/* * 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.api.FeatureColourI; import jalview.datamodel.SearchResults; import jalview.datamodel.SearchResultsI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.gui.JalviewColourChooser.ColourChooserListener; import jalview.io.FeaturesFile; import jalview.schemes.FeatureColour; import jalview.util.ColorUtils; import jalview.util.MessageManager; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; import java.awt.Font; import java.awt.GridLayout; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.util.ArrayList; import java.util.List; import javax.swing.JComboBox; import javax.swing.JLabel; import javax.swing.JPanel; import javax.swing.JScrollPane; import javax.swing.JSpinner; import javax.swing.JTextArea; import javax.swing.JTextField; import javax.swing.SpinnerNumberModel; import javax.swing.SwingConstants; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import javax.swing.event.DocumentEvent; import javax.swing.event.DocumentListener; /** * Provides a dialog allowing the user to add new features, or amend or delete * existing features */ public class FeatureEditor { /* * defaults for creating a new feature are the last created * feature type and group */ static String lastFeatureAdded = "feature_1"; static String lastFeatureGroupAdded = "Jalview"; /* * the sequence(s) with features to be created / amended */ final List sequences; /* * the features (or template features) to be created / amended */ final List features; /* * true if the dialog is to create a new feature, false if * for amend or delete of existing feature(s) */ final boolean forCreate; /* * index into the list of features */ int featureIndex; FeatureColourI oldColour; FeatureColourI featureColour; FeatureRenderer fr; AlignmentPanel ap; JTextField name; JTextField group; JTextArea description; JSpinner start; JSpinner end; JPanel mainPanel; /** * Constructor * * @param alignPanel * @param seqs * @param feats * @param create * if true create a new feature, else amend or delete an existing * feature */ public FeatureEditor(AlignmentPanel alignPanel, List seqs, List feats, boolean create) { ap = alignPanel; fr = alignPanel.getSeqPanel().seqCanvas.fr; sequences = seqs; features = feats; this.forCreate = create; init(); } /** * Initialise the layout and controls */ protected void init() { featureIndex = 0; mainPanel = new JPanel(new BorderLayout()); name = new JTextField(25); name.getDocument().addDocumentListener(new DocumentListener() { @Override public void insertUpdate(DocumentEvent e) { warnIfTypeHidden(mainPanel, name.getText()); } @Override public void removeUpdate(DocumentEvent e) { warnIfTypeHidden(mainPanel, name.getText()); } @Override public void changedUpdate(DocumentEvent e) { warnIfTypeHidden(mainPanel, name.getText()); } }); group = new JTextField(25); group.getDocument().addDocumentListener(new DocumentListener() { @Override public void insertUpdate(DocumentEvent e) { warnIfGroupHidden(mainPanel, group.getText()); } @Override public void removeUpdate(DocumentEvent e) { warnIfGroupHidden(mainPanel, group.getText()); } @Override public void changedUpdate(DocumentEvent e) { warnIfGroupHidden(mainPanel, group.getText()); } }); description = new JTextArea(3, 25); start = new JSpinner(); end = new JSpinner(); start.setPreferredSize(new Dimension(80, 20)); end.setPreferredSize(new Dimension(80, 20)); /* * ensure that start can never be more than end */ start.addChangeListener(new ChangeListener() { @Override public void stateChanged(ChangeEvent e) { Integer startVal = (Integer) start.getValue(); ((SpinnerNumberModel) end.getModel()).setMinimum(startVal); } }); end.addChangeListener(new ChangeListener() { @Override public void stateChanged(ChangeEvent e) { Integer endVal = (Integer) end.getValue(); ((SpinnerNumberModel) start.getModel()).setMaximum(endVal); } }); final JLabel colour = new JLabel(); colour.setOpaque(true); colour.setMaximumSize(new Dimension(30, 16)); colour.addMouseListener(new MouseAdapter() { @Override public void mousePressed(MouseEvent evt) { if (featureColour.isSimpleColour()) { /* * open colour chooser on click in colour panel */ String title = MessageManager .getString("label.select_feature_colour"); ColourChooserListener listener = new ColourChooserListener() { @Override public void colourSelected(Color c) { featureColour = new FeatureColour(c); updateColourButton(mainPanel, colour, featureColour); }; }; JalviewColourChooser.showColourChooser(Desktop.getDesktopPane(), title, featureColour.getColour(), listener); } else { /* * variable colour dialog - on OK, refetch the updated * feature colour and update this display */ final String ft = features.get(featureIndex).getType(); final String type = ft == null ? lastFeatureAdded : ft; FeatureTypeSettings fcc = new FeatureTypeSettings(fr, type); fcc.setRequestFocusEnabled(true); fcc.requestFocus(); fcc.