*/
package jalview.appletgui;
+import jalview.api.FeatureColourI;
import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.GraduatedColor;
+import jalview.io.FeaturesFile;
+import jalview.schemes.FeatureColour;
+import jalview.util.ColorUtils;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import java.awt.Choice;
import java.awt.Color;
import java.awt.Dimension;
+import java.awt.FlowLayout;
import java.awt.Font;
+import java.awt.Frame;
import java.awt.Graphics;
import java.awt.GridLayout;
import java.awt.Label;
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.awt.event.TextEvent;
+import java.awt.event.TextListener;
+import java.util.Hashtable;
+import java.util.List;
/**
* DOCUMENT ME!
* @author $author$
* @version $Revision$
*/
-public class FeatureRenderer extends
- jalview.renderer.seqfeatures.FeatureRenderer
+public class FeatureRenderer
+ extends jalview.renderer.seqfeatures.FeatureRenderer
{
+ /*
+ * creating a new feature defaults to the type and group as
+ * the last one created
+ */
+ static String lastFeatureAdded = "feature_1";
+
+ static String lastFeatureGroupAdded = "Jalview";
+
+ // 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(AlignmentViewport av)
{
super(av);
- setTransparencyAvailable(!System.getProperty("java.version")
- .startsWith("1.1"));
}
- static String lastFeatureAdded;
-
- static String lastFeatureGroupAdded;
-
- static String lastDescriptionAdded;
-
int featureIndex = 0;
boolean deleteFeature = false;
/**
* 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)
+ if (newcol.isSimpleColour())
{
- isGcol = false;
- col = (Color) newcol;
- gcol = null;
- }
- else if (newcol instanceof GraduatedColor)
- {
- isGcol = true;
- gcol = (GraduatedColor) newcol;
- col = null;
+ bg = newcol.getColour();
+ setBackground(bg);
}
else
{
- throw new Error(
- MessageManager
- .getString("error.invalid_colour_for_mycheckbox"));
- }
- if (col != null)
- {
- setBackground(bg = col);
- }
- else
- {
- if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
+ if (newcol.isAboveThreshold())
+ {
+ vlabel += " (>)";
+ }
+ else if (newcol.isBelowThreshold())
{
- vlabel += " "
- + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)"
- : "(<)");
+ vlabel += " (<)";
}
- if (isColourByLabel = gcol.isColourByLabel())
+
+ 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;
}
- boolean amendFeatures(final SequenceI[] sequences,
- final SequenceFeature[] features, boolean newFeatures,
+ /**
+ * Shows a dialog allowing the user to create, or amend or delete, sequence
+ * features. If null in the supplied feature(s), feature type and group
+ * default to those for the last feature created (with initial defaults of
+ * "feature_1" and "Jalview").
+ *
+ * @param sequences
+ * @param features
+ * @param create
+ * @param ap
+ * @return
+ */
+ boolean amendFeatures(final List<SequenceI> sequences,
+ final List<SequenceFeature> features, boolean create,
final AlignmentPanel ap)
{
- Panel bigPanel = new Panel(new BorderLayout());
+ final Panel bigPanel = new Panel(new BorderLayout());
final TextField name = new TextField(16);
- final TextField source = new TextField(16);
+ final TextField group = new TextField(16);
final TextArea description = new TextArea(3, 35);
final TextField start = new TextField(8);
final TextField end = new TextField(8);
Button deleteButton = new Button("Delete");
deleteFeature = false;
+ name.addTextListener(new TextListener()
+ {
+ @Override
+ public void textValueChanged(TextEvent e)
+ {
+ warnIfTypeHidden(ap.alignFrame, name.getText());
+ }
+ });
+ group.addTextListener(new TextListener()
+ {
+ @Override
+ public void textValueChanged(TextEvent e)
+ {
+ warnIfGroupHidden(ap.alignFrame, group.getText());
+ }
+ });
colourPanel = new FeatureColourPanel();
colourPanel.setSize(110, 15);
final FeatureRenderer fr = this;
// /////////////////////////////////////
// /MULTIPLE FEATURES AT SELECTED RESIDUE
- if (!newFeatures && features.length > 1)
