// find all k-tuples. overlapping ones within w discarded
void count_k_tuples(char **seq,char **rseq,int numSeq,int *seqLen,
char **kmer,int numKer,int kmerLen,int *kmerCn) {
register int i,j,k,m,l;
int used,slide,numUniq;
int *uniq,*id;
char *s1,*s2;
s1=alloc_char(kmerLen+1);
s2=alloc_char(kmerLen+1);
uniq=alloc_int(2*kmerLen);
id=alloc_int(2*kmerLen);
for (m=0; m<numKer; m++) kmerCn[m]=0;
for (i=0; i<numSeq; i++) {
for (m=0; m<2*kmerLen; m++) id[m]=-1;
slide=0;
for (j=0; j<seqLen[i]-kmerLen+1; j++) {
for (k=0; k<kmerLen; k++) s1[k]=seq[i][j+k]; s1[k]='\0';
for (k=0; k<kmerLen; k++) s2[k]=rseq[i][seqLen[i]-kmerLen-j+k]; s2[k]='\0';
for (m=0; m<numKer; m++) {
if (strncmp(s1,kmer[m],kmerLen)==0) { id[slide]=m; break; }
}
slide++;
for (m=0; m<numKer; m++) {
if (strncmp(s2,kmer[m],kmerLen)==0) { id[slide]=m; break; }
}
slide++;
if ((slide==2*kmerLen) || (j==seqLen[i]-kmerLen)) {
for (l=0; l<2*kmerLen; l++) uniq[l]=-2;
numUniq=0;
for (k=0; k<2*kmerLen; k++) {
used=0;
for (l=0; l<numUniq; l++) {
if (id[k]==uniq[l]) { used=1; break; }
}
if (!used && id[k]!=-1) {
uniq[numUniq]=id[k]; numUniq++;
}
}
for (l=0; l<numUniq; l++) (kmerCn[uniq[l]])++;
slide=0;
for (m=0; m<2*kmerLen; m++) id[m]=-1;
}
}
}
if (s1) { free(s1); s1=NULL; }
if (s2) { free(s2); s2=NULL; }
if (id) { free(id); id=NULL; }
if (uniq) { free(uniq); uniq=NULL; }
}
static void insert_node(struct node **pn, char c)
{
struct node *n = malloc(sizeof *n);
if (!n)
abort();
n->data = (c) ? alloc_char(c) : NULL;
n->next = *pn;
*pn = n;
}
Ktuples *alloc_ktuples(int numKmer,int kmerLen) {
int i;
Ktuples *tmp=NULL;
tmp=(Ktuples *)calloc(numKmer,sizeof(Ktuples));
for (i=0; i<numKmer; i++) tmp[i].seq=alloc_char(kmerLen+1);
return (tmp);
}
char* convertRString2Char(SEXP rstring)
{
char* charArray;
int rstringlength=length(rstring);
//int i=0;
int lengthcharArray=0;
charArray=alloc_char(rstringlength+1);
strcpy(charArray, CHAR(STRING_ELT(rstring, 0)));
lengthcharArray = (int)(strlen(charArray));
charArray[lengthcharArray]='\0';
return charArray;
}
void print_bed(Sites *site,int nsites,char **geneID,int *seqLen,int pwmLen,int id) {
FILE *f1;
char *fileName,*s1,*chr;
int s,e,e2,len,start;
register int i,j,k;
s1=alloc_char(20);
chr=alloc_char(20);
fileName=alloc_char(500);
/*Rprintf("%d.bed",id);*/
/*f1=fopen(fileName,"w");*/
for (i=0; i<nsites; i++) {
len=strlen(geneID[site[i].seq]);
s=-1; e=-1;
for (j=0; j<len-3; j++) {
if (geneID[site[i].seq][j]=='c' && geneID[site[i].seq][j+1]=='h' && geneID[site[i].seq][j+2]=='r') {
s=j; break;
}
}
for (j=s; j<len; j++) {
if (geneID[site[i].seq][j]==':') {
e=j; break;
}
}
if (s!=-1 && e!=-1) {
for (k=0,j=s; j<e; j++,k++) chr[k]=geneID[site[i].seq][j];
chr[k]='\0';
}
else {
error("%s chr not found! %d %d\n",geneID[site[i].seq],s,e);
/*Rprintf("%s chr not found! %d %d\n",geneID[site[i].seq],s,e); exit(0);*/
}
e2=-1;
for (j=e+1; j<len; j++) {
if (geneID[site[i].seq][j]=='-') {
e2=j; break;
}
}
if (e2!=-1) {
for (k=0,j=e+1; j<e2; j++,k++) s1[k]=geneID[site[i].seq][j];
s1[k]='\0';
start=atoi(s1);
}
else {
error("start not found!\n");
/*Rprintf("start not found!\n"); exit(0);*/
}
if (site[i].rev=='0') {
if (site[i].pos>=0) Rprintf("%s\t%d\t%d\n",chr,site[i].pos+start,site[i].pos+pwmLen+start-1);
}
else {
if (site[i].pos>=0) Rprintf("%s\t%d\t%d\n",chr,seqLen[site[i].seq]-site[i].pos-pwmLen+start,seqLen[site[i].seq]-site[i].pos+start-1);
}
}
/*fclose(f1);*/
if (fileName) { free(fileName); fileName=NULL; }
if (s1) { free(s1); s1=NULL; }
}
void print_motif(Sites *site,int nsites,char **seq,char **rseq,int *seqLen,int pwmLen,int id,double **opwm) {
//FILE *f1;
char *fileName;
register int i,j;
fileName=alloc_char(500);
/*Rprintf("%d.seq",id);*/
//f1=fopen(fileName,"w");
for (i=0; i<nsites; i++) {
if (site[i].rev=='0') {
if (site[i].pos<0) {
//for (j=site[i].pos; j<0; j++) Rprintf("x");
for (j=0; j<pwmLen+site[i].pos; j++) {
switch(seq[site[i].seq][j]) {
//case 'a': Rprintf("a"); break;
//case 'c': Rprintf("c"); break;
//case 'g': Rprintf("g"); break;
//case 't': Rprintf("t"); break;
//case 'n': Rprintf("n"); break;
default: break;
}
}
}
else {
for (j=site[i].pos; j<min(seqLen[site[i].seq],site[i].pos+pwmLen); j++) {
switch(seq[site[i].seq][j]) {
//case 'a': Rprintf("a"); break;
//case 'c': Rprintf("c"); break;
//case 'g': Rprintf("g"); break;
//case 't': Rprintf("t"); break;
//case 'n': Rprintf("n"); break;
default: break;
}
}
}
if (site[i].pos+pwmLen-seqLen[site[i].seq]>0) {
//for (j=seqLen[site[i].seq]; j<site[i].pos+pwmLen; j++) Rprintf("x");
}
//Rprintf("\n");
}
else {
if (site[i].pos<0) {
//for (j=site[i].pos; j<0; j++) Rprintf("x");
for (j=0; j<pwmLen+site[i].pos; j++) {
switch(rseq[site[i].seq][j]) {
// case 'a': Rprintf("a"); break;
// case 'c': Rprintf("c"); break;
// case 'g': Rprintf("g"); break;
// case 't': Rprintf("t"); break;
// case 'n': Rprintf("n"); break;
default: break;
}
}
}
else {
for (j=site[i].pos; j<min(seqLen[site[i].seq],site[i].pos+pwmLen); j++) {
switch(rseq[site[i].seq][j]) {
// case 'a': Rprintf("a"); break;
// case 'c': Rprintf("c"); break;
// case 'g': Rprintf("g"); break;
// case 't': Rprintf("t"); break;
// case 'n': Rprintf("n"); break;
default: break;
}
}
}
if (site[i].pos+pwmLen-seqLen[site[i].seq]>0) {
//for (j=seqLen[site[i].seq]; j<site[i].pos+pwmLen; j++) Rprintf("x");
}
//Rprintf("\n");
}
}
//fclose(f1);
if (fileName) { free(fileName); fileName=NULL; }
// print out individual observed PWM in gadem format
/*-----------------------------------------------------------------------
fileName=alloc_char(500);
Rprintf("%d.mx",id);
f1=fopen(fileName,"w");
Rprintf("4\t%d\n",pwmLen);
for (i=0; i<4; i++) {
for (j=0; j<pwmLen; j++) {
if (j<pwmLen-1) Rprintf("%5.4f\t",opwm[j][i]);
else Rprintf("%5.4f\n",opwm[j][i]);
}
}
fclose(f1);
if (fileName) { free(fileName); fileName=NULL; }
}
-----------------------------------------------------------------------*/
}
SEXP GADEM_Analysis(SEXP sequence,SEXP sizeSeq, SEXP accession, SEXP Rverbose,SEXP RnumWordGroup,SEXP RnumTop3mer,SEXP RnumTop4mer,SEXP RnumTop5mer,SEXP RnumGeneration,SEXP RpopulationSize, SEXP RpValue,SEXP ReValue,SEXP RextTrim,SEXP RminSpaceWidth,SEXP RmaxSpaceWidth,SEXP RuseChIPscore,SEXP RnumEM,SEXP RfEM, SEXP RwidthWt,SEXP RfullScan, SEXP RslideWinPWM,SEXP RstopCriterion,SEXP RnumBackgSets,SEXP RweightType,SEXP RbFileName,SEXP RListPWM,SEXP RminSites,SEXP RmaskR,SEXP Rnmotifs)
{
char *bFileName;
SEXP ResultsGadem;
SEXP RSpwm;
PROTECT(ResultsGadem=NEW_LIST(100));
int increment=0;
double testrand;
//Number of sequences
int numSeq = INTEGER_VALUE(sizeSeq);
// const
// char *Fastaheader[size];
int incr=0;
int longueur=length(sequence);
int IncrementTemp=0;
// basic settings/info
int maxSeqLen,*seqLen; // sequence info
double aveSeqLen; // sequence info
char **seq,**rseq;
int *geneID; // sequence info
char **oseq,**orseq; // copy of the original sequences
char **sseq,**rsseq; // simulated seqs.
