--- /dev/null
+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<SequenceI> sequences;
+
+ /*
+ * the features (or template features) to be created / amended
+ */
+ final List<SequenceFeature> 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<SequenceI> seqs,
+ List<SequenceFeature> 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<String> overlaps = new JComboBox<>();
+ List<String> 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
+ * <ul>
+ * <li>double-click on a sequence - Amend/Delete a selected feature at the
+ * position</li>
+ * <li>Create sequence feature(s) from pop-up menu on selected region</li>
+ * <li>Create features for pattern matches from Find</li>
+ * </ul>
+ * 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;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff