*/
package jalview.gui;
-import jalview.api.FeatureColourI;
-import jalview.datamodel.SearchResults;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.schemes.FeatureColour;
-import jalview.schemes.UserColourScheme;
-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.Arrays;
-import java.util.Comparator;
-
-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;
/**
* DOCUMENT ME!
* @author $author$
* @version $Revision$
*/
-public class FeatureRenderer extends
- jalview.renderer.seqfeatures.FeatureRenderer implements
- jalview.api.FeatureRenderer
+public class FeatureRenderer
+ extends jalview.renderer.seqfeatures.FeatureRenderer
+ implements jalview.api.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(ap.av);
- this.ap = ap;
- if (ap != null && ap.getSeqPanel() != null
- && ap.getSeqPanel().seqCanvas != null
- && ap.getSeqPanel().seqCanvas.fr != null)
- {
- transferSettings(ap.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)
- {
-
- featureIndex = 0;
-
- final JPanel bigPanel = new JPanel(new BorderLayout());
- final JComboBox overlaps;
- final JTextField name = new JTextField(25);
- final JTextField source = new JTextField(25);
- final JTextArea description = new JTextArea(3, 25);
- final JSpinner start = new JSpinner();
- final JSpinner end = new JSpinner();
- start.setPreferredSize(new Dimension(80, 20));
- end.setPreferredSize(new Dimension(80, 20));
- final FeatureRenderer me = this;
- final JLabel colour = new JLabel();
- colour.setOpaque(true);
- // colour.setBorder(BorderFactory.createEtchedBorder());
- colour.setMaximumSize(new Dimension(30, 16));
- colour.addMouseListener(new MouseAdapter()
- {
- FeatureColourChooser fcc = null;
-
- @Override
- public void mousePressed(MouseEvent evt)
- {
- if (fcol.isSimpleColour())
- {
- Color col = JColorChooser.showDialog(Desktop.desktop,
- MessageManager.getString("label.select_feature_colour"),
- fcol.getColour());
- if (col != null)
- {
- fcol = new FeatureColour(col);
- updateColourButton(bigPanel, colour, new FeatureColour(col));
- }
- }
- else
- {
- if (fcc == null)
- {
- final String type = features[featureIndex].getType();
- 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);
- }
- });
-
- }
- }
- }
- });
- JPanel tmp = new JPanel();
- JPanel panel = new JPanel(new GridLayout(3, 1));
-
- // /////////////////////////////////////
- // /MULTIPLE FEATURES AT SELECTED RESIDUE
- if (!newFeatures && features.length > 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++)
- {
- overlaps.addItem(features[i].getType() + "/"
- + features[i].getBegin() + "-" + features[i].getEnd()
- + " (" + features[i].getFeatureGroup() + ")");
- }
-
- tmp.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()));
-
- SearchResults highlight = new SearchResults();
- highlight.addResult(sequences[0], features[index].getBegin(),
- features[index].getEnd());
-
- ap.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
-
- }
- FeatureColourI col = getFeatureStyle(name.getText());
- if (col == null)
- {
- col = new FeatureColour(UserColourScheme
- .createColourFromName(name.getText()));
- }
- oldcol = fcol = col;
- updateColourButton(bigPanel, colour, col);
- }
- });
-
- panel.add(tmp);
- }
- // ////////
- // ////////////////////////////////////
-
- tmp = new JPanel();
- panel.add(tmp);
- tmp.add(new JLabel(MessageManager.getString("label.name:"),
- JLabel.RIGHT));
- tmp.add(name);
-
- tmp = new JPanel();
- panel.add(tmp);
- tmp.add(new JLabel(MessageManager.getString("label.group:"),
- JLabel.RIGHT));
- tmp.add(source);
-
- tmp = new JPanel();
- panel.add(tmp);
- tmp.add(new JLabel(MessageManager.getString("label.colour"),
- JLabel.RIGHT));
- tmp.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);
- bigPanel.add(panel, BorderLayout.NORTH);
-
- panel = new JPanel();
- panel.add(new JLabel(MessageManager.getString("label.description:"),
- JLabel.RIGHT));
- description.setFont(JvSwingUtils.getTextAreaFont());
- description.setLineWrap(true);
- panel.add(new JScrollPane(description));
-
- if (!newFeatures)
- {
- bigPanel.add(panel, BorderLayout.SOUTH);
-
- panel = new JPanel();
- panel.add(new JLabel(MessageManager.getString("label.start"),
- JLabel.RIGHT));
- panel.add(start);
- panel.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)
+ super(alignPanel.av);
+ this.ap = alignPanel;
+ SeqPanel sp = alignPanel.getSeqPanel();
+ if (sp != null && sp.seqCanvas != null && sp.seqCanvas.fr != null)
{
- name.setText(lastFeatureAdded);
- source.setText(lastFeatureGroupAdded);
+ transferSettings(sp.seqCanvas.fr);
}
- else
- {
- name.setText(features[0].getType());
- source.setText(features[0].getFeatureGroup());
- }
-
- 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())));
- Object[] options;
- if (!newFeatures)
- {
- options = new Object[] { "Amend", "Delete", "Cancel" };
- }
- else
- {
- options = new Object[] { "OK", "Cancel" };
- }
-
- String title = newFeatures ? MessageManager
- .getString("label.create_new_sequence_features")
- : MessageManager.formatMessage("label.amend_delete_features",
- new String[] { sequences[0].getName() });
-
- int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
- bigPanel, title, JOptionPane.YES_NO_CANCEL_OPTION,
- JOptionPane.QUESTION_MESSAGE, null, options,
- MessageManager.getString("action.ok"));
-
- jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
-
- if (reply == JOptionPane.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", " ");
- // TODO: determine if the null feature group is valid
- if (lastFeatureGroupAdded.length() < 1)
- {
- lastFeatureGroupAdded = null;
- }
- }
-
- if (!newFeatures)
- {
- SequenceFeature sf = features[featureIndex];
-
- if (reply == JOptionPane.NO_OPTION)
- {
- sequences[0].getDatasetSequence().deleteFeature(sf);
- }
- else if (reply == JOptionPane.YES_OPTION)
- {
- sf.type = lastFeatureAdded;
- sf.featureGroup = lastFeatureGroupAdded;
- sf.description = lastDescriptionAdded;
-
- setColour(sf.type, fcol);
- getFeaturesDisplayed().setVisible(sf.type);
-
- try
- {
- sf.begin = ((Integer) start.getValue()).intValue();
- sf.end = ((Integer) end.getValue()).intValue();
- } catch (NumberFormatException ex)
- {
- }
-
- ffile.parseDescriptionHTML(sf, false);
- }
- }
- else
- // NEW FEATURES ADDED
- {
- if (reply == JOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
- {
- for (int i = 0; i < sequences.length; 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);
- }
-
- if (lastFeatureGroupAdded != null)
- {
- setGroupVisibility(lastFeatureGroupAdded, true);
- }
- setColour(lastFeatureAdded, fcol);
- setVisible(lastFeatureAdded);
-
- findAllFeatures(false);
-
- ap.paintAlignment(true);
-
- return true;
- }
- else
- {
- return false;
- }
- }
-
- ap.paintAlignment(true);
-
- return true;
- }
-
- /**
- * 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.setToolTipText(null);
- colour.setText("");
-
- if (col.isSimpleColour())
- {
- colour.setBackground(col.getColour());
- }
- else
- {
- colour.setBackground(bigPanel.getBackground());
- colour.setForeground(Color.black);
- 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);
}
}
git://source.jalview.org / jalview.git / blobdiff