out: parameter choices read from gui widgets // SimilarityParamsI params = new SimilarityParams( @@ -434,15 +742,15 @@ public class CalculationChooser extends JPanel */ boolean matchGap = doPCA ? false : treeMatchGaps; - return new SimilarityParams(includeGapGap, matchGap, includeGapResidue, matchOnShortestLength); + return new SimilarityParams(includeGapGap, matchGap, includeGapResidue, + matchOnShortestLength); + } /** - * Closes dialog on cancel - * - * @param e + * Closes dialog on Close button press */ - protected void cancel_actionPerformed(ActionEvent e) + protected void close_actionPerformed() { try { @@ -451,4 +759,9 @@ public class CalculationChooser extends JPanel { } } + + public PCAPanel getPcaPanel() + { + return pcaPanel; + } }