@Override
public void analyzeSelf(
String traceFile, String analysisFile, int windowSize, int stepSize, String analysisId)
throws AnalysisException {
try {
AlignmentAnalyses analyses = readAnalyses(analysisFile, getWorkingDir());
if (analysisId == null) {
for (AbstractAnalysis a : analyses.analyses()) {
if (a instanceof ScanAnalysis && a.getId().endsWith("-self-scan")) {
ScanAnalysis sa = (ScanAnalysis) a;
sa.setWindowSize(windowSize);
sa.setStepSize(stepSize);
sa.run(null);
}
}
} else {
ScanAnalysis sa = (ScanAnalysis) analyses.getAnalysis(analysisId);
sa.run(null);
}
} catch (IOException e) {
throw new RuntimeException(e);
} catch (ParameterProblemException e) {
throw new RuntimeException(e);
} catch (FileFormatException e) {
throw new RuntimeException(e);
}
}
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;
}
public GenericTool(ToolConfig toolConfig, File workDir)
throws IOException, ParameterProblemException, FileFormatException {
super(toolConfig, workDir);
blastXml = readAnalyses(getXmlPathAsString() + "blast.xml", getWorkingDir());
blastAnalysis = (BlastAnalysis) blastXml.getAnalysis("blast");
}
@Override
protected void formatDB() throws ApplicationException {
blastAnalysis.formatDB(blastXml.getAlignment());
}