private ScanAnalysis.Result checkBootScan(PhyloClusterAnalysis pca, AbstractSequence s)
throws AnalysisException {
ScanAnalysis sa = null;
try {
sa = (ScanAnalysis) pca.getOwner().getAnalysis(pca.getId() + "-scan");
} catch (Exception e) {
/* If not available */
return null;
}
return sa.run(s);
}
/**
* @param pca phylogenetic analysis to run
* @param s sequence
* @param blastResult genus matched
* @param region region used for this analysis
*/
private void phyloAnalysis(
PhyloClusterAnalysis pca, AbstractSequence s, Result blastResult, Region region)
throws AnalysisException, IOException, ParameterProblemException, FileFormatException {
PhyloClusterAnalysis.Result r = pca.run(s);
ScanAnalysis.Result scanResult = checkBootScan(pca, s);
if (r.haveSupport() && (scanResult == null || scanResult.haveSupport())) {
conclude(
r,
new WString("Supported with phylogenetic analysis and bootstrap {1} (>= {2})")
.arg(r.getConcludedSupport())
.arg(pca.getCutoff()),
"type",
region);
subgenogroupPhyloAnalysis(s, blastResult, region, r.getConcludedCluster());
} else conclude("Could not assign", "Not supported by phylogenetic analysis", "type", region);
}
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;
}