org.biojava.bio.program.das.dasalignment
Class Alignment

java.lang.Object
  extended by org.biojava.bio.program.das.dasalignment.Alignment

public class Alignment
extends 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

Constructor Summary
Alignment()
          Construct a new empty Alignment object.
 
Method Summary
 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 type
static 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 type
 Annotation[] getVectors()
          Returns the shift vectors.
 String toString()
          convert to String.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

Alignment

public Alignment()
Construct a new empty Alignment object.

Method Detail

getVectorAnnotationType

public static AnnotationType getVectorAnnotationType()
define the shift vector annotation type

Returns:
an AnnotationType object representing the shift vector for an object

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.

getScoreAnnotationType

public static AnnotationType getScoreAnnotationType()
define the alignment Score Annotation Type.

Returns:
an AnnotationType object representing the score annotation type

getBlockAnnotationType

public static AnnotationType getBlockAnnotationType()
define the alignment Block Annotation Type.

Returns:
an AnnotationType object representing the block annotation type

getSegmentAnnotationType

public static AnnotationType getSegmentAnnotationType()
define the alignment Segment Annotation Type.

Returns:
an AnnotationType object representing the segment annotation type

getObjectAnnotationType

public static AnnotationType getObjectAnnotationType()
define the alignment object Annotation Type.

Returns:
an AnnotationType object representing the object annotation type

addVector

public void addVector(Annotation vector)
               throws DASException
add Annotation of DAS alignment "vector" type.

Parameters:
vector - a vector
Throws:
DASException - ...
See Also:
getVectorAnnotationType()

addMatrix

public void addMatrix(Annotation matrix)
               throws DASException
add Annotation of DAS alignment "matrix" type.

Parameters:
matrix - a matrix
Throws:
DASException - ...
See Also:
getMatrixAnnotationType()

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()

getObjects

public Annotation[] getObjects()
Returns the Annotation of all objects in this Alignment.

Returns:
an array of Annotation objects

getVectors

public Annotation[] getVectors()
Returns the shift vectors.

Returns:
an array of shift vectors

getMatrices

public Annotation[] getMatrices()
Returns the matrices.

Returns:
an array of the matrices

addScore

public void addScore(Annotation score)
              throws DASException
adds a "Score" Annotation.

Parameters:
score - an Annotation object
Throws:
DASException - ...
See Also:
getScoreAnnotationType()

getScores

public Annotation[] getScores()
get all "Score" Annotations.

Returns:
an array of Annotation objects representing the scores value
Throws:
DASException - ...

addBlock

public void addBlock(Annotation block)
              throws DASException
Add a "Block" Annotation.

Parameters:
block - an Annotation object
Throws:
DASException - ...
See Also:
getBlockAnnotationType()

getBlocks

public Annotation[] getBlocks()
get all Annotations of type "Block".

Returns:
an array of Annotation objects representing the Aligmnent blocks

toString

public String toString()
convert to String.

Overrides:
toString in class Object