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 DAAssembly

java.lang.Object
  extended by 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

Field Summary
protected  Integer assemblyStart
           
protected  Integer assemblyStop
           
protected  uk.ac.roslin.ensembl.model.MappingSet componentMappings
           
protected  uk.ac.roslin.ensembl.model.MappingSet stitchedComponentMappings
           
 
Constructor Summary
DAAssembly()
           
 
Method Summary
static DAAssembly getAssembly(DAAssembledDNASequence parent)
           
static DAAssembly getAssembly(DAAssembledDNASequence parent, Integer start, Integer stop)
           
 Integer getAssemblyStart()
           
 Integer getAssemblyStop()
           
 uk.ac.roslin.ensembl.model.MappingSet getMappings()
           
 DAAssembledDNASequence getParent()
           
 String getReverseComplementSequenceAsString(Integer start, Integer stop)
           
 String getSequenceAsString(Integer start, Integer stop, org.biojava3.core.sequence.Strand strand)
           
 uk.ac.roslin.ensembl.model.MappingSet getStitchedMappings()
           
 uk.ac.roslin.ensembl.model.MappingSet getStitchedMappings(Integer start, Integer stop)
           
 void setAssemblyStart(Integer assemblyStart)
           
 void setAssemblyStop(Integer assemblyStop)
           
 void setParent(uk.ac.roslin.ensembl.model.core.AssembledDNASequence parent)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

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
Constructor Detail

DAAssembly

public DAAssembly()
Method Detail

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

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