Package org.biojava.nbio.alignment.io
Class StockholmStructure
- java.lang.Object
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- org.biojava.nbio.alignment.io.StockholmStructure
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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
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
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
StockholmStructure.DatabaseReference
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Constructor Summary
Constructors Constructor Description StockholmStructure()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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
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 structureList<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()
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Field Detail
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PFAM
public static final String PFAM
- See Also:
- Constant Field Values
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RFAM
public static final String RFAM
- See Also:
- Constant Field Values
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Constructor Detail
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StockholmStructure
public StockholmStructure()
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Method Detail
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getFileAnnotation
public StockholmFileAnnotation getFileAnnotation()
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getConsAnnotation
public org.biojava.nbio.alignment.io.StockholmConsensusAnnotation getConsAnnotation()
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appendToSequence
public void appendToSequence(String seqName, String seqText)
- Parameters:
seqName
-seqText
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getSequences
public Map<String,StringBuffer> getSequences()
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addGSAccessionNumber
public void addGSAccessionNumber(String seqName, String text)
- Parameters:
seqName
-text
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addGSDescription
public void addGSDescription(String seqName, String text)
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addGSdbReference
public void addGSdbReference(String seqName, String text)
- Parameters:
seqName
-text
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addGSOrganismSpecies
public void addGSOrganismSpecies(String seqName, String text)
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addGSOrganismClassification
public void addGSOrganismClassification(String seqName, String text)
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addSurfaceAccessibility
public void addSurfaceAccessibility(String seqName, String text)
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addTransMembrane
public void addTransMembrane(String seqName, String text)
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addPosteriorProbability
public void addPosteriorProbability(String seqName, String text)
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addLigandBinding
public void addLigandBinding(String seqName, String text)
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addActiveSite
public void addActiveSite(String seqName, String text)
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addASPFamPredicted
public void addASPFamPredicted(String seqName, String text)
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addASSwissProt
public void addASSwissProt(String seqName, String text)
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addSecondaryStructure
public void addSecondaryStructure(String seqName, String text)
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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)
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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
- iftrue
, the function will deal with small letters as if they are capital onesforcedSequenceType
- eithernull
,PFAM
, orRFAM
.- Returns:
- Biosequences according to the criteria specified
- See Also:
getBioSequences()
,getBioSequences(boolean)
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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)
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