private XenomeFields constructFieldsByIndex()

in src/main/java/com/epam/fonda/tools/impl/Xenome.java [108:162]
54 lines of code
14 McCabe index (conditional complexity)

    private XenomeFields constructFieldsByIndex(Configuration configuration) {
        XenomeFields xenomeFields = new XenomeFields();
        if (index != null) {
            xenomeFields.index = String.valueOf(index);
        }
        xenomeFields.fastq1 = result.getOut().getMergedFastq1();
        xenomeFields.fastq2 = result.getOut().getMergedFastq2();
        xenomeFields.xenome = validate(configuration.getGlobalConfig().getToolConfig().getXenome(),
                GlobalConfigFormat.XENOME);
        xenomeFields.mouseXenomeIndex = validate(
                configuration.getGlobalConfig().getDatabaseConfig().getMouseXenomeIndex(),
                GlobalConfigFormat.MOUSE_XENOME_INDEX);
        xenomeFields.stmpOutDir = sample.getTmpOutdir();
        if (xenomeFields.index != null) {
            xenomeFields.prefix = format("%s/%s_%s", xenomeFields.stmpOutDir, sample
                    .getName(), xenomeFields.index);
            xenomeFields.humanMergedFastq1 = format("%s/%s_%s_classified_R1.fq.gz",
                    sample.getFastqOutdir(), sample.getName(), xenomeFields.index);
            xenomeFields.humanMergedFastq2 = StringUtils.isBlank(xenomeFields.fastq2) ? null
                    : format("%s/%s_%s_classified_R2.fq.gz", sample.getFastqOutdir(), sample.getName(),
                    xenomeFields.index);
        } else {
            xenomeFields.prefix = format("%s/%s", xenomeFields.stmpOutDir, sample.getName());
            xenomeFields.humanMergedFastq1 = format("%s/%s_classified_R1.fq.gz", sample.getFastqOutdir(),
                    sample.getName());
            xenomeFields.humanMergedFastq2 = StringUtils.isBlank(xenomeFields.fastq2) ? null
                    : format("%s/%s_classified_R2.fq.gz", sample.getFastqOutdir(), sample.getName());
        }

        xenomeFields.humanFastq1 = StringUtils.isBlank(xenomeFields.fastq2)
                ? format("%s_human.fastq", xenomeFields.prefix)
                : format("%s_human_1.fastq", xenomeFields.prefix);
        xenomeFields.humanFastq2 = StringUtils.isBlank(xenomeFields.fastq2) ? null
                : format("%s_human_2.fastq", xenomeFields.prefix);
        xenomeFields.bothFastq1 = StringUtils.isBlank(xenomeFields.fastq2)
                ? format("%s_both.fastq", xenomeFields.prefix)
                : format("%s_both_1.fastq", xenomeFields.prefix);
        xenomeFields.bothFastq2 = StringUtils.isBlank(xenomeFields.fastq2) ? null
                : format("%s_both_2.fastq", xenomeFields.prefix);
        xenomeFields.ambiguousFastq1 = StringUtils.isBlank(xenomeFields.fastq2)
                ? format("%s_ambiguous.fastq", xenomeFields.prefix)
                : format("%s_ambiguous_1.fastq", xenomeFields.prefix);
        xenomeFields.ambiguousFastq2 = StringUtils.isBlank(xenomeFields.fastq2) ? null
                : format("%s_ambiguous_2.fastq", xenomeFields.prefix);
        xenomeFields.convertHumanFastq1 = format("%s_convert_human_1.fastq", xenomeFields.prefix);
        xenomeFields.convertHumanFastq2 = StringUtils.isBlank(xenomeFields.fastq2) ? null
                : format("%s_convert_human_2.fastq", xenomeFields.prefix);
        xenomeFields.convertBothFastq1 = format("%s_convert_both_1.fastq", xenomeFields.prefix);
        xenomeFields.convertBothFastq2 = StringUtils.isBlank(xenomeFields.fastq2) ? null
                : format("%s_convert_both_2.fastq", xenomeFields.prefix);
        xenomeFields.convertAmbiguousFastq1 = format("%s_convert_ambiguous_1.fastq", xenomeFields.prefix);
        xenomeFields.convertAmbiguousFastq2 = StringUtils.isBlank(xenomeFields.fastq2) ? null
                : format("%s_convert_ambiguous_2.fastq", xenomeFields.prefix);
        return xenomeFields;
    }