Initializes a new instance of the QualitativeSequence class with specified alphabet, quality score type, byte array representing symbols and encoded quality scores. Sequence and quality scores are validated with the specified alphabet and specified fastq format respectively.

Initializes a new instance of the QualitativeSequence class with specified alphabet, quality score type, string representing symbols and encoded quality scores. Sequence and quality scores are validated with the specified alphabet and specified fastq format respectively.

Initializes a new instance of the QualitativeSequence class with specified alphabet, quality score type, byte array representing symbols and encoded quality scores.

Initializes a new instance of the QualitativeSequence class with specified alphabet, quality score type, byte array representing symbols and integer array representing base quality scores (Phred or Solexa base according to the FastQ format type).

Initializes a new instance of the QualitativeSequence class with specified alphabet, quality score type, byte array representing symbols and signed byte array representing base quality scores (Phred or Solexa base according to the FastQ format type).

Initializes a new instance of the QualitativeSequence class with specified alphabet, quality score type, string representing symbols and encoded quality scores.

Gets the alphabet to which symbols in this sequence belongs to.

Gets the number of bytes contained in the Sequence.

Gets the quality scores format type. Ex: Illumina/Solexa/Sanger.

Gets or sets the Identifier.

Returns the byte which represents the symbol found at the specified index if within bounds. Note that the index value starts at 0.

Gets or sets the metadata for this qualitative sequence.

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;.

Converts Encoded quality score from to specified format.

Converts Encoded quality scores from to specified format.

Converts Quality score from to specified format.

Converts Quality scores from to specified format.

Converts Quality scores from to specified format.

Converts the current instance to the specified FastQ format type and returns a new instance of QualitativeSequence.

Determines whether the specified object is equal to the current object.

Allows an object to try to free resources and perform other cleanup operations before it is reclaimed by garbage collection.

Return a new QualitativeSequence representing the complement of this QualitativeSequence.

Gets the default quality score for the specified FastQFormatType.

Gets the encoded quality score found at the specified index if within bounds. Note that the index value start at 0.

Gets the encoded quality scores.

Gets an enumerator to the bytes present symbols in this sequence.

Serves as the default hash function.

Gets the maximum encoded quality score for the specified FastQFormatType.

Gets the minimum encoded quality score for the specified FastQFormatType.

Gets the Phred base quality score.

Gets the Phred base quality scores.

Returns base quality scores at specified index. Returns Solexa quality scores if the FastQFormat type of this instance is Solexa Illumina v1.0, else returns Phred quality scores.

Returns base quality scores. Returns Solexa quality scores if the FastQFormat type of this instance is Solexa Illumina v1.0, else returns Phred quality scores.

Return a new QualitativeSequence representing the reverse complement of this QualitativeSequence.

Return a new QualitativeSequence representing this QualitativeSequence with the orientation reversed.

Gets the Solexa base quality score.

Gets the solexa base quality scores.

Return a new QualitativeSequence representing a range (subsequence) of this QualitativeSequence.

Gets the Type of the current instance.

Gets the index of first non-gap symbol.

Returns the position of the first symbol beyond startPos that does not have a Gap symbol.

Gets the index of last non-gap symbol.

Returns the index of last non-gap symbol before the specified end position.

Creates a shallow copy of the current Object.

Returns a string representation of the Qualitative sequence data. This representation will come from the symbols in the alphabet defined for the sequence. Also their Quality scores.

Validates whether the specified encoded quality scores are within the FastQFormatType limit or not.

Maximum encoded quality score for Illumina v1.3 format: 126

Minimum encoded quality score for Illumina v1.3 format: 64

Maximum encoded quality score for Illumina v1.5 format: 126

Minimum encoded quality score for Illumina v1.5 format: 64

Maximum encoded quality score for Illumina v1.8 format: 126

Minimum encoded quality score for Illumina v1.8 format: 33

Phred maximum quality score: 93

Phred minimum quality score: 0

Maximum encoded quality score for Sanger format: 126

Minimum encoded quality score for Sanger format: 33

Maximum encoded quality score for Solexa/Illumina v1.0 format: 126

Minimum encoded quality score for Solexa/Illumina v1.0 format: 59

Solexa maximum quality score: 62

Solexa minimum quality score: -5

Yield an Enumeration of the list with the item appended to the end

Yield a concatenation of the two Enumerable lists

Converts the sequence to a string.

Returns the element at a specified index in a sequence.

Calls an action on each element of a sequence. The action takes one argument: an element. It has no return value.

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.

This checks for a sequence marker to determine if the given ISequence was generated from a reverse complement.

This adds a key to the Metadata to indicate this is a reversed sequence

Shuffles the elements of a sequence.

Creates a string from a sequence of elements. No delimiter is used.

Creates a delimited string from a sequence of elements.

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.

Take the items from a sequence starting with item # start (index 0) and contining for count items.

Creates a HashSet from a sequence. If the sequence is already a HashSet, a new HashSet is still created.

Creates a HashSet from a sequence. If the sequence is already a HashSet, a new HashSet is still created.

Creates a Queue from a sequence. If the sequence is already a Queue, a new Queue is still created.