IQualitativeSequence Interface |
Namespace: Bio
The IQualitativeSequence type exposes the following members.
Name | Description | |
---|---|---|
Alphabet |
Gets alphabet to which this sequence should conform.
(Inherited from ISequence.) | |
Count |
Gets the number of sequence items contained in the Sequence.
(Inherited from ISequence.) | |
FormatType |
Gets the quality scores format type.
Ex: Illumina/Solexa/Sanger.
| |
ID |
Gets or sets an identification provided to distinguish the sequence to others
being worked with.
(Inherited from ISequence.) | |
Item |
Allows the sequence to function like an array, getting and setting
the sequence item at the particular index specified. Note that the
index value starts its count at 0.
(Inherited from ISequence.) | |
Metadata |
Many sequence representations when saved to file also contain
information about that sequence. Unfortunately there is no standard
around what that data may be from format to format. This property
allows a place to put structured metadata that can be accessed by
a particular key.
For example, if species information is stored in a particular Species
class, you could add it to the dictionary by:
mySequence.Metadata["SpeciesInfo"] = mySpeciesInfo;
To fetch the data you would use:
Species mySpeciesInfo = mySequence.Metadata["SpeciesInfo"];
Particular formats may create their own data model class for information
unique to their format as well. Such as:
GenBankMetadata genBankData = new GenBankMetadata();
// ... add population code
mySequence.MetaData["GenBank"] = genBankData;
(Inherited from ISequence.) |
Name | Description | |
---|---|---|
GetComplementedSequence |
Return a sequence representing the complement of this sequence.
(Inherited from ISequence.) | |
GetEncodedQualityScore |
Gets the encoded quality score found at the specified index if within bounds. Note that the index value start at 0.
| |
GetEncodedQualityScores |
Gets the encoded quality scores.
| |
GetEnumerator | Returns an enumerator that iterates through the collection. (Inherited from IEnumerableByte.) | |
GetReverseComplementedSequence |
Return a sequence representing the reverse complement of this sequence.
(Inherited from ISequence.) | |
GetReversedSequence |
Return a sequence representing this sequence with the orientation reversed.
(Inherited from ISequence.) | |
GetSubSequence |
Return a sequence representing a range (subsequence) of this sequence.
(Inherited from ISequence.) | |
IndexOfNonGap |
Gets the index of first non gap symbol.
(Inherited from ISequence.) | |
IndexOfNonGap(Int64) |
Returns the position of the first item beyond startPos that does not
have a Gap symbol.
(Inherited from ISequence.) | |
LastIndexOfNonGap |
Gets the index of last non gap symbol.
(Inherited from ISequence.) | |
LastIndexOfNonGap(Int64) |
Gets the index of last non gap symbol before the specified end position.
(Inherited from ISequence.) |
Name | Description | |
---|---|---|
AppendByte(Byte) | Overloaded.
Yield an Enumeration of the list with the item appended to the end
(Defined by IEnumerableExtensions.) | |
AppendByte(IEnumerableByte) | Overloaded.
Yield a concatenation of the two Enumerable lists
(Defined by IEnumerableExtensions.) | |
ConvertToString |
Converts the sequence to a string.
(Defined by SequenceExtensions.) | |
ElementAtByte |
Returns the element at a specified index in a sequence.
(Defined by IEnumerableExtensions.) | |
ForEachByte(ActionByte) | 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.) | |
ForEachByte(ActionByte, 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.) | |
IsMarkedAsReverseComplement |
This checks for a sequence marker to determine if the given ISequence was generated from
a reverse complement.
(Defined by SequenceExtensions.) | |
MarkAsReverseComplement |
This adds a key to the Metadata to indicate this is a reversed sequence
(Defined by SequenceExtensions.) | |
ShuffleByte |
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.) | |
SubSequenceByte |
Take the items from a sequence starting with item # start (index 0) and contining for count items.
(Defined by IEnumerableExtensions.) | |
ToHashSetByte | Overloaded.
Creates a HashSet from a sequence. If the sequence is already a HashSet, a new HashSet is still created.
(Defined by IEnumerableExtensions.) | |
ToHashSetByte(IEqualityComparerByte) | Overloaded.
Creates a HashSet from a sequence. If the sequence is already a HashSet, a new HashSet is still created.
(Defined by IEnumerableExtensions.) | |
ToQueueByte |
Creates a Queue from a sequence. If the sequence is already a Queue, a new Queue is still created.
(Defined by IEnumerableExtensions.) |