X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCalculationChooser.java;h=f0d9521a9cdc1dca6b8198105c5dd2d087f0f2c1;hb=82de3ff949ae61b771136fbdb49baacc20e652fd;hp=7b3bf220ecdc1f9d676046bf9774c1f0b430736d;hpb=fad1d9c25b785e0d42bbe8cdcd82af1ca8c2276b;p=jalview.git diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java index 7b3bf22..f0d9521 100644 --- a/src/jalview/gui/CalculationChooser.java +++ b/src/jalview/gui/CalculationChooser.java @@ -25,23 +25,31 @@ 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; import java.awt.Color; import java.awt.Component; +import java.awt.Dimension; import java.awt.FlowLayout; import java.awt.Font; import java.awt.GridLayout; +import java.awt.Insets; import java.awt.event.ActionEvent; -import java.awt.event.ItemEvent; -import java.awt.event.ItemListener; +import java.awt.event.ActionListener; +import java.awt.event.FocusEvent; +import java.awt.event.FocusListener; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.beans.PropertyVetoException; import java.util.ArrayList; 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; @@ -68,21 +76,23 @@ public class CalculationChooser extends JPanel private static final Font VERDANA_11PT = new Font("Verdana", 0, 11); + private static final int MIN_TREE_SELECTION = 3; + + private static final int MIN_PCA_SELECTION = 4; + AlignFrame af; JRadioButton pca; - JRadioButton tree; - JRadioButton neighbourJoining; JRadioButton averageDistance; JComboBox modelNames; - private JInternalFrame frame; + JButton calculate; - private ButtonGroup treeTypes; + private JInternalFrame frame; private JCheckBox includeGaps; @@ -92,6 +102,15 @@ public class CalculationChooser extends JPanel private JCheckBox shorterSequence; + final ComboBoxTooltipRenderer renderer = new ComboBoxTooltipRenderer(); + + List tips = new ArrayList<>(); + + /* + * the most recently opened PCA results panel + */ + private PCAPanel pcaPanel; + /** * Constructor * @@ -109,65 +128,91 @@ public class CalculationChooser extends JPanel */ void init() { + setLayout(new BorderLayout()); 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 4 or 5 panels: - * - first with choice of Tree or PCA - * - second with choice of tree method NJ or AV - * - third with choice of score model - * - fourth with score model parameter options [suppressed] - * - fifth with OK and Cancel + * Layout consists of 3 or 4 panels: + * - first with choice of PCA or tree method NJ or AV + * - second with choice of score model + * - third with score model parameter options [suppressed] + * - fourth with OK and Cancel */ - tree = new JRadioButton(MessageManager.getString("label.tree")); - tree.setOpaque(false); pca = new JRadioButton( MessageManager.getString("label.principal_component_analysis")); pca.setOpaque(false); neighbourJoining = new JRadioButton( MessageManager.getString("label.tree_calc_nj")); + neighbourJoining.setSelected(true); averageDistance = new JRadioButton( MessageManager.getString("label.tree_calc_av")); - ItemListener listener = new ItemListener() + neighbourJoining.setOpaque(false); + + JPanel calcChoicePanel = new JPanel(new FlowLayout(FlowLayout.LEFT)); + calcChoicePanel.setOpaque(false); + + // first create the Tree calculation's border panel + JPanel treePanel = new JPanel(new FlowLayout(FlowLayout.LEFT)); + treePanel.setOpaque(false); + + 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.setOpaque(false); + + pcaBorderless.add(pca, FlowLayout.LEFT); + calcChoicePanel.add(pcaBorderless, FlowLayout.LEFT); + + treePanel.add(neighbourJoining); + treePanel.add(averageDistance); + + calcChoicePanel.add(treePanel); + + ButtonGroup calcTypes = new ButtonGroup(); + 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.addItemListener(listener); - tree.addItemListener(listener); - ButtonGroup calcTypes = new ButtonGroup(); - calcTypes.add(pca); - calcTypes.add(tree); - JPanel calcChoicePanel = new JPanel(); - calcChoicePanel.setOpaque(false); - tree.setSelected(true); - calcChoicePanel.add(tree); - calcChoicePanel.add(pca); - - neighbourJoining.setOpaque(false); - treeTypes = new ButtonGroup(); - treeTypes.add(neighbourJoining); - treeTypes.add(averageDistance); - neighbourJoining.setSelected(true); - JPanel treeChoicePanel = new