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IQualitativeSequence Interface
Sequence with qualitative data

Namespace: Bio
Assembly: Bio.Core (in Bio.Core.dll) Version: 2.0.0.1 (2.0.0.1)
Syntax
public interface IQualitativeSequence : ISequence, 
	IEnumerable<byte>, IEnumerable

The IQualitativeSequence type exposes the following members.

Properties
  NameDescription
Public propertyAlphabet
Gets alphabet to which this sequence should conform.
(Inherited from ISequence.)
Public propertyCount
Gets the number of sequence items contained in the Sequence.
(Inherited from ISequence.)
Public propertyFormatType
Gets the quality scores format type. Ex: Illumina/Solexa/Sanger.
Public propertyID
Gets or sets an identification provided to distinguish the sequence to others being worked with.
(Inherited from ISequence.)
Public propertyItem
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.)
Public propertyMetadata
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.)
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Methods
  NameDescription
Public methodGetComplementedSequence
Return a sequence representing the complement of this sequence.
(Inherited from ISequence.)
Public methodGetEncodedQualityScore
Gets the encoded quality score found at the specified index if within bounds. Note that the index value start at 0.
Public methodGetEncodedQualityScores
Gets the encoded quality scores.
Public methodGetEnumerator
Returns an enumerator that iterates through the collection.
(Inherited from IEnumerableByte.)
Public methodGetReverseComplementedSequence
Return a sequence representing the reverse complement of this sequence.
(Inherited from ISequence.)
Public methodGetReversedSequence
Return a sequence representing this sequence with the orientation reversed.
(Inherited from ISequence.)
Public methodGetSubSequence
Return a sequence representing a range (subsequence) of this sequence.
(Inherited from ISequence.)
Public methodIndexOfNonGap
Gets the index of first non gap symbol.
(Inherited from ISequence.)
Public methodIndexOfNonGap(Int64)
Returns the position of the first item beyond startPos that does not have a Gap symbol.
(Inherited from ISequence.)
Public methodLastIndexOfNonGap
Gets the index of last non gap symbol.
(Inherited from ISequence.)
Public methodLastIndexOfNonGap(Int64)
Gets the index of last non gap symbol before the specified end position.
(Inherited from ISequence.)
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Extension Methods
  NameDescription
Public Extension MethodAppendByte(Byte)Overloaded.
Yield an Enumeration of the list with the item appended to the end
(Defined by IEnumerableExtensions.)
Public Extension MethodAppendByte(IEnumerableByte)Overloaded.
Yield a concatenation of the two Enumerable lists
(Defined by IEnumerableExtensions.)
Public Extension MethodConvertToString
Converts the sequence to a string.
(Defined by SequenceExtensions.)
Public Extension MethodElementAtByte
Returns the element at a specified index in a sequence.
(Defined by IEnumerableExtensions.)
Public Extension MethodForEachByte(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.)
Public Extension MethodForEachByte(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.)
Public Extension MethodIsMarkedAsReverseComplement
This checks for a sequence marker to determine if the given ISequence was generated from a reverse complement.
(Defined by SequenceExtensions.)
Public Extension MethodMarkAsReverseComplement
This adds a key to the Metadata to indicate this is a reversed sequence
(Defined by SequenceExtensions.)
Public Extension MethodShuffleByte
Shuffles the elements of a sequence.
(Defined by IEnumerableExtensions.)
Public Extension MethodStringJoinOverloaded.
Creates a string from a sequence of elements. No delimiter is used.
(Defined by IEnumerableExtensions.)
Public Extension MethodStringJoin(String)Overloaded.
Creates a delimited string from a sequence of elements.
(Defined by IEnumerableExtensions.)
Public Extension MethodStringJoin(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.)
Public Extension MethodSubSequenceByte
Take the items from a sequence starting with item # start (index 0) and contining for count items.
(Defined by IEnumerableExtensions.)
Public Extension MethodToHashSetByteOverloaded.
Creates a HashSet from a sequence. If the sequence is already a HashSet, a new HashSet is still created.
(Defined by IEnumerableExtensions.)
Public Extension MethodToHashSetByte(IEqualityComparerByte)Overloaded.
Creates a HashSet from a sequence. If the sequence is already a HashSet, a new HashSet is still created.
(Defined by IEnumerableExtensions.)
Public Extension MethodToQueueByte
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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See Also

Reference