protected int [ ] getSubstitutionScoreVector ( int queryColumn , Subproblem subproblem ) { int [ ] subs = new int [ subproblem . getTargetEndIndex ( ) + 1 ] ; if ( queryColumn > 0 ) { for ( int y = Math . max ( 1 , subproblem . getTargetStartIndex ( ) ) ; y <= subproblem . getTargetEndIndex ( ) ; y ++ ) { subs [ y ] = getSubstitutionScore ( queryColumn , y ) ; } } return subs ; }
Returns score for the alignment of the query column to all target columns