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0. BIOPYTHON mafIO ==================     def mafParsing(self,chrName ):         idx = MafIndex(chrName + ".mafindex", chrName + ".maf", "hg19." + chrName )         multiple_alignment = idx.get_spliced([60000] ,  [60020] , strand = "-")               AlignIO.write(multiple_alignment, "hg19_All.fa", "fasta")         total_bases_tupBel1  = 0;         for seqrec in multiple_alignment:                 if seqrec.id.startswith("tupBel1"): # mm4  tupBel1  tanvir                     # don't count gaps as bases              ...

return the match index /  the next index if no match int findDownstreamStart( int key)     {         int imax = vectNegStart.size();         int imin = 0;         int imid = (imin + imax) / 2;                 if( key <= vectNegStart.get(0))             return 0;         if( key >= vectNegStart.get(imax-1 ))             return imax-1;                     // continue searching while [imin,imax] is not empty         while (imax >= imin)         {             /* calculate the midpoint for roughly e...

// create map LinkedHashMap hashmapGene = new LinkedHashMap() (); // insert element into map             if( hashmapGene.containsKey(geneID) )             {                                GeneInfo gene = hashmapGene.get(geneID);                 gene.determineClass(tmp[3]);                            }else             {                 hashmapGene.put( geneID , new GeneInfo(chrom , st,end, promStartCoord, promEndCoord ,                ...