int allocate_shooter(void){
int mem_points, mem_frames;
FREEMEMORY(shootpointinfo);
FREEMEMORY(shoottimeinfo);
mem_points=max_shooter_points*sizeof(shootpointdata);
mem_frames=nshooter_frames*sizeof(shoottimedata);
PRINTF("shooter point memory requirements\n");
PRINTF("max_shooter_points=%i mem=%i\n",max_shooter_points,mem_points);
PRINTF("nshooter_frames=%i mem=%i\n",nshooter_frames,mem_frames);
if( mem_points<=0||mem_frames<=0||
#ifdef _DEBUG
mem_points>=2000000000||mem_frames>2000000000||
#endif
NewMemory((void **)&shootpointinfo,mem_points)==0||
NewMemory((void **)&shoottimeinfo,mem_frames)==0){
FREEMEMORY(shootpointinfo);
FREEMEMORY(shoottimeinfo);
shooter_active=0;
PRINTF("shooter point memory allocation failed\n");
return 1;
}
return 0;
}
void
freeMatchtype (void *space, void *data)
{
Matchtype *d = (Matchtype*)data;
FREEMEMORY(space, d->pos);
FREEMEMORY(space, data);
}
void
getimbissblast(void *space, IntSequence *query, IntSequence **seqs,
Uint noofseqs, FAlphabet *alphabet, imbissinfo *imbiss){
double *df, *sf, *scr;
double avgsum=0, inputscr=0, lambda=0, K=0;
Uint *sortind, i;
evdparam *evd;
/*frequency of query and database*/
df = dbfreq(space, seqs, noofseqs, alphabet, 1);
sf = seqfreq(space, query, alphabet);
scr = logoddscr(space, df, sf, alphabet);
for (i=0; i < alphabet->domainsize; i++) avgsum += df[i]*scr[i];
for (i=0; i < query->length; i++) inputscr += scr[query->sequence[i]];
sortind = quickSort(space, scr, alphabet->domainsize, cmp_dbl, NULL);
evd=ALLOCMEMORY (space, NULL, evdparam, 1);
evd->noofscores = alphabet->domainsize;
evd->probs = df;
evd->scores = scr;
lambda = uniroot(0, 1, score_evd, 0.0000001, evd);
FREEMEMORY(space, evd);
K = relentropy(space, sortind, scr, alphabet->domainsize, df, lambda);
if (K <= 0) K=1;
imbiss->score = scr;
imbiss->H = 0;
imbiss->K = K;
imbiss->lambda = lambda;
printf("\nBLAST statistics:\n-------------------\n");
printf("E(score): %f\n", avgsum);
printf("inputscr: %f\n", inputscr);
printf("lambda: %19.16e\n", lambda);
printf("check: %19.16e\n",
checklambda(scr, alphabet->domainsize, df, avgsum, lambda));
printf("K: %19.16e\n\n", K);
FREEMEMORY(space, sortind);
FREEMEMORY(space, df);
FREEMEMORY(space, sf);
return;
}
void
bl_radixSortKeyFirst(void *space, void *tosrt,
size_t size, size_t nelem,
Uint bits) {
char *p, *b, *src, *toSort;
Uint *cast;
Uint mask, offset=0, i, key;
Uint cntsize;
Uint *cnt;
toSort = (char*) tosrt;
cntsize = 1 << bits;
cnt = ALLOCMEMORY(space, NULL, Uint, cntsize);
memset(cnt, 0, sizeof(Uint)*cntsize);
b = src = malloc(size*nelem);
mask =~ (UINT_MAX<<bits);
for(; mask; mask <<= bits, offset+=bits) {
for(p=toSort; p < toSort+(nelem*size); p+=size) {
cast = (Uint*)p;
key = (*cast & mask) >> offset;
++cnt[key];
}
for(i=1; i < cntsize; ++i) {
cnt[i]+=cnt[i-1];
}
for(p=toSort+((nelem-1)*size); p >= toSort; p-=size) {
cast = (Uint*)p;
key = (*cast & mask) >> offset;
memmove(b+((cnt[key]-1)*size), p, size);
--cnt[key];
}
p=b; b=toSort; toSort=p;
