Beispiel #1
0
    @Override
    protected void setOptionFromMapEntry(ConanParameter param, String value) {

      Params params = this.getParams();

      if (param.equals(params.getGenomeDir())) {
        this.genomeDir = new File(value);
      } else if (param.equals(params.getGenomeDB())) {
        this.genomeDB = value;
      } else if (param.equals(params.getNovelSplicing())) {
        this.novelSplicing = Integer.parseInt(value) > 0;
      } else if (param.equals(params.getLocalSplicedDist())) {
        this.localSplicedDist = Integer.parseInt(value);
      } else if (param.equals(params.getThreads())) {
        this.threads = Integer.parseInt(value);
      } else if (param.equals(params.getOutputFormat())) {
        this.outputFormat = value;
      } else if (param.equals(params.getNbPaths())) {
        this.nbPaths = Integer.parseInt(value);
      } else if (param.equals(params.getBatch())) {
        this.batch = Integer.parseInt(value);
      } else if (param.equals(params.getExpandOffsets())) {
        this.expandOffsets = value.equalsIgnoreCase("1") ? true : false;
      } else if (param.equals(params.getKmer())) {
        this.kmer = Integer.parseInt(value);
      } else {
        throw new IllegalArgumentException("Unknown param found: " + param);
      }
    }
Beispiel #2
0
    @Override
    protected void setOptionFromMapEntry(ConanParameter param, String value) {

      Params params = this.getParams();

      if (param.equals(params.getJobPrefix())) {
        this.jobPrefix = value;
      } else if (param.equals(params.getRunParallel())) {
        this.runParallel = Boolean.parseBoolean(value);
      } else {
        throw new IllegalArgumentException("Unknown param found: " + param);
      }
    }
Beispiel #3
0
    @Override
    protected void setArgFromMapEntry(ConanParameter param, String value) {

      Params params = this.getParams();

      if (param.equals(params.getRead1())) {
        this.read1 = new File(value);
      } else if (param.equals(params.getRead2())) {
        this.read2 = new File(value);
      } else {
        throw new IllegalArgumentException("Unknown param found: " + param);
      }
    }
Beispiel #4
0
    @Override
    protected void setStdErrRedirectFromMapEntry(ConanParameter param, String value) {

      Params params = this.getParams();

      if (param.equals(params.getLogFile())) {
        this.logFile = new File(value);
      } else {
        throw new IllegalArgumentException("Unknown param found: " + param);
      }
    }