double *bfreq1, *bfreq0=NULL; // base frequencies
double *ChIPScore; // chip score
int maskR; // mask simple repeats before running the algorithm
// pwms
double ***pwm; // initial population of PWMs from spaced dyads
int *pwmLen; // initial pwm lengths
double **opwm2; // EM-derived PWM
double ***opwm; // observed PWMs from identified sites
double ***epwm; // em-optimized PWMs
double **logepwm; // log(em-optimized PWM)
int *pwmnewLen; // final motif length after extending to both ends
// llr score distr.
Pgfs *llrDist; // llr distribution from pgf method
int llrDim; // llr distribution dimension
int **ipwm; // integer pwm for computing llr score distribution
// EM, motif, sites
double pvalueCutoff; // user input, used to determine score cutoff based on ipwm
int *scoreCutoff; // pwm score cutoff for the corresponding p-value cutoff
double logev; // log of E-value of a motif;
int useChIPscore; // indicator for using ChIP-seq score for seq. selection for EM
int numEM; // number of EM steps
double E_valueCutoff; // log E-value cutoff
//int nsitesEM; // number of binding sites in sequences subjected to EM
int minsitesEM; // minimal number of sites in a motif in EM sequences
int *nsites; // number of binding sites in full data
int minsites; // minimal number of sites in a motif in full data
Sites **site; // binding sites in all sequences
int motifCn; // number of motifs sought and found
int extTrim;
int noMotifFound; // none of the dyads in the population resulted in a motif
char **pwmConsensus; // consensus sequences of motifs
double pwmDistCutoff; // test statistic for motif pwm similarity
char *uniqMotif; // motifs in a population unique or not
int numUniq; // number of unique motifs in a population
int slideWinPWM; // sliding window for comparing pwm similarity
int widthWt; // window width in which nucleotides are given large weights for PWM optimization
int fullScan; // scan scan on the original sequences or masked sequences
// background
int numBackgSets;
// weights
double **posWeight; // spatial weights
int weightType; // four weight types 0, 1, 2, 3, or 4
// words for spaced dyad
Words *word; // top-ranked k-mers as the words for spaced dyads
int numTop3mer,numTop4mer,numTop5mer; // No. of top-ranked k-mers as words for dyads
int maxWordSize; // max of the above three
int numWordGroup; // number of non-zero k-mer groups
int minSpaceWidth,maxSpaceWidth; // min and max width of spacer of the spaced dyads
Chrs **dyad; // initial population of "chromosomes"
char **sdyad; // char of spaced dyads
// GA
int populationSize,numGeneration; // GA parameters
double maxpMutationRate;
Fitness *fitness; // "chromosome" fitness
Wheel *wheel; // roulette-wheel selection
// to speed up only select a subset of sequences for EM algorithm
double fEM; // percentage of sequences used in EM algorithm
int numSeqEM; // number of sequences subject to EM
char *Iseq; // Indicator if a sequence is used in EM or not
int *emSeqLen; // length of sequences used in EM
double *maxpFactor;
int numCycle; // number of GADEM cycles
int generationNoMotif; // maximal number of GA generations in a GADEM cycle resulted in no motifs
// mis.
//seed_t seed; // random seed
int motifCn2,id,numCycleNoMotif,verbose,minminSites,nmotifs;
int startPWMfound,stopCriterion;
char *mFileName,*oFileName,*pwmFileName,*tempRbFileName;
time_t start;
int cn[4],bcn[4],*seqCn,*bseqCn,avebnsites,avebnsiteSeq,totalSitesInput;
int i;
int ii=0;
int jjj=0;
/*************/
FILE * output = fopen("output.txt", "w");
/*************/
GetRNGstate();
mFileName=alloc_char(500); mFileName[0]='\0';
oFileName=alloc_char(500); oFileName[0]='\0';
pwmFileName=alloc_char(500); pwmFileName[0]='\0';
bFileName=alloc_char(500); bFileName[0]='\0';
//tempRbFileName=alloc_char(500); tempRbFileName[0]='\0';
seq=NULL; aveSeqLen=0; maxSeqLen=0;
//minsites=-1;
startPWMfound=0;
maxSeqLen=0;
for(incr=1;incr<longueur;incr=incr+2)
{
if (length(STRING_ELT(sequence,(incr)))>maxSeqLen) maxSeqLen=length(STRING_ELT(sequence,(incr)));
}
// fprintf(output,"maxLength=%d",maxSeqLen);
// exit(0);
seq=alloc_char_char(numSeq,maxSeqLen+1);
for(incr=1;incr<longueur;incr=incr+2)
{
for (int j=0; j<length(STRING_ELT(sequence,(incr))); j++)
{
seq[IncrementTemp][j]=CHAR(STRING_ELT(sequence,(incr)))[j];
}
IncrementTemp++;
}
verbose=LOGICAL_VALUE(Rverbose);
numWordGroup=INTEGER_VALUE(RnumWordGroup);
minsites=INTEGER_VALUE(RminSites);
numTop3mer=INTEGER_VALUE(RnumTop3mer);
numTop4mer=INTEGER_VALUE(RnumTop4mer);
numTop5mer=INTEGER_VALUE(RnumTop5mer);
numGeneration=INTEGER_VALUE(RnumGeneration);
populationSize=INTEGER_VALUE(RpopulationSize);
pvalueCutoff=NUMERIC_VALUE(RpValue);
E_valueCutoff=NUMERIC_VALUE(ReValue);
extTrim=INTEGER_VALUE(RextTrim);
minSpaceWidth=INTEGER_VALUE(RminSpaceWidth);
maxSpaceWidth=INTEGER_VALUE(RmaxSpaceWidth);
useChIPscore=NUMERIC_VALUE(RuseChIPscore);
numEM=INTEGER_VALUE(RnumEM);
fEM=NUMERIC_VALUE(RfEM);
widthWt=INTEGER_VALUE(RwidthWt);
fullScan=INTEGER_VALUE(RfullScan);
slideWinPWM=INTEGER_VALUE(RslideWinPWM);
numUniq=populationSize;
stopCriterion=INTEGER_VALUE(RstopCriterion);
numBackgSets=INTEGER_VALUE(RnumBackgSets);
weightType=NUMERIC_VALUE(RweightType);
//const char *tempRbFileName[1];
tempRbFileName = convertRString2Char(RbFileName);
//tempRbFileName[0]=CHAR(STRING_ELT(RbFileName,0));
nmotifs = INTEGER_VALUE(Rnmotifs);
maskR = INTEGER_VALUE(RmaskR);
if(numSeq>MAX_NUM_SEQ)
{
error("Error: maximal number of seqences reached!\nPlease reset MAX_NUM_SEQ in gadem.h and rebuild (see installation)\n");
}
strcpy(bFileName,tempRbFileName);
ChIPScore=alloc_double(MAX_NUM_SEQ);
seqLen=alloc_int(MAX_NUM_SEQ);
geneID=alloc_int(MAX_NUM_SEQ);
// seq=sequences;
// numSeq=size;
int len;
for (i=0; i<numSeq; i++)
{
len=strlen(seq[i]);
seqLen[i]=len;
geneID[i]=INTEGER(accession)[i];
}
aveSeqLen=0;
for (i=0; i<numSeq; i++) aveSeqLen +=seqLen[i]; aveSeqLen /=(double)numSeq;
for (i=0; i<numSeq; i++) {
if (seqLen[i]>maxSeqLen) maxSeqLen=seqLen[i];
}
rseq=alloc_char_char(numSeq,maxSeqLen+1);
oseq=alloc_char_char(numSeq,maxSeqLen+1);
orseq=alloc_char_char(numSeq,maxSeqLen+1);
for (i=0; i<numSeq; i++)
{
if(seqLen[i]>maxSeqLen) maxSeqLen=seqLen[i];
}
reverse_seq(seq,rseq,numSeq,seqLen);
// make a copy of the original sequences both strands
for (i=0; i<numSeq; i++)
{
for (int j=0; j<seqLen[i]; j++)
{
oseq[i][j]=seq[i][j];
orseq[i][j]=rseq[i][j];
}
oseq[i][seqLen[i]]='\0'; orseq[i][seqLen[i]]='\0';
}
if (strcmp(bFileName,"NULL")!= 0)
{
bfreq0=alloc_double(5);
read_background(bFileName,bfreq0);
}
if (GET_LENGTH(RListPWM)!= 0)
{
startPWMfound=1;
}
else { }
// check for input parameters
if(numGeneration<1)
{
error("number of generaton < 1.\n");
}
if(populationSize<1)
{
error("population size < 1.\n");
}
if (minSpaceWidth<0)
{
error("minimal number of unspecified bases in spaced dyads <0.\n");
}
if (maxSpaceWidth<0)
{
error("maximal number of unspecified bases in spaced dyads <0.\n");
