import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.io.FeaturesFile;
import jalview.schemes.FeatureColour;
-import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
import java.awt.event.MouseEvent;
import java.util.Arrays;
import java.util.Comparator;
+import java.util.List;
import javax.swing.JColorChooser;
import javax.swing.JComboBox;
import javax.swing.JLabel;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JSpinner;
import javax.swing.JTextArea;
import javax.swing.JTextField;
import javax.swing.SwingConstants;
+import javax.swing.event.DocumentEvent;
+import javax.swing.event.DocumentListener;
/**
* DOCUMENT ME!
* @version $Revision$
*/
public class FeatureRenderer extends
- jalview.renderer.seqfeatures.FeatureRenderer implements
- jalview.api.FeatureRenderer
+ jalview.renderer.seqfeatures.FeatureRenderer
{
+ /*
+ * defaults for creating a new feature are the last created
+ * feature type and group
+ */
+ static String lastFeatureAdded = "feature_1";
+
+ static String lastFeatureGroupAdded = "Jalview";
+
Color resBoxColour;
AlignmentPanel ap;
/**
- * Creates a new FeatureRenderer object.
+ * Creates a new FeatureRenderer object
*
- * @param av
- * DOCUMENT ME!
+ * @param alignPanel
*/
- public FeatureRenderer(AlignmentPanel ap)
+ public FeatureRenderer(AlignmentPanel alignPanel)
{
- super(ap.av);
- this.ap = ap;
- if (ap != null && ap.getSeqPanel() != null
- && ap.getSeqPanel().seqCanvas != null
- && ap.getSeqPanel().seqCanvas.fr != null)
+ super(alignPanel.av);
+ this.ap = alignPanel;
+ if (alignPanel.getSeqPanel() != null
+ && alignPanel.getSeqPanel().seqCanvas != null
+ && alignPanel.getSeqPanel().seqCanvas.fr != null)
{
- transferSettings(ap.getSeqPanel().seqCanvas.fr);
+ transferSettings(alignPanel.getSeqPanel().seqCanvas.fr);
}
}
- // // /////////////
- // // Feature Editing Dialog
- // // Will be refactored in next release.
-
- static String lastFeatureAdded;
-
- static String lastFeatureGroupAdded;
-
- static String lastDescriptionAdded;
-
FeatureColourI oldcol, fcol;
int featureIndex = 0;
- boolean amendFeatures(final SequenceI[] sequences,
- final SequenceFeature[] features, boolean newFeatures,
- final AlignmentPanel ap)
+ /**
+ * 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
+ * @return
+ */
+ protected boolean amendFeatures(final List<SequenceI> sequences,
+ final List<SequenceFeature> features, boolean create,
+ final AlignmentPanel alignPanel)
{
-
featureIndex = 0;
- final JPanel bigPanel = new JPanel(new BorderLayout());
- final JComboBox overlaps;
+ final JPanel mainPanel = new JPanel(new BorderLayout());
+
final JTextField name = new JTextField(25);
- final JTextField source = 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());
+ }
+ });
+
+ final JTextField 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());
+ }
+ });
+
final JTextArea description = new JTextArea(3, 25);
final JSpinner start = new JSpinner();
final JSpinner end = new JSpinner();
if (col != null)
{
fcol = new FeatureColour(col);
- updateColourButton(bigPanel, colour, new FeatureColour(col));
+ updateColourButton(mainPanel, colour, fcol);
}
}
else
{
if (fcc == null)
{
- final String type = features[featureIndex].getType();
+ final String ft = features.get(featureIndex).getType();
+ final String type = ft == null ? lastFeatureAdded : ft;
fcc = new FeatureColourChooser(me, type);
fcc.setRequestFocusEnabled(true);
fcc.requestFocus();
fcol = fcc.getLastColour();
fcc = null;
setColour(type, fcol);
- updateColourButton(bigPanel, colour, fcol);
+ updateColourButton(mainPanel, colour, fcol);
}
});
}
}
});
- JPanel tmp = new JPanel();
- JPanel panel = new JPanel(new GridLayout(3, 1));
+ JPanel gridPanel = new JPanel(new GridLayout(3, 1));
- // /////////////////////////////////////
- // /MULTIPLE FEATURES AT SELECTED RESIDUE
