public boolean checkReference(SequencesReader sr,Map<String,Long> sequenceNameMap) throws IOException {
  for (  CheckValues cv : mValues) {
    if (!sequenceNameMap.containsKey(cv.getSequenceName())) {
      return false;
    }
    final long sequenceId=sequenceNameMap.get(cv.getSequenceName());
    for (int i=0; i < mChecks.size(); i++) {
      final CheckType check=mChecks.get(i);
      if (!check.checkValue(sr,sequenceId,cv.getValue(i))) {
        return false;
      }
    }
  }
  return true;
}

public boolean checkReference ( SequencesReader sr , Map < String , Long > sequenceNameMap ) throws IOException { for ( CheckValues cv : mValues ) { if ( ! sequenceNameMap . containsKey ( cv . getSequenceName ( ) ) ) { return false ; } final long sequenceId = sequenceNameMap . get ( cv . getSequenceName ( ) ) ; for ( int i = 0 ; i < mChecks . size ( ) ; i ++ ) { final CheckType check = mChecks . get ( i ) ; if ( ! check . checkValue ( sr , sequenceId , cv . getValue ( i ) ) ) { return false ; } } } return true ; }
checks whether given sequences reader matches criteria from loaded manifest