}
if (minSpaceWidth>maxSpaceWidth)
{
error("mingap setting must <= to maxgap setting.\n\n");
}
if (maxSpaceWidth+12>MAX_PWM_LENGTH)
{
error("maxgap setting plus word lengths exceed <MAX_PWM_LENGTH>.\n");
}
if (numEM<0)
{
error("number of EM steps is zero.\n");
}
if (numEM==0)
{
error("number of EM steps = 0, no EM optimization is carried out.\n");
}
if (fullScan!=0 && fullScan!=1)
fullScan=0;
maxWordSize=0;
if (numTop3mer>maxWordSize) maxWordSize=numTop3mer;
if (numTop4mer>maxWordSize) maxWordSize=numTop4mer;
if (numTop5mer>maxWordSize) maxWordSize=numTop5mer;
// any one, two or three: tetramer, pentamer, hexamer
if (numTop3mer==0 && numTop4mer==0 && numTop5mer==0)
{
error("maxw3, maxw4, and maxw5 all zero - no words for spaced dyads.\n");
}
// if (startPWMfound && fEM!=0.5 && fEM!=1.0 & verbose)
// {
// warning("fEM argument is ignored in a seeded analysis\n");
// }
if (startPWMfound)
{
// if(verbose)
// {
// if (populationSize!=10 && populationSize!=100) warning("pop argument is ignored in a seeded analysis, -pop is set to 10.\n");
// if (numGeneration!=1 && numGeneration!=5) warning("gen argument is ignored in a seeded analysis, -gen is set to 1.\n");
// }
fEM=1.0;
populationSize=FIXED_POPULATION; numGeneration=1;
}
// number of sequences for EM
if (fEM>1.0 || fEM<=0.0)
{
error("The fraction of sequences subject to EM is %3.2f.\n",fEM);
}
numSeqEM=(int)(fEM*numSeq);
// memory callocations
Iseq =alloc_char(numSeq+1);
opwm2 =alloc_double_double(MAX_PWM_LENGTH,4);
ipwm =alloc_int_int(MAX_PWM_LENGTH,4);
logepwm=alloc_double_double(MAX_PWM_LENGTH,4);
emSeqLen=alloc_int(numSeqEM);
scoreCutoff=alloc_int(1000);
// scoreCutoff=alloc_int(populationSize);
llrDist=alloc_distr(MAX_DIMENSION);
posWeight=alloc_double_double(numSeq,maxSeqLen);
sseq=alloc_char_char(MAX_NUM_SEQ,maxSeqLen+1);
rsseq=alloc_char_char(MAX_NUM_SEQ,maxSeqLen+1);
bfreq1=base_frequency(numSeq,seq,seqLen);
if (strcmp(bFileName,"NULL") == 0)
{
bfreq0=alloc_double(5);
for (i=0; i<4; i++)
{
bfreq0[i]=bfreq1[i];
}
}
// if minN not specified, set the defaults accordingly
if (minsites==-1)
{
minsites =max(2,(int)(numSeq/20));
}
minsitesEM=(int)(fEM*minsites);
maxpMutationRate=MAXP_MUTATION_RATE;
// determine the distribution and critical cut point
pwmDistCutoff=vector_similarity();
/*---------- select a subset of sequences for EM only --------------*/
if (useChIPscore==1)
{
select_high_scoring_seq_for_EM (ChIPScore,numSeq,numSeqEM,Iseq,fEM);
}
else
{
sample_without_replacement(Iseq,numSeqEM,numSeq);
}
/*-------------------- end of selection --------------------------*/
if (maskR==1) mask_repetitive(geneID,seq,numSeq,seqLen,mFileName);
if (widthWt<20)
{
warning("The window width of sequence centered on the nucleotides having large weights in EM for PWM optimization is small\n Motif longer than %d will not be discovered\n",widthWt);
}
time(&start);
// if (weightType==1 || weightType==3)
//ffprintf(output,fp,"window width of sequence centered on the nucleotides having large weights for PWM optimization: %d\n",widthWt);
//ffprintf(output,fp,"pwm score p-value cutoff for declaring binding site:\t%e\n",pvalueCutoff);
if(verbose)
{
ffprintf(output,output,"==============================================================================================\n");
ffprintf(output,output,"input sequence file: %s\n",mFileName);
fprintf(output,"number of sequences and average length:\t\t\t\t%d %5.1f\n",numSeq,aveSeqLen);
fprintf(output,"Use pgf method to approximate llr null distribution\n");
fprintf(output,"parameters estimated from sequences in: %s\n\n",mFileName);
if (weightType!=0)
fprintf(output,"non-uniform weight applies to each sequence - type:\t\t%d\n",weightType);
fprintf(output,"number of GA generations & population size:\t\t\t%d %d\n\n",numGeneration,populationSize);
fprintf(output,"PWM score p-value cutoff for binding site declaration:\t\t%e\n",pvalueCutoff);
fprintf(output,"ln(E-value) cutoff for motif declaration:\t\t\t%f\n\n",E_valueCutoff);
// fprintf(output,"number (percentage) of sequences selected for EM:\t\t%d(%4.1f\%)\n",numSeqEM,100.0*(double)numSeqEM/(double)numSeq);
fprintf(output,"number of EM steps:\t\t\t\t\t\t%d\n",numEM);
fprintf(output,"minimal no. sites considered for a motif:\t\t\t%d\n\n",minsites);
fprintf(output,"[a,c,g,t] frequencies in input data:\t\t\t\t%f %f %f %f\n",bfreq1[0],bfreq1[1],bfreq1[2],bfreq1[3]);
fprintf(output,"==============================================================================================\n");
}
// if (pgf)
// {
// if (userMarkovOrder!=0 & verbose)
// {
// warning("The user-specified background Markov order (%d) is ignored when -pgf is set to 1\n",userMarkovOrder);
// }
// if (bFileName[0]!='\0' & verbose)
// {
// warning("The user-specified background models: %s are not used when -pgf is set to 1\n",bFileName);
// }
// }
// if (startPWMfound && fEM!=1.0 & verbose)
// {
// warning("fEM argument is ignored in a seeded analysis\n");
// }
// determine seq length by counting only [a,c,g,t], seqLen is used in E-value calculation
// determine the distribution and critical cut point
pwmDistCutoff=vector_similarity();
if (weightType==0) assign_weight_uniform(seqLen,numSeq,posWeight);
else if (weightType==1) assign_weight_triangular(seqLen,numSeq,posWeight);
else if (weightType==2) assign_weight_normal(seqLen,numSeq,posWeight);
else
{
error("Motif prior probability type not found - please choose: 0, 1, or 2\n");
// fprintf(output,"Consider: -posWt 1 for strong central enrichment as in ChIP-seq\n");
// fprintf(output," -posWt 0 for others\n\n");
// exit(0);
}
/* if (startPWMfound) minminSites=minsites;
else minminSites=(int)(0.40*minsitesEM);*/
motifCn=0; noMotifFound=0; numCycle=0; numCycleNoMotif=0;
int compt=0;
int lengthList=GET_LENGTH(RListPWM);
/****************************************/
broadcastOnce(maxSeqLen, numEM, startPWMfound, minminSites, maxpFactor, numSeq, numSeqEM, Iseq, bfreq0, posWeight, weightType, pvalueCutoff, emSeqLen, populationSize);
/****************************************/
do
{
if(!startPWMfound)
{
if(verbose)
{
fprintf(output,"*** Running an unseeded analysis ***\n");
// fprintf(output,"\n|------------------------------------------------------------------|\n");
// fprintf(output,"| |\n");
// fprintf(output,"| *** Running an unseeded analysis *** |\n");
// fprintf(output,"| |\n");
// fprintf(output,"|------------------------------------------------------------------|\n\n");
}
populationSize=INTEGER_VALUE(RpopulationSize);
numGeneration=INTEGER_VALUE(RnumGeneration);
dyad =alloc_chrs(populationSize,4);
wheel =alloc_wheel(populationSize);
fitness=alloc_fitness(populationSize);
maxpFactor=alloc_double(populationSize);
uniqMotif=alloc_char(populationSize+1);
opwm =alloc_double_double_double(populationSize,MAX_PWM_LENGTH,4);
epwm=alloc_double_double_double(populationSize,MAX_PWM_LENGTH,4);
