Package org.biojava.nbio.alignment.io

Class StockholmStructure

  • public class StockholmStructure
extends Object
    Stores all the content of a Stockholm file. N.B.: This structure will undergo several enhancements later on. Don't depend on it in a final code, otherwise it will be hard to maintain. In general, Stockholm File contains the alignment mark-up lines.

    Header Section
    Reference Section
    Comment Section
    Alignment Section
    Sequence letters may include any characters except whitespace. Gaps may be indicated by "." or "-".
    Mark-up lines may include any characters except whitespace. Use underscore ("_") instead of space.
    section field preferred location
    #=GF <feature> <Generic per-File annotation, free text> Above the alignment
    #=GC <feature> <Generic per-Column annotation, exactly 1 char per column> Below the alignment
    #=GS <seqname> <feature> <Generic per-Sequence annotation, free text> Above the alignment or just below the corresponding sequence
    #=GR <seqname> <feature> <Generic per-Residue annotation, exactly 1 char per residue> Just below the corresponding sequence
    Since:
    3.0.5
    Author:
    Amr ALHOSSARY, Marko Vaz

    • Constructor Detail

      • StockholmStructure

        public StockholmStructure()

    • Method Detail

      • getConsAnnotation

        public org.biojava.nbio.alignment.io.StockholmConsensusAnnotation getConsAnnotation()

      • appendToSequence

        public void appendToSequence​(String seqName,
                             String seqText)
        Parameters:
        seqName -
        seqText -

      • addGSAccessionNumber

        public void addGSAccessionNumber​(String seqName,
                                 String text)
        Parameters:
        seqName -
        text -

      • addGSDescription

        public void addGSDescription​(String seqName,
                             String text)

      • addGSdbReference

        public void addGSdbReference​(String seqName,
                             String text)
        Parameters:
        seqName -
        text -

      • addGSOrganismSpecies

        public void addGSOrganismSpecies​(String seqName,
                                 String text)

      • addGSOrganismClassification

        public void addGSOrganismClassification​(String seqName,
                                        String text)

      • addGSLook

        public void addGSLook​(String seqName,
                      String text)

      • addSurfaceAccessibility

        public void addSurfaceAccessibility​(String seqName,
                                    String text)

      • addTransMembrane

        public void addTransMembrane​(String seqName,
                             String text)

      • addPosteriorProbability

        public void addPosteriorProbability​(String seqName,
                                    String text)

      • addLigandBinding

        public void addLigandBinding​(String seqName,
                             String text)

      • addActiveSite

        public void addActiveSite​(String seqName,
                          String text)

      • addASPFamPredicted

        public void addASPFamPredicted​(String seqName,
                               String text)

      • addASSwissProt

        public void addASSwissProt​(String seqName,
                           String text)

      • addIntron

        public void addIntron​(String seqName,
                      String text)

      • addSecondaryStructure

        public void addSecondaryStructure​(String seqName,
                                  String text)

      • getBioSequences

        public List<AbstractSequence<? extends AbstractCompound>> getBioSequences​(boolean ignoreCase,
                                                                          String forcedSequenceType)
        This function tolerates mixed case letters, and allows for forcing the output biosequence type (PFAM/RFAM).
        Parameters:
        ignoreCase - if true, the function will deal with small letters as if they are capital ones
        forcedSequenceType - either null, PFAM, or RFAM.
        Returns:
        Biosequences according to the criteria specified
        See Also:
        getBioSequences(), getBioSequences(boolean)