Besa Fhir Help File

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Class TSequence

Description
Hierarchy
Fields
Methods
Properties

Unit

bsFhir_stu3

Declaration

type TSequence = class(TDomainResource)

Description

Raw data describing a biological sequence. If the element is present, it must have either a @value, an @id, or extensions

Hierarchy

Overview

Methods

Public constructor Create; override;

Properties

Public property identifier : TIdentifierArray read GetidentifierArray;
Public property type_ : string read Gettype_ write Settype_;
Public property type_Element : Tcode read Gettype_Element write Settype_Element;
Public property coordinateSystem : integer read GetcoordinateSystem write SetcoordinateSystem;
Public property coordinateSystemElement : Tinteger read GetcoordinateSystemElement write SetcoordinateSystemElement;
Public property patient : TReference read Getpatient write Setpatient;
Public property specimen : TReference read Getspecimen write Setspecimen;
Public property device : TReference read Getdevice write Setdevice;
Public property performer : TReference read Getperformer write Setperformer;
Public property quantity : TQuantity read Getquantity write Setquantity;
Public property referenceSeq : TSequenceReferenceSeq read GetreferenceSeq write SetreferenceSeq;
Public property variant : TSequenceVariantArray read GetvariantArray;
Public property observedSeq : string read GetobservedSeq write SetobservedSeq;
Public property observedSeqElement : Tstring read GetobservedSeqElement write SetobservedSeqElement;
Public property quality : TSequenceQualityArray read GetqualityArray;
Public property readCoverage : integer read GetreadCoverage write SetreadCoverage;
Public property readCoverageElement : Tinteger read GetreadCoverageElement write SetreadCoverageElement;
Public property repository : TSequenceRepositoryArray read GetrepositoryArray;
Public property pointer : TReferenceArray read GetpointerArray;

Description

Methods

Public constructor Create; override;
 

Properties

Public property identifier : TIdentifierArray read GetidentifierArray;

A unique identifier for this particular sequence instance. This is a FHIR-defined id.

Public property type_ : string read Gettype_ write Settype_;

Amino Acid Sequence/ DNA Sequence / RNA Sequence.

Public property type_Element : Tcode read Gettype_Element write Settype_Element;
 
Public property coordinateSystem : integer read GetcoordinateSystem write SetcoordinateSystem;

Whether the sequence is numbered starting at 0 (0-based numbering or coordinates, inclusive start, exclusive end) or starting at 1 (1-based numbering, inclusive start and inclusive end).

Public property coordinateSystemElement : Tinteger read GetcoordinateSystemElement write SetcoordinateSystemElement;
 
Public property patient : TReference read Getpatient write Setpatient;

The patient whose sequencing results are described by this resource.

Public property specimen : TReference read Getspecimen write Setspecimen;

Specimen used for sequencing.

Public property device : TReference read Getdevice write Setdevice;

The method for sequencing, for example, chip information.

Public property performer : TReference read Getperformer write Setperformer;

The organization or lab that should be responsible for this result.

Public property quantity : TQuantity read Getquantity write Setquantity;

The number of copies of the seqeunce of interest. (RNASeq).

Public property referenceSeq : TSequenceReferenceSeq read GetreferenceSeq write SetreferenceSeq;

A sequence that is used as a reference to describe variants that are present in a sequence analyzed.

Public property variant : TSequenceVariantArray read GetvariantArray;

The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)). This element can represent amino acid or nucleic sequence change(including insertion,deletion,SNP,etc.) It can represent some complex mutation or segment variation with the assist of CIGAR string.

Public property observedSeq : string read GetobservedSeq write SetobservedSeq;

Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall starts from referenceSeq.windowStart and end by referenceSeq.windowEnd.

Public property observedSeqElement : Tstring read GetobservedSeqElement write SetobservedSeqElement;
 
Public property quality : TSequenceQualityArray read GetqualityArray;

An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686)).

Public property readCoverage : integer read GetreadCoverage write SetreadCoverage;

Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.

Public property readCoverageElement : Tinteger read GetreadCoverageElement write SetreadCoverageElement;
 
Public property repository : TSequenceRepositoryArray read GetrepositoryArray;

Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.

Public property pointer : TReferenceArray read GetpointerArray;

Pointer to next atomic sequence which at most contains one variant.

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