Example usage for org.apache.commons.lang ArrayUtils subarray

Introduction

In this page you can find the example usage for org.apache.commons.lang ArrayUtils subarray.

Prototype

public static boolean[] subarray(boolean[] array, int startIndexInclusive, int endIndexExclusive)

Source Link

Document

Produces a new boolean array containing the elements between the start and end indices.

Usage

From source file:uk.ac.ebi.eva.pipeline.io.mappers.AnnotationLineMapper.java

/**
 * From org.opencb.biodata.formats.annotation.io.VepFormatReader#parseVariant(java.lang.String, java.lang.String)
 *///from  w w w. j  a  v  a2 s. c  o  m
private Map<String, String> parseVariant(String variantString, String coordinatesString) {
    //    private Map<String,String> parseVariant(String coordinatesString, String alternativeString) {

    Map<String, String> parsedVariant = new HashMap<>(5);

    try {
        String[] variantLocationFields = coordinatesString.split("[:-]");
        //            parsedVariant.put("chromosome", variantLocationFields[0]);
        //            parsedVariant.put("start", variantLocationFields[1]);
        parsedVariant.put("end",
                (variantLocationFields.length > 2) ? variantLocationFields[2] : variantLocationFields[1]);
    } catch (ArrayIndexOutOfBoundsException e) {
        logger.error("Unexpected format for column 2: " + coordinatesString);
        throw e;
    }

    try {
        // Some VEP examples:
        // 1_718787_-/T    1:718786-718787 T    ...
        // 1_718787_T/-    1:718787        -    ...
        // 1_718788_T/A    1:718788        A    ...
        String[] variantFields = variantString.split("[\\/]");
        //        String[] variantFields = variantString.split("[\\_\\/]");
        String[] leftVariantFields = variantFields[0].split("_");

        // Chr id containing _
        if (leftVariantFields.length > 3) {
            parsedVariant.put("chromosome", String.join("_",
                    (String[]) ArrayUtils.subarray(leftVariantFields, 0, leftVariantFields.length - 2)));
        } else {
            parsedVariant.put("chromosome", leftVariantFields[0]);
        }
        parsedVariant.put("start", leftVariantFields[leftVariantFields.length - 2]);
        parsedVariant.put("reference", leftVariantFields[leftVariantFields.length - 1]);
        parsedVariant.put("alternative", variantFields[1]);
    } catch (ArrayIndexOutOfBoundsException e) {
        logger.error("Unexpected variant format for column 1: " + variantString);
        throw e;
    }

    return parsedVariant;
}

From source file:uk.ac.tgac.rampart.stage.analyse.asm.stats.AssemblyStats.java

public AssemblyStats(String[] stats) {
    this();//from   w w  w  . j  a v  a 2 s.c om

    int i = 0;
    this.index = Integer.parseInt(stats[i++]);
    this.desc = stats[i++];
    this.dataset = stats[i++];
    this.filePath = stats[i++];
    this.bubblePath = stats[i++];
    this.contiguity.parseStrings((String[]) ArrayUtils.subarray(stats, i, i + this.contiguity.getNbMetrics()));
    i += this.contiguity.getNbMetrics();
    this.problems.parseStrings((String[]) ArrayUtils.subarray(stats, i, i + this.problems.getNbMetrics()));
    i += this.problems.getNbMetrics();
    this.conservation
            .parseStrings((String[]) ArrayUtils.subarray(stats, i, i + this.conservation.getNbMetrics()));
    i += this.conservation.getNbMetrics();
    this.finalScore = Double.parseDouble(stats[i++]);
}

From source file:wzw.lang.ArraySupport.java

public static Object[] subarray(Object[] array, int startIndexInclusive, int endIndexExclusive) {
    return ArrayUtils.subarray(array, startIndexInclusive, endIndexExclusive);
}