private int getSubstitutionScore ( float [ ] qv , float [ ] tv ) { float score = 0.0f ; for ( int q = 0 ; q < qv . length ; q ++ ) { if ( qv [ q ] > 0.0f ) { for ( int t = 0 ; t < tv . length ; t ++ ) { if ( tv [ t ] > 0.0f ) { score += qv [ q ] * tv [ t ] * getSubstitutionMatrix ( ) . getValue ( cslist . get ( q ) , cslist . get ( t ) ) ; } } } } return Math . round ( score ) ; }
helper method that scores alignment of two column vectors