+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * 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 jalview.util.dialogrunner.RunResponse;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
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;
+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;
+
/**
* Provides a dialog allowing the user to add new features, or amend or delete
* existing features
static String lastFeatureGroupAdded = "Jalview";
/*
- * index into a list of features if more than one selected for editing
+ * 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;
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)
+ 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();
}
/**
- * Presents a dialog allowing the user to add new features, or amend or delete
- * existing features. Currently this can be on
- * <ul>
- * <li>double-click on a sequence - Amend/Delete features at position</li>
- * <li>Create sequence feature 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").
- *
- * @param sequences
- * the sequences features are to be created on (if creating
- * features), or a single sequence (if amending features)
- * @param features
- * the current features at the position (if amending), or template
- * new feature(s) with start/end position set (if creating)
- * @param create
- * true to create features, false to amend or delete
- * @param alignPanel
- * @param responseHandler
- * boolean true RunResponse is run if features are created
+ * Initialise the layout and controls
*/
- public boolean amendFeatures(final List<SequenceI> sequences,
- final List<SequenceFeature> features, boolean create,
- final Runnable responseHandler)
+ protected void init()
{
featureIndex = 0;
-
- final JPanel mainPanel = new JPanel(new BorderLayout());
-
- final JTextField name = new JTextField(25);
+
+ mainPanel = new JPanel(new BorderLayout());
+
+ name = new JTextField(25);
name.getDocument().addDocumentListener(new DocumentListener()
{
@Override
{
warnIfTypeHidden(mainPanel, name.getText());
}
-
+
@Override
public void removeUpdate(DocumentEvent e)
{
warnIfTypeHidden(mainPanel, name.getText());
}
-
+
@Override
public void changedUpdate(DocumentEvent e)
{
warnIfTypeHidden(mainPanel, name.getText());
}
});
-
- final JTextField group = new JTextField(25);
+
+ group = new JTextField(25);
group.getDocument().addDocumentListener(new DocumentListener()
{
@Override
{
warnIfGroupHidden(mainPanel, group.getText());
}
-
+
@Override
public void removeUpdate(DocumentEvent e)
{
warnIfGroupHidden(mainPanel, group.getText());
}
-
+
@Override
public void changedUpdate(DocumentEvent e)
{
warnIfGroupHidden(mainPanel, group.getText());
}
});
-
- final JTextArea description = new JTextArea(3, 25);
- final JSpinner start = new JSpinner();
- final JSpinner end = new JSpinner();
+
+ 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.setBorder(BorderFactory.createEtchedBorder());
colour.setMaximumSize(new Dimension(30, 16));
colour.addMouseListener(new MouseAdapter()
{
- /*
- * open colour chooser on click in colour panel
- */
@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()
*/
final String ft = features.get(featureIndex).getType();
final String type = ft == null ? lastFeatureAdded : ft;
- FeatureTypeSettings fcc = new FeatureTypeSettings(
- fr, type);
+ FeatureTypeSettings fcc = new FeatureTypeSettings(fr, type);
fcc.setRequestFocusEnabled(true);
fcc.requestFocus();
fcc.addActionListener(new ActionListener()
}
});
JPanel gridPanel = new JPanel(new GridLayout(3, 1));
-
- if (!create && features.size() > 1)
+
+ if (!forCreate && features.size() > 1)
{
/*
* more than one feature at selected position -
added.add(text);
}
choosePanel.add(overlaps);
-
+
overlaps.addItemListener(new ItemListener()
{
@Override
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, false);
+
+ ap.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
}
FeatureColourI col = fr.getFeatureStyle(name.getText());
if (col == null)
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"),
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 (!create)
+
+ if (!forCreate)
{
mainPanel.add(descriptionPanel, BorderLayout.SOUTH);
-
+
JPanel startEndPanel = new JPanel();
startEndPanel.add(new JLabel(MessageManager.getString("label.start"),
JLabel.RIGHT));
{
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)
: 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);
- Object[] options;
- if (!create)
+ }
+
+ /**
+ * 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(ap.alignFrame)
+ .setResponseHandler(0, okAction)
+ .setResponseHandler(2, cancelAction);
+ if (!forCreate)
{
- options = new Object[] { MessageManager.getString("label.amend"),
- MessageManager.getString("action.delete"),
+ 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
{
- options = new Object[] { MessageManager.getString("action.ok"),
+ 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") };
}
-
- String title = create
- ? MessageManager.getString("label.create_new_sequence_features")
- : MessageManager.formatMessage("label.amend_delete_features",
- new String[]
- { sequences.get(0).getName() });
-
- /*
- * register responses and show the dialog
- */
- JvOptionPane.newOptionDialog(Desktop.desktop).response(
-
- new RunResponse(JvOptionPane.OK_OPTION)
- {
- 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 (create)
- {
- // NEW FEATURES ADDED
- 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();
-
- responseHandler.run();
- }
- } else {
- SequenceFeature sf = features.get(featureIndex);
- /*
- * Feature amended - YES_OPTION corresponds to the Amend button
- * 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 :-)
- }
-
- /*
- * replace the feature by deleting it and adding a new one
- * (to ensure integrity of SequenceFeatures data store)
- */
- sequences.get(0).deleteFeature(sf);
- SequenceFeature newSf = new SequenceFeature(sf, enteredType,
- newBegin, newEnd, enteredGroup, sf.getScore());
- newSf.setDescription(enteredDescription);
- new FeaturesFile().parseDescriptionHTML(newSf, false);
- // amend features dialog only updates one sequence at a time
- sequences.get(0).addSequenceFeature(newSf);
-
- if (refreshSettings)
- {
- fr.featuresAdded();
- }
- }
- ap.getSeqPanel().seqCanvas.highlightSearchResults(null,
- false);
- ap.paintAlignment(true, true);
- }
- }).response(new RunResponse(JvOptionPane.NO_OPTION)
- {
- public void run()
- {
- SequenceFeature sf = features.get(featureIndex);
- /*
- * NO_OPTION corresponds to the Delete button
- */
- sequences.get(0).getDatasetSequence().deleteFeature(sf);
- // update Feature Settings for removal of feature / group
- fr.featuresAdded();
- ap.getSeqPanel().seqCanvas.highlightSearchResults(null,
- false);
- ap.paintAlignment(true, true);
- }
- }).defaultResponse(new Runnable()
+
+ 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)
{
- public void run()
- {
- ap.getSeqPanel().seqCanvas.highlightSearchResults(null,
- false);
- ap.paintAlignment(true, true);
- }
- }).showInternalDialog(mainPanel, title,
- JvOptionPane.YES_NO_CANCEL_OPTION,
- JvOptionPane.QUESTION_MESSAGE, null, options,
- MessageManager.getString("action.ok"));
- return true;
+ 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;
}
/**
{
colour.removeAll();
colour.setIcon(null);
- colour.setToolTipText(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);
}
}
}
}
+ /**
+ * 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;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff