IPairwiseSequenceAlignment Interface

An IPairwiseSequenceAlignment is the result of running a Pairwise alignment algorithm on a set of two sequences.

Namespace: Bio.Algorithms.Alignment
Assembly: Bio.Core (in Bio.Core.dll) Version: 2.0.0.1 (2.0.0.1)

Syntax

public interface IPairwiseSequenceAlignment : ISequenceAlignment, 
	ICollection<PairwiseAlignedSequence>, IEnumerable<PairwiseAlignedSequence>, IEnumerable

Public Interface IPairwiseSequenceAlignment
	Inherits ISequenceAlignment, ICollection(Of PairwiseAlignedSequence), IEnumerable(Of PairwiseAlignedSequence), 
	IEnumerable

public interface class IPairwiseSequenceAlignment : ISequenceAlignment, 
	ICollection<PairwiseAlignedSequence^>, IEnumerable<PairwiseAlignedSequence^>, IEnumerable

type IPairwiseSequenceAlignment =  
    interface
        interface ISequenceAlignment
        interface ICollection<PairwiseAlignedSequence>
        interface IEnumerable<PairwiseAlignedSequence>
        interface IEnumerable
    end

The IPairwiseSequenceAlignment type exposes the following members.

Properties

	Name	Description
	AlignedSequences	Gets list of the IAlignedSequences which contains aligned sequences with score, offset and consensus . (Inherited from ISequenceAlignment.)
	Count	Gets the number of elements contained in the ICollectionT. (Inherited from ICollectionPairwiseAlignedSequence.)
	Documentation	Gets or sets Documentation object is intended for tracking the history, provenance, and experimental context of a sequence. The user can adopt any desired convention for use of this object. (Inherited from ISequenceAlignment.)
	FirstSequence	Gets accessor for the first sequence.
	IsReadOnly	Gets a value indicating whether the ICollectionT is read-only. (Inherited from ICollectionPairwiseAlignedSequence.)
	Metadata	Gets any additional information about the Alignment. (Inherited from ISequenceAlignment.)
	PairwiseAlignedSequences	Gets list of the (output) aligned sequences with score, offset and consensus.
	SecondSequence	Gets accessor for the second sequence.
	Sequences	Gets list of sequences. (Inherited from ISequenceAlignment.)

Top

Methods

	Name	Description
	Add	Adds an item to the ICollectionT. (Inherited from ICollectionPairwiseAlignedSequence.)
	AddSequence	Add a new Aligned Sequence Object to the end of the list.
	Clear	Removes all items from the ICollectionT. (Inherited from ICollectionPairwiseAlignedSequence.)
	Contains	Determines whether the ICollectionT contains a specific value. (Inherited from ICollectionPairwiseAlignedSequence.)
	CopyTo	Copies the elements of the ICollectionT to an Array, starting at a particular Array index. (Inherited from ICollectionPairwiseAlignedSequence.)
	GetEnumerator	Returns an enumerator that iterates through the collection. (Inherited from IEnumerablePairwiseAlignedSequence.)
	Remove	Removes the first occurrence of a specific object from the ICollectionT. (Inherited from ICollectionPairwiseAlignedSequence.)

Top

Extension Methods

	Name	Description
	AppendPairwiseAlignedSequence(PairwiseAlignedSequence)	Overloaded. Yield an Enumeration of the list with the item appended to the end (Defined by IEnumerableExtensions.)
	AppendPairwiseAlignedSequence(IEnumerablePairwiseAlignedSequence)	Overloaded. Yield a concatenation of the two Enumerable lists (Defined by IEnumerableExtensions.)
	ElementAtPairwiseAlignedSequence	Returns the element at a specified index in a sequence. (Defined by IEnumerableExtensions.)
	ForEachPairwiseAlignedSequence(ActionPairwiseAlignedSequence)	Overloaded. Calls an action on each element of a sequence. The action takes one argument: an element. It has no return value. (Defined by IEnumerableExtensions.)
	ForEachPairwiseAlignedSequence(ActionPairwiseAlignedSequence, Int32)	Overloaded. Calls an action on each element of a sequence. The action takes two arguments: an element and the index of the element. It has no return value. (Defined by IEnumerableExtensions.)
	ShufflePairwiseAlignedSequence	Shuffles the elements of a sequence. (Defined by IEnumerableExtensions.)
	StringJoin	Overloaded. Creates a string from a sequence of elements. No delimiter is used. (Defined by IEnumerableExtensions.)
	StringJoin(String)	Overloaded. Creates a delimited string from a sequence of elements. (Defined by IEnumerableExtensions.)
	StringJoin(String, Int32, String)	Overloaded. Creates a delimited string from a sequence of elements. At most maxLength elements will be used and "..." shows that more elements were in the list. (Defined by IEnumerableExtensions.)
	SubSequencePairwiseAlignedSequence	Take the items from a sequence starting with item # start (index 0) and contining for count items. (Defined by IEnumerableExtensions.)
	ToHashSetPairwiseAlignedSequence	Overloaded. Creates a HashSet from a sequence. If the sequence is already a HashSet, a new HashSet is still created. (Defined by IEnumerableExtensions.)
	ToHashSetPairwiseAlignedSequence(IEqualityComparerPairwiseAlignedSequence)	Overloaded. Creates a HashSet from a sequence. If the sequence is already a HashSet, a new HashSet is still created. (Defined by IEnumerableExtensions.)
	ToQueuePairwiseAlignedSequence	Creates a Queue from a sequence. If the sequence is already a Queue, a new Queue is still created. (Defined by IEnumerableExtensions.)

Top

Remarks

this is just a storage object – it’s up to an algorithm object to fill it in. for efficiency’s sake, we are leaving it up to calling code to keep track of the input sequences, if desired.

Reference

Bio.Algorithms.Alignment Namespace