memset(cnt, 0, sizeof(Uint)*cntsize);
}
if(toSort == src) memcpy(b, toSort, size*nelem);
FREEMEMORY(space, src);
FREEMEMORY(space, cnt);
return;
}
void free_skybox(void){
int i;
skyboxdata *skyi;
for(i=0;i<nskyboxinfo;i++){
int j;
skyi = skyboxinfo + i;
for(j=0;j<6;j++){
FREEMEMORY(skyi->face[j].file);
}
}
FREEMEMORY(skyboxinfo);
nskyboxinfo=0;
}
void copy_args(int *argc, char **aargv, char ***argv_sv){
#ifdef WIN32
char *filename=NULL;
char **argv=NULL;
int filelength=1024,openfile;
int i;
if(NewMemory((void **)&argv,(*argc+1)*sizeof(char **))!=0){
*argv_sv=argv;
for(i=0;i<*argc;i++){
argv[i]=aargv[i];
}
if(*argc==1){
if(NewMemory((void **)&filename,(unsigned int)(filelength+1))!=0){
openfile=0;
OpenSMVFile(filename,filelength,&openfile);
if(openfile==1&&ResizeMemory((void **)&filename,strlen(filename)+1)!=0){
*argc=2;
argv[1]=filename;
}
else{
FREEMEMORY(filename);
}
}
}
}
else{
*argc=0;
}
#else
*argv_sv=aargv;
#endif
}
/*------------------------------ destructSufArr ------------------------------
*
* destruct a suffix array.
*
*/
void
destructSufArr (void *space, Suffixarray *arr)
{
FREEMEMORY(space, arr->suftab);
if (arr->lcptab != NULL)
FREEMEMORY(space, arr->lcptab);
if (arr->inv_suftab != NULL)
FREEMEMORY(space, arr->inv_suftab);
if (arr->suffixptr != NULL)
FREEMEMORY(space, arr->suffixptr);
if (arr->seq != NULL)
destructMultiSeq(space, arr->seq);
FREEMEMORY(space, arr);
return ;
}
void loadskytexture(char *filebase, texturedata *texti){
char *filebuffer=NULL;
int texwid, texht;
int errorcode;
unsigned char *floortex;
trim(filebase);
texti->name=0;
texti->loaded=0;
if(strcmp(filebase,"NULL")==0)return;
NewMemory((void **)&filebuffer,strlen(filebase)+1);
STRCPY(filebuffer,filebase);
glGenTextures(1,&texti->name);
glBindTexture(GL_TEXTURE_2D,texti->name);
floortex=readpicture(filebuffer,&texwid,&texht,0);
if(floortex==NULL){
FREEMEMORY(filebuffer);
return;
}
errorcode=gluBuild2DMipmaps(GL_TEXTURE_2D,4, texwid, texht, GL_RGBA, GL_UNSIGNED_BYTE, floortex);
if(errorcode!=0){
FREEMEMORY(floortex);
FREEMEMORY(filebuffer);
return;
}
FREEMEMORY(floortex);
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MAG_FILTER, GL_LINEAR);
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MAG_FILTER, GL_LINEAR);
#ifdef pp_GPU
if(gpuactive==1){
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_S, GL_CLAMP_TO_EDGE);
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_T, GL_CLAMP_TO_EDGE);
}
else{
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_S, GL_CLAMP);
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_T, GL_CLAMP);
}
#else
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_S, GL_CLAMP);
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_T, GL_CLAMP);
#endif
texti->file=filebuffer;
texti->loaded=1;
return;
}
void
bl_radixSortUint(void *space, Uint *toSort,
size_t nelem,
Uint bits) {
Uint *p, *b, *src;
Uint mask, offset=0, i, key;
Uint cntsize;
Uint *cnt;
cntsize = 1 << bits;
cnt = ALLOCMEMORY(space, NULL, Uint, cntsize);
