public int getBlastWordSize ( ) { if ( param . containsKey ( WORD_SIZE ) ) { return Integer . parseInt ( getAlignmentOption ( WORD_SIZE ) ) ; } // return default word size value try { BlastProgramEnum programType = getBlastProgram ( ) ; switch ( programType ) { case blastn : return 11 ; case megablast : return 28 ; case blastp : case blastx : case tblastn : case tblastx : return 3 ; default : throw new UnsupportedOperationException ( "Blast program " + programType . name ( ) + " is not supported." ) ; } } catch ( IllegalArgumentException e ) { throw new IllegalArgumentException ( "Blast program " + getBlastProgram ( ) + " is not supported." , e ) ; } }
Returns the value of the WORD_SIZE parameter used for this blast run