Description:

This set of functions are the responsible of memory management, allocating main geneid data structures, from predictions to parameters and statistical models, as well as temporary structures reset in every fragment of the input sequence.

Briefing:

account* RequestMemoryAccounting()

Memory for account data structure.

char* RequestMemorySequence(long L)

Memory for a DNA sequence.

packSites* RequestMemorySites()

Memory for main structure pack of sites (forward or reverse sense) and every type of signal: acceptor and donor splice sites, start and stop in translation.

packExons* RequestMemoryExons()

Memory for pack of exons and every type of exons: NUMEXONS is modified (divided) by RSINGL, RFIRST, RINTER, RTERMI and RORF ratios because some type of exons (internal and terminal) appear more frequently than others.

exonGFF* RequestMemorySortExons()

Memory to sort exons found in the current fragment.

packEvidence* RequestMemoryEvidence()

Memory for input annotations (evidences).

packHSP* RequestMemoryHomology()

Memory for input similarity to protein regions (homology).

packExternalInformation* RequestMemoryExternalInformation()

Memory for external information (dictionary of Locus names)

packGC* RequestMemoryGC()

Memory for the precomputed array of G/C's and N's nucleotides on a DNA subsequence.

gparam* RequestMemoryParams()

Memory for the statistical model of one isochore loading from the parameter file: profiles, Markov initial/transition arrays, exon scoring parameters. Memory for temporary arrays which compute accumulated sum of penta/hexanucleotides in every split.

gparam ** RequestMemoryIsochoresParams()

Memory for the array of isochores and their common information: gene model dictionary and allowed distances arrays.

void RequestMemoryProfile(profile* p)

Memory for every position containing a Markov chain inside in a Position Weight Array (profile).

packGenes* RequestMemoryGenes()

Memory for the main structure, Ghost exon, best partial genes (Ga) and sorting by donor functions (d-array) in every gene class, necessary in genamic.

packDump* RequestMemoryDumpster()

Memory for backup information between two fragments: sites, exons and a hash table useful to save only once every exon and avoid usual redundancy between best partial genes (they share most exons).

dict* RequestMemoryAaDictionary()

Memory for the genetic code, a hash table to translate from predicted genes or exons into proteins.

Enrique Blanco Garcia © 2003