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 GapSequence

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.GapSequence
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.CoreObject, uk.ac.roslin.ensembl.model.core.DNASequence, uk.ac.roslin.ensembl.model.IdentifiableObject, uk.ac.roslin.ensembl.model.MappableObject

public class GapSequence
extends DADNASequence

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
 
Method Summary
 int getLength()
           
 String getReverseComplementSequenceAsString()
           
 String getReverseComplementSequenceAsString(Integer start, Integer stop)
           
 String getSequenceAsString()
           
 String getSequenceAsString(Integer start, Integer stop)
           
 String getSequenceAsString(Integer start, Integer stop, org.biojava3.core.sequence.Strand strand)
           
static GapSequence makeGap(Integer length)
           
 String toString()
           
 
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, 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
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 org.biojava3.core.sequence.template.Sequence
countCompounds, getAsList, getCompoundAt, getCompoundSet, getIndexOf, getInverse, getLastIndexOf, getSubSequence
 
Methods inherited from interface java.lang.Iterable
iterator
 
Methods inherited from interface org.biojava3.core.sequence.template.Accessioned
getAccession
 

Method Detail

makeGap

public static GapSequence makeGap(Integer length)

getSequenceAsString

public String getSequenceAsString()
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>

getReverseComplementSequenceAsString

public String getReverseComplementSequenceAsString()
Specified by:
getReverseComplementSequenceAsString in interface uk.ac.roslin.ensembl.model.core.DNASequence
Overrides:
getReverseComplementSequenceAsString in class DADNASequence

getSequenceAsString

public String getSequenceAsString(Integer start,
                                  Integer stop)
Specified by:
getSequenceAsString in interface uk.ac.roslin.ensembl.model.core.DNASequence
Overrides:
getSequenceAsString in class DADNASequence

getSequenceAsString

public String getSequenceAsString(Integer start,
                                  Integer stop,
                                  org.biojava3.core.sequence.Strand strand)
Overrides:
getSequenceAsString in class org.biojava3.core.sequence.template.AbstractSequence<org.biojava3.core.sequence.compound.NucleotideCompound>

getReverseComplementSequenceAsString

public String getReverseComplementSequenceAsString(Integer start,
                                                   Integer stop)
Specified by:
getReverseComplementSequenceAsString in interface uk.ac.roslin.ensembl.model.core.DNASequence
Overrides:
getReverseComplementSequenceAsString in class DADNASequence

toString

public String toString()
Overrides:
toString in class DADNASequence

getLength

public int getLength()
Specified by:
getLength in interface org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>
Overrides:
getLength in class DADNASequence

Ensembl Datasource Aware Module
v1.09

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