com.intel.genomicsdb.GenomicsDBPartitionInfo.java Source code

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Here is the source code for com.intel.genomicsdb.GenomicsDBPartitionInfo.java

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/*
* The MIT License (MIT)
* Copyright (c) 2016 Intel Corporation
*
* Permission is hereby granted, free of charge, to any person obtaining a copy of
* this software and associated documentation files (the "Software"), to deal in
* the Software without restriction, including without limitation the rights to
* use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
* the Software, and to permit persons to whom the Software is furnished to do so,
* subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
* FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
* COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
* IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
* CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/

package com.intel.genomicsdb;

import com.fasterxml.jackson.databind.ObjectMapper;

import java.io.IOException;
import java.io.Serializable;

/**
 * Maintain global information on how variant data is partitioned
 * across multiple nodes (if loaded with mpiexec)
 *
 * The assumption is that every object described one partition as:
 * {"begin": 0, "workspace":"/home/forall/tiledb-ws",
 *  "array": "test0", "vcf_output_filename":"/home/forall/lihao/mytest/test0.vcf.gz" }
 */
class GenomicsDBPartitionInfo implements Serializable {

    private Integer beginPosition;
    private String tileDBWorkspace;
    private String tileDBArrayName;
    private String VCFOutputFileName;

    public GenomicsDBPartitionInfo(Integer pos, String workspace, String arrayName, String vcfOutput) {
        beginPosition = pos;
        tileDBWorkspace = workspace;
        tileDBArrayName = arrayName;
        VCFOutputFileName = vcfOutput;
    }

    @Override
    public String toString() {
        String out = beginPosition.toString() + " ";
        out += tileDBWorkspace + " ";
        out += tileDBArrayName + " ";
        out += VCFOutputFileName;
        return out;
    }

    /**
     * Create a JSON string from the partition info object
     *
     * @return  A JSON string of the partition info
     * @throws IOException write throws IOException
     */
    public String toJSON() throws IOException {
        ObjectMapper mapper = new ObjectMapper();
        mapper.writeValueAsString(toString());
        return mapper.toString();
    }
}