Class FastaAFPChainConverter

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static AFPChain cpFastaToAfpChain​(java.io.File fastaFile, Structure structure, int cpSite)
      Takes a structure and sequence corresponding to an alignment between a structure or sequence and itself (or even a structure with a sequence), where the result has a circular permutation site cpSite residues to the right.
      static AFPChain cpFastaToAfpChain​(java.lang.String first, java.lang.String second, Structure structure, int cpSite)  
      static AFPChain cpFastaToAfpChain​(ProteinSequence first, ProteinSequence second, Structure structure, int cpSite)
      Takes a structure and sequence corresponding to an alignment between a structure or sequence and itself (or even a structure with a sequence), where the result has a circular permutation site cpSite residues to the right.
      static AFPChain fastaFileToAfpChain​(java.io.File fastaFile, Structure structure1, Structure structure2)
      Reads the file fastaFile, expecting exactly two sequences which give a pairwise alignment.
      static AFPChain fastaStringToAfpChain​(java.lang.String sequence1, java.lang.String sequence2, Structure structure1, Structure structure2)
      Returns an AFPChain corresponding to the alignment between structure1 and structure2, which is given by the gapped protein sequences sequence1 and sequence2.
      static AFPChain fastaToAfpChain​(java.lang.String sequence1, java.lang.String sequence2, Structure structure1, Structure structure2)
      TODO Write comment
      static AFPChain fastaToAfpChain​(java.util.Map<java.lang.String,​ProteinSequence> sequences, Structure structure1, Structure structure2)
      Uses two sequences each with a corresponding structure to create an AFPChain corresponding to the alignment.
      static AFPChain fastaToAfpChain​(SequencePair<Sequence<AminoAcidCompound>,​AminoAcidCompound> alignment, Structure structure1, Structure structure2)
      Provided only for convenience.
      static AFPChain fastaToAfpChain​(ProteinSequence sequence1, ProteinSequence sequence2, Structure structure1, Structure structure2)
      Returns an AFPChain corresponding to the alignment between structure1 and structure2, which is given by the gapped protein sequences sequence1 and sequence2.
      static java.util.List<java.lang.Object> getAlignedUserCollection​(java.lang.String sequence)
      Takes a protein sequence string with capital and lowercase letters and sets its user collection to record which letters are uppercase (aligned) and which are lowercase (unaligned).
      static void main​(java.lang.String[] args)
      Prints out the XML representation of an AFPChain from a file containing exactly two FASTA sequences.
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait