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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.GapSequence
public class GapSequence
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 |
Method Summary | |
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int |
getLength()
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String |
getReverseComplementSequenceAsString()
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String |
getReverseComplementSequenceAsString(Integer start,
Integer stop)
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String |
getSequenceAsString()
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String |
getSequenceAsString(Integer start,
Integer stop)
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String |
getSequenceAsString(Integer start,
Integer stop,
org.biojava3.core.sequence.Strand strand)
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static GapSequence |
makeGap(Integer length)
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String |
toString()
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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, getMappedRegions, getMappings, getMappings, getName, getObjectTypeMappings, getRegistry, getSchemaVersion, getSpecies, getType, setCoordSystem, setDaoFactory, setDBSeqLength, setId, setName, setRegistry, setSequenceStorage, setSpecies |
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 org.biojava3.core.sequence.template.Sequence |
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countCompounds, getAsList, getCompoundAt, getCompoundSet, getIndexOf, getInverse, getLastIndexOf, 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 |
Method Detail |
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public static GapSequence makeGap(Integer length)
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()
getReverseComplementSequenceAsString
in interface uk.ac.roslin.ensembl.model.core.DNASequence
getReverseComplementSequenceAsString
in class DADNASequence
public String getSequenceAsString(Integer start, Integer stop)
getSequenceAsString
in interface uk.ac.roslin.ensembl.model.core.DNASequence
getSequenceAsString
in class DADNASequence
public String getSequenceAsString(Integer start, Integer stop, org.biojava3.core.sequence.Strand strand)
getSequenceAsString
in class org.biojava3.core.sequence.template.AbstractSequence<org.biojava3.core.sequence.compound.NucleotideCompound>
public String getReverseComplementSequenceAsString(Integer start, Integer stop)
getReverseComplementSequenceAsString
in interface uk.ac.roslin.ensembl.model.core.DNASequence
getReverseComplementSequenceAsString
in class DADNASequence
public String toString()
toString
in class DADNASequence
public int getLength()
getLength
in interface org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>
getLength
in class DADNASequence
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Ensembl Datasource Aware Module v1.09 |
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