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()));
}
}
int start, int stop, AlignmentI alignment, String method)
{
sortByFeature(
- featureLabel == null ? null
- : Arrays.asList(new String[] { featureLabel }),
- groupLabel == null ? null : Arrays
- .asList(new String[] { groupLabel }), start, stop,
- alignment, method);
+ featureLabel == null ? null : Arrays.asList(new String[]
+ { featureLabel }),
+ groupLabel == null ? null : Arrays.asList(new String[]
+ { groupLabel }), start, stop, alignment, method);
}
private static boolean containsIgnoreCase(final String lab,
if (method != FEATURE_SCORE && method != FEATURE_LABEL
&& method != FEATURE_DENSITY)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_sortbyfeature"));
+ throw new Error(MessageManager
+ .getString("error.implementation_error_sortbyfeature"));
}
boolean ignoreScore = method != FEATURE_SCORE;
*/
boolean noOverlap = seqs[i].findIndex(feature.getBegin()) > stop + 1
|| seqs[i].findIndex(feature.getEnd()) < start + 1;
- boolean skipFeatureType = featureLabels != null
- && !AlignmentSorter.containsIgnoreCase(feature.type,
- featureLabels);
+ boolean skipFeatureType = featureLabels != null && !AlignmentSorter
+ .containsIgnoreCase(feature.type, featureLabels);
boolean skipFeatureGroup = groupLabels != null
- && (feature.getFeatureGroup() != null && !AlignmentSorter
- .containsIgnoreCase(feature.getFeatureGroup(),
- groupLabels));
+ && (feature.getFeatureGroup() != null
+ && !AlignmentSorter.containsIgnoreCase(
+ feature.getFeatureGroup(), groupLabels));
if (noOverlap || skipFeatureType || skipFeatureGroup)
{
// forget about this feature
String[] labs = new String[fs.length];
for (int l = 0; l < labs.length; l++)
{
- labs[l] = (fs[l].getDescription() != null ? fs[l]
- .getDescription() : fs[l].getType());
+ labs[l] = (fs[l].getDescription() != null
+ ? fs[l].getDescription()
+ : fs[l].getType());
}
QuickSort.sort(labs, ((Object[]) feats[i]));
}