Class GffRecord
Represent a record from a GFF or GTF file.

Implements FormattedFileRecordConcept
All Impl'd AssignableConcept, CopyConstructibleConcept, DefaultConstructibleConcept, FormattedFileRecordConcept
Defined in <seqan/gff_io.h>
Signature class GffRecord;

Member Function Overview

Member Functions Inherited From AssignableConcept

Interface Function Overview

Interface Functions Inherited From AssignableConcept

Member Variable Overview

Member Functions Detail

static float INVALID_SCORE()

Returns invalid score (NaN float value).

The term x != x (for float x is only true if x is a NaN.

Interface Functions Detail

void clear(record);

Reset a GffRecord object.


record The GffRecord to reset.

Member Variables Detail

__int32 GffRecord::beginPos

The begin position of the record.

__int32 GffRecord::endPos

The end position of the record.

GFF and GTF use 1-based positions in text, but they are stored as 0-based coordinates.

__int32 GffRecord::INVALID_IDX

Static member with invalid/sentinel rID value.

char GffRecord::phase

The phase of the record.

For features of type "CDS", the phase indicates where the feature begins with reference to the reading frame. The phase is one of the integers 0, 1, or 2, indicating the number of bases that should be removed from the beginning of this feature to reach the first base of the next codon.

CharString GffRecord::ref

The sequence name of the record.

The ID of the landmark used to establish the coordinate system for the current feature, most often the contig/chromosome name.

float GffRecord::score

The score of the record.

CharString GffRecord::source

The source of the record.

The source is a free text qualifier intended to describe the algorithm or operating procedure that generated this feature.

char GffRecord::strand

The strand the record belongs to.

The strand of the feature. + for positive strand (relative to the landmark), - for minus strand, and . for features that are not stranded.

TCharStringSet GffRecord::tagNames

The names of the attributes of the record, StringSet of CharString.

For each value there is a name associated in tagNames.

TCharStringSet GffRecord::tagValues

The values of the attributes of the record, StringSet of CharString.


For each name there is a value associated in GffRecord::tagValues.

CharString GffRecord::type

The type of the record.