BitSet bs = new BitSet();
boolean searchSelection = viewport.getSelectionGroup() != null
&& !extendCurrent;
- SequenceCollectionI sqcol = searchSelection ? viewport
- .getSelectionGroup() : viewport.getAlignment();
+ SequenceCollectionI sqcol = searchSelection
+ ? viewport.getSelectionGroup()
+ : viewport.getAlignment();
int nseq = findColumnsWithFeature(featureType, sqcol, bs);
{
String key = searchSelection ? "label.no_feature_found_selection"
: "label.no_feature_of_type_found";
- avcg.setStatus(MessageManager.formatMessage(key,
- new String[] { featureType }));
+ avcg.setStatus(
+ MessageManager.formatMessage(key, new String[]
+ { featureType }));
if (!extendCurrent)
{
cs.clear();
* @param bs
* @return
*/
- int findColumnsWithFeature(String featureType,
- SequenceCollectionI sqcol, BitSet bs)
+ int findColumnsWithFeature(String featureType, SequenceCollectionI sqcol,
+ BitSet bs)
{
- FeatureRenderer fr = alignPanel == null ? null : alignPanel
- .getFeatureRenderer();
+ FeatureRenderer fr = alignPanel == null ? null
+ : alignPanel.getFeatureRenderer();
final int startColumn = sqcol.getStartRes() + 1; // converted to base 1
final int endColumn = sqcol.getEndRes() + 1;
if (sq != null)
{
// int ist = sq.findPosition(sqcol.getStartRes());
- List<SequenceFeature> sfs = sq.findFeatures(startColumn,
- endColumn, featureType);
+ List<SequenceFeature> sfs = sq.findFeatures(startColumn, endColumn,
+ featureType);
boolean found = false;
for (SequenceFeature sf : sfs)
@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
else
{
avcg.setStatus(MessageManager
- .formatMessage("No highlighted regions marked"));
+ .getString("label.no_highlighted_regions_marked"));
if (!extendCurrent)
{
cs.clear();