- if (!newFeatures && features.length > 1)
+ if (!create && features.size() > 1)
{
- panel = new JPanel(new GridLayout(4, 1));
- tmp = new JPanel();
- tmp.add(new JLabel(MessageManager.getString("label.select_feature")
+ /*
+ * more than one feature at selected position - add a drop-down
+ * to choose the feature to amend
+ */
+ gridPanel = new JPanel(new GridLayout(4, 1));
+ JPanel choosePanel = new JPanel();
+ choosePanel.add(new JLabel(MessageManager
+ .getString("label.select_feature")
+ ":"));
- overlaps = new JComboBox();
- for (int i = 0; i < features.length; i++)
+ final JComboBox<String> overlaps = new JComboBox<String>();
+ for (SequenceFeature sf : features)
{
- overlaps.addItem(features[i].getType() + "/"
- + features[i].getBegin() + "-" + features[i].getEnd()
- + " (" + features[i].getFeatureGroup() + ")");
+ String text = sf.getType() + "/" + sf.getBegin() + "-"
+ + sf.getEnd() + " (" + sf.getFeatureGroup() + ")";
+ overlaps.addItem(text);
}
-
- tmp.add(overlaps);
+ choosePanel.add(overlaps);
overlaps.addItemListener(new ItemListener()
{
if (index != -1)
{
featureIndex = index;
- name.setText(features[index].getType());
- description.setText(features[index].getDescription());
- source.setText(features[index].getFeatureGroup());
- start.setValue(new Integer(features[index].getBegin()));
- end.setValue(new Integer(features[index].getEnd()));
+ 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()));
SearchResultsI highlight = new SearchResults();
- highlight.addResult(sequences[0], features[index].getBegin(),
- features[index].getEnd());
+ highlight.addResult(sequences.get(0), sf.getBegin(),
+ sf.getEnd());
- ap.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
+ alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
}
FeatureColourI col = getFeatureStyle(name.getText());
if (col == null)
{
- col = new FeatureColour(UserColourScheme
+ col = new FeatureColour(ColorUtils
.createColourFromName(name.getText()));
}
oldcol = fcol = col;
- updateColourButton(bigPanel, colour, col);
+ updateColourButton(mainPanel, colour, col);
}
});
- panel.add(tmp);
+ gridPanel.add(choosePanel);
}
- // ////////
- // ////////////////////////////////////
- tmp = new JPanel();
- panel.add(tmp);
- tmp.add(new JLabel(MessageManager.getString("label.name:"),
+ JPanel namePanel = new JPanel();
+ gridPanel.add(namePanel);
+ namePanel.add(new JLabel(MessageManager.getString("label.name:"),
JLabel.RIGHT));
- tmp.add(name);
+ namePanel.add(name);
- tmp = new JPanel();
- panel.add(tmp);
- tmp.add(new JLabel(MessageManager.getString("label.group:"),
+ JPanel groupPanel = new JPanel();
+ gridPanel.add(groupPanel);
+ groupPanel.add(new JLabel(MessageManager.getString("label.group:"),
JLabel.RIGHT));
- tmp.add(source);
+ groupPanel.add(group);
- tmp = new JPanel();
- panel.add(tmp);
- tmp.add(new JLabel(MessageManager.getString("label.colour"),
+ JPanel colourPanel = new JPanel();
+ gridPanel.add(colourPanel);
+ colourPanel.add(new JLabel(MessageManager.getString("label.colour"),
JLabel.RIGHT));
- tmp.add(colour);
+ colourPanel.add(colour);
colour.setPreferredSize(new Dimension(150, 15));
colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
colour.setForeground(Color.black);
colour.setVerticalAlignment(SwingConstants.CENTER);
colour.setHorizontalTextPosition(SwingConstants.CENTER);
colour.setVerticalTextPosition(SwingConstants.CENTER);
- bigPanel.add(panel, BorderLayout.NORTH);
+ mainPanel.add(gridPanel, BorderLayout.NORTH);
- panel = new JPanel();
- panel.add(new JLabel(MessageManager.getString("label.description:"),
+ JPanel descriptionPanel = new JPanel();
+ descriptionPanel.add(new JLabel(MessageManager
+ .getString("label.description:"),
JLabel.RIGHT));
description.setFont(JvSwingUtils.getTextAreaFont());
description.setLineWrap(true);
- panel.add(new JScrollPane(description));
