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Ensembl Datasource Aware Module v1.09 |
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java.lang.Objectorg.biojava3.core.sequence.template.AbstractSequence<org.biojava3.core.sequence.compound.NucleotideCompound>
org.biojava3.core.sequence.DNASequence
uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
uk.ac.roslin.ensembl.datasourceaware.core.DAAssembledDNASequence
public class DAAssembledDNASequence
Nested Class Summary |
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Nested classes/interfaces inherited from class org.biojava3.core.sequence.DNASequence |
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org.biojava3.core.sequence.DNASequence.DNAType |
Nested classes/interfaces inherited from class org.biojava3.core.sequence.template.AbstractSequence |
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org.biojava3.core.sequence.template.AbstractSequence.AnnotationType |
Field Summary |
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Fields inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence |
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comparaFactories, coordSystem, daoFactory, DBSeqLength, dbSpeciesName, dbVersion, id, mappedRegions, mappings, name, objectTypeMappings, registry, schemaVersion, seqRegionID, species |
Constructor Summary | |
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DAAssembledDNASequence()
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DAAssembledDNASequence(uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory factory)
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Method Summary | |
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DAAssembly |
getCompleteAssembly()
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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)
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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)
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String |
getSequenceAsString(Integer begin,
Integer end,
org.biojava3.core.sequence.Strand strand)
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Methods inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence |
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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 |
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getComplement, getDNAType, getGCCount, getReverse, getReverseComplement, getRNASequence, getRNASequence, getRNASequence, getRNASequence, main, setDNAType |
Methods inherited from class org.biojava3.core.sequence.template.AbstractSequence |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface uk.ac.roslin.ensembl.model.core.DNASequence |
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getCoordSystem, getDBSeqLength, getGenesOnRegion, getGenesOnRegion, getGenesOnRegion, getMappedRegions, getName, getObjectTypeMappings, setCoordSystem, setDBSeqLength, setName |
Methods inherited from interface uk.ac.roslin.ensembl.model.core.CoreObject |
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getAssembly, getSpecies, setSpecies |
Methods inherited from interface uk.ac.roslin.ensembl.model.MappableObject |
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addMapping, clearAllMappings, getMappings, getMappings |
Methods inherited from interface uk.ac.roslin.ensembl.model.IdentifiableObject |
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getDBVersion, getHashID, getId, getSchemaVersion, getType, setId |
Methods inherited from interface org.biojava3.core.sequence.template.Sequence |
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countCompounds, getAsList, getCompoundAt, getCompoundSet, getIndexOf, getInverse, getLastIndexOf, getLength, getSubSequence |
Methods inherited from interface java.lang.Iterable |
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iterator |
Methods inherited from interface org.biojava3.core.sequence.template.Accessioned |
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getAccession |
Constructor Detail |
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public DAAssembledDNASequence()
public DAAssembledDNASequence(uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory factory)
Method Detail |
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public DAAssembly getCompleteAssembly()
getCompleteAssembly
in interface uk.ac.roslin.ensembl.model.core.AssembledDNASequence
public String getSequenceAsString(Integer begin, Integer end)
getSequenceAsString
in interface uk.ac.roslin.ensembl.model.core.DNASequence
getSequenceAsString
in class DADNASequence
begin
- end
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public String getSequenceAsString(Integer begin, Integer end, org.biojava3.core.sequence.Strand strand)
getSequenceAsString
in class org.biojava3.core.sequence.template.AbstractSequence<org.biojava3.core.sequence.compound.NucleotideCompound>
begin
- end
- strand
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public String getSequenceAsString()
getSequenceAsString
in interface org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>
getSequenceAsString
in class org.biojava3.core.sequence.template.AbstractSequence<org.biojava3.core.sequence.compound.NucleotideCompound>
public String getReverseComplementSequenceAsString(Integer begin, Integer end)
getReverseComplementSequenceAsString
in interface uk.ac.roslin.ensembl.model.core.DNASequence
getReverseComplementSequenceAsString
in class DADNASequence
begin
- end
- strand
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public String getReverseComplementSequenceAsString()
getReverseComplementSequenceAsString
in interface uk.ac.roslin.ensembl.model.core.DNASequence
getReverseComplementSequenceAsString
in class DADNASequence
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