Ensembl Datasource Aware Module v1.09
© Roslin Institute 2010. GNU General Public License, version3
Ensembl Datasource Aware Module
v1.09

uk.ac.roslin.ensembl.datasourceaware.core
Class DAAssembledDNASequence

java.lang.Object
  extended by org.biojava3.core.sequence.template.AbstractSequence<org.biojava3.core.sequence.compound.NucleotideCompound>
      extended by org.biojava3.core.sequence.DNASequence
          extended by uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
              extended by uk.ac.roslin.ensembl.datasourceaware.core.DAAssembledDNASequence
All Implemented Interfaces:
Serializable, Iterable<org.biojava3.core.sequence.compound.NucleotideCompound>, org.biojava3.core.sequence.template.Accessioned, org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>, uk.ac.roslin.ensembl.model.core.AssembledDNASequence, uk.ac.roslin.ensembl.model.core.CoreObject, uk.ac.roslin.ensembl.model.core.DNASequence, uk.ac.roslin.ensembl.model.IdentifiableObject, uk.ac.roslin.ensembl.model.MappableObject
Direct Known Subclasses:
DAChromosome

public class DAAssembledDNASequence
extends DADNASequence
implements uk.ac.roslin.ensembl.model.core.AssembledDNASequence

Author:
paterson
See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from class org.biojava3.core.sequence.DNASequence
org.biojava3.core.sequence.DNASequence.DNAType
 
Nested classes/interfaces inherited from class org.biojava3.core.sequence.template.AbstractSequence
org.biojava3.core.sequence.template.AbstractSequence.AnnotationType
 
Field Summary
 
Fields inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
comparaFactories, coordSystem, daoFactory, DBSeqLength, dbSpeciesName, dbVersion, id, mappedRegions, mappings, name, objectTypeMappings, registry, schemaVersion, seqRegionID, species
 
Constructor Summary
DAAssembledDNASequence()
           
DAAssembledDNASequence(uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory factory)
           
 
Method Summary
 DAAssembly getCompleteAssembly()
           
 String getReverseComplementSequenceAsString()
          Default case is to assume strand is positive because only CDSSequence can be either positive or negative Strand.
 String getReverseComplementSequenceAsString(Integer begin, Integer end)
           
 String getSequenceAsString()
          Default case is to assume strand is positive because only CDSSequence can be either positive or negative Strand.
 String getSequenceAsString(Integer begin, Integer end)
           
 String getSequenceAsString(Integer begin, Integer end, org.biojava3.core.sequence.Strand strand)
           
 
Methods inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
addMapping, clearAllMappings, getAssembly, getBioEnd, getComparaDivision, getComparaFactory, getComparaFactory, getCoordSystem, getDaoFactory, getDBName, getDBSeqLength, getDBVersion, getGenesOnRegion, getGenesOnRegion, getGenesOnRegion, getHashID, getId, getLength, getMappedRegions, getMappings, getMappings, getName, getObjectTypeMappings, getRegistry, getSchemaVersion, getSpecies, getType, setCoordSystem, setDaoFactory, setDBSeqLength, setId, setName, setRegistry, setSequenceStorage, setSpecies, toString
 
Methods inherited from class org.biojava3.core.sequence.DNASequence
getComplement, getDNAType, getGCCount, getReverse, getReverseComplement, getRNASequence, getRNASequence, getRNASequence, getRNASequence, main, setDNAType
 
