gps = jalview.analysis.Grouping.makeGroupsFromCols(
(sg == null) ? viewport.getAlignment().getSequencesArray()
: sg.getSequences().toArray(new SequenceI[0]),
- cs, viewport.getAlignment().getGroups());
+ cs, viewport.getAlignment().getGroups(),
+ viewport.getAlignment().getHiddenColumns());
}
}
if (gps != null)
viewport.getAlignment().addGroup(gps[g]);
if (colours != null)
{
- gps[g].setColourScheme(colours.getInstance(viewport, gps[g],
- viewport.getHiddenRepSequences()));
+ gps[g].setColourScheme(colours.getInstance(viewport, gps[g]));
}
Color col = new Color((int) (Math.random() * 255),
(int) (Math.random() * 255), (int) (Math.random() * 255));
// JBPNote this routine could also mark rows, not just columns.
// need a decent query structure to allow all types of feature searches
BitSet bs = new BitSet();
- SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null
- || extendCurrent) ? viewport.getAlignment()
- : viewport.getSelectionGroup();
+ boolean searchSelection = viewport.getSelectionGroup() != null
+ && !extendCurrent;
+ SequenceCollectionI sqcol = searchSelection ? viewport
+ .getSelectionGroup() : viewport.getAlignment();
int nseq = findColumnsWithFeature(featureType, sqcol, bs);
}
else
{
- avcg.setStatus(MessageManager
- .formatMessage("label.no_feature_of_type_found", new String[]
- { featureType }));
+ String key = searchSelection ? "label.no_feature_found_selection"
+ : "label.no_feature_of_type_found";
+ avcg.setStatus(MessageManager.formatMessage(key,
+ new String[] { featureType }));
if (!extendCurrent)
{
cs.clear();
@Override
public void sortAlignmentByFeatureDensity(List<String> typ)
{
- sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
+ String methodText = MessageManager.getString("label.sort_by_density");
+ sortByFeatures(typ, methodText, AlignmentSorter.FEATURE_DENSITY);
}
- protected void sortBy(List<String> typ, String methodText,
+ /**
+ * Sorts the alignment (or current selection) by either average score or density
+ * of the specified feature types, and adds to the command history. If
+ * {@code types} is null, all visible feature types are used for the sort. If no
+ * feature types apply, does nothing.
+ *
+ * @param types
+ * @param methodText
+ * - text shown in Undo/Redo command
+ * @param method
+ * - passed to
+ * jalview.analysis.AlignmentSorter.sortByFeatures()
+ */
+ protected void sortByFeatures(List<String> types, String methodText,
final String method)
{
FeatureRenderer fr = alignPanel.getFeatureRenderer();
- if (typ == null && fr != null)
+ if (types == null && fr != null)
+ {
+ types = fr.getDisplayedFeatureTypes();
+ }
+ if (types.isEmpty())
{
- typ = fr.getDisplayedFeatureTypes();
+ return; // nothing to do
}
List<String> gps = null;
if (fr != null)
stop = al.getWidth();
}
SequenceI[] oldOrder = al.getSequencesArray();
- AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
+ AlignmentSorter.sortByFeature(types, gps, start, stop, al, method);
avcg.addHistoryItem(new OrderCommand(methodText, oldOrder,
viewport.getAlignment()));
alignPanel.paintAlignment(true, false);
@Override
public void sortAlignmentByFeatureScore(List<String> typ)
{
- sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
+ String methodText = MessageManager.getString("label.sort_by_score");
+ sortByFeatures(typ, methodText, AlignmentSorter.FEATURE_SCORE);
}
@Override