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

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	StockholmStructure.DatabaseReference

Field Summary

Fields

Modifier and Type	Field and Description
static String	PFAM
static String	RFAM

Constructor Summary

Constructors

Constructor and Description
StockholmStructure()

Method Summary

Methods

Modifier and Type	Method and Description
void	addActiveSite(String seqName, String text)
void	addASPFamPredicted(String seqName, String text)
void	addASSwissProt(String seqName, String text)
void	addGSAccessionNumber(String seqName, String text)
void	addGSdbReference(String seqName, String text)
void	addGSDescription(String seqName, String text)
void	addGSLook(String seqName, String text)
void	addGSOrganismClassification(String seqName, String text)
void	addGSOrganismSpecies(String seqName, String text)
void	addIntron(String seqName, String text)
void	addLigandBinding(String seqName, String text)
void	addPosteriorProbability(String seqName, String text)
void	addSecondaryStructure(String seqName, String text)
void	addSequence(String seqName, String seqText) Deprecated. Use appendToSequence(String,String) instead
void	addSurfaceAccessibility(String seqName, String text)
void	addTransMembrane(String seqName, String text)
void	appendToSequence(String seqName, String seqText)
List<AbstractSequence<? extends AbstractCompound>>	getBioSequences() used to retrieve sequences from the structure
List<AbstractSequence<? extends AbstractCompound>>	getBioSequences(boolean ignoreCase) Because some database files have incorrectly small letters (e.g.
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).
org.biojava.nbio.alignment.io.StockholmConsensusAnnotation	getConsAnnotation()
StockholmFileAnnotation	getFileAnnotation()
Map<String,StringBuffer>	getSequences()
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

PFAM

public static final String PFAM

See Also:

Constant Field Values

RFAM

public static final String RFAM

See Also:

Constant Field Values

Constructor Detail

StockholmStructure

public StockholmStructure()

Method Detail

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(boolean), getBioSequences(boolean, String)

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)

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:

getBioSequences(), getBioSequences(boolean, String)

toString

public String toString()

Overrides:

toString in class Object