memset(cnt, 0, sizeof(Uint)*cntsize);
b = src = malloc(sizeof(Uint)*nelem);
mask =~ (UINT_MAX<<bits);
for(; mask; mask <<= bits, offset+=bits) {
for(p=toSort; p < toSort+nelem; ++p) {
key = (*p & mask) >> offset;
++cnt[key];
}
for(i=1; i < cntsize; ++i) {
cnt[i]+=cnt[i-1];
}
for(p=toSort+((nelem-1)); p >= toSort; --p) {
key = (*p & mask) >> offset;
b[cnt[key]-1] = *p;
--cnt[key];
}
p=b; b=toSort; toSort=p;
memset(cnt, 0, sizeof(Uint)*cntsize);
}
if(toSort == src) memcpy(b, toSort, sizeof(Uint)*nelem);
FREEMEMORY(space, src);
FREEMEMORY(space, cnt);
return;
}
void Get_Slice_Bounds(void) {
int i;
int endiandata;
endiandata=getendian();
if(endianswitch==1)endiandata=1-endiandata;
PRINTF("Determining slice file bounds\n");
for(i=0; i<nsliceinfo; i++) {
slice *slicei;
slicei = sliceinfo + i;
slicei->inuse_getbounds=0;
}
#ifdef pp_THREAD
mt_update_slice_hist();
#else
update_slice_hist();
#endif
for(i=0; i<nsliceinfo; i++) {
slice *slicei;
int j;
slicei = sliceinfo + i;
if(slicei->dup==1)continue;
for(j=i+1; j<nsliceinfo; j++) {
slice *slicej;
slicej = sliceinfo + j;
if(strcmp(slicei->label.shortlabel,slicej->label.shortlabel)!=0)continue;
merge_histogram(slicei->histogram,slicej->histogram);
}
slicei->valmax=get_histogram_value(slicei->histogram,0.99);
slicei->valmin=get_histogram_value(slicei->histogram,0.01);
slicei->setvalmax=1;
slicei->setvalmin=1;
for(j=i+1; j<nsliceinfo; j++) {
slice *slicej;
slicej = sliceinfo + j;
if(strcmp(slicei->label.shortlabel,slicej->label.shortlabel)!=0)continue;
slicej->valmax=slicei->valmax;
slicej->valmin=slicei->valmin;
slicej->setvalmax=1;
slicej->setvalmin=1;
}
}
for(i=0; i<nsliceinfo; i++) {
slice *slicei;
slicei = sliceinfo + i;
FREEMEMORY(slicei->histogram);
}
}
int main(int argc, char** argv) {
char* content;
Uint contentlen,i,j;
stringset_t *set, *set2, **csv;
int space;
content = readfile(&space, "casessmall.rtxt", &contentlen);
printf("read file of length: %d\n", contentlen);
set = tokensToStringset(&space, "\n", content, contentlen);
FREEMEMORY(&space, content);
printf("file contained %d lines\n", set->noofstrings);
for(i=0; i < set->noofstrings; i++) {
set2 = tokensToStringset(&space, ",", set->strings[i].str, set->strings[i].len);
for(j=0; j < set2->noofstrings; j++) {
printf("%s,", set2->strings[j].str);
}
printf("\n");
destructStringset(&space, set2);
}
destructStringset(&space, set);
printf("reading csv ...\n");
csv = readcsv(&space, "cases.rtxt", ",", &contentlen);
for (i=0; i < contentlen; i++) {
for(j=0; j < csv[i]->noofstrings; j++) {
printf("%s",csv[i]->strings[j].str);
}
destructStringset(&space, csv[i]);
printf("\n");
}
FREEMEMORY(&space, csv);
return EXIT_SUCCESS;
}
char *
printSequence (void *space, CharSequence *s, Uint cols)
{
Uint i, c, k, pos=0, l=0, width=0;
char *buf, *buf2;
stringset_t *entries;
entries=initStringset(space);
for (i=0; i < s->length; i++)
{
/*buf = ALLOCMEMORY(space, NULL, char, 32);
buf = my_itoa(s->sequence[i], buf, 10);*/
