true);
for (int i = 0; i < nSeq; i++)
{
- scores[i] = (float) PIDModel.computePID(align.getSequenceAt(i)
- .getSequenceAsString(), refSeq, pidParams);
+ scores[i] = (float) PIDModel.computePID(
+ align.getSequenceAt(i).getSequenceAsString(), refSeq,
+ pidParams);
seqs[i] = align.getSequenceAt(i);
}
}
else
{
- setReverseOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
+ setReverseOrder(align,
+ vectorSubsetToArray(tmp, align.getSequences()));
}
}
if (tmp.size() != nSeq)
{
- System.err
- .println("WARNING: tmp.size()="
- + tmp.size()
- + " != nseq="
- + nSeq
- + " in getOrderByTree - tree contains sequences not in alignment");
+ System.err.println("WARNING: tmp.size()=" + tmp.size() + " != nseq="
+ + nSeq
+ + " in getOrderByTree - tree contains sequences not in alignment");
}
}
}
else
{
- setReverseOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
+ setReverseOrder(align,
+ vectorSubsetToArray(tmp, align.getSequences()));
}
}
public static String FEATURE_DENSITY = "density";
- private static boolean containsIgnoreCase(final String lab,
- final List<String> labs)
- {
- if (labs == null)
- {
- return true;
- }
- if (lab == null)
- {
- return false;
- }
- for (String label : labs)
- {
- if (lab.equalsIgnoreCase(label))
- {
- return true;
- }
- }
- return false;
- }
-
/**
* Sort sequences by feature score or density, optionally restricted by
* feature types, feature groups, or alignment start/end positions.
* get sequence residues overlapping column region
* and features for residue positions and specified types
*/
- // TODO new method findPositions(startCol, endCol)? JAL-2544
- int startResidue = seqs[i].findPosition(startCol);
- int endResidue = seqs[i].findPosition(endCol);
String[] types = featureTypes == null ? null : featureTypes
.toArray(new String[featureTypes.size()]);
- List<SequenceFeature> sfs = seqs[i].getFeatures().findFeatures(
- startResidue, endResidue, types);
+ List<SequenceFeature> sfs = seqs[i].findFeatures(startCol + 1,
+ endCol + 1, types);
seqScores[i] = 0;
scores[i] = 0.0;
{
SequenceFeature sf = it.next();
+ /*
+ * accept all features with null or empty group, otherwise
+ * check group is one of the currently visible groups
+ */
String featureGroup = sf.getFeatureGroup();
if (groups != null && featureGroup != null
+ && !"".equals(featureGroup)
&& !groups.contains(featureGroup))
{
it.remove();