/**
* 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");
}
}
