| DeltaAlignment Class |
Represents a alignment object in terms of delta.
Delta is an encoded representation of alignments between input sequences.
It contains the start and end indices of alignment in reference and
query sequence followed by error values and list of integer in
following lines. Each integer represent an insertion (+ve) in reference
sequence and deletion (-ve) in reference sequence.
This class represents such alignment with required properties and
utility methods.
Inheritance HierarchyNamespace: Bio.Algorithms.Alignment
Assembly: Bio.Core (in Bio.Core.dll) Version: 2.0.0.1 (2.0.0.1)
SyntaxThe DeltaAlignment type exposes the following members.
Constructors| Name | Description | |
|---|---|---|
 | DeltaAlignment |
Initializes a new instance of the DeltaAlignment class
|
Properties| Name | Description | |
|---|---|---|
 | DeltaReferencePosition |
Gets or sets the value of delta reference position
|
| Deltas |
Gets list of integers that pointing the insertion and
deletion indices
|
| Errors |
Gets or sets errors
|
| FirstSequenceEnd |
Gets or sets the end index of first sequence
|
| FirstSequenceStart |
Gets or sets the start index of first sequence
|
| Id |
Id for this Delta alignment.
Note: As file position is used as ID in case of comparative assembly steps, this value may vary from step to step.
For example: if 0 is the id for a delta alignment in 2nd step then the same delta alignment
can have 500 as id in 3rd step.
This change in id may happen due to the sorting of delta or ignoring some other delta alignments etc.
|
| IsReverseQueryDirection |
Returns TRUE if this is a REVERSE query sequence direction
|
| NonAlphas |
Gets or sets number of non alphabets encountered during alignment
|
| QueryDirection |
Gets or sets the query sequence direction FORWARD or REVERSE
When this is reverse, the second offsets will be reversed in output
|
| QuerySequence |
Gets query sequence id
|
| ReferenceSequence |
Gets reference sequence
|
| SecondSequenceEnd |
Gets or sets the end index of second sequence
|
| SecondSequenceStart |
Gets or sets the start index of second sequence
|
| SimilarityErrors |
Gets or sets similarity errors
|
Methods| Name | Description | |
|---|---|---|
| ConvertDeltaToSequences |
Convert the delta alignment object to its sequence representation
|
| 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.) |
| 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.) |
| ToString |
Converts Ref ID, Query Id, Ref start, Ref End, Query start, Query End to string.
(Overrides ObjectToString.) |
See Also