maltcms.datastructures.fragments

Class PairwiseAlignment

java.lang.Object

maltcms.datastructures.fragments.PairwiseAlignment

All Implemented Interfaces:

IWorkflowElement, IConfigurable, IFileFragmentProvider, IXMLSerializable, Serializable

public class PairwiseAlignment
extends Object
implements IFileFragmentProvider, IConfigurable, IWorkflowElement

Implementation of IFileFragmentProvider for PairwiseAlignment.

Author:

Nils.Hoffmann@cebitec.uni-bielefeld.de

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
PairwiseAlignment()

Method Summary

Methods

Modifier and Type	Method and Description
void	appendXML(org.jdom.Element e)
void	configure(org.apache.commons.configuration.Configuration cfg)
IArrayD2Double	getAlignment()
DefaultPairSet<IAnchor>	getAnchors() Retrieve paired anchors
String	getArrayDistanceClassName()
IRecurrence	getCd()
Class<?>	getCreator()
IArrayD2Double	getDistance()
IFileFragment	getFf()
List<Tuple2DI>	getInterppath()
List<Tuple2DI>	getPath()
ArrayByte.D2	getPredecessors()
PairwiseFeatureSimilarity	getPwd()
int	getQuerysize()
IFileFragment	getRef()
int	getRefsize()
ArrayDouble.D0	getResult()
ArrayDouble.D1	getResultVector()
IFileFragment	getTarget()
IWorkflow	getWorkflow()
WorkflowSlot	getWorkflowSlot()
boolean	isMinimize()
boolean	isNormalizeByMapWeights()
boolean	isSaveCDM()
boolean	isSavePWDM()
IFileFragment	provideFileFragment()
void	setAlignment(IArrayD2Double al)
void	setAnchors(DefaultPairSet<IAnchor> anchors) Set paired anchors
void	setArrayDistanceClassName(String arrayDistanceClassName)
void	setCd(IRecurrence cd)
void	setCreator(Class<?> creator)
void	setCumulativeDistance(DtwRecurrence cd1)
void	setDistance(IArrayD2Double distance)
void	setFf(IFileFragment ff)
void	setFileFragments(IFileFragment ref1, IFileFragment target1, Class<?> creator1)
void	setInterppath(List<Tuple2DI> interppath)
void	setIsMinimizing(boolean b)
void	setMinimize(boolean isMinimize)
void	setNormalizeByMapLength(boolean normalizeByMapWeights)
void	setNumberOfScansQuery(int n)
void	setNumberOfScansReference(int n)
void	setPairwiseDistance(PairwiseFeatureSimilarity pwd1)
void	setPairwiseDistances(IArrayD2Double pwd1)
void	setPath(List<Tuple2DI> path1)
void	setPredecessors(ArrayByte.D2 predecessors)
void	setPwd(PairwiseFeatureSimilarity pwd)
void	setQuerysize(int querysize)
void	setRef(IFileFragment ref)
void	setRefsize(int refsize)
void	setResult(double d)
void	setSaveCDM(boolean saveCDM)
void	setSavePWDM(boolean savePWDM)
void	setTarget(IFileFragment target)
void	setTraceMatrix(ArrayByte.D2 predecessors1)
void	setWorkflow(IWorkflow iw1)

Methods inherited from class java.lang.Object

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

Constructor Detail

PairwiseAlignment

public PairwiseAlignment()

Method Detail

getInterppath

public List<Tuple2DI> getInterppath()

setInterppath

public void setInterppath(List<Tuple2DI> interppath)

appendXML

public void appendXML(org.jdom.Element e)

Specified by:

appendXML in interface IXMLSerializable

configure

public void configure(org.apache.commons.configuration.Configuration cfg)

Specified by:

configure in interface IConfigurable

getAlignment

public IArrayD2Double getAlignment()

Returns:

the alignment

getArrayDistanceClassName

public String getArrayDistanceClassName()

Returns:

the arrayDistanceClassName

getCd

public IRecurrence getCd()

Returns:

the cumulativeDistanceClass

getCreator

public Class<?> getCreator()

Returns:

the creator

getDistance

public IArrayD2Double getDistance()

Returns:

the distance

getFf

public IFileFragment getFf()

Returns:

the ff

getAnchors

public DefaultPairSet<IAnchor> getAnchors()

