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();
static int findColumnsWithFeature(String featureType,
SequenceCollectionI sqcol, BitSet bs)
{
- final int startPosition = sqcol.getStartRes() + 1; // converted to base 1
- final int endPosition = sqcol.getEndRes() + 1;
+ final int startColumn = sqcol.getStartRes() + 1; // converted to base 1
+ final int endColumn = sqcol.getEndRes() + 1;
List<SequenceI> seqs = sqcol.getSequences();
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());
+ List<SequenceFeature> sfs = sq.findFeatures(startColumn,
+ endColumn, featureType);
+
+ if (!sfs.isEmpty())
{
- int ist = sq.findIndex(sq.getStart());
- int iend = sq.findIndex(sq.getEnd());
- if (iend < startPosition || ist > endPosition)
- {
- // sequence not in region
- continue;
- }
- for (SequenceFeature sf : sfs)
+ nseq++;
+ }
+
+ for (SequenceFeature sf : sfs)
+ {
+ int sfStartCol = sq.findIndex(sf.getBegin());
+ int sfEndCol = sq.findIndex(sf.getEnd());
+
+ if (sf.isContactFeature())
{
- // future functionality - featureType == null means mark columns
- // containing all displayed features
- if (sf != null && (featureType.equals(sf.getType())))
+ /*
+ * 'contact' feature - check for 'start' or 'end'
+ * position within the selected region
+ */
+ if (sfStartCol >= startColumn && sfStartCol <= endColumn)
+ {
+ bs.set(sfStartCol - 1);
+ }
+ if (sfEndCol >= startColumn && sfEndCol <= endColumn)
{
- // 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());
-
- 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 (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
- }
+ bs.set(sfEndCol - 1);
}
+ continue;
}
- }
- if (sequenceHasFeature)
- {
- nseq++;
+ /*
+ * contiguous feature - select feature positions (if any)
+ * within the selected region
+ */
+ if (sfStartCol < startColumn)
+ {
+ sfStartCol = startColumn;
+ }
+ // not sure what the point of this is
+ // if (sfStartCol < ist)
+ // {
+ // sfStartCol = ist;
+ // }
+ if (sfEndCol > endColumn)
+ {
+ sfEndCol = endColumn;
+ }
+ for (; sfStartCol <= sfEndCol; sfStartCol++)
+ {
+ 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();
}
// JBPNote this routine could also mark rows, not just columns.
BitSet bs = new BitSet();
- SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null || extendCurrent) ? viewport
- .getAlignment() : viewport.getSelectionGroup();
+ 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.
{
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")
git://source.jalview.org / jalview.git / blobdiff