pwmConsensus=alloc_char_char(populationSize,MAX_PWM_LENGTH+1);
pwm =alloc_double_double_double(populationSize,MAX_PWM_LENGTH,4);
pwmLen=alloc_int(populationSize);
sdyad =alloc_char_char(populationSize,MAX_PWM_LENGTH+1);
word =alloc_word(numWordGroup,maxWordSize);
minminSites=(int)(0.40*minsitesEM);
// identify top-ranked k-mers (k=3,4,5) for spaced dyads
if(verbose)
fprintf(output,"GADEM cycle %2d: enumerate and count k-mers... ",numCycle+1);
numWordGroup=word_for_dyad(word,seq,rseq,numSeq,seqLen,bfreq1,&numTop3mer,&numTop4mer,&numTop5mer);
if(verbose)
fprintf(output,"Done.\n");
// generating a "population" of spaced dyads
if(verbose)
fprintf(output,"Initializing GA... ");
initialisation(dyad,populationSize,numWordGroup,word,minSpaceWidth,maxSpaceWidth,maxpFactor);
if(verbose)
fprintf(output,"Done.\n");
}
else
{
if(verbose)
{
fprintf(output,"*** Running an seeded analysis ***\n");
// fprintf(output,"\n|------------------------------------------------------------------|\n");
// fprintf(output,"| |\n");
// fprintf(output,"| *** Running a seeded analysis *** |\n");
// fprintf(output,"| |\n");
// fprintf(output,"|------------------------------------------------------------------|\n\n");
}
populationSize=FIXED_POPULATION;
dyad =alloc_chrs(populationSize,4);
pwm=alloc_double_double_double(populationSize,MAX_PWM_LENGTH,4);
pwmLen=alloc_int(populationSize);
maxpFactor=alloc_double(populationSize);
uniqMotif=alloc_char(populationSize+1);
opwm =alloc_double_double_double(populationSize,MAX_PWM_LENGTH,4);
epwm=alloc_double_double_double(populationSize,MAX_PWM_LENGTH,4);
pwmConsensus=alloc_char_char(populationSize,MAX_PWM_LENGTH+1);
sdyad =alloc_char_char(populationSize,MAX_PWM_LENGTH+1);
word =alloc_word(numWordGroup,maxWordSize);
wheel =alloc_wheel(populationSize);
fitness=alloc_fitness(populationSize);
minminSites=minsites;
int lengthMatrix;
lengthMatrix=GET_LENGTH(VECTOR_ELT(RListPWM,compt));
RSpwm=allocMatrix(REALSXP,4,(lengthMatrix/4));
RSpwm=VECTOR_ELT(RListPWM,compt);
pwmLen[0]=read_pwm0(RSpwm,pwm[0],lengthMatrix);
for(i=1; i<populationSize; i++)
{
for (int j=0; j<pwmLen[0]; j++)
{
for (int k=0; k<4; k++)
{
pwm[i][j][k]=pwm[0][j][k];
}
}
pwmLen[i]=pwmLen[0];
}
for (i=0; i<populationSize; i++)
{
maxpFactor[i]=FIXED_MAXPF*(i+1);
standardize_pwm(pwm[i],pwmLen[i]);
consensus_pwm(pwm[i],pwmLen[i],pwmConsensus[i]);
strcpy(sdyad[i],pwmConsensus[i]);
}
}
generationNoMotif=0;
for (jjj=0; jjj<numGeneration; jjj++)
{
// convert spaced dyads to letter probability matrix
if (!startPWMfound)
{
dyad_to_pwm(word,populationSize,dyad,pwm,pwmLen);
}
/*
DO_APPLY(populationCalculation(maxSeqLen, numEM, fitness+ii,
startPWMfound, minminSites, maxpFactor[ii],
numSeq, numSeqEM, seq, rseq, seqLen, Iseq,
bfreq0, posWeight, weightType,
pvalueCutoff, emSeqLen,
pwm[ii], pwmLen[ii], epwm[ii], opwm[ii],
pwmConsensus[ii], scoreCutoff+ii, sdyad[ii], ii),
populationSize, ii);
*/
/* Create the structure to send to all the other slaves */
broadcastEveryCycle(Iseq, pwm, pwmLen, pwmConsensus, scoreCutoff, sdyad, populationSize);
populationCalculation(maxSeqLen, numEM, fitness+ii,
startPWMfound, minminSites, maxpFactor[ii],
numSeq, numSeqEM, seq, rseq, seqLen, Iseq,
bfreq0, posWeight, weightType,
pvalueCutoff, emSeqLen,
pwm[ii], pwmLen[ii], epwm[ii], opwm[ii],
pwmConsensus[ii], scoreCutoff+ii, sdyad[ii], ii);
/* Receive the analyzed data from all the other slaves and compile them */
//getPopCalcResults(...);
// for (i=0; i<5; i++)
// {
// fprintf(output,"fitness.value=%lf\n",fitness[i].value);
// fprintf(output,"fitness.index=%d\n",fitness[i].index);
// fprintf(output,"maxpfactor=%lf\n",maxpFactor[i]);
// fprintf(output,"scoreCutoff=%d\n",scoreCutoff[i]);
// fprintf(output," spacedDyad: %s\n",sdyad[i]);
//
// for (l=0; l<pwmLen[i]; l++)
// {
// for (m=0; m<4; m++)
// {
// fprintf(output,"opwm[%d][%d][%d]=%lf ",i,l,m,opwm[i][l][m]);
// fprintf(output,"epwm[%d][%d][%d]=%lf ",i,l,m,epwm[i][l][m]);
// fprintf(output,"pwm[%d][%d][%d]=%lf ",i,l,m,pwm[i][l][m]);
// }
// fprintf(output,"\n");
// }
// fprintf(output,"\n");
// }
//
// testrand=runif(0,1);
// fprintf(output,"testrand1=%lf\n",testrand);
if (populationSize>1)
{
sort_fitness(fitness,populationSize);
}
// for (i=0; i<5; i++)
// {
// fprintf(output,"fitness.value=%lf\n",fitness[i].value);
// fprintf(output,"fitness.index=%d\n",fitness[i].index);
// }
numUniq=check_pwm_uniqueness_dist(opwm, pwmLen,
populationSize, fitness,
pwmDistCutoff, E_valueCutoff,
uniqMotif, slideWinPWM);
// for (i=0; i<5; i++)
// {
// fprintf(output,"fitness.value=%lf\n",fitness[i].value);
// fprintf(output,"fitness.index=%d\n",fitness[i].index);
// fprintf(output,"maxpfactor=%lf\n",maxpFactor[i]);
// fprintf(output,"scoreCutoff=%d\n",scoreCutoff[i]);
// fprintf(output," spacedDyad: %s\n",sdyad[i]);
//
// for (l=0; l<pwmLen[i]; l++)
// {
// for (m=0; m<4; m++)
// {
// fprintf(output,"opwm[%d][%d][%d]=%lf",i,l,m,opwm[i][l][m]);
// }
// fprintf(output,"\n");
// }
// fprintf(output,"\n");
// }
if(verbose)
{
fprintf(output,"GADEM cycle[%3d] generation[%3d] number of unique motif: %d\n",numCycle+1,jjj+1,numUniq);
for (i=0; i<populationSize; i++)
{
if (uniqMotif[i]=='1')
{
fprintf(output," spacedDyad: %s ",sdyad[fitness[i].index]);
for (int j=strlen(sdyad[fitness[i].index]); j<maxSpaceWidth+10; j++) fprintf(output," ");
fprintf(output,"motifConsensus: %s ",pwmConsensus[fitness[i].index]);
for (int j=strlen(sdyad[fitness[i].index]); j<maxSpaceWidth+10; j++) fprintf(output," ");
fprintf(output," %3.2f fitness: %7.2f\n",maxpFactor[fitness[i].index],fitness[i].value);
}
}
fprintf(output,"\n");
}
if (jjj<numGeneration-1)
{
// fitness based selection with replacement
roulett_wheel_fitness(fitness,populationSize,wheel);
// mutation and crossover operations
if (populationSize>1)
{
testrand=runif(0,1);
if (testrand>=0.5)
{
mutation(dyad,numWordGroup,word,minSpaceWidth,maxSpaceWidth,wheel,populationSize,fitness,uniqMotif,
maxpFactor,maxpMutationRate);
}
else
{
crossover(dyad,numWordGroup,word,minSpaceWidth,maxSpaceWidth,wheel,populationSize,fitness,uniqMotif, maxpFactor,maxpMutationRate);
}
}
else
{
mutation(dyad,numWordGroup,word,minSpaceWidth,maxSpaceWidth,wheel,populationSize,fitness,uniqMotif, maxpFactor,maxpMutationRate);
}
}
}
if((numCycle+1)< lengthList)
{
compt++;
}
else
{
startPWMfound=0;
}
numCycle++;
site=alloc_site_site(numUniq+1,MAX_SITES);
nsites=alloc_int(numUniq+1);
pwmnewLen=alloc_int(numUniq+1); // after base extension and trimming
seqCn=alloc_int(MAX_NUM_SEQ);
bseqCn=alloc_int(MAX_NUM_SEQ);
// final step user-specified background model is used
motifCn2=0; // motifCn per GADEM cycle
for (ii=0; ii<populationSize; ii++)
{
id=fitness[ii].index;
if(uniqMotif[ii]=='0')
{
continue;
}
// approximate the exact llr distribution using Staden's method
// if(verbose)
// {
// fprintf(output,"Approximate the exact pwm llr score distribution using the pgf method.\n");
