import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
import jalview.io.FeaturesFile;
+import jalview.schemes.ColourSchemeI;
import jalview.util.MessageManager;
import java.awt.Color;
viewport.getAlignment().deleteAllGroups();
viewport.clearSequenceColours();
viewport.setSelectionGroup(null);
+ ColourSchemeI colours = viewport.getGlobalColourScheme();
// set view properties for each group
for (int g = 0; g < gps.length; g++)
{
// gps[g].setShowunconserved(viewport.getShowUnconserved());
gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
viewport.getAlignment().addGroup(gps[g]);
- Color col = new Color((int) (Math.random() * 255),
- (int) (Math.random() * 255), (int) (Math.random() * 255));
- col = col.brighter();
- for (SequenceI sq : gps[g].getSequences(null))
+ if (colours != null)
{
- viewport.setSequenceColour(sq, col);
+ gps[g].setColourScheme(colours.getInstance(viewport, gps[g]));
}
+ Color col = new Color((int) (Math.random() * 255),
+ (int) (Math.random() * 255), (int) (Math.random() * 255));
+ gps[g].idColour = col;
+ viewport.setUpdateStructures(true);
+ viewport.addSequenceGroup(gps[g]);
}
return true;
}
// 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[]
+ String key = searchSelection ? "label.no_feature_found_selection"
+ : "label.no_feature_of_type_found";
+ avcg.setStatus(
+ MessageManager.formatMessage(key, new String[]
{ featureType }));
if (!extendCurrent)
{
* @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
- public boolean parseFeaturesFile(String file, DataSourceType protocol,
+ public boolean parseFeaturesFile(Object file, DataSourceType protocol,
boolean relaxedIdMatching)
{
boolean featuresAdded = false;
else
{
avcg.setStatus(MessageManager
- .formatMessage("No highlighted regions marked"));
+ .getString("label.no_highlighted_regions_marked"));
if (!extendCurrent)
{
cs.clear();