X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FFeatureEditor.java;fp=src%2Fjalview%2Fgui%2FFeatureEditor.java;h=d547c5882bc4e61f23da6733a9da3676713efd72;hb=4f30214e8098748469c6a4269ac2ed6c5750e4b0;hp=0000000000000000000000000000000000000000;hpb=9dabc02511e3a334a5749a504f57f69d6c9017bd;p=jalview.git diff --git a/src/jalview/gui/FeatureEditor.java b/src/jalview/gui/FeatureEditor.java new file mode 100644 index 0000000..d547c58 --- /dev/null +++ b/src/jalview/gui/FeatureEditor.java @@ -0,0 +1,717 @@ +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.getDesktop(), + 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(Desktop.desktop) + .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; + + 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() + { + 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(); + + 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; + } + +}