Class StockholmStructure


  • public class StockholmStructure
    extends java.lang.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 AL-Hossary, Marko Vaz
    • Constructor Detail

      • StockholmStructure

        public StockholmStructure()
    • Method Detail

      • getConsAnnotation

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

        @Deprecated
        public void addSequence​(java.lang.String seqName,
                                java.lang.String seqText)
        Deprecated.
        Actually this function should be called appendToSequence
        Parameters:
        seqName -
        seqText -
      • appendToSequence

        public void appendToSequence​(java.lang.String seqName,
                                     java.lang.String seqText)
        Parameters:
        seqName -
        seqText -
      • getSequences

        public java.util.Map<java.lang.String,​java.lang.StringBuffer> getSequences()
      • addGSAccessionNumber

        public void addGSAccessionNumber​(java.lang.String seqName,
                                         java.lang.String text)
        Parameters:
        seqName -
        text -
      • addGSDescription

        public void addGSDescription​(java.lang.String seqName,
                                     java.lang.String text)
      • addGSdbReference

        public void addGSdbReference​(java.lang.String seqName,
                                     java.lang.String text)
        Parameters:
        seqName -
        text -
      • addGSOrganismSpecies

        public void addGSOrganismSpecies​(java.lang.String seqName,
                                         java.lang.String text)
      • addGSOrganismClassification

        public void addGSOrganismClassification​(java.lang.String seqName,
                                                java.lang.String text)
      • addGSLook

        public void addGSLook​(java.lang.String seqName,
                              java.lang.String text)
      • addSurfaceAccessibility

        public void addSurfaceAccessibility​(java.lang.String seqName,
                                            java.lang.String text)
      • addTransMembrane

        public void addTransMembrane​(java.lang.String seqName,
                                     java.lang.String text)
      • addPosteriorProbability

        public void addPosteriorProbability​(java.lang.String seqName,
                                            java.lang.String text)
      • addLigandBinding

        public void addLigandBinding​(java.lang.String seqName,
                                     java.lang.String text)
      • addActiveSite

        public void addActiveSite​(java.lang.String seqName,
                                  java.lang.String text)
      • addASPFamPredicted

        public void addASPFamPredicted​(java.lang.String seqName,
                                       java.lang.String text)
      • addASSwissProt

        public void addASSwissProt​(java.lang.String seqName,
                                   java.lang.String text)
      • addIntron

        public void addIntron​(java.lang.String seqName,
                              java.lang.String text)
      • addSecondaryStructure

        public void addSecondaryStructure​(java.lang.String seqName,
                                          java.lang.String text)
      • getBioSequences

        public java.util.List<AbstractSequence<? extends AbstractCompound>> getBioSequences​(boolean ignoreCase,
                                                                                            java.lang.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)
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object