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java.lang.Objectorg.biojava.bio.program.das.dasalignment.Alignment
public class Alignment
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)
Constructor Summary | |
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Alignment()
Construct a new empty Alignment object. |
Method Summary | |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public Alignment()
Method Detail |
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public static AnnotationType getVectorAnnotationType()
public static AnnotationType getMatrixAnnotationType()
public static AnnotationType getScoreAnnotationType()
public static AnnotationType getBlockAnnotationType()
public static AnnotationType getSegmentAnnotationType()
public static AnnotationType getObjectAnnotationType()
public void addVector(Annotation vector) throws DASException
vector
- a vector
DASException
- ...getVectorAnnotationType()
public void addMatrix(Annotation matrix) throws DASException
matrix
- a matrix
DASException
- ...getMatrixAnnotationType()
public void addObject(Annotation object) throws DASException
object
- an Annotation object
DASException
- ...getObjectAnnotationType()
public Annotation[] getObjects()
public Annotation[] getVectors()
public Annotation[] getMatrices()
public void addScore(Annotation score) throws DASException
score
- an Annotation object
DASException
- ...getScoreAnnotationType()
public Annotation[] getScores()
DASException
- ...public void addBlock(Annotation block) throws DASException
block
- an Annotation object
DASException
- ...getBlockAnnotationType()
public Annotation[] getBlocks()
public String toString()
toString
in class Object
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