+
+ /**
+ * 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)
+ {
+ boolean sequenceHasFeature = false;
+ if (sq != null)
+ {
+ SequenceFeature[] sfs = sq.getSequenceFeatures();
+ if (sfs != null)
+ {
+ 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)
+ {
+ // 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());
+
+ 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
+ }
+ }
+ }
+ }
+
+ if (sequenceHasFeature)
+ {
+ nseq++;
+ }
+ }
+ }
+ return nseq;
+ }
+
+ @Override
+ public void sortAlignmentByFeatureDensity(List<String> typ)
+ {
+ sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
+ }
+
+ protected void sortBy(List<String> typ, String methodText,
+ final String method)
+ {
+ FeatureRenderer fr = alignPanel.getFeatureRenderer();
+ if (typ == null && fr != null)
+ {
+ typ = fr.getDisplayedFeatureTypes();
+ }
+ List<String> gps = null;
+ if (fr != null)
+ {
+ gps = fr.getDisplayedFeatureGroups();
+ }
+ AlignmentI al = viewport.getAlignment();
+
+ int start, stop;
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (sg != null)
+ {
+ start = sg.getStartRes();
+ stop = sg.getEndRes();
+ }
+ else
+ {
+ start = 0;
+ stop = al.getWidth();
+ }
+ SequenceI[] oldOrder = al.getSequencesArray();
+ AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
+ avcg.addHistoryItem(new OrderCommand(methodText, oldOrder, viewport
+ .getAlignment()));
+ alignPanel.paintAlignment(true);
+
+ }
+
+ @Override
+ public void sortAlignmentByFeatureScore(List<String> typ)
+ {
+ sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
+ }
+
+ @Override
+ public boolean parseFeaturesFile(String file, DataSourceType protocol,
+ boolean relaxedIdMatching)
+ {
+ boolean featuresFile = false;
+ try
+ {
+ featuresFile = new FeaturesFile(false, file, protocol).parse(viewport
+ .getAlignment().getDataset(), alignPanel.getFeatureRenderer()
+ .getFeatureColours(), false, relaxedIdMatching);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ if (featuresFile)
+ {
+ avcg.refreshFeatureUI(true);
+ if (alignPanel.getFeatureRenderer() != null)
+ {
+ // update the min/max ranges where necessary
+ alignPanel.getFeatureRenderer().findAllFeatures(true);
+ }
+ if (avcg.getFeatureSettingsUI() != null)
+ {
+ avcg.getFeatureSettingsUI().discoverAllFeatureData();
+ }
+ alignPanel.paintAlignment(true);
+ }
+
+ 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;
+ }
+
+}