private AbstractSequence cutRegion(
AbstractSequence s, BlastAnalysis.Result blastResult, BlastAnalysis.Region region) {
int rs = Math.max(0, region.getBegin() - blastResult.getStart());
int re = Math.min(s.getLength(), s.getLength() - (blastResult.getEnd() - region.getEnd()));
AbstractSequence s2 = re > rs ? new SubSequence(s.getName(), s.getDescription(), s, rs, re) : s;
return s2;
}
@Override
public void analyze(AbstractSequence s) throws AnalysisException {
/*
* First perform the blast analysis.
*/
BlastAnalysis.Result blastResult = blastAnalysis.run(s);
if (blastResult.haveSupport()) {
Cluster c = blastResult.getConcludedCluster();
analyseClaster(c, s);
/*
* Reverse complement the sequence for subsequent analyses.
*/
if (blastResult.isReverseComplement()) s = s.reverseCompliment();
boolean haveConclusion = false;
try {
/*
* Perhaps we have a full-genome analysis?
*/
PhyloClusterAnalysis pca = getPhyloAnalysis(c.getId(), null, null);
if (pca != null) {
phyloAnalysis(pca, s, blastResult, null);
haveConclusion = true;
}
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);
if (!regions.isEmpty()) {
for (Region region : regions) {
pca = getPhyloAnalysis(c.getId(), null, region);
if (pca != null) {
AbstractSequence s2 = cutRegion(s, blastResult, region);
phyloAnalysis(pca, s2, blastResult, region);
haveConclusion = true;
}
}
}
} catch (IOException e) {
throw new AnalysisException("", s, e);
} catch (ParameterProblemException e) {
throw new AnalysisException("", s, e);
} catch (FileFormatException e) {
throw new AnalysisException("", s, e);
}
/*
* If no conclusion: conclude the blast result
*/
if (!haveConclusion)
if (blastAnalysis.getAbsCutoff() != null && blastAnalysis.getRelativeCutoff() != null)
conclude(
blastResult,
"Assigned based on BLAST absolute score >= "
+ blastAnalysis.getAbsCutoff()
+ " and relative score >= "
+ blastAnalysis.getRelativeCutoff(),
null);
else if (blastAnalysis.getAbsCutoff() != null)
conclude(
blastResult,
"Assigned based on BLAST absolute score >= " + blastAnalysis.getAbsCutoff(),
null);
else if (blastAnalysis.getRelativeCutoff() != null)
conclude(
blastResult,
"Assigned based on BLAST relative score >= " + blastAnalysis.getAbsCutoff(),
null);
} else {
if (blastAnalysis.getAbsCutoff() != null && blastAnalysis.getRelativeCutoff() != null)
conclude(
"Unassigned",
"Unassigned based on BLAST absolute score >= "
+ blastAnalysis.getAbsCutoff()
+ " and relative score >= "
+ blastAnalysis.getRelativeCutoff(),
null);
else if (blastAnalysis.getAbsCutoff() != null)
conclude(
"Unassigned",
"Unassigned based on BLAST absolute score >= " + blastAnalysis.getAbsCutoff(),
null);
else if (blastAnalysis.getRelativeCutoff() != null)
conclude(
"Unassigned",
"Unassigned based on BLAST relative score >= " + blastAnalysis.getAbsCutoff(),
null);
}
}