import java.awt.event.ItemListener;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
+import java.util.ArrayList;
import java.util.Arrays;
import java.util.Comparator;
import java.util.List;
* @author $author$
* @version $Revision$
*/
-public class FeatureRenderer extends
- jalview.renderer.seqfeatures.FeatureRenderer
+public class FeatureRenderer
+ extends jalview.renderer.seqfeatures.FeatureRenderer
{
/*
* defaults for creating a new feature are the last created
if (col != null)
{
fcol = new FeatureColour(col);
- updateColourButton(mainPanel, colour, new FeatureColour(col));
+ updateColourButton(mainPanel, colour, fcol);
}
}
else
if (!create && features.size() > 1)
{
/*
- * more than one feature at selected position - add a drop-down
- * to choose the feature to amend
+ * more than one feature at selected position -
+ * add a drop-down to choose the feature to amend
+ * space pad text if necessary to make entries distinct
*/
gridPanel = new JPanel(new GridLayout(4, 1));
JPanel choosePanel = new JPanel();
- choosePanel.add(new JLabel(MessageManager
- .getString("label.select_feature")
- + ":"));
- final JComboBox<String> overlaps = new JComboBox<String>();
+ choosePanel.add(new JLabel(
+ MessageManager.getString("label.select_feature") + ":"));
+ final JComboBox<String> overlaps = new JComboBox<>();
+ List<String> added = new ArrayList<>();
for (SequenceFeature sf : features)
{
- String text = sf.getType() + "/" + sf.getBegin() + "-"
- + sf.getEnd() + " (" + sf.getFeatureGroup() + ")";
+ String text = String.format("%s/%d-%d (%s)", sf.getType(),
+ sf.getBegin(), sf.getEnd(), sf.getFeatureGroup());
+ while (added.contains(text))
+ {
+ text += " ";
+ }
overlaps.addItem(text);
+ added.add(text);
}
choosePanel.add(overlaps);
highlight.addResult(sequences.get(0), sf.getBegin(),
sf.getEnd());
- alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
-
+ alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(
+ highlight, false);
}
FeatureColourI col = getFeatureStyle(name.getText());
if (col == null)
{
- col = new FeatureColour(ColorUtils
- .createColourFromName(name.getText()));
+ col = new FeatureColour(
+ ColorUtils.createColourFromName(name.getText()));
}
oldcol = fcol = col;
updateColourButton(mainPanel, colour, col);
mainPanel.add(gridPanel, BorderLayout.NORTH);
JPanel descriptionPanel = new JPanel();
- descriptionPanel.add(new JLabel(MessageManager
- .getString("label.description:"),
- JLabel.RIGHT));
+ descriptionPanel.add(new JLabel(
+ MessageManager.getString("label.description:"), JLabel.RIGHT));
description.setFont(JvSwingUtils.getTextAreaFont());
description.setLineWrap(true);
descriptionPanel.add(new JScrollPane(description));
end.setValue(new Integer(firstFeature.getEnd()));
description.setText(firstFeature.getDescription());
updateColourButton(mainPanel, colour,
- (oldcol = fcol = getFeatureStyle(name.getText())));
+ (oldcol = fcol = getFeatureStyle(featureType)));
Object[] options;
if (!create)
{
MessageManager.getString("action.cancel") };
}
- String title = create ? MessageManager
- .getString("label.create_new_sequence_features")
+ String title = create
+ ? MessageManager.getString("label.create_new_sequence_features")
: MessageManager.formatMessage("label.amend_delete_features",
- new String[] { sequences.get(0).getName() });
+ new String[]
+ { sequences.get(0).getName() });
/*
* show the dialog
FeaturesFile ffile = new FeaturesFile();
- if (reply == JvOptionPane.OK_OPTION && name.getText().length() > 0)
+ final String enteredType = name.getText().trim();
+ final String enteredGroup = group.getText().trim();
+ final String enteredDescription = description.getText().replaceAll("\n", " ");
+
+ if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0)
{
/*
* update default values only if creating using default values
*/
if (useLastDefaults)
{
- lastFeatureAdded = name.getText().trim();
- lastFeatureGroupAdded = group.getText().trim();
+ lastFeatureAdded = enteredType;
+ lastFeatureGroupAdded = enteredGroup;
// TODO: determine if the null feature group is valid
if (lastFeatureGroupAdded.length() < 1)
{
{
/*
* YES_OPTION corresponds to the Amend button
- * need to refresh Feature Settings if type, group or colour changed
+ * need to refresh Feature Settings if type, group or colour changed;
+ * note we don't force the feature to be visible - the user has been
+ * warned if a hidden feature type or group was entered
*/
- sf.type = name.getText().trim();
- sf.featureGroup = group.getText().trim();
- sf.description = description.getText().replaceAll("\n", " ");
- boolean refreshSettings = (!featureType.equals(sf.type) || !featureGroup
- .equals(sf.featureGroup));
+ boolean refreshSettings = (!featureType.equals(enteredType) || !featureGroup
+ .equals(enteredGroup));
refreshSettings |= (fcol != oldcol);
-
- setColour(sf.type, fcol);
-
+ setColour(enteredType, fcol);
+ int newBegin = sf.begin;
+ int newEnd = sf.end;
try
{
- sf.begin = ((Integer) start.getValue()).intValue();
- sf.end = ((Integer) end.getValue()).intValue();
+ newBegin = ((Integer) start.getValue()).intValue();
+ newEnd = ((Integer) end.getValue()).intValue();
} catch (NumberFormatException ex)
{
+ // JSpinner doesn't accept invalid format data :-)
}
- ffile.parseDescriptionHTML(sf, false);
+ /*
+ * 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(enteredDescription);
+ ffile.parseDescriptionHTML(newSf, false);
+ // amend features dialog only updates one sequence at a time
+ sequences.get(0).addSequenceFeature(newSf);
+
if (refreshSettings)
{
featuresAdded();
else
// NEW FEATURES ADDED
{
- if (reply == JvOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
+ if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0)
{
for (int i = 0; i < sequences.size(); i++)
{
SequenceFeature sf = features.get(i);
- sf.type = name.getText().trim();
- // fix for JAL-1538 - always set feature group here
- sf.featureGroup = group.getText().trim();
- sf.description = description.getText().replaceAll("\n", " ");
- sequences.get(i).addSequenceFeature(sf);
- ffile.parseDescriptionHTML(sf, false);
+ SequenceFeature sf2 = new SequenceFeature(enteredType,
+ enteredDescription, sf.getBegin(), sf.getEnd(),
+ enteredGroup);
+ ffile.parseDescriptionHTML(sf2, false);
+ sequences.get(i).addSequenceFeature(sf2);
}
- setColour(lastFeatureAdded, fcol);
+ setColour(enteredType, fcol);
featuresAdded();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
return true;
}
}
}
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
return true;
}
{
String msg = MessageManager.formatMessage("label.warning_hidden",
MessageManager.getString("label.group"), group);
- JvOptionPane.showMessageDialog(panel, msg, "", JvOptionPane.OK_OPTION);
+ JvOptionPane.showMessageDialog(panel, msg, "",
+ JvOptionPane.OK_OPTION);
}
}
git://source.jalview.org / jalview.git / blobdiff