uk.ac.roslin.ensembl.datasourceaware.core

Class DAAssembly

java.lang.Object

uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly

All Implemented Interfaces:

Assembly

public class DAAssembly
extends Object
implements Assembly

Author:

paterson

Field Summary

Fields

Modifier and Type	Field and Description
protected Integer	assemblyStart
protected Integer	assemblyStop
protected MappingSet	componentMappings
protected boolean	hasPAR
protected MappingSet	pARMappings
protected MappingSet	stitchedComponentMappings

Constructor Summary

Constructors

Constructor and Description
DAAssembly()

Method Summary

Methods

Modifier and Type	Method and Description
static DAAssembly	getAssembly(DAAssembledDNASequence parent)
static DAAssembly	getAssembly(DAAssembledDNASequence parent, Integer start, Integer stop)
Integer	getAssemblyStart()
Integer	getAssemblyStop()
MappingSet	getMappings() Returns the MappingSet 'componentMappings' of all of the mappings of all of the DNASequences that make up this assembly.
String	getPaddedReverseComplementSequenceAsString(Integer start, Integer stop) Returns a String representation of the reverse complement of theassembly sequence for the given range.
String	getPaddedSequenceAsString(Integer start, Integer stop) Returns a String representation of the assembly sequence for the given range.
DAAssembledDNASequence	getParent() Returns the DAAssembledDNASequence that this assembly holds (its 'Parent').
String	getReverseComplementSequenceAsString(Integer start, Integer stop) Returns a String representation of the reverse complement of the assembly sequence for the given range.
String	getSequenceAsString(Integer start, Integer stop) Returns a String representation of the assembly sequence for the given range.
MappingSet	getStitchedMappings() Returns the MappingSet 'stitchedComponentMappings' of all of the mappings of all of the DNASequences that make up this assembly, that have been 'edited', i.e. stitched together into a single continuous gap free assembly.
MappingSet	getStitchedMappings(Integer start, Integer stop) For a given range, returns a subset of the MappingSet 'stitchedComponentMappings' of all of the mappings of all of the DNASequences that make up this assembly, that have been 'edited', i.e. stitched together into a single continuous gap free assembly.
void	setAssemblyStart(Integer assemblyStart)
void	setAssemblyStop(Integer assemblyStop)
void	setParent(AssembledDNASequence parent) Sets the DAAssembledDNASequence that this assembly holds (its 'Parent').
protected MappingSet	stitchComponents() Protected method to join together (stitch) all of the component sub-sequences of the assembly, together with GapSequences to form a single continuous ungapped assembly, held in the MappingSet 'stitchedComponentMappings';

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

componentMappings

protected MappingSet componentMappings

pARMappings

protected MappingSet pARMappings

stitchedComponentMappings

protected MappingSet stitchedComponentMappings

assemblyStart

protected Integer assemblyStart

assemblyStop

protected Integer assemblyStop

hasPAR

protected boolean hasPAR

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()

Returns the DAAssembledDNASequence that this assembly holds (its 'Parent').

Specified by:

getParent in interface Assembly

setParent

public void setParent(AssembledDNASequence parent)

Sets the DAAssembledDNASequence that this assembly holds (its 'Parent').

Specified by:

setParent in interface Assembly

getAssemblyStart

public Integer getAssemblyStart()

Specified by:

getAssemblyStart in interface Assembly

setAssemblyStart

public void setAssemblyStart(Integer assemblyStart)

Specified by:

setAssemblyStart in interface Assembly

getAssemblyStop

public Integer getAssemblyStop()

Specified by:

getAssemblyStop in interface Assembly

setAssemblyStop

public void setAssemblyStop(Integer assemblyStop)

Specified by:

setAssemblyStop in interface Assembly

getMappings

public MappingSet getMappings()
                       throws DAOException

Returns the MappingSet 'componentMappings' of all of the mappings of all of the DNASequences that make up this assembly. Triggers a lazy load if not already set.

Specified by:

getMappings in interface Assembly

Throws:

DAOException

getStitchedMappings

public MappingSet getStitchedMappings()
                               throws DAOException

Returns the MappingSet 'stitchedComponentMappings' of all of the mappings of all of the DNASequences that make up this assembly, that have been 'edited', i.e. stitched together into a single continuous gap free assembly. Triggers method 'stitchComponents' if not yet set .

Specified by:

getStitchedMappings in interface Assembly

Throws:

DAOException

getStitchedMappings

public MappingSet getStitchedMappings(Integer start,
                             Integer stop)
                               throws DAOException,
                                      RangeException

For a given range, returns a subset of the MappingSet 'stitchedComponentMappings' of all of the mappings of all of the DNASequences that make up this assembly, that have been 'edited', i.e. stitched together into a single continuous gap free assembly. Triggers method 'stitchComponents' if not yet set .

Throws:

DAOException

RangeException

stitchComponents

protected MappingSet stitchComponents()
                               throws DAOException

Protected method to join together (stitch) all of the component sub-sequences of the assembly, together with GapSequences to form a single continuous ungapped assembly, held in the MappingSet 'stitchedComponentMappings';

Throws:

DAOException

getReverseComplementSequenceAsString

public String getReverseComplementSequenceAsString(Integer start,
                                          Integer stop)
                                            throws RangeException,
                                                   DAOException

Returns a String representation of the reverse complement of the assembly sequence for the given range. If there is no sequence for this assembly null is returned. If the given range is greater than the assembly coordinates, a RangeException is thrown (try using getPaddedReverseComplementSequenceAsString(int,int) instead).

Parameters:

start -

stop -

Throws:

RangeException

DAOException

getPaddedReverseComplementSequenceAsString

public String getPaddedReverseComplementSequenceAsString(Integer start,
                                                Integer stop)
                                                  throws DAOException

Returns a String representation of the reverse complement of theassembly sequence for the given range. If there is no sequence for this assembly null is returned. If the given range is greater than the assembly coordinates, the result is padded upstream and/or downstream.

Parameters:

start -

stop -

Throws:

RangeException

DAOException

getSequenceAsString

public String getSequenceAsString(Integer start,
                         Integer stop)
                           throws RangeException,
                                  DAOException

Returns a String representation of the assembly sequence for the given range. If there is no sequence for this assembly null is returned. If the given range is greater than the assembly coordinates, a RangeException is thrown (try using getPaddedSequenceAsString(int,int) instead).

Parameters:

start -

stop -

Throws:

RangeException

DAOException

getPaddedSequenceAsString

public String getPaddedSequenceAsString(Integer start,
                               Integer stop)
                                 throws DAOException

Returns a String representation of the assembly sequence for the given range. If there is no sequence for this assembly null is returned. If the given range is greater than the assembly coordinates, the result is padded upstream and/or downstream.

Parameters:

start -

stop -

Returns:

String representation of the Assembly Sequence

Throws:

DAOException