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;
final JSpinner end = new JSpinner();
start.setPreferredSize(new Dimension(80, 20));
end.setPreferredSize(new Dimension(80, 20));
- final FeatureRenderer me = this;
final JLabel colour = new JLabel();
colour.setOpaque(true);
// colour.setBorder(BorderFactory.createEtchedBorder());
colour.setMaximumSize(new Dimension(30, 16));
colour.addMouseListener(new MouseAdapter()
{
- FeatureColourChooser fcc = null;
-
+ /*
+ * open colour chooser on click in colour panel
+ */
@Override
public void mousePressed(MouseEvent evt)
{
}
else
{
- if (fcc == null)
+ /*
+ * variable colour dialog - on OK, refetch the updated
+ * feature colour and update this display
+ */
+ final String ft = features.get(featureIndex).getType();
+ final String type = ft == null ? lastFeatureAdded : ft;
+ FeatureTypeSettings fcc = new FeatureTypeSettings(
+ FeatureRenderer.this, type);
+ fcc.setRequestFocusEnabled(true);
+ fcc.requestFocus();
+ fcc.addActionListener(new ActionListener()
{
- final String ft = features.get(featureIndex).getType();
- final String type = ft == null ? lastFeatureAdded : ft;
- fcc = new FeatureColourChooser(me, type);
- fcc.setRequestFocusEnabled(true);
- fcc.requestFocus();
-
- fcc.addActionListener(new ActionListener()
+ @Override
+ public void actionPerformed(ActionEvent e)
{
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- fcol = fcc.getLastColour();
- fcc = null;
- setColour(type, fcol);
- updateColourButton(mainPanel, colour, fcol);
- }
- });
-
- }
+ fcol = FeatureRenderer.this.getFeatureStyle(ft);
+ setColour(type, fcol);
+ updateColourButton(mainPanel, colour, fcol);
+ }
+ });
}
}
});
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>();
+ 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)
FeaturesFile ffile = new FeaturesFile();
- String enteredType = name.getText().trim();
+ 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)
{
/*
if (useLastDefaults)
{
lastFeatureAdded = enteredType;
- lastFeatureGroupAdded = group.getText().trim();
+ 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 = enteredType;
- 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();
for (int i = 0; i < sequences.size(); i++)
{
SequenceFeature sf = features.get(i);
- sf.type = enteredType;
- // 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(enteredType, fcol);
featuresAdded();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
return true;
}
}
}
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
return true;
}
git://source.jalview.org / jalview.git / blobdiff