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { featureColour = fr.getFeatureStyle(ft); fr.setColour(type, featureColour); updateColourButton(mainPanel, colour, featureColour); } }); } } }); JPanel gridPanel = new JPanel(new GridLayout(3, 1)); if (!forCreate && features.size() > 1) { /* * more than one feature at selected position - * add a drop-down to choose the feature to amend * space pad text if necessary to make entries distinct */ gridPanel = new JPanel(new GridLayout(4, 1)); JPanel choosePanel = new JPanel(); choosePanel.add(new JLabel( MessageManager.getString("label.select_feature") + ":")); final JComboBox overlaps = new JComboBox<>(); List added = new ArrayList<>(); for (SequenceFeature sf : features) { String text = String.format("%s/%d-%d (%s)", sf.getType(), sf.getBegin(), sf.getEnd(), sf.getFeatureGroup()); while (added.contains(text)) { text += " "; } overlaps.addItem(text); added.add(text); } choosePanel.add(overlaps); overlaps.addItemListener(new ItemListener() { @Override public void itemStateChanged(ItemEvent e) { int index = overlaps.getSelectedIndex(); if (index != -1) { featureIndex = index; SequenceFeature sf = features.get(index); name.setText(sf.getType()); description.setText(sf.getDescription()); group.setText(sf.getFeatureGroup()); start.setValue(new Integer(sf.getBegin())); end.setValue(new Integer(sf.getEnd())); ((SpinnerNumberModel) start.getModel()).setMaximum(sf.getEnd()); ((SpinnerNumberModel) end.getModel()).setMinimum(sf.getBegin()); SearchResultsI highlight = new SearchResults(); highlight.addResult(sequences.get(0), sf.getBegin(), sf.getEnd()); ap.getSeqPanel().seqCanvas.highlightSearchResults(highlight); } FeatureColourI col = fr.getFeatureStyle(name.getText()); if (col == null) { col = new FeatureColour( ColorUtils.createColourFromName(name.getText())); } oldColour = featureColour = col; updateColourButton(mainPanel, colour, col); } }); gridPanel.add(choosePanel); } JPanel namePanel = new JPanel(); gridPanel.add(namePanel); namePanel.add(new JLabel(MessageManager.getString("label.name:"), JLabel.RIGHT)); namePanel.add(name); JPanel groupPanel = new JPanel(); gridPanel.add(groupPanel); groupPanel.add(new JLabel(MessageManager.getString("label.group:"), JLabel.RIGHT)); groupPanel.add(group); JPanel colourPanel = new JPanel(); gridPanel.add(colourPanel); colourPanel.add(new JLabel(MessageManager.getString("label.colour"), JLabel.RIGHT)); colourPanel.add(colour); colour.setPreferredSize(new Dimension(150, 15)); colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9)); colour.setForeground(Color.black); colour.setHorizontalAlignment(SwingConstants.CENTER); colour.setVerticalAlignment(SwingConstants.CENTER); colour.setHorizontalTextPosition(SwingConstants.CENTER); colour.setVerticalTextPosition(SwingConstants.CENTER); mainPanel.add(gridPanel, BorderLayout.NORTH); JPanel descriptionPanel = new JPanel(); descriptionPanel.add(new JLabel( MessageManager.getString("label.description:"), JLabel.RIGHT)); description.setFont(JvSwingUtils.getTextAreaFont()); description.setLineWrap(true); descriptionPanel.add(new JScrollPane(description)); if (!forCreate) { mainPanel.add(descriptionPanel, BorderLayout.SOUTH); JPanel startEndPanel = new JPanel(); startEndPanel.add(new JLabel(MessageManager.getString("label.start"), JLabel.RIGHT)); startEndPanel.add(start); startEndPanel.add(new JLabel(MessageManager.getString("label.end"), JLabel.RIGHT)); startEndPanel.add(end); mainPanel.add(startEndPanel, BorderLayout.CENTER); } else { mainPanel.add(descriptionPanel, BorderLayout.CENTER); } /* * default feature type and group to that of the first feature supplied, * or to the last feature created if not supplied (null value) */ SequenceFeature firstFeature = features.get(0); boolean useLastDefaults = firstFeature.getType() == null; final String featureType = useLastDefaults ? lastFeatureAdded : firstFeature.getType(); final String featureGroup = useLastDefaults ? lastFeatureGroupAdded : firstFeature.getFeatureGroup(); name.setText(featureType); group.setText(featureGroup); start.setValue(new Integer(firstFeature.getBegin())); end.setValue(new Integer(firstFeature.getEnd())); ((SpinnerNumberModel) start.getModel()).setMaximum(firstFeature.getEnd()); ((SpinnerNumberModel) end.getModel()).setMinimum(firstFeature.getBegin()); description.setText(firstFeature.getDescription()); featureColour = fr.getFeatureStyle(featureType); oldColour = featureColour; updateColourButton(mainPanel, colour, oldColour); } /** * Presents a dialog allowing the user to add new features, or amend or delete * an existing feature. Currently this can be on *
