*/
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.schemes.GraduatedColor;
+import jalview.io.FeaturesFile;
+import jalview.schemes.FeatureColour;
+import jalview.util.ColorUtils;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
import java.awt.event.ItemListener;
import java.awt.event.MouseAdapter;
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;
* @author $author$
* @version $Revision$
*/
-public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRenderer implements jalview.api.FeatureRenderer
+public class FeatureRenderer extends
+ jalview.renderer.seqfeatures.FeatureRenderer
{
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();
- this.ap = ap;
- this.av = ap.av;
- 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);
}
}
static String lastDescriptionAdded;
- Object oldcol, fcol;
+ 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>
+ *
+ * @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 features with start/end position set (if creating)
+ * @param create
+ * true to create features, false to amend or delete
+ * @param featureType
+ * the feature type to set on new features; if null, defaults to the
+ * type of the last new feature created if any, failing that to
+ * "feature_1"
+ * @param alignPanel
+ * @return
+ */
+ protected boolean amendFeatures(final List<SequenceI> sequences,
+ final List<SequenceFeature> features, boolean create,
+ final AlignmentPanel alignPanel, String featureType)
{
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);
final JTextArea description = new JTextArea(3, 25);
{
FeatureColourChooser fcc = null;
+ @Override
public void mousePressed(MouseEvent evt)
{
- if (fcol instanceof Color)
+ if (fcol.isSimpleColour())
{
Color col = JColorChooser.showDialog(Desktop.desktop,
- MessageManager.getString("label.select_feature_colour"), ((Color) fcol));
+ MessageManager.getString("label.select_feature_colour"),
+ fcol.getColour());
if (col != null)
{
- fcol = col;
- updateColourButton(bigPanel, colour, col);
+ fcol = new FeatureColour(col);
+ updateColourButton(mainPanel, colour, new FeatureColour(col));
}
}
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();
fcc.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
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")));
- overlaps = new JComboBox();
- for (int i = 0; i < features.length; i++)
+ /*
+ * 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")
+ + ":"));
+ 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()
{
+ @Override
public void itemStateChanged(ItemEvent e)
{
int index = overlaps.getSelectedIndex();
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());
+ source.setText(sf.getFeatureGroup());
+ start.setValue(new Integer(sf.getBegin()));
+ end.setValue(new Integer(sf.getEnd()));
- SearchResults highlight = new SearchResults();
- highlight.addResult(sequences[0], features[index].getBegin(),
- features[index].getEnd());
+ SearchResultsI highlight = new SearchResults();
+ highlight.addResult(sequences.get(0), sf.getBegin(),
+ sf.getEnd());
- ap.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
+ alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
}
- Object col = getFeatureStyle(name.getText());
+ FeatureColourI col = getFeatureStyle(name.getText());
if (col == null)
{
- col = new jalview.schemes.UserColourScheme()
- .createColourFromName(name.getText());
+ 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"), JLabel.RIGHT));
- tmp.add(name);
+ JPanel namePanel = new JPanel();
+ gridPanel.add(namePanel);
+ namePanel.add(new JLabel(MessageManager.getString("label.name:"),
+ JLabel.RIGHT));
+ 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(source);
- 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);
+ startEndPanel.add(end);
+ mainPanel.add(startEndPanel, BorderLayout.CENTER);
}
else
{
- bigPanel.add(panel, BorderLayout.CENTER);
+ mainPanel.add(descriptionPanel, BorderLayout.CENTER);
}
- if (lastFeatureAdded == null)
+ SequenceFeature firstFeature = features.get(0);
+ if (featureType != null)
{
- if (features[0].type != null)
- {
- lastFeatureAdded = features[0].type;
- }
- else
+ lastFeatureAdded = featureType;
+ }
+ else
+ {
+ if (lastFeatureAdded == null)
{
- lastFeatureAdded = "feature_1";
+ if (firstFeature.type != null)
+ {
+ lastFeatureAdded = firstFeature.type;
+ }
+ else
+ {
+ lastFeatureAdded = "feature_1";
+ }
}
}
if (lastFeatureGroupAdded == null)
{
- if (features[0].featureGroup != null)
