private List<Region> findOverlappingRegions(Result blastResult) {
List<Region> result = new ArrayList<Region>();
for (BlastAnalysis.Region region : blastResult.getReference().getRegions())
if (region.overlaps(blastResult.getStart(), blastResult.getEnd(), MINIMUM_REGION_OVERLAP))
result.add(region);
return result;
}
private boolean subgenogroupPhyloAnalysis(
AbstractSequence s, Result blastResult, Region region, Cluster typeCluster)
throws AnalysisException, IOException, ParameterProblemException, FileFormatException {
PhyloClusterAnalysis a =
getPhyloAnalysis(blastResult.getConcludedCluster().getId(), typeCluster.getId(), region);
if (a == null) {
if (region != null) {
region = null;
a =
getPhyloAnalysis(
blastResult.getConcludedCluster().getId(), typeCluster.getId(), region);
if (a == null) return false;
} else {
List<Region> regions = Collections.emptyList();
if (blastResult.getReference() != null)
/*
* Perhaps we have an analysis for the region covered by the input sequence ?
*/
regions = findOverlappingRegions(blastResult);
boolean result = false;
for (Region r : regions)
if (subgenogroupPhyloAnalysis(s, blastResult, r, typeCluster)) result = true;
return result;
}
}
if (region != null) s = cutRegion(s, blastResult, region);
PhyloClusterAnalysis.Result r = a.run(s);
ScanAnalysis.Result scanResult = checkBootScan(a, s);
String phyloName = "phylogenetic subgenogroup analysis within " + typeCluster.getId();
/*
* If we are clustering with the outgroup, then clearly we could not identify a variant.
*
* WARNING: the following test is based on a variant cluster to start with the same
* name as the genotype for which it is a variant!
* This is to differentiate with the outgroup. It would be better to mark the
* outgroup with some attribute ?
*/
if (r == null
|| (scanResult != null && !scanResult.haveSupport())
|| r.getConcludedCluster() == null
|| !r.getConcludedCluster().getId().contains(typeCluster.getId())
|| !r.haveSupport())
conclude("Could not assign", "Not supported by " + phyloName, "subtype", region);
else
conclude(
r,
new WString("Supported with " + phyloName + " and bootstrap {1} (>= {2})")
.arg(r.getConcludedSupport())
.arg(a.getCutoff()),
"subtype",
region);
return true;
}