import jalview.datamodel.SequenceI;
import jalview.io.FeaturesFile;
import jalview.schemes.FeatureColour;
-import jalview.schemes.UserColourScheme;
+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.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!
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;
}
- 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() + "");
SearchResultsI highlight = new SearchResults();
- highlight.addResult(sequences[0], features[index].getBegin(),
- features[index].getEnd());
+ highlight.addResult(sequences.get(0), sf.getBegin(),
+ sf.getEnd());
ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
FeatureColourI col = getFeatureStyle(name.getText());
if (col == null)
{
- Color generatedColour = UserColourScheme
- .createColourFromName(name.getText());
+ Color generatedColour = ColorUtils.createColourFromName(name
+ .getText());
col = new FeatureColour(generatedColour);
}
tmp = new Panel();
panel.add(tmp);
tmp.add(new Label(MessageManager.getString("label.group:"), Label.RIGHT));
- tmp.add(source);
+ tmp.add(group);
tmp = new Panel();
panel.add(tmp);
Label.RIGHT));
panel.add(new ScrollPane().add(description));
- if (!newFeatures)
+ if (!create)
{
bigPanel.add(panel, BorderLayout.SOUTH);
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
+ /*
+ * 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());
+ 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
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, 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, 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(sf.type) || !featureGroup
+ .equals(sf.featureGroup));
+
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, new FeatureColour(newColour)); // was fcol
- setVisible(lastFeatureAdded);
- findAllFeatures(false); // different to original applet behaviour ?
- // findAllFeatures();
+ setColour(enteredType, new FeatureColour(newColour)); // was fcol
+ featuresAdded();
}
else
{
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);
+ }
}
git://source.jalview.org / jalview.git / blobdiff