@Override
public void configure(final Set<Parameter> conf) throws EoulsanException {
// The merge does not need any parameter
for (Parameter p : conf) {
throw new EoulsanException(
"Unknown parameter for " + getFormat().getName() + " merger: " + p.getName());
}
}
/**
* Set the constants values
*
* @param parameters a set with the parameters
* @throws EoulsanException if an error occurs while evaluating the parameters
*/
private void addConstants(final Set<Parameter> parameters) throws EoulsanException {
if (parameters == null) {
return;
}
for (Parameter p : parameters) {
if (!"".equals(p.getName())) {
addConstant(p.getName(), p.getValue(), true);
}
}
}
/**
* Set the "gtf.feature.exon" and "gtf.tag.exon.parent.transcript" parameter from the expression
* step parameters.
*
* @param context the context of the task
* @throws EoulsanException if more than one expression step exists
*/
private void searchExpressionStepParameters(final TaskContext context) throws EoulsanException {
int count = 0;
for (Step step : context.getWorkflow().getSteps()) {
if (AbstractExpressionModule.MODULE_NAME.equals(step.getModuleName())) {
for (Parameter p : step.getParameters()) {
switch (p.getName()) {
case AbstractExpressionModule.OLD_GENOMIC_TYPE_PARAMETER_NAME:
case AbstractExpressionModule.GENOMIC_TYPE_PARAMETER_NAME:
gtfFeatureExon = p.getStringValue();
break;
case AbstractExpressionModule.OLD_ATTRIBUTE_ID_PARAMETER_NAME:
case AbstractExpressionModule.ATTRIBUTE_ID_PARAMETER_NAME:
gtfTagExonParentTranscript = p.getStringValue();
break;
default:
break;
}
}
count++;
}
}
if (count == 0) {
throw new EoulsanException("No expression step found in the workflow");
}
if (count > 1) {
throw new EoulsanException("Found more than one expression step in the workflow");
}
}
@Override
public void configure(final StepConfigurationContext context, final Set<Parameter> stepParameters)
throws EoulsanException {
if (stepParameters == null) {
throw new EoulsanException("No parameters set in " + getName() + " generator");
}
for (Parameter p : stepParameters) {
switch (p.getName()) {
case "overhang":
this.overhang = p.getIntValueGreaterOrEqualsTo(1);
break;
case "gtf.file":
Modules.renamedParameter(context, p, "use.gtf.file");
case "use.gtf.file":
this.gtfFile = p.getBooleanValue();
break;
case "file.chr.start.end":
this.chrStartEndFilename = p.getStringValue();
break;
case "gtf.feature.exon":
this.gtfFeatureExon = p.getStringValue();
break;
case "gtf.tag.exon.parent.transcript":
this.gtfTagExonParentTranscript = p.getStringValue();
break;
case "genome.sa.index.nbases":
this.genomeSAindexNbases = p.getIntValueGreaterOrEqualsTo(0);
break;
case "genome.chr.bin.nbits":
this.genomeChrBinNbits = p.getIntValueGreaterOrEqualsTo(0);
break;
case "use.expression.step.parameters":
this.useExpressionStepParameters = p.getBooleanValue();
break;
case "local.threads":
this.localThreads = p.getIntValueGreaterOrEqualsTo(1);
break;
case "max.local.threads":
this.maxLocalThreads = p.getIntValueGreaterOrEqualsTo(1);
break;
case "features.file.format":
switch (p.getLowerStringValue()) {
case "gtf":
this.gtfFormat = true;
break;
case "gff":
case "gff3":
this.gtfFormat = false;
break;
default:
Modules.badParameterValue(context, p, "Unknown annotation file format");
break;
}
break;
default:
throw new EoulsanException(
"Unknown parameter for " + getName() + " step: " + p.getName());
}
}
}