private PhyloClusterAnalysis getPhyloAnalysis(String genusId, String typeId, Region region)
throws IOException, ParameterProblemException, FileFormatException {
String alignmentId = genusId;
if (region != null) alignmentId += "-" + region.getName();
String analysisId;
if (typeId != null) analysisId = "phylo-minor-" + typeId;
else analysisId = "phylo-major";
PhyloClusterAnalysis result = phyloAnalyses.get(alignmentId + "-" + analysisId);
if (result == null) {
String f = "phylo-" + alignmentId + ".xml";
if (new File(getXmlPathAsString() + f).canRead()) {
AlignmentAnalyses analyses = readAnalyses(getXmlPathAsString() + f, getWorkingDir());
analyses.setRegion(region);
if (analyses.haveAnalysis(analysisId)) {
result = (PhyloClusterAnalysis) analyses.getAnalysis(analysisId);
phyloAnalyses.put(alignmentId + "-" + analysisId, result);
}
}
}
return result;
}
