Ensembl Datasource Aware Module v1.09
© Roslin Institute 2010. GNU General Public License, version3
uk.ac.roslin.ensembl.datasourceaware.core
Class DAAssembly
java.lang.Object
uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly
- All Implemented Interfaces:
- uk.ac.roslin.ensembl.model.core.Assembly
public class DAAssembly
- extends Object
- implements uk.ac.roslin.ensembl.model.core.Assembly
- Author:
- paterson
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
componentMappings
protected uk.ac.roslin.ensembl.model.MappingSet componentMappings
stitchedComponentMappings
protected uk.ac.roslin.ensembl.model.MappingSet stitchedComponentMappings
assemblyStart
protected Integer assemblyStart
assemblyStop
protected Integer assemblyStop
DAAssembly
public DAAssembly()
getAssembly
public static DAAssembly getAssembly(DAAssembledDNASequence parent)
getAssembly
public static DAAssembly getAssembly(DAAssembledDNASequence parent,
Integer start,
Integer stop)
getParent
public DAAssembledDNASequence getParent()
- Specified by:
getParent
in interface uk.ac.roslin.ensembl.model.core.Assembly
setParent
public void setParent(uk.ac.roslin.ensembl.model.core.AssembledDNASequence parent)
- Specified by:
setParent
in interface uk.ac.roslin.ensembl.model.core.Assembly
getAssemblyStart
public Integer getAssemblyStart()
- Specified by:
getAssemblyStart
in interface uk.ac.roslin.ensembl.model.core.Assembly
setAssemblyStart
public void setAssemblyStart(Integer assemblyStart)
- Specified by:
setAssemblyStart
in interface uk.ac.roslin.ensembl.model.core.Assembly
getAssemblyStop
public Integer getAssemblyStop()
- Specified by:
getAssemblyStop
in interface uk.ac.roslin.ensembl.model.core.Assembly
setAssemblyStop
public void setAssemblyStop(Integer assemblyStop)
- Specified by:
setAssemblyStop
in interface uk.ac.roslin.ensembl.model.core.Assembly
getMappings
public uk.ac.roslin.ensembl.model.MappingSet getMappings()
throws uk.ac.roslin.ensembl.exception.DAOException
- Specified by:
getMappings
in interface uk.ac.roslin.ensembl.model.core.Assembly
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getStitchedMappings
public uk.ac.roslin.ensembl.model.MappingSet getStitchedMappings()
throws uk.ac.roslin.ensembl.exception.DAOException
- Specified by:
getStitchedMappings
in interface uk.ac.roslin.ensembl.model.core.Assembly
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getStitchedMappings
public uk.ac.roslin.ensembl.model.MappingSet getStitchedMappings(Integer start,
Integer stop)
throws uk.ac.roslin.ensembl.exception.DAOException
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getSequenceAsString
public String getSequenceAsString(Integer start,
Integer stop,
org.biojava3.core.sequence.Strand strand)
throws uk.ac.roslin.ensembl.exception.RangeException,
uk.ac.roslin.ensembl.exception.DAOException
- Throws:
uk.ac.roslin.ensembl.exception.RangeException
uk.ac.roslin.ensembl.exception.DAOException
getReverseComplementSequenceAsString
public String getReverseComplementSequenceAsString(Integer start,
Integer stop)
throws uk.ac.roslin.ensembl.exception.RangeException,
uk.ac.roslin.ensembl.exception.DAOException
- Throws:
uk.ac.roslin.ensembl.exception.RangeException
uk.ac.roslin.ensembl.exception.DAOException
Ensembl Datasource Aware Module v1.09
© Roslin Institute 2010. GNU General Public License, version3