+ if (!create && features.size() > 1)
{
panel = new Panel(new GridLayout(4, 1));
tmp = new Panel();
tmp.add(new Label("Select Feature: "));
overlaps = new Choice();
- for (int i = 0; i < features.length; i++)
+ for (SequenceFeature sf : features)
{
- String item = features[i].getType() + "/" + features[i].getBegin()
- + "-" + features[i].getEnd();
-
- if (features[i].getFeatureGroup() != null)
+ String item = sf.getType() + "/" + sf.getBegin() + "-"
+ + sf.getEnd();
+ if (sf.getFeatureGroup() != null)
{
- item += " (" + features[i].getFeatureGroup() + ")";
+ item += " (" + sf.getFeatureGroup() + ")";
}
-
overlaps.addItem(item);
}
if (index != -1)
{
featureIndex = index;
- name.setText(features[index].getType());
- description.setText(features[index].getDescription());
- source.setText(features[index].getFeatureGroup());
- start.setText(features[index].getBegin() + "");
- end.setText(features[index].getEnd() + "");
+ SequenceFeature sf = features.get(index);
+ name.setText(sf.getType());
+ description.setText(sf.getDescription());
+ group.setText(sf.getFeatureGroup());
+ start.setText(sf.getBegin() + "");
+ end.setText(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.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(source);
+ tmp.add(new Label(MessageManager.getString("label.group:"),
+ Label.RIGHT));
+ tmp.add(group);
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)
+ if (!create)
{
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);
}
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
- {
- lastFeatureAdded = "Jalview";
- }
- }
-
- String title = newFeatures ? MessageManager
- .getString("label.create_new_sequence_features")
+ /*
+ * use defaults for type and group (and update them on Confirm) only
+ * if feature type has not been supplied by the caller
+ * (e.g. for Amend, or create features from Find)
+ */
+ SequenceFeature firstFeature = features.get(0);
+ boolean useLastDefaults = firstFeature.getType() == null;
+ String featureType = useLastDefaults ? lastFeatureAdded
+ : firstFeature.getType();
+ String featureGroup = useLastDefaults ? lastFeatureGroupAdded
+ : firstFeature.getFeatureGroup();
+
+ 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() });
final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
240);
dialog.setMainPanel(bigPanel);
- if (newFeatures)
- {
- name.setText(lastFeatureAdded);
- source.setText(lastFeatureGroupAdded);
- }
- else
+ name.setText(featureType);
+ group.setText(featureGroup);
+
+ if (!create)
{
dialog.ok.setLabel(MessageManager.getString("label.amend"));
dialog.buttonPanel.add(deleteButton, 1);
dialog.setVisible(false);
}
});
- name.setText(features[0].getType());
- source.setText(features[0].getFeatureGroup());
}
- 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());
+ start.setText(firstFeature.getBegin() + "");
+ end.setText(firstFeature.getEnd() + "");
+ description.setText(firstFeature.getDescription());
+ // 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()
{
@Override
- public void mousePressed(java.awt.event.MouseEvent evt)
+ 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', ' ');
- }
+ /*
+ * only update default type and group if we used defaults
+ */
+ final String enteredType = name.getText().trim();
+ final String enteredGroup = group.getText().trim();
+ final String enteredDesc = description.getText().replace('\n', ' ');
- if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1)
+ if (dialog.accept && useLastDefaults)
{
- lastFeatureGroupAdded = null;
+ lastFeatureAdded = enteredType;
+ lastFeatureGroupAdded = enteredGroup;
}
- if (!newFeatures)
+ if (!create)
{
-
- SequenceFeature sf = features[featureIndex];
+ SequenceFeature sf = features.get(featureIndex);
if (dialog.accept)
{
- sf.type = lastFeatureAdded;
- sf.featureGroup = lastFeatureGroupAdded;
- sf.description = lastDescriptionAdded;
if (!colourPanel.isGcol)
{
// update colour - otherwise its already done.