+ descriptionPanel.add(new JScrollPane(description));
- if (!newFeatures)
+ if (!create)
{
- bigPanel.add(panel, BorderLayout.SOUTH);
+ mainPanel.add(descriptionPanel, BorderLayout.SOUTH);
- panel = new JPanel();
- panel.add(new JLabel(MessageManager.getString("label.start"),
+ JPanel startEndPanel = new JPanel();
+ startEndPanel.add(new JLabel(MessageManager.getString("label.start"),
JLabel.RIGHT));
- panel.add(start);
- panel.add(new JLabel(MessageManager.getString("label.end"),
+ startEndPanel.add(start);
+ startEndPanel.add(new JLabel(MessageManager.getString("label.end"),
JLabel.RIGHT));
- panel.add(end);
- bigPanel.add(panel, BorderLayout.CENTER);
- }
- else
- {
- bigPanel.add(panel, BorderLayout.CENTER);
- }
-
- if (lastFeatureAdded == null)
- {
- if (features[0].type != null)
- {
- lastFeatureAdded = features[0].type;
- }
- else
- {
- lastFeatureAdded = "feature_1";
- }
- }
-
- if (lastFeatureGroupAdded == null)
- {
- if (features[0].featureGroup != null)
- {
- lastFeatureGroupAdded = features[0].featureGroup;
- }
- else
- {
- lastFeatureGroupAdded = "Jalview";
- }
- }
-
- if (newFeatures)
- {
- name.setText(lastFeatureAdded);
- source.setText(lastFeatureGroupAdded);
+ startEndPanel.add(end);
+ mainPanel.add(startEndPanel, BorderLayout.CENTER);
}
else
{
- name.setText(features[0].getType());
- source.setText(features[0].getFeatureGroup());
+ mainPanel.add(descriptionPanel, BorderLayout.CENTER);
}
- start.setValue(new Integer(features[0].getBegin()));
- end.setValue(new Integer(features[0].getEnd()));
- description.setText(features[0].getDescription());
- updateColourButton(bigPanel, colour,
- (oldcol = fcol = getFeatureStyle(name.getText())));
+ /*
+ * 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()));
+ description.setText(firstFeature.getDescription());
+ updateColourButton(mainPanel, colour,
+ (oldcol = fcol = getFeatureStyle(featureType)));
Object[] options;
- if (!newFeatures)
+ if (!create)
{
- options = new Object[] { "Amend", "Delete", "Cancel" };
+ options = new Object[] { MessageManager.getString("label.amend"),
+ MessageManager.getString("action.delete"),
+ MessageManager.getString("action.cancel") };
}
else
{
- options = new Object[] { "OK", "Cancel" };
+ options = new Object[] { MessageManager.getString("action.ok"),
+ MessageManager.getString("action.cancel") };
}
- String title = newFeatures ? MessageManager
+ String title = create ? MessageManager
.getString("label.create_new_sequence_features")
: MessageManager.formatMessage("label.amend_delete_features",
- new String[] { sequences[0].getName() });
+ new String[] { sequences.get(0).getName() });
+ /*
+ * show the dialog
+ */
int reply = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
- bigPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION,
+ mainPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION,
JvOptionPane.QUESTION_MESSAGE, null, options,
MessageManager.getString("action.ok"));
- jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
+ FeaturesFile ffile = new FeaturesFile();
- if (reply == JvOptionPane.OK_OPTION && name.getText().length() > 0)
+ final String enteredType = name.getText().trim();
+ final String enteredGroup = group.getText().trim();
+ final String enteredDescription = description.getText().replaceAll("\n", " ");
+
+ if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0)
{
- // This ensures that the last sequence
- // is refreshed and new features are rendered
- lastSeq = null;
- lastFeatureAdded = name.getText().trim();
- lastFeatureGroupAdded = source.getText().trim();
- lastDescriptionAdded = description.getText().replaceAll("\n", " ");
- // TODO: determine if the null feature group is valid
- if (lastFeatureGroupAdded.length() < 1)
+ /*
+ * update default values only if creating using default values
+ */
+ if (useLastDefaults)
