private static List < Monomer > getMonomersRNAOnlyBase ( MonomerNotationUnitRNA rna , MonomerStore monomerStore ) throws HELM2HandledException { try { List < Monomer > monomers = new ArrayList < Monomer > ( ) ; for ( MonomerNotationUnit unit : rna . getContents ( ) ) { String id = unit . getUnit ( ) . replace ( "[" , "" ) ; id = id . replace ( "]" , "" ) ; Monomer mon = MethodsMonomerUtils . getMonomer ( rna . getType ( ) , id , "" ) ; if ( mon . getMonomerType ( ) . equals ( Monomer . BRANCH_MOMONER_TYPE ) ) { monomers . add ( mon ) ; } } return monomers ; } catch ( Exception e ) { e . printStackTrace ( ) ; throw new HELM2HandledException ( e . getMessage ( ) ) ; } }
method to get only the nucleotide base for one MonomerNotationUnitRNA