JPanel(); - treeChoicePanel.setOpaque(false); - treeChoicePanel.add(neighbourJoining); - treeChoicePanel.add(averageDistance); + pca.addActionListener(calcChanged); + neighbourJoining.addActionListener(calcChanged); + averageDistance.addActionListener(calcChanged); /* * score models drop-down - with added tooltips! */ modelNames = buildModelOptionsList(); - JPanel scoreModelPanel = new JPanel(new FlowLayout(FlowLayout.LEFT)); + JPanel scoreModelPanel = new JPanel(new FlowLayout(FlowLayout.CENTER)); scoreModelPanel.setOpaque(false); - scoreModelPanel.add(modelNames, FlowLayout.LEFT); + scoreModelPanel.add(modelNames); /* * score model parameters @@ -187,53 +232,53 @@ public class CalculationChooser extends JPanel /* * OK / Cancel buttons */ - JButton ok = new JButton(MessageManager.getString("action.ok")); - 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.cancel")); - 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); - this.add(treeChoicePanel); - this.add(scoreModelPanel); + this.add(calcChoicePanel, BorderLayout.CENTER); + calcChoicePanel.add(scoreModelPanel); if (includeParams) { - this.add(paramsPanel); + scoreModelPanel.add(paramsPanel); } - this.add(actionPanel); + this.add(actionPanel, BorderLayout.SOUTH); int width = 350; - int height = includeParams ? 400 : 220; + int height = includeParams ? 420 : 240; + + setMinimumSize(new Dimension(325, height - 10)); String title = MessageManager.getString("label.choose_calculation"); if (af.getViewport().viewName != null) { title = title + " (" + af.getViewport().viewName + ")"; } - Desktop.addInternalFrame(frame, - title, width, - height, false); - + Desktop.addInternalFrame(frame, title, width, height, false); + calcChoicePanel.doLayout(); + revalidate(); /* * null the AlignmentPanel's reference to the dialog when it is closed */ @@ -250,6 +295,80 @@ public class CalculationChooser extends JPanel } /** + * 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 @@ -257,86 +376,150 @@ 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(); + final JComboBox scoreModelsCombo = new JComboBox<>(); + 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); } /** - * Open and calculate the selected tree on 'OK' + * 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 void ok_actionPerformed() + 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() { boolean doPCA = pca.isSelected(); - ScoreModelI sm = ScoreModels.getInstance().forName( - modelNames.getSelectedItem().toString()); + String modelName = modelNames.getSelectedItem().toString(); SimilarityParamsI params = getSimilarityParameters(doPCA); if (doPCA) { - openPcaPanel(sm, params); + openPcaPanel(modelName, params); } else { - openTreePanel(sm, params); + openTreePanel(modelName, params); } // closeFrame(); @@ -345,41 +528,63 @@ public class CalculationChooser extends JPanel /** * Open a new Tree panel on the desktop * - * @param sm + * @param modelName * @param params */ - protected void openTreePanel(ScoreModelI sm, SimilarityParamsI params) + protected void openTreePanel(String modelName, SimilarityParamsI params) { - String treeType = neighbourJoining.isSelected() ? TreeBuilder.NEIGHBOUR_JOINING + /* + * 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; + } + + String treeType = neighbourJoining.isSelected() + ? TreeBuilder.NEIGHBOUR_JOINING : TreeBuilder.AVERAGE_DISTANCE; - af.newTreePanel(treeType, sm, params); + af.newTreePanel(treeType, modelName, params); } /** * Open a new PCA panel on the desktop * - * @param sm + * @param modelName * @param params */ - protected void openPcaPanel(ScoreModelI sm, SimilarityParamsI params) + protected void openPcaPanel(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)) + && (viewport.getSelectionGroup().getSize() < MIN_PCA_SELECTION) + && (viewport.getSelectionGroup().getSize() > 0)) + || (viewport.getAlignment().getHeight() < MIN_PCA_SELECTION)) { - JvOptionPane - .showInternalMessageDialog( - this, - MessageManager - .getString("label.principal_component_analysis_must_take_least_four_input_sequences"), - MessageManager - .getString("label.sequence_selection_insufficient"), - JvOptionPane.WARNING_MESSAGE); + 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, sm, params); + pcaPanel = new PCAPanel(af.alignPanel, modelName, params); } /** @@ -421,15 +626,14 @@ 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 { @@ -438,4 +642,9 @@ public class CalculationChooser extends JPanel { } } + + public PCAPanel getPcaPanel() + { + return pcaPanel; + } }