/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.appletgui;
-import java.util.*;
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.GraduatedColor;
import jalview.util.MessageManager;
-import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.Choice;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.GridLayout;
+import java.awt.Label;
+import java.awt.Panel;
+import java.awt.ScrollPane;
+import java.awt.TextArea;
+import java.awt.TextField;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
/**
* DOCUMENT ME!
* @author $author$
* @version $Revision$
*/
-public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRenderer
+public class FeatureRenderer extends
+ jalview.renderer.seqfeatures.FeatureRenderer
{
-
- // Holds web links for feature groups and feature types
- // in the form label|link
- Hashtable featureLinks = null;
-
/**
* Creates a new FeatureRenderer object.
*
* @param av
* DOCUMENT ME!
*/
- public FeatureRenderer(AlignViewport av)
+ public FeatureRenderer(AlignmentViewport av)
{
super();
this.av = av;
-
- setTransparencyAvailable(!System.getProperty("java.version").startsWith("1.1"));
}
static String lastFeatureAdded;
}
else
{
- throw new Error(MessageManager.getString("error.invalid_colour_for_mycheckbox"));
+ throw new Error(
+ MessageManager
+ .getString("error.invalid_colour_for_mycheckbox"));
}
if (col != null)
{
super(null);
}
+ @Override
public void paint(Graphics g)
{
Dimension d = getSize();
+ "-" + features[i].getEnd();
if (features[i].getFeatureGroup() != null)
+ {
item += " (" + features[i].getFeatureGroup() + ")";
+ }
overlaps.addItem(item);
}
overlaps.addItemListener(new java.awt.event.ItemListener()
{
+ @Override
public void itemStateChanged(java.awt.event.ItemEvent e)
{
int index = overlaps.getSelectedIndex();
}
}
- String title = newFeatures ? MessageManager.getString("label.create_new_sequence_features")
- : MessageManager.formatMessage("label.amend_delete_features", new String[]{sequences[0].getName()});
+ String title = newFeatures ? MessageManager
+ .getString("label.create_new_sequence_features")
+ : MessageManager.formatMessage("label.amend_delete_features",
+ new String[] { sequences[0].getName() });
final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
240);
dialog.buttonPanel.add(deleteButton, 1);
deleteButton.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
deleteFeature = true;
start.setText(features[0].getBegin() + "");
end.setText(features[0].getEnd() + "");
description.setText(features[0].getDescription());
- Color col = getColour(name.getText());
- if (col == null)
- {
- col = new jalview.schemes.UserColourScheme()
- .createColourFromName(name.getText());
- }
Object fcol = getFeatureStyle(name.getText());
// simply display the feature color in a box
colourPanel.updateColor(fcol);
// TODO: render the graduated color in the box.
colourPanel.addMouseListener(new java.awt.event.MouseAdapter()
{
+ @Override
public void mousePressed(java.awt.event.MouseEvent evt)
{
if (!colourPanel.isGcol)
}
if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1)
+ {
lastFeatureGroupAdded = null;
+ }
if (!newFeatures)
{
}
ffile.parseDescriptionHTML(sf, false);
- setVisible(lastFeatureAdded); // if user edited name then make sure new type is visible
+ setVisible(lastFeatureAdded); // if user edited name then make sure new
+ // type is visible
}
if (deleteFeature)
{
ffile.parseDescriptionHTML(features[i], false);
}
- col = colourPanel.getBackground();
+ Color newColour = colourPanel.getBackground();
// setColour(lastFeatureAdded, fcol);
if (lastFeatureGroupAdded != null)
{
setGroupVisibility(lastFeatureGroupAdded, true);
}
- setColour(lastFeatureAdded, fcol);
+ setColour(lastFeatureAdded, newColour); // was fcol
setVisible(lastFeatureAdded);
- findAllFeatures(false); // different to original applet behaviour ?
+ findAllFeatures(false); // different to original applet behaviour ?
// findAllFeatures();
}
else