Ensembl Model v1.09
© Roslin Institute 2010. GNU General Public License, version3
uk.ac.roslin.ensembl.model.core
Interface DNASequence
- All Superinterfaces:
- org.biojava3.core.sequence.template.Accessioned, CoreObject, IdentifiableObject, Iterable<org.biojava3.core.sequence.compound.NucleotideCompound>, MappableObject, org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>, Serializable
- All Known Subinterfaces:
- AssembledDNASequence, Chromosome
public interface DNASequence
- extends CoreObject, MappableObject, org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>
- Author:
- paterson
Methods inherited from interface org.biojava3.core.sequence.template.Sequence |
countCompounds, getAsList, getCompoundAt, getCompoundSet, getIndexOf, getInverse, getLastIndexOf, getLength, getSequenceAsString, getSubSequence |
Methods inherited from interface org.biojava3.core.sequence.template.Accessioned |
getAccession |
getDBSeqLength
Integer getDBSeqLength()
setDBSeqLength
void setDBSeqLength(Integer seqLength)
getCoordSystem
CoordinateSystem getCoordSystem()
setCoordSystem
void setCoordSystem(CoordinateSystem coordSystem)
getName
String getName()
setName
void setName(String name)
getGenesOnRegion
List<? extends Gene> getGenesOnRegion(Coordinate coord)
throws DAOException
- Throws:
DAOException
getGenesOnRegion
List<? extends Gene> getGenesOnRegion(Integer start,
Integer stop)
throws DAOException
- Throws:
DAOException
getGenesOnRegion
List<? extends Gene> getGenesOnRegion(Integer start,
Integer stop,
Coordinate.Strand strand)
throws DAOException
- Throws:
DAOException
getSequenceAsString
String getSequenceAsString(Integer begin,
Integer end)
getReverseComplementSequenceAsString
String getReverseComplementSequenceAsString(Integer begin,
Integer end)
getReverseComplementSequenceAsString
String getReverseComplementSequenceAsString()
getObjectTypeMappings
HashMap<ObjectType,? extends MappingSet> getObjectTypeMappings()
getMappedRegions
HashMap<ObjectType,CoordinateSet> getMappedRegions()
Ensembl Model v1.09
© Roslin Institute 2010. GNU General Public License, version3