/*************************************************************************
 * tranSMART - translational medicine data mart
 *
 * Copyright 2008-2012 Janssen Research & Development, LLC.
 *
 * This product includes software developed at Janssen Research & Development, LLC.
 *
 * This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License 
 * as published by the Free Software  * Foundation, either version 3 of the License, or (at your option) any later version, along with the following terms:
 * 1.	You may convey a work based on this program in accordance with section 5, provided that you retain the above notices.
 * 2.	You may convey verbatim copies of this program code as you receive it, in any medium, provided that you retain the above notices.
 *
 * This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS    * FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License along with this program.  If not, see <http://www.gnu.org/licenses/>.
 *
 *
 ******************************************************************/


package i2b2

/**
 * This class contains SNP data from multiple datasets. 
 */
class SnpDatasetListByProbe {
    String trialName;
    List<Long> patientNumList_1;
    List<Long> patientNumList_2;
    List<SnpDataset> datasetList;    // The list of SnpDataset in the order of final xcn file
    List<String> datasetNameForSNPViewerList;
    //	The list of SnpDataset names in the order of final xcn file, like S1_ and S2_
    Map<Long, SnpDataset[]> snpDatasetBySubjectMap;    // <PatientNum, [Normal Dataset, Disease Dataset]>
    Map<Long, Integer> datasetCompactLocationMap;    // <dataset ID, order in the compacted String>
    Map<String, List<SnpDataByProbe>> snpDataByChromMap;
    // <Chrom, List<SnpDataByProbe> in the order of chromPos>

    public SnpDatasetListByProbe() {
        datasetList = new ArrayList<SnpDataset>();
        datasetNameForSNPViewerList = new ArrayList<String>();
        snpDatasetBySubjectMap = new HashMap<Long, SnpDataset[]>();
        snpDataByChromMap = new HashMap<String, List<SnpDataByProbe>>();
        datasetCompactLocationMap = new HashMap<Long, Integer>();
    }
}
