private static List < Monomer > getMonomersRNA ( MonomerNotationUnitRNA rna , MonomerStore monomerStore , int position ) throws HELM2HandledException { try { List < Monomer > monomers = new ArrayList < Monomer > ( ) ; for ( int index = 0 ; index < rna . getContents ( ) . size ( ) ; index ++ ) { String id = rna . getContents ( ) . get ( index ) . getUnit ( ) ; if ( rna . getContents ( ) . get ( index ) . getUnit ( ) . startsWith ( "[" ) && rna . getContents ( ) . get ( index ) . getUnit ( ) . endsWith ( "]" ) ) { id = id . substring ( 1 , id . length ( ) - 1 ) ; } /* Special case */ if ( rna . getContents ( ) . size ( ) == 1 && position == 0 ) { monomers . add ( MethodsMonomerUtils . getMonomer ( rna . getType ( ) , id , "P" ) ) ; } else { monomers . add ( MethodsMonomerUtils . getMonomer ( rna . getType ( ) , id , rna . getInformation ( ) . get ( index ) ) ) ; } } return monomers ; } catch ( Exception e ) { e . printStackTrace ( ) ; throw new HELM2HandledException ( e . getMessage ( ) ) ; } }
method to get all monomers for MonomerNotationUnitRNA