// }
log_ratio_to_int(epwm[id],ipwm,pwmLen[id],bfreq0);
// compute score distribution of the (int)PWM using Staden's method
llrDim=pwm_score_dist(ipwm,pwmLen[id],llrDist,bfreq0);
//fprintf(output,"Avant ScoreCutoff %d \n",scoreCutoff[id]);
scoreCutoff[id]=determine_cutoff(llrDist,llrDim,pvalueCutoff);
//fprintf(output,"Apres ScoreCutoff %d \n",scoreCutoff[id]);
if(fullScan)
{
nsites[motifCn2]=scan_llr_pgf(llrDist,llrDim,site[motifCn2],numSeq,oseq,orseq,seqLen,ipwm,pwmLen[id],scoreCutoff[id],bfreq0);
}
else
{
nsites[motifCn2]=scan_llr_pgf(llrDist,llrDim,site[motifCn2],numSeq,seq,rseq,seqLen,ipwm,pwmLen[id],scoreCutoff[id],bfreq0);
}
if (nsites[motifCn2]>=max(2,minsites))
{
for (int j=0; j<numSeq; j++) seqCn[j]=0;
for (int j=0; j<nsites[motifCn2]; j++) seqCn[site[motifCn2][j].seq]++;
for (int j=0; j<4; j++) cn[j]=0;
for (int j=0; j<numSeq; j++)
{
if (seqCn[j]==0) cn[0]++;
if (seqCn[j]==1) cn[1]++;
if (seqCn[j]==2) cn[2]++;
if (seqCn[j]>2) cn[3]++;
}
totalSitesInput=nsites[motifCn2];
if (extTrim)
{
if (fullScan)
{
extend_alignment(site[motifCn2],numSeq,oseq,orseq,seqLen,nsites[motifCn2],pwmLen[id],&(pwmnewLen[motifCn2]));
}
else
{
extend_alignment(site[motifCn2],numSeq,seq,rseq,seqLen,nsites[motifCn2],pwmLen[id],&(pwmnewLen[motifCn2]));
}
}
else
{
pwmnewLen[motifCn2]=pwmLen[id];
}
if (fullScan)
{
align_sites_count(site[motifCn2],oseq,orseq,nsites[motifCn2],pwmnewLen[motifCn2],opwm2);
}
else
{
align_sites_count(site[motifCn2],seq,rseq,nsites[motifCn2],pwmnewLen[motifCn2],opwm2);
}
standardize_pwm(opwm2,pwmnewLen[motifCn2]);
logev=E_value(opwm2,nsites[motifCn2],bfreq0,pwmnewLen[motifCn2],numSeq,seqLen);
if (logev<=E_valueCutoff)
{
consensus_pwm(opwm2,pwmnewLen[motifCn2],pwmConsensus[id]);
if (fullScan)
{
SET_VECTOR_ELT(ResultsGadem,increment,print_result_R(site[motifCn2],nsites[motifCn2],numSeq,oseq,orseq,seqLen,logev,opwm2,pwmnewLen[motifCn2],motifCn+1,sdyad[id],pwmConsensus[id],numCycle,pvalueCutoff,maxpFactor[id],geneID));
increment++;
print_motif(site[motifCn2],nsites[motifCn2],oseq,orseq,seqLen,pwmnewLen[motifCn2],motifCn+1,opwm2);
}
else
{
SET_VECTOR_ELT(ResultsGadem,increment,print_result_R(site[motifCn2],nsites[motifCn2],numSeq,seq,rseq,seqLen,logev,opwm2,pwmnewLen[motifCn2],
motifCn+1,sdyad[id],pwmConsensus[id],numCycle,pvalueCutoff,maxpFactor[id],geneID));
increment++;
print_motif(site[motifCn2],nsites[motifCn2],seq,rseq,seqLen,pwmnewLen[motifCn2],motifCn+1,opwm2);
}
mask_sites(nsites[motifCn2],seq,rseq,seqLen,site[motifCn2],pwmnewLen[motifCn2]);
/* ----------------------compute the average number of sites in background sequences ----------------------*/
avebnsites=0; avebnsiteSeq=0;
for (i=0; i<numBackgSets; i++)
{
simulate_background_seq(bfreq0,numSeq,seqLen,sseq);
reverse_seq(sseq,rsseq,numSeq,seqLen);
nsites[motifCn2]=scan_llr_pgf(llrDist,llrDim,site[motifCn2],numSeq,sseq,rsseq,seqLen,ipwm,pwmLen[id],scoreCutoff[id],bfreq0);
for (int j=0; j<numSeq; j++) bseqCn[j]=0;
for (int j=0; j<nsites[motifCn2]; j++) bseqCn[site[motifCn2][j].seq]++;
for (int j=0; j<4; j++) bcn[j]=0;
for (int j=0; j<numSeq; j++)
{
if (bseqCn[j]==0) bcn[0]++;
if (bseqCn[j]==1) bcn[1]++;
if (bseqCn[j]==2) bcn[2]++;
if (bseqCn[j]>2) bcn[3]++;
}
//ffprintf(output,fq,"background set[%2d] Seqs with 0,1,2,>2 sites: %d %d %d %d\n",i+1,bcn[0],bcn[1],bcn[2],bcn[3]);
avebnsites+=nsites[motifCn2]; avebnsiteSeq+=(numSeq-bcn[0]);
}
avebnsites/=numBackgSets; avebnsiteSeq/=numBackgSets;
/* -----------------end compute the average number of sites in background sequences ----------------------*/
motifCn++; motifCn2++;
//if((numCycle+1) > lengthList & fixSeeded)
// {
// numCycleNoMotif=1;
// startPWMfound=1;
// } else {
numCycleNoMotif=0;
// }
}
}
}
/* for (int i=0; i<motifCn2; i++)
{
mask_sites(nsites[i],seq,rseq,seqLen,site[i],pwmnewLen[i]);
} */
if (site[0])
{
free(site[0]);
site[0]=NULL;
}
if (site)
{
free(site);
site=NULL;
}
if (nsites)
{
free(nsites);
nsites=NULL;
}
if (pwmnewLen)
{
free(pwmnewLen);
pwmnewLen=NULL;
}
if (motifCn2==0)
numCycleNoMotif++;
if (motifCn==nmotifs)
{
fprintf(output,"Maximal number of motifs (%d) reached\n",nmotifs);
break;
}
if (numCycleNoMotif==stopCriterion)
noMotifFound=1;
}while (!noMotifFound);
// fclose(fp);
/*if (!startPWMfound) {
if (dyad[0]) { free(dyad[0]); dyad[0]=NULL; }
if (dyad) { free(dyad); dyad=NULL; }
}*/
if (seqLen)
{
free(seqLen);
seqLen=NULL;
}
if (pwm[0][0])
{
free(pwm[0][0]);
pwm[0][0]=NULL;
}
if (pwm[0])
{
free(pwm[0]);
pwm[0]=NULL;
}
if (pwm)
{
free(pwm);
pwm=NULL;
}
if (opwm2[0])
{
free(opwm2[0]);
opwm2[0]=NULL;
}
if (opwm2)
{
free(opwm2);
opwm2=NULL;
}
if (opwm[0][0])
{
free(opwm[0][0]);
opwm[0][0]=NULL;
}
if (opwm[0])
{
free(opwm[0]);
opwm[0]=NULL;
}
if (opwm)
{
free(opwm);
opwm=NULL;
}
if(ipwm[0])
{
free(ipwm[0]);
ipwm[0]=NULL;
}
if (ipwm)
{
free(ipwm);
ipwm=NULL;
}
if (pwmLen)
{
free(pwmLen);
pwmLen=NULL;
}
if (seq[0]) { free(seq[0]); seq[0]=NULL; }
if (seq) { free(seq); seq=NULL; }
// if (rseq[0]) { free(rseq[0]); rseq[0]=NULL; }
// if (rseq) { free(rseq); rseq=NULL; }
// if (oseq[0]) { free(oseq[0]); oseq[0]=NULL; }
// if (oseq) { free(oseq); oseq=NULL; }
// if (orseq[0]) { free(orseq[0]); orseq[0]=NULL; }
// if (orseq) { free(orseq); orseq=NULL; }
if (bfreq1)
{
free(bfreq1);
bfreq1=NULL;
}
if (bfreq0)
{
free(bfreq0);
bfreq0=NULL;
}
if (wheel)
{
free(wheel);
wheel=NULL;
}
if (fitness)
{
free(fitness);
fitness=NULL;
}
if (mFileName)
{
free(mFileName);
mFileName=NULL;
}
if (oFileName)
{
free(oFileName);
oFileName=NULL;
}
if (pwmFileName)
{
free(pwmFileName);
pwmFileName=NULL;
}
if (sdyad[0])
{
free(sdyad[0]);
sdyad[0]=NULL;
}
if (sdyad)
{
free(sdyad);
sdyad=NULL;
}
if (pwmConsensus[0])
{
free(pwmConsensus[0]);
pwmConsensus[0]=NULL;
}
if (pwmConsensus)
{
free(pwmConsensus);
pwmConsensus=NULL;
}
//if (!startPWMfound && word) destroy_word(word,numWordGroup);
PutRNGstate();
UNPROTECT(1);
return(ResultsGadem);
}
void read_background(char *filename,double *bfreq) {
FILE *fp;
char *buffer,*tok,letter[2];
int i,len,numTab;
double sum;
fp=fopen(filename,"r");
if (!fp)
{
error("Incorrect filename for background model\n");
}
buffer=alloc_char(250);
for (i=0; i<4; i++) bfreq[i]=-1;
while (!feof(fp)) {
if (fgets(buffer,250,fp)>0) {
if (buffer[0]=='#') continue;
len=strlen(buffer);
buffer[len-1]='\0';
numTab=0;
for (i=0; i<len; i++) {
if (buffer[i]=='\0') numTab++;
}
if (numTab>0) {
tok=strtok(buffer,"\t");
if (strlen(tok)>1) continue;
letter[0]=tok[0];
tok=strtok(0,"\t");
if (letter[0]=='A' || letter[0]=='a') {
if (bfreq[0]==-1) bfreq[0]=atof(tok);
}
else if (letter[0]=='C' || letter[0]=='c') {
if (bfreq[1]==-1) bfreq[1]=atof(tok);
}
else if (letter[0]=='G' || letter[0]=='g') {
if (bfreq[2]==-1) bfreq[2]=atof(tok);
}
else if (letter[0]=='T' || letter[0]=='t') {
if (bfreq[3]==-1) bfreq[3]=atof(tok);
}
else { fprintf(output,"Error reading %s: non-[A,C,G,T]\n",filename); exit(0); }
}
else {
tok=strtok(buffer," ");
