Class Alignment
- java.lang.Object
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- org.biojava.bio.program.das.dasalignment.Alignment
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public class Alignment extends java.lang.Object
Alignment object to contain/manage a DAS alignment. see also DAS specification at http://www.sanger.ac.uk/xml/das/documentation/new_spec.html supports also structure alignments (optional shift vector and rotation matrix for objects)- Since:
- 1.4
- Author:
- Andreas Prlic
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Constructor Summary
Constructors Constructor Description Alignment()
Construct a new empty Alignment object.
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addBlock(Annotation block)
Add a "Block" Annotation.void
addMatrix(Annotation matrix)
add Annotation of DAS alignment "matrix" type.void
addObject(Annotation object)
add Annotation of DAS alignment "object" type.void
addScore(Annotation score)
adds a "Score" Annotation.void
addVector(Annotation vector)
add Annotation of DAS alignment "vector" type.static AnnotationType
getBlockAnnotationType()
define the alignment Block Annotation Type.Annotation[]
getBlocks()
get all Annotations of type "Block".Annotation[]
getMatrices()
Returns the matrices.static AnnotationType
getMatrixAnnotationType()
define the rotation matrix annotation typestatic AnnotationType
getObjectAnnotationType()
define the alignment object Annotation Type.Annotation[]
getObjects()
Returns the Annotation of all objects in this Alignment.static AnnotationType
getScoreAnnotationType()
define the alignment Score Annotation Type.Annotation[]
getScores()
get all "Score" Annotations.static AnnotationType
getSegmentAnnotationType()
define the alignment Segment Annotation Type.static AnnotationType
getVectorAnnotationType()
define the shift vector annotation typeAnnotation[]
getVectors()
Returns the shift vectors.java.lang.String
toString()
convert to String.
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Method Detail
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getVectorAnnotationType
public static AnnotationType getVectorAnnotationType()
define the shift vector annotation type- Returns:
- an AnnotationType object representing the shift vector for an object
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getMatrixAnnotationType
public static AnnotationType getMatrixAnnotationType()
define the rotation matrix annotation type- Returns:
- an AnnotationType object representing the rotation matrix for an object in a structure alignment.
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getScoreAnnotationType
public static AnnotationType getScoreAnnotationType()
define the alignment Score Annotation Type.- Returns:
- an AnnotationType object representing the score annotation type
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getBlockAnnotationType
public static AnnotationType getBlockAnnotationType()
define the alignment Block Annotation Type.- Returns:
- an AnnotationType object representing the block annotation type
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getSegmentAnnotationType
public static AnnotationType getSegmentAnnotationType()
define the alignment Segment Annotation Type.- Returns:
- an AnnotationType object representing the segment annotation type
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getObjectAnnotationType
public static AnnotationType getObjectAnnotationType()
define the alignment object Annotation Type.- Returns:
- an AnnotationType object representing the object annotation type
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addVector
public void addVector(Annotation vector) throws DASException
add Annotation of DAS alignment "vector" type.- Parameters:
vector
- a vector- Throws:
DASException
- ...- See Also:
getVectorAnnotationType()
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addMatrix
public void addMatrix(Annotation matrix) throws DASException
add Annotation of DAS alignment "matrix" type.- Parameters:
matrix
- a matrix- Throws:
DASException
- ...- See Also:
getMatrixAnnotationType()
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addObject
public void addObject(Annotation object) throws DASException
add Annotation of DAS alignment "object" type.- Parameters:
object
- an Annotation object- Throws:
DASException
- ...- See Also:
getObjectAnnotationType()
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getObjects
public Annotation[] getObjects()
Returns the Annotation of all objects in this Alignment.- Returns:
- an array of Annotation objects
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getVectors
public Annotation[] getVectors()
Returns the shift vectors.- Returns:
- an array of shift vectors
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getMatrices
public Annotation[] getMatrices()
Returns the matrices.- Returns:
- an array of the matrices
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addScore
public void addScore(Annotation score) throws DASException
adds a "Score" Annotation.- Parameters:
score
- an Annotation object- Throws:
DASException
- ...- See Also:
getScoreAnnotationType()
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getScores
public Annotation[] getScores()
get all "Score" Annotations.- Returns:
- an array of Annotation objects representing the scores value
- Throws:
DASException
- ...
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addBlock
public void addBlock(Annotation block) throws DASException
Add a "Block" Annotation.- Parameters:
block
- an Annotation object- Throws:
DASException
- ...- See Also:
getBlockAnnotationType()
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getBlocks
public Annotation[] getBlocks()
get all Annotations of type "Block".- Returns:
- an array of Annotation objects representing the Aligmnent blocks
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toString
public java.lang.String toString()
convert to String.- Overrides:
toString
in classjava.lang.Object
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