addString(space, entries, s->sequence[i], strlen(s->sequence[i]));
if(SETSTRLEN(entries, i) > width)
width = SETSTRLEN(entries, i);
}
/*add spacer*/
width++;
c = cols / (width+1);
l = (s->descrlen+2)+(s->namelen+2)+(s->length*(width+1))+((entries->noofstrings/c)*(5+1+1));
buf = ALLOCMEMORY(space, NULL, char, l);
memset(&buf[pos++], '>', 1);
memmove(&buf[pos], s->url, s->urllen);
pos+=s->urllen;
memset(&buf[pos++], '\n', 1);
memset(&buf[pos++], '>', 1);
memmove(&buf[pos], s->alphabetname, s->namelen);
pos+=s->namelen;
memset(&buf[pos++], '\n', 1);
for (i=0; i < entries->noofstrings; i++) {
if((i%c) == 0) {
memset(&buf[pos++], '\n', 1);
buf2 = ALLOCMEMORY(space, NULL, char, 5);
buf2 = my_itoa(i, buf2, 10);
memset(&buf[pos], ' ', 5-strlen(buf2));
pos += 5-strlen(buf2);
memmove(&buf[pos], buf2, strlen(buf2));
pos += strlen(buf2);
memset(&buf[pos++], '\t', 1);
FREEMEMORY(space, buf2);
}
k = (width-SETSTRLEN(entries,i));
memset(&buf[pos], ' ', k);
pos += k;
memmove(&buf[pos], SETSTR(entries, i), SETSTRLEN(entries, i));
pos += SETSTRLEN(entries, i);
}
void mt_compress_all(void){
int i;
pthread_t *thread_ids;
int *index;
NewMemory((void **)&thread_ids,mt_nthreads*sizeof(pthread_t));
NewMemory((void **)&index,mt_nthreads*sizeof(int));
NewMemory((void **)&threadinfo,mt_nthreads*sizeof(threaddata));
for(i=0;i<mt_nthreads;i++){
index[i]=i;
pthread_create(&thread_ids[i],NULL,compress_all,&index[i]);
threadinfo[i].stat=-1;
}
for(i=0;i<mt_nthreads;i++){
pthread_join(thread_ids[i],NULL);
}
print_summary();
FREEMEMORY(thread_ids);
FREEMEMORY(index);
FREEMEMORY(threadinfo);
}
void mt_update_slice_hist(void) {
pthread_t *thread_ids;
int i;
NewMemory((void **)&thread_ids,mt_nthreads*sizeof(pthread_t));
for(i=0; i<mt_nthreads; i++) {
pthread_create(&thread_ids[i],NULL,MT_update_slice_hist,NULL);
}
for(i=0; i<mt_nthreads; i++) {
pthread_join(thread_ids[i],NULL);
}
FREEMEMORY(thread_ids);
}
void update_slice_hist(void) {
int i;
for(i=0; i<nsliceinfo; i++) {
slice *slicei;
int unit1;
FILE_SIZE lenfile;
int error1;
float slicetime1, *sliceframe;
int sliceframesize;
int is1, is2, js1, js2, ks1, ks2;
int testslice;
slicei = sliceinfo + i;
LOCK_SLICE_BOUND;
if(slicei->inuse_getbounds==1) {
UNLOCK_SLICE_BOUND;
continue;
}
slicei->inuse_getbounds=1;
UNLOCK_SLICE_BOUND;
PRINTF(" Examining %s\n",slicei->file);
lenfile=strlen(slicei->file);
LOCK_COMPRESS;
FORTget_file_unit(&unit1,&slicei->unit_start);
FORTopenslice(slicei->file,&unit1,&is1,&is2,&js1,&js2,&ks1,&ks2,&error1,lenfile);
UNLOCK_COMPRESS;
sliceframesize=(is2+1-is1)*(js2+1-js1)*(ks2+1-ks1);
NewMemory((void **)&sliceframe,sliceframesize*sizeof(float));
init_histogram(slicei->histogram);
testslice=0;
while(error1==0) {
FORTgetsliceframe(&unit1, &is1, &is2, &js1, &js2, &ks1, &ks2, &slicetime1, sliceframe, &testslice,&error1);
update_histogram(sliceframe,sliceframesize,slicei->histogram);
}
FREEMEMORY(sliceframe);
LOCK_COMPRESS;
FORTclosefortranfile(&unit1);
UNLOCK_COMPRESS;
}
}