letter[0]=tok[0];
if (strlen(tok)>1) continue;
tok=strtok(0," ");
if (letter[0]=='A' || letter[0]=='a') {
if (bfreq[0]==-1) bfreq[0]=atof(tok);
}
else if (letter[0]=='C' || letter[0]=='c') {
if (bfreq[1]==-1) bfreq[1]=atof(tok);
}
else if (letter[0]=='G' || letter[0]=='g') {
if (bfreq[2]==-1) bfreq[2]=atof(tok);
}
else if (letter[0]=='T' || letter[0]=='t') {
if (bfreq[3]==-1) bfreq[3]=atof(tok);
}
else { fprintf(output,"Error reading %s: non-[A,C,G,T]\n",filename); exit(0); }
}
}
}
fclose(fp);
for (i=0; i<4; i++) {
if (bfreq[i]==-1) {
switch (i) {
case 0: fprintf(output,"freq. for 'a' not found in %s\n",filename); break;
case 1: fprintf(output,"freq. for 'c' not found in %s\n",filename); break;
case 2: fprintf(output,"freq. for 'g' not found in %s\n",filename); break;
case 3: fprintf(output,"freq. for 't' not found in %s\n",filename); break;
default: break;
}
exit(0);
}
}
sum=0; for (i=0; i<4; i++) sum +=bfreq[i];
if (fabs(sum-1.0)>0.001) {
fprintf(output,"Warning: frequenices do not add to 1.0\n");
fprintf(output,"Please check %s\n",filename);
exit(0);
}
if (buffer) { free(buffer); buffer=NULL; }
}
struct response *evresp_itp(char *stalst, char *chalst, char *net_code,
char *locidlst, char *date_time, char *units,
char *file, double *freqs, int nfreqs,
char *rtype, char *verbose, int start_stage,
int stop_stage, int stdio_flag,
int listinterp_out_flag, int listinterp_in_flag,
double listinterp_tension, int useTotalSensitivityFlag)
{
struct channel this_channel;
struct scn *scn;
struct string_array *sta_list, *chan_list;
struct string_array *locid_list;
int i, j, k, count = 0, which_matched, test = 1, mode, new_file;
int locid_pos;
int err_type;
char out_name[MAXLINELEN], locid[LOCIDLEN+1];
char *locid_ptr, *end_locid_ptr;
struct matched_files *flst_head = (struct matched_files *)NULL;
struct matched_files *flst_ptr = NULL, *output_files = NULL;
struct file_list *lst_ptr = NULL, *tmp_ptr = NULL, *out_file = NULL, *tmp_file = NULL;
struct response *resp = NULL, *next_ptr = NULL;
struct response *prev_ptr = (struct response *)NULL;
struct response *first_resp = (struct response *)NULL;
struct complex *output = NULL;
struct scn_list *scns = NULL;
FILE *fptr = NULL;
double *freqs_orig = NULL; /* for saving the original frequencies */
int nfreqs_orig;
/* Let's save the original frequencies requested by a user since they can be overwritten */
/* if we process blockette 55 IGD for version 3.2.17 of evalresp*/
nfreqs_orig = nfreqs;
freqs_orig = (double *) malloc(sizeof(double) * nfreqs_orig);
memcpy (freqs_orig, freqs, sizeof(double) * nfreqs_orig);
/* set 'GblChanPtr' to point to 'this_channel' */
GblChanPtr = &this_channel;
/* clear out the FirstLine buffer */
memset(FirstLine, 0, sizeof(FirstLine));
/* if the verbose flag is set, then print some diagnostic output (other than
errors) */
if(verbose && !strcmp(verbose,"-v")) {
fprintf(stderr, "<< EVALRESP RESPONSE OUTPUT V%s >>\n", REVNUM);
fflush(stderr);
}
/* first, determine the values of Pi and twoPi for use in evaluating
the instrument responses later */
Pi = acos(-1.0);
twoPi = 2.0 * Pi;
/* set the values of first_units and last_units to null strings */
strncpy(this_channel.staname,"",STALEN);
strncpy(this_channel.network,"",NETLEN);
strncpy(this_channel.locid,"",LOCIDLEN);
strncpy(this_channel.chaname,"",CHALEN);
strncpy(this_channel.beg_t,"",DATIMLEN);
strncpy(this_channel.end_t,"",DATIMLEN);
strncpy(this_channel.first_units,"",MAXLINELEN);
strncpy(this_channel.last_units,"",MAXLINELEN);
/* and initialize the linked list of pointers to filters */
this_channel.first_stage = (struct stage *)NULL;
/* parse the "stalst" string to form a list of stations */
for(i = 0; i < (int)strlen(stalst); i++) {
if(stalst[i] == ',')
stalst[i] = ' ';
}
sta_list = ev_parse_line(stalst);
/* remove any blank spaces from the beginning and end of the string */
locid_ptr = locidlst; locid_pos = 0;
strncpy(locid, "", LOCIDLEN);
while(*locid_ptr && *locid_ptr == ' ') locid_ptr++;
end_locid_ptr = locid_ptr + strlen(locid_ptr) - 1;
while(end_locid_ptr > locid_ptr && *end_locid_ptr == ' ') end_locid_ptr--;
strncpy(locid, locid_ptr, (end_locid_ptr - locid_ptr + 1));
/* parse the "locidlst" string to form a list of channels */
locid_list = parse_delim_line(locid,",");
/* parse the "chalst" string to form a list of channels */
for(i = 0; i < (int)strlen(chalst); i++) {
if(chalst[i] == ',')
chalst[i] = ' ';
}
chan_list = ev_parse_line(chalst);
/* then form a set of network-station-locid-channel tuples to search for */
scns = alloc_scn_list(chan_list->nstrings*sta_list->nstrings*locid_list->nstrings);
for(i = 0; i < sta_list->nstrings; i++) {
for(j = 0; j < locid_list->nstrings; j++) {
for(k = 0; k < chan_list->nstrings; k++, count++) {
scn = scns->scn_vec[count];
strncpy(scn->station, sta_list->strings[i], STALEN);
if(strlen(locid_list->strings[j]) == strspn(locid_list->strings[j], " "))
memset(scn->locid, 0, LOCIDLEN);
else
strncpy(scn->locid, locid_list->strings[j], LOCIDLEN);
strncpy(scn->channel, chan_list->strings[k], CHALEN);
strncpy(scn->network, net_code, NETLEN);
}
}
}
#ifdef LOG_LABEL
sprintf(myLabel, "[%s.%s.%s.%s]", scn->network, scn->station, scn->locid, scn->channel);
#else
myLabel[0] = '\0';
#endif
/* if input is from stdin, set fptr to stdin, else find whatever matching
files there are */
if(stdio_flag) {
fptr = stdin;
mode = 0;
}
else {
flst_head = find_files(file, scns, &mode);
flst_ptr = flst_head;
}
/* find the responses for each of the station channel pairs as they
occur in the file */
if(!mode && !stdio_flag) {
curr_file = file;
if((fptr = fopen(file,"r")) == (FILE *)NULL) {
#ifdef LIB_MODE
fprintf(stderr, "%s failed to open file %s\n", myLabel, file);
return NULL;
#else
error_exit(OPEN_FILE_ERROR,"failed to open file %s", file);
#endif
}
}
/* allocate space for the first response */
resp = alloc_response(nfreqs);
for(i = 0; i < scns->nscn && (mode || test); i++) {
/* allocate space for 'matched_files' pointer used to determine if a
file has already been read */
if(!stdio_flag)
output_files = alloc_matched_files();
/* then check the mode to determine if are parsing one file or a list
of files (note: if input is from stdin, is one file) */
if(!mode) {
which_matched = 0;
while(test && which_matched >= 0) {
if(!(err_type = setjmp(jump_buffer))) {
new_file = 0;
which_matched = find_resp(fptr, scns, date_time, &this_channel);
#ifdef LIB_MODE /* IGD 25-Sep-2007 Looks like we do not need this: function returns anyway */
// if(which_matched < 0) {
// if(!stdio_flag) /* if not input from console then */
// fclose(fptr); /* close input file
// return NULL;
// }
#endif
/* found a station-channel-network that matched. First construct
an output filename and compare to other output files. If this
filename doesn't match any of them, (or if it is the first
file found) parse the channel's response information.
