Interface SequencePair<S extends Sequence<C>,​C extends Compound>

    • Method Detail

      • getCompoundInQueryAt

        C getCompoundInQueryAt​(int alignmentIndex)
        Returns the Compound in query sequence at given column index in alignment.
        Parameters:
        alignmentIndex - column index in alignment
        Returns:
        the query sequence element
        Throws:
        java.lang.IndexOutOfBoundsException - if alignmentIndex < 1 or alignmentIndex > Profile.getLength()
      • getCompoundInTargetAt

        C getCompoundInTargetAt​(int alignmentIndex)
        Returns the Compound in target sequence at given column index in alignment.
        Parameters:
        alignmentIndex - column index in alignment
        Returns:
        the target sequence element
        Throws:
        java.lang.IndexOutOfBoundsException - if alignmentIndex < 1 or alignmentIndex > Profile.getLength()
      • getIndexInQueryAt

        int getIndexInQueryAt​(int alignmentIndex)
        Returns the query index corresponding to a given alignment column.
        Parameters:
        alignmentIndex - column index in alignment
        Returns:
        index in query Sequence
        Throws:
        java.lang.IndexOutOfBoundsException - if alignmentIndex < 1 or alignmentIndex > Profile.getLength()
      • getIndexInQueryForTargetAt

        int getIndexInQueryForTargetAt​(int targetIndex)
        Returns the query index corresponding to a given target index.
        Parameters:
        targetIndex - index in target Sequence
        Returns:
        index in query Sequence
        Throws:
        java.lang.IndexOutOfBoundsException - if targetIndex < 1 or targetIndex > getTarget().getLength()
      • getIndexInTargetAt

        int getIndexInTargetAt​(int alignmentIndex)
        Returns the target index corresponding to a given alignment column.
        Parameters:
        alignmentIndex - column index in alignment
        Returns:
        index in target Sequence
        Throws:
        java.lang.IndexOutOfBoundsException - if alignmentIndex < 1 or alignmentIndex > Profile.getLength()
      • getIndexInTargetForQueryAt

        int getIndexInTargetForQueryAt​(int queryIndex)
        Returns the target index corresponding to a given query index.
        Parameters:
        queryIndex - index in query Sequence
        Returns:
        index in target Sequence
        Throws:
        java.lang.IndexOutOfBoundsException - if queryIndex < 1 or queryIndex > getQuery().getLength()
      • getNumIdenticals

        int getNumIdenticals()
        Returns the number of indices for which both the query and target sequences have an identical Compound.
        Returns:
        the number of identical indices
      • getNumSimilars

        int getNumSimilars()
        Returns the number of indices for which both the query and target sequences have a similar Compound.
        Returns:
        the number of similar indices