X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCalculationChooser.java;h=183419e7c2768cdd862c9ab5ffca284b466718ec;hb=7e82e1fed011077e5cd4cc40ac8ad3519d7c47a8;hp=05f1fbad3e8602308369f1a2ae00e7ef277cd6db;hpb=2a35abbd49049cce7f7bb1abb0543e444e72485c;p=jalview.git diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java index 05f1fba..183419e 100644 --- a/src/jalview/gui/CalculationChooser.java +++ b/src/jalview/gui/CalculationChooser.java @@ -25,6 +25,7 @@ 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; @@ -74,6 +75,10 @@ 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; @@ -84,7 +89,7 @@ public class CalculationChooser extends JPanel JComboBox modelNames; - JButton ok; + JButton calculate; private JInternalFrame frame; @@ -96,6 +101,15 @@ 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 * @@ -143,6 +157,7 @@ public class CalculationChooser extends JPanel 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); @@ -154,20 +169,19 @@ 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); @@ -177,7 +191,7 @@ public class CalculationChooser extends JPanel calcTypes.add(pca); calcTypes.add(neighbourJoining); calcTypes.add(averageDistance); - + ActionListener calcChanged = new ActionListener() { @Override @@ -189,6 +203,7 @@ public class CalculationChooser extends JPanel pca.addActionListener(calcChanged); neighbourJoining.addActionListener(calcChanged); averageDistance.addActionListener(calcChanged); + /* * score models drop-down - with added tooltips! */ @@ -216,30 +231,30 @@ public class CalculationChooser extends JPanel /* * 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); @@ -255,14 +270,12 @@ 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(); /* @@ -290,18 +303,27 @@ public class CalculationChooser extends JPanel { size = af.getViewport().getSelectionGroup().getSize(); } - if (!(checkEnabled(pca, size, 4) - | checkEnabled(neighbourJoining, size, 3) | checkEnabled( - averageDistance, size, 3))) + + /* + * 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) { - ok.setToolTipText(null); - ok.setEnabled(true); + calculate.setToolTipText(null); + calculate.setEnabled(true); } else { - ok.setEnabled(false); + calculate.setEnabled(false); } - updateScoreModels(comboBox, tips); + updateScoreModels(modelNames, tips); } /** @@ -314,12 +336,12 @@ public class CalculationChooser extends JPanel * - size of input to calculation * @param minsize * - minimum size for calculation - * @return true if size < minsize *and* calc.isSelected + * @return true if size >= minsize and calc.isSelected */ private boolean checkEnabled(JRadioButton calc, int size, int minsize) { - String ttip = MessageManager.formatMessage( - "label.you_need_more_than_n_sequences", minsize); + String ttip = MessageManager + .formatMessage("label.you_need_at_least_n_sequences", minsize); calc.setEnabled(size >= minsize); if (!calc.isEnabled()) @@ -333,22 +355,18 @@ public class CalculationChooser extends JPanel if (calc.isSelected()) { modelNames.setEnabled(calc.isEnabled()); - if (!calc.isEnabled()) + if (calc.isEnabled()) { - ok.setEnabled(false); - ok.setToolTipText(ttip); return true; } + else + { + calculate.setToolTipText(ttip); + } } return false; } - final JComboBox comboBox = new JComboBox(); - - final ComboBoxTooltipRenderer renderer = new ComboBoxTooltipRenderer(); - - List tips = new ArrayList(); - /** * A rather elaborate helper method (blame Swing, not me) that builds a * drop-down list of score models (by name) with descriptions as tooltips. @@ -357,7 +375,8 @@ public class CalculationChooser extends JPanel */ protected JComboBox buildModelOptionsList() { - comboBox.setRenderer(renderer); + final JComboBox scoreModelsCombo = new JComboBox(); + scoreModelsCombo.setRenderer(renderer); /* * show tooltip on mouse over the combobox @@ -369,35 +388,37 @@ public class CalculationChooser extends JPanel @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(comboBox, tips); + updateScoreModels(scoreModelsCombo, tips); /* * set the list of tooltips on the combobox's renderer */ renderer.setTooltips(tips); - return comboBox; + return scoreModelsCombo; } - private void updateScoreModels(JComboBox comboBox, List tips) + private void updateScoreModels(JComboBox comboBox, + List toolTips) { Object curSel = comboBox.getSelectedItem(); - tips.clear(); - DefaultComboBoxModel model = new DefaultComboBoxModel(); + toolTips.clear(); + DefaultComboBoxModel model = new DefaultComboBoxModel(); /* * now we can actually add entries to the combobox, @@ -427,7 +448,7 @@ public class CalculationChooser extends JPanel tooltip = MessageManager.getStringOrReturn("label.score_model_", sm.getName()); } - tips.add(tooltip); + toolTips.add(tooltip); } } if (selectedIsPresent) @@ -441,7 +462,7 @@ public class CalculationChooser extends JPanel /** * 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(); @@ -467,7 +488,25 @@ public class CalculationChooser extends JPanel */ 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, modelName, params); } @@ -481,22 +520,26 @@ public class CalculationChooser extends JPanel 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, modelName, params); + pcaPanel = new PCAPanel(af.alignPanel, modelName, params); } /** @@ -538,15 +581,14 @@ 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 { @@ -555,4 +597,9 @@ public class CalculationChooser extends JPanel { } } + + public PCAPanel getPcaPanel() + { + return pcaPanel; + } }