org.biojava3.alignment.io
Class StockholmStructure

java.lang.Object
  org.biojava3.alignment.io.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

Nested Class Summary

static class

StockholmStructure.DatabaseReference

Constructor Summary

StockholmStructure()

Method Summary

void	addActiveSite(java.lang.String seqName, java.lang.String text)
void	addASPFamPredicted(java.lang.String seqName, java.lang.String text)
void	addASSwissProt(java.lang.String seqName, java.lang.String text)
void	addGSAccessionNumber(java.lang.String seqName, java.lang.String text)
void	addGSdbReference(java.lang.String seqName, java.lang.String text)
void	addGSDescription(java.lang.String seqName, java.lang.String text)
void	addGSLook(java.lang.String seqName, java.lang.String text)
void	addGSOrganismClassification(java.lang.String seqName, java.lang.String text)
void	addGSOrganismSpecies(java.lang.String seqName, java.lang.String text)
void	addIntron(java.lang.String seqName, java.lang.String text)
void	addLigandBinding(java.lang.String seqName, java.lang.String text)
void	addPosteriorProbability(java.lang.String seqName, java.lang.String text)
void	addSecondaryStructure(java.lang.String seqName, java.lang.String text)
void	addSequence(java.lang.String seqName, java.lang.String seqText) Actually this function should be called appendToSequence
void	addSurfaceAccessibility(java.lang.String seqName, java.lang.String text)
void	addTransMembrane(java.lang.String seqName, java.lang.String text)
java.util.List<AbstractSequence<? extends AbstractCompound>>	getBioSequences()
java.util.List<AbstractSequence<? extends AbstractCompound>>	getBioSequences(boolean ignoreCase) Because some database files have incorrectly small letters (e.g.
org.biojava3.alignment.io.StockholmConsensusAnnotation	getConsAnnotation()
StockholmFileAnnotation	getFileAnnotation()
java.util.Map<java.lang.String,java.lang.StringBuffer>	getSequences()
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

StockholmStructure

public StockholmStructure()

Method Detail

getFileAnnotation

public StockholmFileAnnotation getFileAnnotation()

getConsAnnotation

public org.biojava3.alignment.io.StockholmConsensusAnnotation getConsAnnotation()

addSequence

public void addSequence(java.lang.String seqName,
                        java.lang.String seqText)

Actually this function should be called appendToSequence

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()

Returns:

getBioSequences

public java.util.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 - if true, the function will deal with small letters as if they are capital ones

Returns:

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object