+ if (firstFeature.featureGroup != null)
{
- lastFeatureGroupAdded = features[0].featureGroup;
+ lastFeatureGroupAdded = firstFeature.featureGroup;
}
else
{
}
}
- if (newFeatures)
+ if (create)
{
name.setText(lastFeatureAdded);
source.setText(lastFeatureGroupAdded);
}
else
{
- name.setText(features[0].getType());
- source.setText(features[0].getFeatureGroup());
+ name.setText(firstFeature.getType());
+ source.setText(firstFeature.getFeatureGroup());
}
- start.setValue(new Integer(features[0].getBegin()));
- end.setValue(new Integer(features[0].getEnd()));
- description.setText(features[0].getDescription());
- updateColourButton(bigPanel, colour,
+ start.setValue(new Integer(firstFeature.getBegin()));
+ end.setValue(new Integer(firstFeature.getEnd()));
+ description.setText(firstFeature.getDescription());
+ updateColourButton(mainPanel, colour,
(oldcol = fcol = getFeatureStyle(name.getText())));
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.getString("label.create_new_sequence_features")
- : MessageManager.formatMessage("label.amend_delete_features", new String[]{sequences[0].getName()});
+ String title = create ? MessageManager
+ .getString("label.create_new_sequence_features")
+ : MessageManager.formatMessage("label.amend_delete_features",
+ new String[] { sequences.get(0).getName() });
- int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
- bigPanel, title, JOptionPane.YES_NO_CANCEL_OPTION,
- JOptionPane.QUESTION_MESSAGE, null, options, MessageManager.getString("action.ok"));
+ /*
+ * show the dialog
+ */
+ int reply = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
+ 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 == JOptionPane.OK_OPTION && name.getText().length() > 0)
+ if (reply == JvOptionPane.OK_OPTION && name.getText().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", " ");
}
}
- if (!newFeatures)
+ if (!create)
{
- SequenceFeature sf = features[featureIndex];
+ SequenceFeature sf = features.get(featureIndex);
- if (reply == JOptionPane.NO_OPTION)
+ if (reply == JvOptionPane.NO_OPTION)
{
- sequences[0].getDatasetSequence().deleteFeature(sf);
+ /*
+ * NO_OPTION corresponds to the Delete button
+ */
+ sequences.get(0).getDatasetSequence().deleteFeature(sf);
}
- else if (reply == JOptionPane.YES_OPTION)
+ else if (reply == JvOptionPane.YES_OPTION)
{
+ /*
+ * YES_OPTION corresponds to the Amend button
+ */
+ boolean typeChanged = !lastFeatureAdded.equals(sf.type);
sf.type = lastFeatureAdded;
sf.featureGroup = lastFeatureGroupAdded;
sf.description = lastDescriptionAdded;
}
ffile.parseDescriptionHTML(sf, false);
+ if (typeChanged)
+ {
+ findAllFeatures();
+ }
}
}
else
// NEW FEATURES ADDED
{
- if (reply == JOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
+ if (reply == JvOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
{
- for (int i = 0; i < sequences.length; i++)
+ for (int i = 0; i < sequences.size(); i++)
{
- features[i].type = lastFeatureAdded;
+ SequenceFeature sf = features.get(i);
+ sf.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);
+ sf.featureGroup = lastFeatureGroupAdded;
+ sf.description = lastDescriptionAdded;
+ sequences.get(i).addSequenceFeature(sf);
+ ffile.parseDescriptionHTML(sf, false);
}
if (lastFeatureGroupAdded != null)
findAllFeatures(false);
- ap.paintAlignment(true);
+ alignPanel.paintAlignment(true);
return true;
}
}
}
- ap.paintAlignment(true);
+ alignPanel.paintAlignment(true);
return true;
}
-
/**
* update the amend feature button dependent on the given style
*
* @param bigPanel
* @param col
- * @param col2
+ * @param col
*/
protected void updateColourButton(JPanel bigPanel, JLabel colour,
- Object col2)
+ FeatureColourI col)
{
colour.removeAll();
colour.setIcon(null);
colour.setToolTipText(null);
colour.setText("");
- if (col2 instanceof Color)
+ if (col.isSimpleColour())
{
- colour.setBackground((Color) col2);
+ colour.setBackground(col.getColour());
}
else
{
colour.setBackground(bigPanel.getBackground());
colour.setForeground(Color.black);
- FeatureSettings.renderGraduatedColor(colour, (GraduatedColor) col2);
- // colour.setForeground(colour.getBackground());
+ FeatureSettings.renderGraduatedColor(colour, col);
}
}
+
+ /**
+ * Orders features in render precedence (last in order is last to render, so
+ * displayed on top of other features)
+ *
+ * @param order
+ */
+ public void orderFeatures(Comparator<String> order)
+ {
+ Arrays.sort(renderOrder, order);
+ }
}