SequenceGroup[] gps = null;
if (sg != null && (cs == null || cs.isEmpty()))
{
- gps = jalview.analysis.Grouping.makeGroupsFrom(viewport
- .getSequenceSelection(), viewport.getAlignmentView(true)
- .getSequenceStrings(viewport.getGapCharacter()), viewport
- .getAlignment().getGroups());
+ gps = jalview.analysis.Grouping.makeGroupsFrom(
+ viewport.getSequenceSelection(),
+ viewport.getAlignmentView(true)
+ .getSequenceStrings(viewport.getGapCharacter()),
+ viewport.getAlignment().getGroups());
}
else
{
{
gps = jalview.analysis.Grouping.makeGroupsFromCols(
(sg == null) ? viewport.getAlignment().getSequencesArray()
- : sg.getSequences().toArray(new SequenceI[0]), cs,
- viewport.getAlignment().getGroups());
+ : sg.getSequences().toArray(new SequenceI[0]),
+ cs, viewport.getAlignment().getGroups());
}
}
if (gps != null)
// 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();
+ SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null
+ || extendCurrent) ? viewport.getAlignment()
+ : viewport.getSelectionGroup();
int nseq = findColumnsWithFeature(featureType, sqcol, bs);
{
viewport.setColumnSelection(cs);
alignPanel.paintAlignment(true);
- int columnCount = invert ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
- - bs.cardinality()
+ 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"),
+ "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")
}
else
{
- avcg.setStatus(MessageManager.formatMessage(
- "label.no_feature_of_type_found",
- new String[] { featureType }));
+ avcg.setStatus(MessageManager
+ .formatMessage("label.no_feature_of_type_found", new String[]
+ { featureType }));
if (!extendCurrent)
{
cs.clear();
SequenceFeature[] sfs = sq.getSequenceFeatures();
if (sfs != null)
{
- /*
- * 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)
// - findIndex wastes time by starting from first character and
// counting
- int i = sq.findIndex(sf.getBegin());
- int j = sq.findIndex(sf.getEnd());
- if (j < startPosition || i > endPosition)
+ int sfStartCol = sq.findIndex(sf.getBegin());
+ int sfEndCol = sq.findIndex(sf.getEnd());
+
+ if (sf.isContactFeature())
+ {
+ /*
+ * 'contact' feature - check for 'start' or 'end'
+ * position within the selected region
+ */
+ if (sfStartCol >= startPosition
+ && sfStartCol <= endPosition)
+ {
+ bs.set(sfStartCol - 1);
+ sequenceHasFeature = true;
+ }
+ if (sfEndCol >= startPosition && sfEndCol <= endPosition)
+ {
+ bs.set(sfEndCol - 1);
+ sequenceHasFeature = true;
+ }
+ continue;
+ }
+
+ /*
+ * contiguous feature - select feature positions (if any)
+ * within the selected region
+ */
+ if (sfStartCol > endPosition || sfEndCol < startPosition)
{
// feature is outside selected region
continue;
}
sequenceHasFeature = true;
- if (i < startPosition)
+ if (sfStartCol < startPosition)
{
- i = startPosition;
+ sfStartCol = startPosition;
}
- if (i < ist)
+ if (sfStartCol < ist)
{
- i = ist;
+ sfStartCol = ist;
}
- if (j > endPosition)
+ if (sfEndCol > endPosition)
{
- j = endPosition;
+ sfEndCol = endPosition;
}
- for (; i <= j; i++)
+ for (; sfStartCol <= sfEndCol; sfStartCol++)
{
- bs.set(i - 1); // convert to base 0
+ bs.set(sfStartCol - 1); // convert to base 0
}
}
}
}
SequenceI[] oldOrder = al.getSequencesArray();
AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
- avcg.addHistoryItem(new OrderCommand(methodText, oldOrder, viewport
- .getAlignment()));
+ avcg.addHistoryItem(new OrderCommand(methodText, oldOrder,
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
boolean featuresFile = false;
try
{
- featuresFile = new FeaturesFile(false, file, protocol).parse(viewport
- .getAlignment().getDataset(), alignPanel.getFeatureRenderer()
- .getFeatureColours(), false, relaxedIdMatching);
+ featuresFile = new FeaturesFile(false, file, protocol).parse(
+ viewport.getAlignment().getDataset(),
+ alignPanel.getFeatureRenderer().getFeatureColours(), false,
+ relaxedIdMatching);
} catch (Exception ex)
{
ex.printStackTrace();
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;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff