/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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.schemes.AnnotationColourGradient;
-import jalview.schemes.GraduatedColor;
+import jalview.api.FeatureColourI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.io.FeaturesFile;
+import jalview.schemes.FeatureColour;
+import jalview.util.ColorUtils;
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;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.Hashtable;
/**
* 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
* Creates a new FeatureRenderer object.
*
* @param av
- * DOCUMENT ME!
*/
- public FeatureRenderer(AlignViewport av)
+ public FeatureRenderer(AlignmentViewport av)
{
- super();
- this.av = av;
+ super(av);
- setTransparencyAvailable(!System.getProperty("java.version").startsWith("1.1"));
}
static String lastFeatureAdded;
/**
* render a feature style in the amend feature dialog box
*/
- public void updateColor(Object newcol)
+ public void updateColor(FeatureColourI newcol)
{
-
- Color bg, col = null;
- GraduatedColor gcol = null;
+ Color bg = null;
String vlabel = "";
- if (newcol instanceof Color)
- {
- isGcol = false;
- col = (Color) newcol;
- gcol = null;
- }
- else if (newcol instanceof GraduatedColor)
- {
- isGcol = true;
- gcol = (GraduatedColor) newcol;
- col = null;
- }
- else
- {
- throw new Error("Invalid color for MyCheckBox");
- }
- if (col != null)
+ if (newcol.isSimpleColour())
{
- setBackground(bg = col);
+ bg = newcol.getColour();
+ setBackground(bg);
}
else
{
- if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
+ if (newcol.isAboveThreshold())
{
- vlabel += " "
- + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)"
- : "(<)");
+ vlabel += " (>)";
}
- if (isColourByLabel = gcol.isColourByLabel())
+ else if (newcol.isBelowThreshold())
+ {
+ vlabel += " (<)";
+ }
+
+ if (isColourByLabel = newcol.isColourByLabel())
{
setBackground(bg = Color.white);
vlabel += " (by Label)";
}
else
{
- setBackground(bg = gcol.getMinColor());
- maxCol = gcol.getMaxColor();
+ setBackground(bg = newcol.getMinColour());
+ maxCol = newcol.getMaxColour();
}
}
label = vlabel;
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();
start.setText(features[index].getBegin() + "");
end.setText(features[index].getEnd() + "");
- SearchResults highlight = new SearchResults();
+ SearchResultsI highlight = new SearchResults();
highlight.addResult(sequences[0], features[index].getBegin(),
features[index].getEnd());
ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
}
- Object col = getFeatureStyle(name.getText());
+ FeatureColourI col = getFeatureStyle(name.getText());
if (col == null)
{
- col = new jalview.schemes.UserColourScheme()
+ Color generatedColour = ColorUtils
.createColourFromName(name.getText());
+ col = new FeatureColour(generatedColour);
}
colourPanel.updateColor(col);
tmp = new Panel();
panel.add(tmp);
- tmp.add(new Label("Name: ", Label.RIGHT));
+ tmp.add(new Label(MessageManager.getString("label.name:"), Label.RIGHT));
tmp.add(name);
tmp = new Panel();
panel.add(tmp);
- tmp.add(new Label("Group: ", Label.RIGHT));
+ tmp.add(new Label(MessageManager.getString("label.group:"), Label.RIGHT));
tmp.add(source);
tmp = new Panel();
panel.add(tmp);
- tmp.add(new Label("Colour: ", Label.RIGHT));
+ tmp.add(new Label(MessageManager.getString("label.colour"), Label.RIGHT));
tmp.add(colourPanel);
bigPanel.add(panel, BorderLayout.NORTH);
panel = new Panel();
- panel.add(new Label("Description: ", Label.RIGHT));
+ panel.add(new Label(MessageManager.getString("label.description:"),
+ Label.RIGHT));
panel.add(new ScrollPane().add(description));
if (!newFeatures)
bigPanel.add(panel, BorderLayout.SOUTH);
panel = new Panel();
- panel.add(new Label(" Start:", Label.RIGHT));
+ panel.add(new Label(MessageManager.getString("label.start"),
+ Label.RIGHT));
panel.add(start);
- panel.add(new Label(" End:", Label.RIGHT));
+ panel.add(new Label(MessageManager.getString("label.end"),
+ Label.RIGHT));
panel.add(end);
bigPanel.add(panel, BorderLayout.CENTER);
}
}
}
- String title = newFeatures ? "Create New Sequence Feature(s)"
- : "Amend/Delete Features for " + 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());
+ // lookup (or generate) the feature colour
+ FeatureColourI fcol = getFeatureStyle(name.getText());
// simply display the feature color in a box
colourPanel.updateColor(fcol);
dialog.setResizable(true);
// TODO: render the graduated color in the box.
- colourPanel.addMouseListener(new java.awt.event.MouseAdapter()
+ colourPanel.addMouseListener(new MouseAdapter()
{
- public void mousePressed(java.awt.event.MouseEvent evt)
+ @Override
+ public void mousePressed(MouseEvent evt)
{
if (!colourPanel.isGcol)
{
}
else
{
- FeatureColourChooser fcc = new FeatureColourChooser(
- ap.alignFrame, name.getText());
+ new FeatureColourChooser(ap.alignFrame, name.getText());
dialog.transferFocus();
}
}
});
dialog.setVisible(true);
- jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
+ FeaturesFile ffile = new FeaturesFile();
if (dialog.accept)
{
- // 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().replace('\n', ' ');
}
if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1)
+ {
lastFeatureGroupAdded = null;
+ }
if (!newFeatures)
{
if (!colourPanel.isGcol)
{
// update colour - otherwise its already done.
- setColour(sf.type, colourPanel.getBackground());
+ setColour(sf.type, new FeatureColour(colourPanel.getBackground()));
}
try
{
}
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, new FeatureColour(newColour)); // was fcol
setVisible(lastFeatureAdded);
- findAllFeatures(false); // different to original applet behaviour ?
+ findAllFeatures(false); // different to original applet behaviour ?
// findAllFeatures();
}
else