Retrieve paired anchors

Returns:

setAnchors

public void setAnchors(DefaultPairSet<IAnchor> anchors)

Set paired anchors

Parameters:

anchors -

getWorkflow

public IWorkflow getWorkflow()

Specified by:

getWorkflow in interface IWorkflowElement

getPath

public List<Tuple2DI> getPath()

Returns:

the path

getPredecessors

public ArrayByte.D2 getPredecessors()

Returns:

the predecessors

getPwd

public PairwiseFeatureSimilarity getPwd()

Returns:

the pwd

getQuerysize

public int getQuerysize()

Returns:

the querysize

getRef

public IFileFragment getRef()

Returns:

the ref

getRefsize

public int getRefsize()

Returns:

the refsize

getResult

public ArrayDouble.D0 getResult()

Returns:

the result

getResultVector

public ArrayDouble.D1 getResultVector()

Returns:

the resultVector

getTarget

public IFileFragment getTarget()

Returns:

the target

getWorkflowSlot

public WorkflowSlot getWorkflowSlot()

Specified by:

getWorkflowSlot in interface IWorkflowElement

isMinimize

public boolean isMinimize()

Returns:

the isMinimize

isNormalizeByMapWeights

public boolean isNormalizeByMapWeights()

Returns:

the normalizeAlignmentValueByMapWeights

isSaveCDM

public boolean isSaveCDM()

Returns:

the saveCDM

isSavePWDM

public boolean isSavePWDM()

Returns:

the savePWDM

provideFileFragment

public IFileFragment provideFileFragment()

Specified by:

provideFileFragment in interface IFileFragmentProvider

setAlignment

public void setAlignment(IArrayD2Double al)

setArrayDistanceClassName

public void setArrayDistanceClassName(String arrayDistanceClassName)

Parameters:

arrayDistanceClassName - the arrayDistanceClassName to set

setCd

public void setCd(IRecurrence cd)

Parameters:

cumulativeDistanceClass - the cumulativeDistanceClass to set

setCreator

public void setCreator(Class<?> creator)

Parameters:

creator - the creator to set

setCumulativeDistance

public void setCumulativeDistance(DtwRecurrence cd1)

setDistance

public void setDistance(IArrayD2Double distance)

Parameters:

distance - the distance to set

setFf

public void setFf(IFileFragment ff)

Parameters:

ff - the ff to set

setFileFragments

public void setFileFragments(IFileFragment ref1,
                    IFileFragment target1,
                    Class<?> creator1)

setIsMinimizing

public void setIsMinimizing(boolean b)

setWorkflow

public void setWorkflow(IWorkflow iw1)

Specified by:

setWorkflow in interface IWorkflowElement

setMinimize

public void setMinimize(boolean isMinimize)

Parameters:

isMinimize - the isMinimize to set

setNormalizeByMapLength

public void setNormalizeByMapLength(boolean normalizeByMapWeights)

Parameters:

normalizeAlignmentValueByMapWeights - the normalizeAlignmentValueByMapWeights to set

setNumberOfScansQuery

public void setNumberOfScansQuery(int n)

setNumberOfScansReference

public void setNumberOfScansReference(int n)

setPairwiseDistance

public void setPairwiseDistance(PairwiseFeatureSimilarity pwd1)

setPairwiseDistances

public void setPairwiseDistances(IArrayD2Double pwd1)

setPath

public void setPath(List<Tuple2DI> path1)

setPredecessors

public void setPredecessors(ArrayByte.D2 predecessors)

Parameters:

predecessors - the predecessors to set

setPwd

public void setPwd(PairwiseFeatureSimilarity pwd)

Parameters:

pwd - the pwd to set

setQuerysize

public void setQuerysize(int querysize)

Parameters:

querysize - the querysize to set

setRef

public void setRef(IFileFragment ref)

Parameters:

ref - the ref to set

setRefsize

public void setRefsize(int refsize)

Parameters:

refsize - the refsize to set

setResult

public void setResult(double d)

setSaveCDM

public void setSaveCDM(boolean saveCDM)

Parameters:

saveCDM - the saveCDM to set

setSavePWDM

public void setSavePWDM(boolean savePWDM)

Parameters:

savePWDM - the savePWDM to set

setTarget

public void setTarget(IFileFragment target)

Parameters:

target - the target to set

setTraceMatrix

public void setTraceMatrix(ArrayByte.D2 predecessors1)