import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
import jalview.io.FeaturesFile;
import jalview.util.MessageManager;
int nseq = 0;
for (SequenceI sq : seqs)
{
- boolean sequenceHasFeature = false;
if (sq != null)
{
- SequenceFeature[] sfs = sq.getSequenceFeatures();
- if (sfs != null)
+ int ist = sq.findPosition(sqcol.getStartRes());
+ int iend = sq.findPosition(sqcol.getEndRes()); // see JAL-2526
+ List<SequenceFeature> sfs = sq.getFeatures().findFeatures(ist,
+ iend, featureType);
+ boolean overlap = false;
+ for (SequenceFeature sf : sfs)
{
- /*
- * check whether the feature start/end (base 1)
- * overlaps the selection start/end
- */
- int ist = sq.findIndex(sq.getStart());
- int iend = sq.findIndex(sq.getEnd());
- if (iend < startPosition || ist > endPosition)
+ // future functionality - featureType == null means mark columns
+ // containing all displayed features
+ if (sf != null && (featureType.equals(sf.getType())))
{
- // sequence not in region
- continue;
- }
- for (SequenceFeature sf : sfs)
- {
- // future functionality - featureType == null means mark columns
- // containing all displayed features
- if (sf != null && (featureType.equals(sf.getType())))
- {
- // optimisation - could consider 'spos,apos' like cursor argument
- // - findIndex wastes time by starting from first character and
- // counting
+ int sfStartCol = sq.findIndex(sf.getBegin());
+ int sfEndCol = sq.findIndex(sf.getEnd()); // inefficient - JAL-2526
- int i = sq.findIndex(sf.getBegin());
- int j = sq.findIndex(sf.getEnd());
- if (j < startPosition || i > endPosition)
- {
- // feature is outside selected region
- continue;
- }
- sequenceHasFeature = true;
- if (i < startPosition)
- {
- i = startPosition;
- }
- if (i < ist)
- {
- i = ist;
- }
- if (j > endPosition)
+ if (sf.isContactFeature())
+ {
+ /*
+ * 'contact' feature - check for 'start' or 'end'
+ * position within the selected region
+ */
+ if (sfStartCol >= startPosition && sfStartCol <= endPosition)
{
- j = endPosition;
+ bs.set(sfStartCol - 1);
+ overlap = true;
}
- for (; i <= j; i++)
+ if (sfEndCol >= startPosition && sfEndCol <= endPosition)
{
- bs.set(i - 1); // convert to base 0
+ bs.set(sfEndCol - 1);
+ overlap = true;
}
+ continue;
+ }
+
+ /*
+ * contiguous feature - select feature positions (if any)
+ * within the selected region
+ */
+ if (sfStartCol < startPosition)
+ {
+ sfStartCol = startPosition;
+ }
+ if (sfStartCol < ist)
+ {
+ sfStartCol = ist;
+ }
+ if (sfEndCol > endPosition)
+ {
+ sfEndCol = endPosition;
+ }
+ for (; sfStartCol <= sfEndCol; sfStartCol++)
+ {
+ bs.set(sfStartCol - 1); // convert to base 0
+ overlap = true;
}
}
}
-
- if (sequenceHasFeature)
+ if (overlap)
{
nseq++;
}
}
@Override
- public boolean parseFeaturesFile(String file, String protocol,
+ public boolean parseFeaturesFile(String file, DataSourceType protocol,
boolean relaxedIdMatching)
{
boolean featuresFile = false;
return featuresFile;
}
+
+ @Override
+ public boolean markHighlightedColumns(boolean invert,
+ boolean extendCurrent, boolean toggle)
+ {
+ if (!viewport.hasSearchResults())
+ {
+ // do nothing if no selection exists
+ return false;
+ }
+ // JBPNote this routine could also mark rows, not just columns.
+ BitSet bs = new BitSet();
+ SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null || extendCurrent) ? viewport
+ .getAlignment() : viewport.getSelectionGroup();
+
+ // this could be a lambda... - the remains of the method is boilerplate,
+ // except for the different messages for reporting selection.
+ int nseq = viewport.getSearchResults().markColumns(sqcol, bs);
+
+ ColumnSelection cs = viewport.getColumnSelection();
+ if (cs == null)
+ {
+ cs = new ColumnSelection();
+ }
+
+ if (bs.cardinality() > 0 || invert)
+ {
+ boolean changed = cs.markColumns(bs, sqcol.getStartRes(),
+ sqcol.getEndRes(), invert, extendCurrent, toggle);
+ if (changed)
+ {
+ viewport.setColumnSelection(cs);
+ alignPanel.paintAlignment(true);
+ int columnCount = invert ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
+ - bs.cardinality()
+ : bs.cardinality();
+ avcg.setStatus(MessageManager.formatMessage(
+ "label.view_controller_toggled_marked",
+ new String[] {
+ toggle ? MessageManager.getString("label.toggled")
+ : MessageManager.getString("label.marked"),
+ String.valueOf(columnCount),
+ invert ? MessageManager
+ .getString("label.not_containing")
+ : MessageManager.getString("label.containing"),
+ "Highlight", Integer.valueOf(nseq).toString() }));
+ return true;
+ }
+ }
+ else
+ {
+ avcg.setStatus(MessageManager
+ .formatMessage("No highlighted regions marked"));
+ if (!extendCurrent)
+ {
+ cs.clear();
+ alignPanel.paintAlignment(true);
+ }
+ }
+ return false;
+ }
+
}