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
}
- static String lastFeatureAdded;
-
- static String lastFeatureGroupAdded;
-
- static String lastDescriptionAdded;
-
int featureIndex = 0;
boolean deleteFeature = false;
/**
* Shows a dialog allowing the user to create, or amend or delete, sequence
- * features.
+ * 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
- * @param featureType
* @return
*/
boolean amendFeatures(final SequenceI[] sequences,
final SequenceFeature[] features, boolean create,
- final AlignmentPanel ap, String featureType)
+ final AlignmentPanel ap)
{
final Panel bigPanel = new Panel(new BorderLayout());
final TextField name = new TextField(16);
bigPanel.add(panel, BorderLayout.CENTER);
}
- if (featureType != null)
- {
- lastFeatureAdded = featureType;
- }
- else
- {
- 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";
- }
- }
+ /*
+ * 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)
+ */
+ boolean useLastDefaults = features[0].getType() == null;
+ String featureType = useLastDefaults ? lastFeatureAdded : features[0]
+ .getType();
+ String featureGroup = useLastDefaults ? lastFeatureGroupAdded
+ : features[0].getFeatureGroup();
String title = create ? MessageManager
.getString("label.create_new_sequence_features")
dialog.setMainPanel(bigPanel);
- if (create)
- {
- name.setText(lastFeatureAdded);
- group.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());
- group.setText(features[0].getFeatureGroup());
}
start.setText(features[0].getBegin() + "");
FeaturesFile ffile = new FeaturesFile();
- if (dialog.accept)
- {
- lastFeatureAdded = name.getText().trim();
- lastFeatureGroupAdded = group.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 (!create)
{
-
SequenceFeature sf = features[featureIndex];
if (dialog.accept)
{
- boolean typeOrGroupChanged = (!lastFeatureAdded.equals(sf.type) || !lastFeatureGroupAdded
- .equals(sf.featureGroup));
- sf.type = lastFeatureAdded;
- sf.featureGroup = lastFeatureGroupAdded;
- sf.description = lastDescriptionAdded;
if (!colourPanel.isGcol)
{
// update colour - otherwise its already done.
setColour(sf.type, 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[0].deleteFeature(sf);
+ SequenceFeature newSf = new SequenceFeature(sf, newBegin, newEnd,
+ enteredGroup, sf.getScore());
+ newSf.setDescription(enteredDesc);
+ ffile.parseDescriptionHTML(newSf, false);
+ // amend features dialog only updates one sequence at a time
+ sequences[0].addSequenceFeature(newSf);
+ boolean typeOrGroupChanged = (!featureType.equals(sf.type) || !featureGroup
+ .equals(sf.featureGroup));
+
ffile.parseDescriptionHTML(sf, false);
if (typeOrGroupChanged)
{
// ensure Feature Settings reflects removal of feature / group
featuresAdded();
}
-
}
else
{
{
for (int i = 0; i < sequences.length; 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[i];
+ SequenceFeature sf2 = new SequenceFeature(enteredType,
+ enteredDesc, sf.getBegin(), sf.getEnd(), enteredGroup);
+ ffile.parseDescriptionHTML(sf2, false);
+ sequences[i].addSequenceFeature(sf2);
}
Color newColour = colourPanel.getBackground();
// setColour(lastFeatureAdded, fcol);
- setColour(lastFeatureAdded, new FeatureColour(newColour)); // was fcol
+ setColour(enteredType, new FeatureColour(newColour)); // was fcol
featuresAdded();
}
else