    *
  • double-click on a sequence - Amend/Delete a selected feature at the * position
  • *
  • Create sequence feature(s) from pop-up menu on selected region
  • *
  • Create features for pattern matches from Find
  • *
* If the supplied feature type is null, show (and update on confirm) the type * and group of the last new feature created (with initial defaults of * "feature_1" and "Jalview"). */ public void showDialog() { Runnable okAction = forCreate ? getCreateAction() : getAmendAction(); Runnable cancelAction = getCancelAction(); /* * set dialog action handlers for OK (create/Amend) and Cancel options * also for Delete if applicable (when amending features) */ JvOptionPane dialog = JvOptionPane.newOptionDialog(ap.alignFrame) .setResponseHandler(0, okAction) .setResponseHandler(2, cancelAction); if (!forCreate) { dialog.setResponseHandler(1, getDeleteAction()); } String title = null; Object[] options = null; if (forCreate) { title = MessageManager .getString("label.create_new_sequence_features"); options = new Object[] { MessageManager.getString("action.ok"), MessageManager.getString("action.cancel") }; } else { title = MessageManager.formatMessage("label.amend_delete_features", new String[] { sequences.get(0).getName() }); options = new Object[] { MessageManager.getString("label.amend"), MessageManager.getString("action.delete"), MessageManager.getString("action.cancel") }; } dialog.showInternalDialog(mainPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION, JvOptionPane.PLAIN_MESSAGE, null, options, MessageManager.getString("action.ok")); } /** * Answers an action to run on Cancel in the dialog. This is just to remove * any feature highlighting from the display. Changes in the dialog are not * applied until it is dismissed with OK, Amend or Delete, so there are no * updates to reset on Cancel. * * @return */ protected Runnable getCancelAction() { Runnable okAction = new Runnable() { @Override public void run() { ap.highlightSearchResults(null); ap.paintAlignment(false, false); } }; return okAction; } /** * Returns the action to be run on OK in the dialog when creating one or more * sequence features. Note these may have a pre-supplied feature type (such as * a Find pattern), or none, in which case the feature type and group default * to those last added through this dialog. The action includes refreshing the * Feature Settings panel (if it is open), to show any new feature type, or * amended colour for an existing type. * * @return */ protected Runnable getCreateAction() { Runnable okAction = new Runnable() { boolean useLastDefaults = features.get(0).getType() == null; @Override public void run() { final String enteredType = name.getText().trim(); final String enteredGroup = group.getText().trim(); final String enteredDescription = description.getText() .replaceAll("\n", " "); if (enteredType.length() > 0) { /* * update default values only if creating using default values */ if (useLastDefaults) { lastFeatureAdded = enteredType; lastFeatureGroupAdded = enteredGroup; // TODO: determine if the null feature group is valid if (lastFeatureGroupAdded.length() < 1) { lastFeatureGroupAdded = null; } } } if (enteredType.length() > 0) { for (int i = 0; i < sequences.size(); i++) { SequenceFeature sf = features.get(i); SequenceFeature sf2 = new SequenceFeature(enteredType, enteredDescription, sf.getBegin(), sf.getEnd(), enteredGroup); new FeaturesFile().parseDescriptionHTML(sf2, false); sequences.get(i).addSequenceFeature(sf2); } fr.setColour(enteredType, featureColour); fr.featuresAdded(); repaintPanel(); } } }; return okAction; } /** * Answers the action to run on Delete in the dialog. Note this includes * refreshing the Feature Settings (if open) in case the only instance of a * feature type or