Description:

To exchange frame and remainder in reverse exons is necessary because while during exon construction, frame and remainder are dependent on the sense of reading (frame for the first uncomplete codon, following the reading sense, and remainder for the end), in genamic assembling frame is always associated to the left (geographical) uncomplete codon and remainder to the right one. Thus, gene assembling is reduced to assemble the pieces according only to some restrictions such as allowed rules (gene model) or frame-remainder constraints, forgetting different exon properties.

Briefing:

void SwitchFrames(exonGFF* e, long n)

Exchanging/restore frame and remainder in the exons predicted during current sequence fragment (only reverse exons).

void SwitchFramesDa(packGenes* pg, int nclass)

Exchanging frame and remainder in the exons saved during previous fragment processing into the d-array (only reverse exons). Using the flag selected, because some exons might be in more than one list and this change must be only once. This exchange will be restored after finishing genamic processing.

void SwitchFramesDb(packGenes* pg, int nclass)

Restore frame and remainder only in the exons saved during previous fragment processing into the d-array (only reverse exons). Using the flag selected, because some exons might be in more than one list and this change must be only once. (Note: Exons predicted in the current fragment will not have raised the flag selected. Thus, although they are right now in the d-array, their frame and remainder will not change during this function)

void UndoFrames(exonGFF* e, long n)

Restore frame and remainder in the input set of exons when they have been loaded from a gff file (partial prediction, only assembling).

Enrique Blanco Garcia © 2001