import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
import jalview.io.FeaturesFile;
import jalview.util.MessageManager;
// 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();
- int alw, alStart;
- SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null ? viewport
- .getAlignment() : viewport.getSelectionGroup());
- alStart = sqcol.getStartRes();
- alw = sqcol.getEndRes() + 1;
- List<SequenceI> seqs = sqcol.getSequences();
- int nseq = 0;
- for (SequenceI sq : seqs)
- {
- int tfeat = 0;
- if (sq != null)
- {
- SequenceFeature[] sf = sq.getSequenceFeatures();
- if (sf != null)
- {
- int ist = sq.findIndex(sq.getStart());
- int iend = sq.findIndex(sq.getEnd());
- if (iend < alStart || ist > alw)
- {
- // sequence not in region
- continue;
- }
- for (SequenceFeature sfpos : sf)
- {
- // future functionalty - featureType == null means mark columns
- // containing all displayed features
- if (sfpos != null && (featureType.equals(sfpos.getType())))
- {
- tfeat++;
- // optimisation - could consider 'spos,apos' like cursor argument
- // - findIndex wastes time by starting from first character and
- // counting
-
- int i = sq.findIndex(sfpos.getBegin());
- int j = sq.findIndex(sfpos.getEnd());
- if (j < alStart || i > alw)
- {
- // feature is outside selected region
- continue;
- }
- if (i < alStart)
- {
- i = alStart;
- }
- if (i < ist)
- {
- i = ist;
- }
- if (j > alw)
- {
- j = alw;
- }
- for (; i <= j; i++)
- {
- bs.set(i - 1);
- }
- }
- }
- }
+ SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null || extendCurrent) ? viewport
+ .getAlignment() : viewport.getSelectionGroup();
+
+ int nseq = findColumnsWithFeature(featureType, sqcol, bs);
- if (tfeat > 0)
- {
- nseq++;
- }
- }
- }
ColumnSelection cs = viewport.getColumnSelection();
+ if (cs == null)
+ {
+ cs = new ColumnSelection();
+ }
+
if (bs.cardinality() > 0 || invert)
{
- boolean changed = false;
- if (cs == null)
- {
- cs = new ColumnSelection();
- }
- else
- {
- if (!extendCurrent)
- {
- changed = !cs.isEmpty();
- cs.clear();
- }
- }
- if (invert)
- {
- // invert only in the currently selected sequence region
- for (int i = bs.nextClearBit(alStart), ibs = bs.nextSetBit(alStart); i >= alStart
- && i < (alw);)
- {
- if (ibs < 0 || i < ibs)
- {
- changed = true;
- if (toggle && cs.contains(i))
- {
- cs.removeElement(i++);
- }
- else
- {
- cs.addElement(i++);
- }
- }
- else
- {
- i = bs.nextClearBit(ibs);
- ibs = bs.nextSetBit(i);
- }
- }
- }
- else
- {
- for (int i = bs.nextSetBit(alStart); i >= alStart; i = bs
- .nextSetBit(i + 1))
- {
- changed = true;
- if (toggle && cs.contains(i))
- {
- cs.removeElement(i);
- }
- else
- {
- cs.addElement(i);
- }
- }
- }
+ 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[] {
- MessageManager.getString(toggle ? "label.toggled"
- : "label.marked"),
- String.valueOf(invert ? alw - alStart
- - bs.cardinality() : bs.cardinality()),
- MessageManager
- .getString(invert ? "label.not_containing"
- : "label.containing"),
+ toggle ? MessageManager.getString("label.toggled")
+ : MessageManager.getString("label.marked"),
+ String.valueOf(columnCount),
+ invert ? MessageManager
+ .getString("label.not_containing")
+ : MessageManager.getString("label.containing"),
featureType, Integer.valueOf(nseq).toString() }));
return true;
}
avcg.setStatus(MessageManager.formatMessage(
"label.no_feature_of_type_found",
new String[] { featureType }));
- if (!extendCurrent && cs != null)
+ if (!extendCurrent)
{
cs.clear();
alignPanel.paintAlignment(true);
return false;
}
+ /**
+ * Sets a bit in the BitSet for each column (base 0) in the sequence
+ * collection which includes the specified feature type. Returns the number of
+ * sequences which have the feature in the selected range.
+ *
+ * @param featureType
+ * @param sqcol
+ * @param bs
+ * @return
+ */
+ 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;
+ List<SequenceI> seqs = sqcol.getSequences();
+ int nseq = 0;
+ for (SequenceI sq : seqs)
+ {
+ if (sq != 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)
+ {
+ // future functionality - featureType == null means mark columns
+ // containing all displayed features
+ if (sf != null && (featureType.equals(sf.getType())))
+ {
+ int sfStartCol = sq.findIndex(sf.getBegin());
+ int sfEndCol = sq.findIndex(sf.getEnd()); // inefficient - JAL-2526
+
+ if (sf.isContactFeature())
+ {
+ /*
+ * 'contact' feature - check for 'start' or 'end'
+ * position within the selected region
+ */
+ if (sfStartCol >= startPosition && sfStartCol <= endPosition)
+ {
+ bs.set(sfStartCol - 1);
+ overlap = true;
+ }
+ if (sfEndCol >= startPosition && sfEndCol <= endPosition)
+ {
+ 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 (overlap)
+ {
+ nseq++;
+ }
+ }
+ }
+ return nseq;
+ }
+
@Override
public void sortAlignmentByFeatureDensity(List<String> typ)
{
}
@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;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff