Class JoiningSequenceReader<C extends Compound>

  • Type Parameters:
    C - Tyoe of compound to hold
    All Implemented Interfaces:
    java.lang.Iterable<C>, Accessioned, ProxySequenceReader<C>, Sequence<C>, SequenceReader<C>

    public class JoiningSequenceReader<C extends Compound>
    extends java.lang.Object
    implements ProxySequenceReader<C>
    This reader actually proxies onto multiple types of sequence in order to allow a number of sequence objects to act as if they are one sequence. The code takes in any number of sequences, records the minimum and maximum bounds each sequence covers with respect to 1 position indexing and then binary searches these when a position is requested. Because of this 0 length Sequences are excluded during construction. Performance is not as good as if you are using a flat sequence however the speed of lookup is more than adaquate for most situations. Using the iterator gives the best performance as this does not rely on the binary search mechanism instead iterating through each sequence in turn.
    Author:
    ayates
    • Constructor Detail

      • JoiningSequenceReader

        public JoiningSequenceReader​(Sequence<C>... sequences)
        Allows creation of the store from Vargs Sequence objects. CompoundSet defaults to the first element of the array (assuming there are elements available during construction otherwise we will throw an illegal state exception).
      • JoiningSequenceReader

        public JoiningSequenceReader​(java.util.List<Sequence<C>> sequences)
        Allows creation of the store from List>. CompoundSet defaults to the first element of the List (assuming there are elements available during construction otherwise we will throw an illegal state exception).
      • JoiningSequenceReader

        public JoiningSequenceReader​(CompoundSet<C> compoundSet,
                                     Sequence<C>... sequences)
      • JoiningSequenceReader

        public JoiningSequenceReader​(CompoundSet<C> compoundSet,
                                     java.util.List<Sequence<C>> sequences)
    • Method Detail

      • getCompoundAt

        public C getCompoundAt​(int position)
        Description copied from interface: Sequence
        Returns the Compound at the given biological index
        Specified by:
        getCompoundAt in interface Sequence<C extends Compound>
        Parameters:
        position - Biological index (1 to n)
        Returns:
        Compound at the specified position
      • getLength

        public int getLength()
        Description copied from interface: Sequence
        Returns the length of the Sequence
        Specified by:
        getLength in interface Sequence<C extends Compound>
      • iterator

        public java.util.Iterator<C> iterator()
        Iterator implementation which attempts to move through the 2D structure attempting to skip onto the next sequence as & when it is asked to
        Specified by:
        iterator in interface java.lang.Iterable<C extends Compound>
      • countCompounds

        public int countCompounds​(C... compounds)
        Description copied from interface: Sequence
        Returns the number of times we found a compound in the Sequence
        Specified by:
        countCompounds in interface Sequence<C extends Compound>
        Parameters:
        compounds - Vargs of the compounds to count
        Returns:
        Number of times a compound was found
      • getAccession

        public AccessionID getAccession()
                                 throws java.lang.UnsupportedOperationException
        Description copied from interface: Accessioned
        Returns the AccessionID this location is currently bound with
        Specified by:
        getAccession in interface Accessioned
        Throws:
        java.lang.UnsupportedOperationException
      • getAsList

        public java.util.List<C> getAsList()
        Description copied from interface: Sequence
        Returns the Sequence as a List of compounds
        Specified by:
        getAsList in interface Sequence<C extends Compound>
      • equals

        public boolean equals​(java.lang.Object o)
        Overrides:
        equals in class java.lang.Object
      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class java.lang.Object
      • getIndexOf

        public int getIndexOf​(C compound)
        Description copied from interface: Sequence
        Scans through the Sequence looking for the first occurrence of the given compound
        Specified by:
        getIndexOf in interface Sequence<C extends Compound>
        Parameters:
        compound - Compounds to look for
        Returns:
        Index of the first position of the compound in the sequence (1 to n)
      • getLastIndexOf

        public int getLastIndexOf​(C compound)
        Description copied from interface: Sequence
        Scans through the Sequence looking for the last occurrence of the given compound
        Specified by:
        getLastIndexOf in interface Sequence<C extends Compound>
        Parameters:
        compound - Compounds to look for
        Returns:
        Index of the last position of the compound in the sequence (1 to n)
      • getSequenceAsString

        public java.lang.String getSequenceAsString()
        Description copied from interface: Sequence
        Returns the String representation of the Sequence
        Specified by:
        getSequenceAsString in interface Sequence<C extends Compound>
      • getSubSequence

        public SequenceView<C> getSubSequence​(java.lang.Integer start,
                                              java.lang.Integer end)
        Description copied from interface: Sequence
        Returns a portion of the sequence from the different positions. This is indexed from 1
        Specified by:
        getSubSequence in interface Sequence<C extends Compound>
        Parameters:
        start - Biological index start; must be greater than 0
        end - Biological end; must be less than length + 1
        Returns:
        A SequenceView of the offset
      • getInverse

        public SequenceView<C> getInverse()
        Description copied from interface: Sequence
        Does the right thing to get the inverse of the current Sequence. This means either reversing the Sequence and optionally complementing the Sequence.
        Specified by:
        getInverse in interface Sequence<C extends Compound>