Otherwise skip it (since a match has already been found) */
sprintf(out_name,"%s.%s.%s.%s",this_channel.network,
this_channel.staname,this_channel.locid,
this_channel.chaname);
#ifdef LOG_LABEL
sprintf(myLabel, "[%s]", out_name);
#else
myLabel[0] = '\0';
#endif
if(!stdio_flag) {
tmp_file = output_files->first_list;
for(k = 0; k < output_files->nfiles; k++) {
out_file = tmp_file;
if(!strcmp(out_file->name,out_name))
break;
tmp_file = out_file->next_file;
}
}
if((stdio_flag && !new_file) || !output_files->nfiles) {
if(!stdio_flag) {
output_files->nfiles++;
out_file = alloc_file_list();
output_files->first_list = out_file;
out_file->name = alloc_char(strlen(out_name)+1);
strcpy(out_file->name,out_name);
}
new_file = 1;
}
else if((stdio_flag && !new_file) || k == output_files->nfiles) {
if(!stdio_flag) {
output_files->nfiles++;
out_file->next_file = alloc_file_list();
tmp_file = out_file->next_file;
out_file = tmp_file;
out_file->name = alloc_char(strlen(out_name)+1);
strcpy(out_file->name,out_name);
}
new_file = 1;
}
else
new_file = 0;
if(new_file && which_matched >= 0) {
/* fill in station-channel-net information for the response */
strncpy(resp->station,this_channel.staname,STALEN);
strncpy(resp->locid,this_channel.locid,LOCIDLEN);
strncpy(resp->channel,this_channel.chaname,CHALEN);
strncpy(resp->network,this_channel.network,NETLEN);
output = resp->rvec;
/* found a station channel pair that matched a response, so parse
the response into a channel/filter list */
test = parse_channel(fptr, &this_channel);
if(listinterp_in_flag &&
this_channel.first_stage->first_blkt->type == LIST)
{ /* flag set for interpolation and stage type is "List" */
interpolate_list_blockette(
&(this_channel.first_stage->first_blkt->blkt_info.list.freq),
&(this_channel.first_stage->first_blkt->blkt_info.list.amp),
&(this_channel.first_stage->first_blkt->blkt_info.list.phase),
&(this_channel.first_stage->first_blkt->blkt_info.list.nresp),
freqs,nfreqs,listinterp_tension);
}
/* check the filter sequence that was just read */
check_channel(&this_channel);
/* If we process blockette 55, we should recompute resp->rvec */
/* because the number of output responses is generally different from */
/* what is the user requested */
/*if we don't use blockette 55, we should set the frequencies to the original */
/* user defined position if we did mess up with frequencies in -possible - blockette 55*/
/* containing previous file. Modifications by I.Dricker IGD*/
free(resp->rvec);
/* 'freqs' array is passed in and should not be freed -- 10/18/2005 -- [ET] */
/* free(freqs); */
if (this_channel.first_stage->first_blkt != NULL && this_channel.first_stage->first_blkt->type == LIST)
{
/*to prevent segmentation in case of bogus input files */
nfreqs = this_channel.first_stage->first_blkt->blkt_info.list.nresp;
freqs = (double *) malloc(sizeof(double) * nfreqs); /* malloc a new vector */
memcpy (freqs, this_channel.first_stage->first_blkt->blkt_info.list.freq, sizeof(double) * nfreqs); /*cp*/
resp->rvec = alloc_complex(nfreqs);
output=resp->rvec;
resp->nfreqs = nfreqs;
resp->freqs = (double *) malloc(sizeof(double) * nfreqs); /* malloc a new vector */
memcpy (resp->freqs, this_channel.first_stage->first_blkt->blkt_info.list.freq, sizeof(double) * nfreqs); /*cp*/
}
else
{
nfreqs = nfreqs_orig;
freqs = (double *) malloc(sizeof(double) * nfreqs); /* malloc a new vector */
memcpy (freqs, freqs_orig, sizeof(double) * nfreqs); /*cp*/
resp->rvec = alloc_complex(nfreqs);
output=resp->rvec;
resp->nfreqs = nfreqs;
resp->freqs = (double *) malloc(sizeof(double) * nfreqs); /* malloc a new vector */
memcpy (resp->freqs, freqs_orig, sizeof(double) * nfreqs); /*cp*/
}
/* normalize the response of the filter sequence */
norm_resp(&this_channel, start_stage, stop_stage);
/* calculate the response at the requested frequencies */
calc_resp(&this_channel, freqs, nfreqs, output, units,
start_stage, stop_stage, useTotalSensitivityFlag);
/* diagnostic output, if the user requested it */
if(verbose && !strcmp(verbose,"-v")) {
print_chan(&this_channel, start_stage, stop_stage,
stdio_flag, listinterp_out_flag, listinterp_in_flag, useTotalSensitivityFlag);
}
free(freqs); /* free array that was allocated above */
/* and, finally, free the memory associated with this channel/filter
list and continue searching for the next match */
free_channel(&this_channel);
if(first_resp == (struct response *)NULL) {
first_resp = resp;
}
next_ptr = alloc_response(nfreqs);
resp->next = next_ptr;
prev_ptr = resp;
resp = next_ptr;
}
else {
strncpy(FirstLine,"",MAXLINELEN);
test = next_resp(fptr);
}
}
else {
if(new_file)
output_files->nfiles--;
free_channel(&this_channel);
/* catch errors that cause parsing to fail midstream */
if(err_type == PARSE_ERROR || err_type == UNRECOG_FILTYPE ||
err_type == UNDEF_SEPSTR || err_type == IMPROP_DATA_TYPE ||
err_type == RE_COMP_FAILED || err_type == UNRECOG_UNITS) {
strncpy(FirstLine,"",MAXLINELEN);
test = next_resp(fptr);
}
else if(err_type == UNDEF_PREFIX) {
test = 0;
}
}
}
if(!stdio_flag)
free_matched_files(output_files); /* added 3/28/2006 -- [ET] */
/* allocated one too many responses */
free_response(resp);
if(prev_ptr != (struct response *)NULL)
prev_ptr->next = (struct response *)NULL;
break;
}
else if(mode) {
lst_ptr = flst_ptr->first_list;
scn = scns->scn_vec[i];
next_scn:
for(j = 0; j < flst_ptr->nfiles; j++) {
if(!stdio_flag) {
fptr = fopen(lst_ptr->name,"r");
}
if(fptr != (FILE *)NULL) {
curr_file = lst_ptr->name;
look_again:
if(!(err_type = setjmp(jump_buffer))) {
new_file = 0;
which_matched = get_resp(fptr, scn, date_time, &this_channel);
#ifdef LIB_MODE /* IGD 25-Sep-2007 Looks like we do not need this: function returns anyway */
// if(which_matched < 1) {
// if(!stdio_flag) /* if not input from console then */
// fclose(fptr); /* close input file */
// return NULL;
// }
#endif
if(which_matched >= 0) {
/* found a station-channel-network that matched. First construct
an output filename and compare to other output files. If this
filename doesn't match any of them, (or if it is the first
file found) parse the channel's response information.
