PairwiseSequenceAlignment Class

A simple implementation of IPairwiseSequenceAlignment that stores the results as list of Aligned Sequences.

Inheritance Hierarchy

SystemObject
Bio.Algorithms.AlignmentPairwiseSequenceAlignment

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

Syntax

C++

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public class PairwiseSequenceAlignment : IPairwiseSequenceAlignment, 
	ISequenceAlignment, ICollection<PairwiseAlignedSequence>, IEnumerable<PairwiseAlignedSequence>, 
	IEnumerable

Public Class PairwiseSequenceAlignment
	Implements IPairwiseSequenceAlignment, ISequenceAlignment, ICollection(Of PairwiseAlignedSequence), 
	IEnumerable(Of PairwiseAlignedSequence), IEnumerable

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

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

The PairwiseSequenceAlignment type exposes the following members.

Constructors

	Name	Description
	PairwiseSequenceAlignment	Initializes a new instance of the PairwiseSequenceAlignment class Constructs an empty PairwiseSequenceAlignment.
	PairwiseSequenceAlignment(ISequence, ISequence)	Initializes a new instance of the PairwiseSequenceAlignment class Constructs PairwiseSequenceAlignment with input sequences.

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Properties

	Name	Description
	AlignedSequences	Gets list of the (output) aligned sequences.
	Count	Gets number of aligned sequence objects in the PairwiseSequenceAlignment.
	Documentation	Gets or sets Documentation object is intended for tracking the history, provenance, and experimental context of a PairwiseSequenceAlignment. The user can adopt any desired convention for use of this object.
	FirstSequence	Gets accessor for the first sequence.
	IsReadOnly	Gets or sets a value indicating whether PairwiseSequenceAlignment is read-only or not.
	Item	Returns the nth aligned sequence in the alignment.
	Metadata	Gets any additional information about the Alignment.
	PairwiseAlignedSequences	Gets the list of alignments.
	SecondSequence	Gets accessor for the second sequence.
	Sequences	Gets list of sequences involved in this alignment.

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Methods

	Name	Description
	Add	Adds an aligned sequence to the list of aligned sequences in the PairwiseSequenceAlignment. Throws exception if sequence alignment is read only.
	AddSequence	Add a new Aligned Sequence Object to the end of the list.
	Clear	Clears the PairwiseSequenceAlignment Throws exception if PairwiseSequenceAlignment is read only.
	Contains	Returns true if the PairwiseSequenceAlignment contains the aligned sequence in the list of aligned sequences.
	CopyTo	Copies the aligned sequences from the PairwiseSequenceAlignment into an existing aligned sequence array.
	Equals	Determines whether the specified object is equal to the current object. (Inherited from Object.)
	Finalize	Allows an object to try to free resources and perform other cleanup operations before it is reclaimed by garbage collection. (Inherited from Object.)
	GetEnumerator	Returns an enumerator for the aligned sequences in the PairwiseSequenceAlignment.
	GetHashCode	Serves as the default hash function. (Inherited from Object.)
	GetType	Gets the Type of the current instance. (Inherited from Object.)
	MemberwiseClone	Creates a shallow copy of the current Object. (Inherited from Object.)
	Remove	Removes item from the list of aligned sequences in the PairwiseSequenceAlignment. Throws exception if PairwiseSequenceAlignment is read only.
	ToString	Converts the Aligned Sequences to string. (Overrides ObjectToString.)

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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.)

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Reference

Bio.Algorithms.Alignment Namespace