group has been deleted. * * @return */ protected Runnable getDeleteAction() { Runnable deleteAction = new Runnable() { @Override public void run() { SequenceFeature sf = features.get(featureIndex); sequences.get(0).getDatasetSequence().deleteFeature(sf); fr.featuresAdded(); ap.getSeqPanel().seqCanvas.highlightSearchResults(null); ap.paintAlignment(true, true); } }; return deleteAction; } /** * update the amend feature button dependent on the given style * * @param bigPanel * @param col * @param col */ protected void updateColourButton(JPanel bigPanel, JLabel colour, FeatureColourI col) { colour.removeAll(); colour.setIcon(null); colour.setText(""); if (col.isSimpleColour()) { colour.setToolTipText(null); colour.setBackground(col.getColour()); } else { colour.setBackground(bigPanel.getBackground()); colour.setForeground(Color.black); colour.setToolTipText(FeatureSettings.getColorTooltip(col, false)); FeatureSettings.renderGraduatedColor(colour, col); } } /** * Show a warning message if the entered group is one that is currently hidden * * @param panel * @param group */ protected void warnIfGroupHidden(JPanel panel, String group) { if (!fr.isGroupVisible(group)) { String msg = MessageManager.formatMessage("label.warning_hidden", MessageManager.getString("label.group"), group); JvOptionPane.showMessageDialog(panel, msg, "", JvOptionPane.OK_OPTION); } } /** * Show a warning message if the entered type is one that is currently hidden * * @param panel * @param type */ protected void warnIfTypeHidden(JPanel panel, String type) { if (fr.getRenderOrder().contains(type)) { if (!fr.showFeatureOfType(type)) { String msg = MessageManager.formatMessage("label.warning_hidden", MessageManager.getString("label.feature_type"), type); JvOptionPane.showMessageDialog(panel, msg, "", JvOptionPane.OK_OPTION); } } } /** * On closing the dialog - ensure feature display is turned on, to show any * new features - remove highlighting of the last selected feature - repaint * the panel to show any changes */ protected void repaintPanel() { ap.alignFrame.showSeqFeatures.setSelected(true); ap.av.setShowSequenceFeatures(true); ap.av.setSearchResults(null); ap.paintAlignment(true, true); } /** * Returns the action to be run on OK in the dialog when amending a feature. * Note this may include refreshing the Feature Settings panel (if it is * open), if feature type, group or colour has changed (but not for * description or extent). * * @return */ protected Runnable getAmendAction() { Runnable okAction = new Runnable() { boolean useLastDefaults = features.get(0).getType() == null; String featureType = name.getText(); String featureGroup = group.getText(); @Override public void run() { final String enteredType = name.getText().trim(); final String enteredGroup = group.getText().trim(); final String enteredDescription = description.getText() .replaceAll("\n", " "); if (enteredType.length() > 0) { /* * update default values only if creating using default values */ if (useLastDefaults) { lastFeatureAdded = enteredType; lastFeatureGroupAdded = enteredGroup; // TODO: determine if the null feature group is valid if (lastFeatureGroupAdded.length() < 1) { lastFeatureGroupAdded = null; } } } SequenceFeature sf = features.get(featureIndex); /* * Need to refresh Feature Settings if type, group or colour changed; * note we don't force the feature to be visible - the user has been * warned if a hidden feature type or group was entered */ boolean refreshSettings = (!featureType.equals(enteredType) || !featureGroup.equals(enteredGroup)); refreshSettings |= (featureColour != oldColour); fr.setColour(enteredType, featureColour); int newBegin = sf.begin; int newEnd = sf.end; try { newBegin = ((Integer) start.getValue()).intValue(); newEnd = ((Integer) end.getValue()).intValue(); } catch (NumberFormatException ex) { // JSpinner doesn't accept invalid format data :-) } /* * 'amend' the feature by deleting it and adding a new one * (to ensure integrity of SequenceFeatures data store) * note this dialog only updates one sequence at a time */ sequences.get(0).deleteFeature(sf); SequenceFeature newSf = new SequenceFeature(sf, enteredType, newBegin, newEnd, enteredGroup, sf.getScore()); newSf.setDescription(enteredDescription); new FeaturesFile().parseDescriptionHTML(newSf, false); sequences.get(0).addSequenceFeature(newSf); if (refreshSettings) { fr.featuresAdded(); } repaintPanel(); } }; return okAction; } }