public static AFPChain fastaToAfpChain ( SequencePair < Sequence < AminoAcidCompound > , AminoAcidCompound > alignment , Structure structure1 , Structure structure2 ) throws StructureException { List < AlignedSequence < Sequence < AminoAcidCompound > , AminoAcidCompound > > seqs = alignment . getAlignedSequences ( ) ; StringBuilder sb1 = new StringBuilder ( ) ; for ( AminoAcidCompound a : seqs . get ( 0 ) ) { sb1 . append ( a . getBase ( ) ) ; } try { ProteinSequence seq1 = new ProteinSequence ( sb1 . toString ( ) ) ; StringBuilder sb2 = new StringBuilder ( ) ; for ( AminoAcidCompound a : seqs . get ( 1 ) ) { sb1 . append ( a . getBase ( ) ) ; } ProteinSequence seq2 = new ProteinSequence ( sb2 . toString ( ) ) ; LinkedHashMap < String , ProteinSequence > map = new LinkedHashMap < String , ProteinSequence > ( ) ; map . put ( structure1 . getName ( ) , seq1 ) ; map . put ( structure2 . getName ( ) , seq2 ) ; return fastaToAfpChain ( map , structure1 , structure2 ) ; } catch ( CompoundNotFoundException e ) { logger . error ( "Unexpected error while creating protein sequences: {}. This is most likely a bug." , e . getMessage ( ) ) ; return null ; } }
Provided only for convenience .