Package org.biojava.nbio.alignment.io

Class StockholmStructure

java.lang.Object
org.biojava.nbio.alignment.io.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 AL-Hossary, Marko Vaz

  • Field Details

  • Constructor Details

    • StockholmStructure

      public StockholmStructure()

  • Method Details

    • getFileAnnotation

      public StockholmFileAnnotation getFileAnnotation()

    • getConsAnnotation

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

    • addSequence

      @Deprecated public void addSequence(String seqName, String seqText)
      Deprecated.
      Use appendToSequence(String,String) instead
      Actually this function should be called appendToSequence
      Parameters:
      seqName -
      seqText -

    • appendToSequence

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

    • getSequences

      public Map<String,StringBuffer> getSequences()

    • 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()
      used to retrieve sequences from the structure
      Returns:
      Biosequences (case sensitive)
      See Also:

    • 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

      public List<AbstractSequence<? extends AbstractCompound>> getBioSequences(boolean ignoreCase)
      Because some database files have incorrectly small letters (e.g. Pfam23 structure PF00389.22 sequence TKRA_BACSU/6-322), this function is used to ignore the small letters case.
      Parameters:
      ignoreCase -
      Returns:
      See Also:

    • toString

      public String toString()
      Overrides:
      toString in class Object