X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCalculationChooser.java;fp=src%2Fjalview%2Fgui%2FCalculationChooser.java;h=a9f396634a63e9746e8ce405380ada7ec38b087e;hb=f063821ed0be9c1581af74643a1aa5798731af65;hp=0000000000000000000000000000000000000000;hpb=fd18e2c73cd015d4e38ad91da0e5d7532ff0ef42;p=jalview.git diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java new file mode 100644 index 0000000..a9f3966 --- /dev/null +++ b/src/jalview/gui/CalculationChooser.java @@ -0,0 +1,595 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +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; +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.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; +import javax.swing.JInternalFrame; +import javax.swing.JLabel; +import javax.swing.JLayeredPane; +import javax.swing.JPanel; +import javax.swing.JRadioButton; +import javax.swing.event.InternalFrameAdapter; +import javax.swing.event.InternalFrameEvent; + +/** + * A dialog where a user can choose and action Tree or PCA calculation options + */ +public class CalculationChooser extends JPanel +{ + /* + * flag for whether gap matches residue in the PID calculation for a Tree + * - true gives Jalview 2.10.1 behaviour + * - set to false (using Groovy) for a more correct tree + * (JAL-374) + */ + private static boolean treeMatchGaps = true; + + 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 neighbourJoining; + + JRadioButton averageDistance; + + JComboBox modelNames; + + JButton calculate; + + private JInternalFrame frame; + + private JCheckBox includeGaps; + + private JCheckBox matchGaps; + + private JCheckBox includeGappedColumns; + + private JCheckBox shorterSequence; + + final ComboBoxTooltipRenderer renderer = new ComboBoxTooltipRenderer(); + + List tips = new ArrayList(); + + /** + * Constructor + * + * @param af + */ + public CalculationChooser(AlignFrame alignFrame) + { + this.af = alignFrame; + init(); + af.alignPanel.setCalculationDialog(this); + } + + /** + * Lays out the panel and adds it to the desktop + */ + 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 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 + */ + 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")); + 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); + + treePanel.setBorder(BorderFactory + .createTitledBorder(MessageManager.getString("label.tree"))); + + // 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 actionPerformed(ActionEvent e) + { + validateCalcTypes(); + } + }; + 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.CENTER)); + scoreModelPanel.setOpaque(false); + scoreModelPanel.add(modelNames); + + /* + * score model parameters + */ + JPanel paramsPanel = new JPanel(new GridLayout(5, 1)); + paramsPanel.setOpaque(false); + includeGaps = new JCheckBox("Include gaps"); + matchGaps = new JCheckBox("Match gaps"); + includeGappedColumns = new JCheckBox("Include gapped columns"); + shorterSequence = new JCheckBox("Match on shorter sequence"); + paramsPanel.add(new JLabel("Pairwise sequence scoring options")); + paramsPanel.add(includeGaps); + paramsPanel.add(matchGaps); + paramsPanel.add(includeGappedColumns); + paramsPanel.add(shorterSequence); + + /* + * OK / Cancel buttons + */ + calculate = new JButton(MessageManager.getString("action.calculate")); + calculate.setFont(VERDANA_11PT); + calculate.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + calculate_actionPerformed(); + } + }); + 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) + { + close_actionPerformed(); + } + }); + JPanel actionPanel = new JPanel(); + actionPanel.setOpaque(false); + actionPanel.add(calculate); + actionPanel.add(close); + + boolean includeParams = false; + this.add(calcChoicePanel, BorderLayout.CENTER); + calcChoicePanel.add(scoreModelPanel); + if (includeParams) + { + scoreModelPanel.add(paramsPanel); + } + this.add(actionPanel, BorderLayout.SOUTH); + + int width = 350; + 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); + calcChoicePanel.doLayout(); + revalidate(); + /* + * null the AlignmentPanel's reference to the dialog when it is closed + */ + frame.addInternalFrameListener(new InternalFrameAdapter() + { + @Override + public void internalFrameClosed(InternalFrameEvent evt) + { + af.alignPanel.setCalculationDialog(null); + }; + }); + + 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 + * over it (without opening the list). + */ + protected JComboBox buildModelOptionsList() + { + 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 + */ + final MouseAdapter mouseListener = new MouseAdapter() + { + @Override + public void mouseEntered(MouseEvent e) + { + scoreModelsCombo.setToolTipText( + tips.get(scoreModelsCombo.getSelectedIndex())); + } + + @Override + public void mouseExited(MouseEvent e) + { + scoreModelsCombo.setToolTipText(null); + } + }; + 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(); + + /* + * 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()) + { + 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) + { + tooltip = MessageManager.getStringOrReturn("label.score_model_", + sm.getName()); + } + toolTips.add(tooltip); + } + } + if (selectedIsPresent) + { + model.setSelectedItem(curSel); + } + // finally, update the model + comboBox.setModel(model); + } + + /** + * Open and calculate the selected tree or PCA on 'OK' + */ + protected void calculate_actionPerformed() + { + boolean doPCA = pca.isSelected(); + String modelName = modelNames.getSelectedItem().toString(); + SimilarityParamsI params = getSimilarityParameters(doPCA); + + if (doPCA) + { + openPcaPanel(modelName, params); + } + else + { + openTreePanel(modelName, params); + } + + // closeFrame(); + } + + /** + * Open a new Tree panel on the desktop + * + * @param modelName + * @param params + */ + protected void openTreePanel(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) + { + 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, modelName, params); + } + + /** + * Open a new PCA panel on the desktop + * + * @param modelName + * @param 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() < 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.WARNING_MESSAGE); + return; + } + new PCAPanel(af.alignPanel, modelName, params); + } + + /** + * + */ + protected void closeFrame() + { + try + { + frame.setClosed(true); + } catch (PropertyVetoException ex) + { + } + } + + /** + * Returns a data bean holding parameters for similarity (or distance) model + * calculation + * + * @param doPCA + * @return + */ + protected SimilarityParamsI getSimilarityParameters(boolean doPCA) + { + // commented out: parameter choices read from gui widgets + // SimilarityParamsI params = new SimilarityParams( + // includeGappedColumns.isSelected(), matchGaps.isSelected(), + // includeGaps.isSelected(), shorterSequence.isSelected()); + + boolean includeGapGap = true; + boolean includeGapResidue = true; + boolean matchOnShortestLength = false; + + /* + * 'matchGaps' flag is only used in the PID calculation + * - set to false for PCA so that PCA using PID reproduces SeqSpace PCA + * - set to true for Tree to reproduce Jalview 2.10.1 calculation + * - set to false for Tree for a more correct calculation (JAL-374) + */ + boolean matchGap = doPCA ? false : treeMatchGaps; + + return new SimilarityParams(includeGapGap, matchGap, includeGapResidue, + matchOnShortestLength); + } + + /** + * Closes dialog on Close button press + */ + protected void close_actionPerformed() + { + try + { + frame.setClosed(true); + } catch (Exception ex) + { + } + } +}