Ensembl Model v1.09
© Roslin Institute 2010. GNU General Public License, version3
Ensembl Model
v1.09

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

Method Summary
 CoordinateSystem getCoordSystem()
           
 Integer getDBSeqLength()
           
 List<? extends Gene> getGenesOnRegion(Coordinate coord)
           
 List<? extends Gene> getGenesOnRegion(Integer start, Integer stop)
           
 List<? extends Gene> getGenesOnRegion(Integer start, Integer stop, Coordinate.Strand strand)
           
 HashMap<ObjectType,CoordinateSet> getMappedRegions()
           
 String getName()
           
 HashMap<ObjectType,? extends MappingSet> getObjectTypeMappings()
           
 String getReverseComplementSequenceAsString()
           
 String getReverseComplementSequenceAsString(Integer begin, Integer end)
           
 String getSequenceAsString(Integer begin, Integer end)
           
 void setCoordSystem(CoordinateSystem coordSystem)
           
 void setDBSeqLength(Integer seqLength)
           
 void setName(String name)
           
 
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, getSequenceAsString, getSubSequence
 
Methods inherited from interface java.lang.Iterable
iterator
 
Methods inherited from interface org.biojava3.core.sequence.template.Accessioned
getAccession
 

Method Detail

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

Ensembl Model v1.09
© Roslin Institute 2010. GNU General Public License, version3