Otherwise skip it (since a match has already been found) */
sprintf(out_name,"%s.%s.%s.%s",this_channel.network,
this_channel.staname,this_channel.locid,
this_channel.chaname);
#ifdef LOG_LABEL
sprintf (myLabel, "[%s]", out_name);
#else
myLabel[0] = '\0';
#endif
tmp_file = output_files->first_list;
for(k = 0; k < output_files->nfiles; k++) {
out_file = tmp_file;
if(!strcmp(out_file->name,out_name))
break;
tmp_file = out_file->next_file;
}
if(!output_files->nfiles) {
output_files->nfiles++;
out_file = alloc_file_list();
output_files->first_list = out_file;
out_file->name = alloc_char(strlen(out_name)+1);
strcpy(out_file->name,out_name);
new_file = 1;
}
else if(k == output_files->nfiles) {
output_files->nfiles++;
out_file->next_file = alloc_file_list();
tmp_file = out_file->next_file;
out_file = tmp_file;
out_file->name = alloc_char(strlen(out_name)+1);
strcpy(out_file->name,out_name);
new_file = 1;
}
else
new_file = 0;
if(new_file) {
/* fill in station-channel-net information for the response */
strncpy(resp->station,this_channel.staname,STALEN);
strncpy(resp->locid,this_channel.locid,LOCIDLEN);
strncpy(resp->channel,this_channel.chaname,CHALEN);
strncpy(resp->network,this_channel.network,NETLEN);
output = resp->rvec;
/* parse the response into a channel/filter list */
test = parse_channel(fptr, &this_channel);
/* IGD 01/04/01 Add code preventing a user from defining output units as DIS and ACC if
the input units are PRESSURE after */
if (strncmp (this_channel.first_units, "PA -",4) == 0) {
if (strcmp(units, "VEL") != 0) {
if(strcmp(units, "DEF") != 0) {
fprintf(stderr, "%s WARNING: OUTPUT %s does not make sense if INPUT is PRESSURE\n",
myLabel, units);
strcpy (units, "VEL");
fprintf(stderr, "%s OUTPUT units are reset and interpreted as PRESSURE\n", myLabel);
}
}
}
/* IGD 08/21/06 Add code preventing a user from defining output units as DIS and ACC if
the input units are TESLA */
if (strncmp (this_channel.first_units, "T -", 3) == 0) {
if (strcmp(units, "VEL") != 0) {
if(strcmp(units, "DEF") != 0) {
fprintf(stderr, "%s WARNING: OUTPUT %s does not make sense if INPUT is MAGNETIC FLUX\n",
myLabel, units);
strcpy (units, "VEL");
fprintf(stderr, "%s OUTPUT units are reset and interpreted as TESLA\n", myLabel);
}
}
}
if(listinterp_in_flag &&
this_channel.first_stage->first_blkt->type == LIST) {
/* flag set for interpolation and stage type is "List" */
interpolate_list_blockette(
&(this_channel.first_stage->first_blkt->blkt_info.list.freq),
&(this_channel.first_stage->first_blkt->blkt_info.list.amp),
&(this_channel.first_stage->first_blkt->blkt_info.list.phase),
&(this_channel.first_stage->first_blkt->blkt_info.list.nresp),
freqs,nfreqs,listinterp_tension);
}
/* check the filter sequence that was just read */
check_channel(&this_channel);
/* If we process blockette 55, we should recompute resp->rvec */
/* because the number of output responses is generally different from */
/* what is the user requested */
/*if we don't use blockette 55, we should set the frequencies to the original */
/* user defined position if we did mess up with frequencies in -possible - blockette 55*/
/* containing previous file. Modifications by I.Dricker / IGD */
free(resp->rvec);
/* 'freqs' array is passed in and should not be freed -- 10/18/2005 -- [ET] */
/* free(freqs); */
if (this_channel.first_stage->first_blkt != NULL && this_channel.first_stage->first_blkt->type == LIST) {
/* This is to prevent segmentation if the response input is bogus responses */
nfreqs = this_channel.first_stage->first_blkt->blkt_info.list.nresp;
freqs = (double *) malloc(sizeof(double) * nfreqs); /* malloc a new vector */
memcpy (freqs, this_channel.first_stage->first_blkt->blkt_info.list.freq, sizeof(double) * nfreqs); /*cp*/
resp->rvec = alloc_complex(nfreqs);
output=resp->rvec;
resp->nfreqs = nfreqs;
resp->freqs = (double *) malloc(sizeof(double) * nfreqs); /* malloc a new vector */
memcpy (resp->freqs, this_channel.first_stage->first_blkt->blkt_info.list.freq, sizeof(double) * nfreqs); /*cp*/
}
else {
nfreqs = nfreqs_orig;
freqs = (double *) malloc(sizeof(double) * nfreqs); /* malloc a new vector */
memcpy (freqs, freqs_orig, sizeof(double) * nfreqs); /*cp*/
resp->rvec = alloc_complex(nfreqs);
output=resp->rvec;
resp->nfreqs = nfreqs;
resp->freqs = (double *) malloc(sizeof(double) * nfreqs); /* malloc a new vector */
memcpy (resp->freqs, freqs_orig, sizeof(double) * nfreqs); /*cp*/
}
/* normalize the response of the filter sequence */
norm_resp(&this_channel, start_stage, stop_stage);
/* calculate the response at the requested frequencies */
calc_resp(&this_channel, freqs, nfreqs, output, units,
start_stage, stop_stage, useTotalSensitivityFlag);
/* diagnostic output, if the user requested it */
if(verbose && !strcmp(verbose,"-v")) {
print_chan(&this_channel, start_stage, stop_stage,
stdio_flag, listinterp_out_flag, listinterp_in_flag, useTotalSensitivityFlag);
}
free(freqs); /* free array that was allocated above */
/* and, finally, free the memory associated with this
channel/filter list and continue searching for the
next match */
free_channel(&this_channel);
if(first_resp == (struct response *)NULL) {
first_resp = resp;
}
next_ptr = alloc_response(nfreqs);
resp->next = next_ptr;
prev_ptr = resp;
resp = next_ptr;
}
FirstField = 0;
strncpy(FirstLine,"",MAXLINELEN);
if(!stdio_flag) {
fclose(fptr);
}
}
else {
strncpy(FirstLine,"",MAXLINELEN);
test = next_resp(fptr);
if (!test) {
if(!stdio_flag) {
fclose(fptr);
}
}
}
/* if not the last file in the list, move on to the next one */
if(lst_ptr->next_file != (struct file_list *)NULL) {
tmp_ptr = lst_ptr->next_file;
lst_ptr = tmp_ptr;
}
}
else {
if (new_file)
output_files->nfiles--;
/* catch errors that cause parsing to fail midstream */
if(err_type == PARSE_ERROR || err_type == UNRECOG_FILTYPE ||
err_type == UNDEF_SEPSTR || err_type == IMPROP_DATA_TYPE ||
err_type == RE_COMP_FAILED || err_type == UNRECOG_UNITS) {
strncpy(FirstLine,"",MAXLINELEN);
test = next_resp(fptr);
}
else if(err_type == UNDEF_PREFIX) {
test = 0;
}
free_channel(&this_channel);
if (!test) {
FirstField = 0;
strncpy(FirstLine,"",MAXLINELEN);
if(!stdio_flag) {
fclose(fptr);
}
}
else
goto look_again;
/* if not the last file in the list, move on to the next one */
if(lst_ptr->next_file != (struct file_list *)NULL) {
tmp_ptr = lst_ptr->next_file;
lst_ptr = tmp_ptr;
}
}
}
}
/* if not the last station-channel-network in the list,
move on to the next one */
if(i < (scns->nscn-1)) {
flst_ptr = flst_ptr->ptr_next;
lst_ptr = flst_ptr->first_list;
i++;
scn = scns->scn_vec[i];
goto next_scn;
}
if(!stdio_flag)
free_matched_files(output_files);
/* allocated one too many responses */
free_response(resp);
if(prev_ptr != (struct response *)NULL)
prev_ptr->next = (struct response *)NULL;
} /* end else if mode */
} /* end for loop */
/* added file close if single input file -- 2/13/2006 -- [ET]: */
if(!mode && !stdio_flag) /* if single file was opened then */
fclose(fptr); /* close input file */
/* and print a list of WARNINGS about the station-channel pairs that were not
found in the input RESP files */
for(i = 0; i < scns->nscn; i++) {
scn = scns->scn_vec[i];
if(!scn->found) {
fprintf(stderr,"%s WARNING: no response found for NET=%s,STA=%s,LOCID=%s,CHAN=%s,DATE=%s\n",
myLabel, scn->network, scn->station, scn->locid, scn->channel, date_time);
fflush(stderr);
}
}
free_scn_list(scns);
if(flst_head != (struct matched_files *)NULL)
free_matched_files(flst_head);
free_string_array(chan_list);
free_string_array(locid_list);
free_string_array(sta_list);
free(freqs_orig); /* added 3/28/2006 -- [ET] */
return(first_resp);
}
