private static float calculateExtinctionFromPeptide ( List < Monomer > monomers ) throws IOException , HELM2HandledException { if ( null == monomers || monomers . isEmpty ( ) ) { return 0.0f ; } Map < String , Integer > countMap = new HashMap < String , Integer > ( ) ; for ( Monomer monomer : monomers ) { if ( aminoAcidMap . containsKey ( monomer . getAlternateId ( ) ) ) { int count = 1 ; if ( countMap . containsKey ( monomer . getAlternateId ( ) ) ) { count = count + countMap . get ( monomer . getAlternateId ( ) ) ; } countMap . put ( monomer . getAlternateId ( ) , count ) ; } } float result = 0.0f ; Set < String > keys = countMap . keySet ( ) ; for ( Iterator < String > it = keys . iterator ( ) ; it . hasNext ( ) ; ) { String key = it . next ( ) ; int count = countMap . get ( key ) ; float factor = aminoAcidMap . get ( key ) ; result = result + factor * count ; } return BigDecimal . valueOf ( result ) . floatValue ( ) ; }
method to calculate the extinction coefficient for peptide