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commit -m "Cleaned code for thermodynamics properties and added Melting Temperature for approximate version of strict repeats. Also cleaned printing code.

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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@223 60f365c0-8329-0410-b2a4-ec073aeeaa1d
This commit is contained in:
Eric Coissac
2009-07-13 09:26:19 +00:00
parent 91753ace82
commit e79738e170
8 changed files with 305 additions and 564 deletions
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37
src/libecoprimer/pairs.c
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@ -156,16 +156,14 @@ ppairtree_t buildPrimerPairs(pecodnadb_t seqdb,uint32_t seqdbsize,pprimercount_t
{
uint32_t i;
ppairtree_t primerpairs;
primerpairs = initpairtree(NULL);
for (i=0; i < seqdbsize; i++)
{
buildPrimerPairsForOneSeq(i, seqdb, primers, primerpairs, options);
}
return primerpairs;
}
#define DMAX (2000000000)
@ -187,7 +185,11 @@ static void buildPrimerPairsForOneSeq(uint32_t seqid,
bool_t bswp;
size_t distance;
bool_t strand;
//char prmr[50];
//float mtemp;
//prmr[options->primer_length] = '\0';
for (i=0;i < primers->size; i++)
{
matchcount+=primers->primers[i].directCount[seqid];
@ -272,10 +274,12 @@ static void buildPrimerPairsForOneSeq(uint32_t seqid,
current.outexample=0;
current.curseqid = 0;
current.refsequence=-1;
//current.p1temp = 100;
//current.p1mintemp = 100;
//current.p2temp = 100;
//current.p2mintemp = 100;
// Standardize the pair
strand = current.p2->word > current.p1->word;
if (!strand)
{
@ -309,6 +313,10 @@ static void buildPrimerPairsForOneSeq(uint32_t seqid,
//else
// pcurrent->outexample++;
//for each pair we save current sequence id in the pair
//when we see this pair for the first time in currnet sequence
//because we want to increment inexample & outexample count
//only once for one sequence
if (pcurrent->curseqid != (seqid+1))
{
if (seqdb[seqid]->isexample)
@ -359,6 +367,23 @@ static void buildPrimerPairsForOneSeq(uint32_t seqid,
else
pcurrent->pcr.amplifias[pcurrent->pcr.ampcount].amplifia= seqdb[seqid]->SQ + matches[j].position - 1 ;
/*strncpy (prmr, seqdb[seqid]->SQ + matches[i].position, options->primer_length);
mtemp = nparam_CalcSelfTM (options->pnparm, prmr, options->primer_length) - 273.0;
if (mtemp < pcurrent->p1mintemp)
pcurrent->p1mintemp = mtemp;
//fprintf (stderr, "prmr1: %s\n", seqdb[seqid]->SQ);
strncpy (prmr, seqdb[seqid]->SQ + matches[j].position, options->primer_length);
mtemp = nparam_CalcSelfTM (options->pnparm, prmr, options->primer_length) - 273.0;
if (mtemp < pcurrent->p2mintemp)
pcurrent->p2mintemp = mtemp;
//fprintf (stderr, "prmr2: %s\n", prmr);
if (pcurrent->p1temp == 100)
pcurrent->p1temp = nparam_CalcSelfTM (options->pnparm, ecoUnhashWord(pcurrent->p1->word, options->primer_length), 0) - 273.0;
if (pcurrent->p2temp == 100)
pcurrent->p2temp = nparam_CalcSelfTM (options->pnparm, ecoUnhashWord(pcurrent->p2->word, options->primer_length), 0) - 273.0;
*/
pcurrent->pcr.ampcount++;
// fprintf(stderr,"%c%c W1 : %s direct : %c",
// "bG"[(int)pcurrent->p1->good],