CSC

The GAnnotations Structure

typedef struct { 
    GCardinal type;
    GCardinal position; 
    GCardinal length; 
    GCardinal strand; 
    GCardinal annotation; 
    GCardinal next;
} GAnnotations; 

The annotations (aka tags) are comments attached to segments of readings or contig consensus sequences. The location is stored as position and length in the original orientation, so complementing a reading does not require edits to the annotations. Consensus sequences are always considered uncomplemented and so complementing a contig does require complementing of annotations that are stored on the consensus.

The annotations can be linked together to form linked lists, sorted on ascending position. The GReadings and GContigs structures contain an annotations field which holds the annotation number of the left most (original orientation) annotation.

Unused annotations are kept in an unsorted linked list referenced by the free_annotatons field of the GDatabase structure.

type

The type of the annotation; a 4 byte integer which the user sees as a 4 character string.

position

The position of the left end of the annotation.

length

The length of the annotation.

strand

The annotation strand. 0 for positive, 1 for negative, and 2 for both.

annotation

The record number of the text string containing a comment for the annotation. Zero means no comment.

next

The annotation number of the next annotation in the linked list, or zero if this is the last in this linked list.