{
- lastFeatureGroupAdded = null;
+ lastFeatureAdded = enteredType;
+ lastFeatureGroupAdded = enteredGroup;
+ // TODO: determine if the null feature group is valid
+ if (lastFeatureGroupAdded.length() < 1)
+ {
+ lastFeatureGroupAdded = null;
+ }
}
}
- if (!newFeatures)
+ if (!create)
{
- SequenceFeature sf = features[featureIndex];
+ SequenceFeature sf = features.get(featureIndex);
if (reply == JvOptionPane.NO_OPTION)
{
- sequences[0].getDatasetSequence().deleteFeature(sf);
+ /*
+ * NO_OPTION corresponds to the Delete button
+ */
+ sequences.get(0).getDatasetSequence().deleteFeature(sf);
+ // update Feature Settings for removal of feature / group
+ featuresAdded();
}
else if (reply == JvOptionPane.YES_OPTION)
{
- sf.type = lastFeatureAdded;
- sf.featureGroup = lastFeatureGroupAdded;
- sf.description = lastDescriptionAdded;
-
- setColour(sf.type, fcol);
- getFeaturesDisplayed().setVisible(sf.type);
-
+ /*
+ * 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 |= (fcol != oldcol);
+ setColour(enteredType, fcol);
+ int newBegin = sf.begin;
+ int newEnd = sf.end;
try
{
- sf.begin = ((Integer) start.getValue()).intValue();
- sf.end = ((Integer) end.getValue()).intValue();
+ newBegin = ((Integer) start.getValue()).intValue();
+ newEnd = ((Integer) end.getValue()).intValue();
} catch (NumberFormatException ex)
{
+ // JSpinner doesn't accept invalid format data :-)
}
- ffile.parseDescriptionHTML(sf, false);
+ /*
+ * 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, newBegin, newEnd,
+ enteredGroup, sf.getScore());
+ sf.setDescription(enteredDescription);
+ ffile.parseDescriptionHTML(newSf, false);
+ // amend features dialog only updates one sequence at a time
+ sequences.get(0).addSequenceFeature(newSf);
+
+ if (refreshSettings)
+ {
+ featuresAdded();
+ }
}
}
else
// NEW FEATURES ADDED
{
- if (reply == JvOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
+ if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0)
{
- for (int i = 0; i < sequences.length; i++)
+ for (int i = 0; i < sequences.size(); i++)
{
- features[i].type = lastFeatureAdded;
- // fix for JAL-1538 - always set feature group here
- features[i].featureGroup = lastFeatureGroupAdded;
- features[i].description = lastDescriptionAdded;
- sequences[i].addSequenceFeature(features[i]);
- ffile.parseDescriptionHTML(features[i], false);
+ SequenceFeature sf = features.get(i);
+ SequenceFeature sf2 = new SequenceFeature(enteredType,
+ enteredDescription, sf.getBegin(), sf.getEnd(),
+ enteredGroup);
+ ffile.parseDescriptionHTML(sf2, false);
+ sequences.get(i).addSequenceFeature(sf2);
}
- if (lastFeatureGroupAdded != null)
- {
- setGroupVisibility(lastFeatureGroupAdded, true);
- }
- setColour(lastFeatureAdded, fcol);
- setVisible(lastFeatureAdded);
+ setColour(enteredType, fcol);
- findAllFeatures(false);
+ featuresAdded();
- ap.paintAlignment(true);
+ alignPanel.paintAlignment(true);
return true;
}
}
}
- ap.paintAlignment(true);
+ alignPanel.paintAlignment(true);
return true;
}
/**
+ * 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 (getRenderOrder().contains(type))
+ {
+ if (!showFeatureOfType(type))
+ {
+ String msg = MessageManager.formatMessage("label.warning_hidden",
+ MessageManager.getString("label.feature_type"), type);
+ JvOptionPane.showMessageDialog(panel, msg, "",
+ JvOptionPane.OK_OPTION);
+ }
+ }
+ }
+
+ /**
+ * 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 (featureGroups.containsKey(group) && !featureGroups.get(group))
+ {
+ String msg = MessageManager.formatMessage("label.warning_hidden",
+ MessageManager.getString("label.group"), group);
+ JvOptionPane.showMessageDialog(panel, msg, "", JvOptionPane.OK_OPTION);
+ }
+ }
+
+ /**
* update the amend feature button dependent on the given style
*
* @param bigPanel
git://source.jalview.org / jalview.git / blobdiff