Class Alignment


  • 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
    • 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
      • 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
      • getScores

        public Annotation[] getScores()
        get all "Score" Annotations.
        Returns:
        an array of Annotation objects representing the scores value
        Throws:
        DASException - ...
      • getBlocks

        public Annotation[] getBlocks()
        get all Annotations of type "Block".
        Returns:
        an array of Annotation objects representing the Aligmnent blocks
      • toString

        public java.lang.String toString()
        convert to String.
        Overrides:
        toString in class java.lang.Object