- setColour(sf.type, colourPanel.getBackground());
+ setColour(enteredType,
+ new FeatureColour(colourPanel.getBackground()));
}
+ int newBegin = sf.begin;
+ int newEnd = sf.end;
try
{
- sf.begin = Integer.parseInt(start.getText());
- sf.end = Integer.parseInt(end.getText());
+ newBegin = Integer.parseInt(start.getText());
+ newEnd = Integer.parseInt(end.getText());
} catch (NumberFormatException ex)
{
+ //
}
+ /*
+ * 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, enteredType,
+ newBegin, newEnd, enteredGroup, sf.getScore());
+ newSf.setDescription(enteredDesc);
+ ffile.parseDescriptionHTML(newSf, false);
+ // amend features dialog only updates one sequence at a time
+ sequences.get(0).addSequenceFeature(newSf);
+ boolean typeOrGroupChanged = (!featureType.equals(newSf.getType())
+ || !featureGroup.equals(newSf.getFeatureGroup()));
+
ffile.parseDescriptionHTML(sf, false);
- setVisible(lastFeatureAdded); // if user edited name then make sure new
- // type is visible
+ if (typeOrGroupChanged)
+ {
+ featuresAdded();
+ }
}
if (deleteFeature)
{
- sequences[0].deleteFeature(sf);
+ sequences.get(0).deleteFeature(sf);
+ // ensure Feature Settings reflects removal of feature / group
+ featuresAdded();
}
-
}
else
{
+ /*
+ * adding feature(s)
+ */
if (dialog.accept && name.getText().length() > 0)
{
- for (int i = 0; i < sequences.length; i++)
+ for (int i = 0; i < sequences.size(); i++)
{
- features[i].type = lastFeatureAdded;
- 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,
+ enteredDesc, sf.getBegin(), sf.getEnd(), enteredGroup);
+ ffile.parseDescriptionHTML(sf2, false);
+ sequences.get(i).addSequenceFeature(sf2);
}
Color newColour = colourPanel.getBackground();
// setColour(lastFeatureAdded, fcol);
- if (lastFeatureGroupAdded != null)
- {
- setGroupVisibility(lastFeatureGroupAdded, true);
- }
- setColour(lastFeatureAdded, newColour); // was fcol
- setVisible(lastFeatureAdded);
- findAllFeatures(false); // different to original applet behaviour ?
- // findAllFeatures();
+ setColour(enteredType, new FeatureColour(newColour)); // was fcol
+ featuresAdded();
}
else
{
}
// findAllFeatures();
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
return true;
}
+
+ protected void warnIfGroupHidden(Frame frame, String group)
+ {
+ if (featureGroups.containsKey(group) && !featureGroups.get(group))
+ {
+ String msg = MessageManager.formatMessage("label.warning_hidden",
+ MessageManager.getString("label.group"), group);
+ showWarning(frame, msg);
+ }
+ }
+
+ protected void warnIfTypeHidden(Frame frame, String type)
+ {
+ if (getRenderOrder().contains(type))
+ {
+ if (!showFeatureOfType(type))
+ {
+ String msg = MessageManager.formatMessage("label.warning_hidden",
+ MessageManager.getString("label.feature_type"), type);
+ showWarning(frame, msg);
+ }
+ }
+ }
+
+ /**
+ * @param frame
+ * @param msg
+ */
+ protected void showWarning(Frame frame, String msg)
+ {
+ JVDialog d = new JVDialog(frame, "", true, 350, 200);
+ Panel mp = new Panel();
+ d.ok.setLabel(MessageManager.getString("action.ok"));
+ d.cancel.setVisible(false);
+ mp.setLayout(new FlowLayout());
+ mp.add(new Label(msg));
+ d.setMainPanel(mp);
+ d.setVisible(true);
+ }
}