Methods inherited from class org.biojava3.core.sequence.template.AbstractSequence
addFeature, addFeature, addNote, countCompounds, getAccession, getAnnotationType, getAsList, getBioBegin, getCompoundAt, getCompoundSet, getDatabaseReferences, getDescription, getFeatures, getFeatures, getFeatures, getFeaturesByType, getFeaturesKeyWord, getIndexOf, getInverse, getLastIndexOf, getNotesList, getOriginalHeader, getParentSequence, getProxySequenceReader, getSequenceScore, getSource, getSubSequence, getTaxonomy, getUserCollection, iterator, removeFeature, removeNote, setAccession, setAnnotationType, setBioBegin, setBioEnd, setCompoundSet, setDatabaseReferences, setDescription, setFeaturesKeyWord, setNotesList, setOriginalHeader, setParentSequence, setProxySequenceReader, setSequenceScore, setSource, setTaxonomy, setUserCollection
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface uk.ac.roslin.ensembl.model.core.DNASequence
getCoordSystem, getDBSeqLength, getGenesOnRegion, getGenesOnRegion, getGenesOnRegion, getMappedRegions, getName, getObjectTypeMappings, setCoordSystem, setDBSeqLength, setName
 
Methods inherited from interface uk.ac.roslin.ensembl.model.core.CoreObject
getAssembly, getSpecies, setSpecies
 
Methods inherited from interface uk.ac.roslin.ensembl.model.MappableObject
addMapping, clearAllMappings, getMappings, getMappings
 
Methods inherited from interface uk.ac.roslin.ensembl.model.IdentifiableObject
getDBVersion, getHashID, getId, getSchemaVersion, getType, setId
 
Methods inherited from interface org.biojava3.core.sequence.template.Sequence
countCompounds, getAsList, getCompoundAt, getCompoundSet, getIndexOf, getInverse, getLastIndexOf, getLength, getSubSequence
 
Methods inherited from interface java.lang.Iterable
iterator
 
Methods inherited from interface org.biojava3.core.sequence.template.Accessioned
getAccession
 

Constructor Detail

DAAssembledDNASequence

public DAAssembledDNASequence()

DAAssembledDNASequence

public DAAssembledDNASequence(uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory factory)
Method Detail

getCompleteAssembly

public DAAssembly getCompleteAssembly()
Specified by:
getCompleteAssembly in interface uk.ac.roslin.ensembl.model.core.AssembledDNASequence

getSequenceAsString

public String getSequenceAsString(Integer begin,
                                  Integer end)
Specified by:
getSequenceAsString in interface uk.ac.roslin.ensembl.model.core.DNASequence
Overrides:
getSequenceAsString in class DADNASequence
Parameters:
begin -
end -
Returns:

getSequenceAsString

public String getSequenceAsString(Integer begin,
                                  Integer end,
                                  org.biojava3.core.sequence.Strand strand)
Overrides:
getSequenceAsString in class org.biojava3.core.sequence.template.AbstractSequence<org.biojava3.core.sequence.compound.NucleotideCompound>
Parameters:
begin -
end -
strand -
Returns:

getSequenceAsString

public String getSequenceAsString()
Default case is to assume strand is positive because only CDSSequence can be either positive or negative Strand.

Specified by:
getSequenceAsString in interface org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>
Overrides:
getSequenceAsString in class org.biojava3.core.sequence.template.AbstractSequence<org.biojava3.core.sequence.compound.NucleotideCompound>
Returns:

getReverseComplementSequenceAsString

public String getReverseComplementSequenceAsString(Integer begin,
                                                   Integer end)
Specified by:
getReverseComplementSequenceAsString in interface uk.ac.roslin.ensembl.model.core.DNASequence
Overrides:
getReverseComplementSequenceAsString in class DADNASequence
Parameters:
begin -
end -
strand -
Returns:

getReverseComplementSequenceAsString

public String getReverseComplementSequenceAsString()
Default case is to assume strand is positive because only CDSSequence can be either positive or negative Strand.

Specified by:
getReverseComplementSequenceAsString in interface uk.ac.roslin.ensembl.model.core.DNASequence
Overrides:
getReverseComplementSequenceAsString in class DADNASequence
Returns:

Ensembl Datasource Aware Module
v1.09

Ensembl Datasource Aware Module v1.09
© Roslin Institute 2010. GNU General Public License, version3