vector_t *decodeCantor(void *space, Uint code, Uint n) {
Uint i;
vector_t *v = NULL;
vector_t *r = NULL;
v=ALLOCMEMORY(space, v, vector_t, 1);
INITVECTOR(v);
for (i=0; i < (n-1); i++) {
r = decode_2tupel_cantor(space, code);
APPENDVEC(space, v, VECTOR(r,0));
code = VECTOR(r,1);
FREEMEMORY(space, r);
}
APPENDVEC(space, v, VECTOR(r,1));
return (v);
}
double
swconstfilter(void *space, Matchtype *m, IntSequence *a, IntSequence *b,
Uint *ptr, Uint len, Uint pos, void *info) {
imbissinfo *imbiss;
int *swres;
double t;
imbiss = (imbissinfo*) info;
t=scorefilter(space, m, a, b, ptr, len, pos, info);
if (m->count == imbiss->minseeds) {
swres = swgapless(space, a->sequence, a->length,
b->sequence, b->length,
constscr, imbiss->swscores);
m->swscore= swres[arraymax(swres, (a->length+1)*(b->length+1))];
FREEMEMORY(space, swres);
}
return t;
}
int
latexscores (void *space, Matchtype *m, IntSequence **s, Uint len, Uint match,
void *info)
{
int sw;
double explambda, E;
/*FILE* fp;*/
struct salami_info* salami;
imbissinfo *imbiss;
stringset_t *query;
imbiss = (imbissinfo*) info;
if (m->count <= imbiss->minseeds) return 0;
if (match > imbiss->noofhits) return -1;
query = tokensToStringset(space, "/.",
s[m->id]->url, strlen(s[m->id]->url));
explambda = exp(-imbiss->lambda * m->blast );
E = imbiss->K*2500000*imbiss->substrlen*explambda;
sw = floor(m->swscore);
salami = doWurstAlignment(space, m, s, len, imbiss->query);
printf("%s & %s & %.2f & %d & %.2f & %.2f & %.2f & %.2f\\\\ \n",
query->strings[query->noofstrings-1].str, s[m->id]->description,
m->score, sw, salami->sw_score_tot, salami->id ,log10(E), salami->rmsd);
/* latexWurstAlignment(space, m, s, len, ((imbissinfo*)info)->query);
*/
FREEMEMORY(space, salami);
destructStringset(space, query);
return 1;
}
Matchtype*
selectScoreSWconst(void *space, Matchtype *m, Uint k,
IntSequence *a, IntSequence **s, void *info) {
Uint l, i;
int *swres;
imbissinfo *imbiss;
imbiss = (imbissinfo*) info;
qsort(m, k, sizeof(Matchtype), cmp_score);
l=0;
for (i=k; i > 0 && l < 1000; i--) {
if (m[i-1].count >= imbiss->minseeds) {
swres = swgapless(space,
a->sequence, a->length,
s[m[i-1].id]->sequence, s[m[i-1].id]->length,
constscr, imbiss->swscores
/*subscr, info*/
);
m[i-1].swscore= swres[arraymax(swres,
(a->length+1)*(s[m[i-1].id]->length+1))];
FREEMEMORY(space, swres);
} else {
m[i-1].swscore = 0;
}
l++;
}
qsort(m, k, sizeof(Matchtype), cmp_swscore);
return m;
}
void
destructinterval(void *space, void *data) {
FREEMEMORY(space, (PairUint*) data);
}
void readhrr(int flag, int *errorcode){
FILE *HRRFILE;
int ntimeshrr, nfirst;
char buffer[LENBUFFER];
float *hrrtime, *hrrval;
int display=0;
int ntimes_saved;
*errorcode=0;
if(hrrinfo!=NULL){
display = hrrinfo->display;
FREEMEMORY(hrrinfo->times_csv);
FREEMEMORY(hrrinfo->times);
FREEMEMORY(hrrinfo->hrrval_csv);
FREEMEMORY(hrrinfo->hrrval);
FREEMEMORY(hrrinfo->timeslist);
}
FREEMEMORY(hrrinfo);
if(flag==UNLOAD)return;
NewMemory((void **)&hrrinfo,sizeof(hrrdata));
hrrinfo->file=hrr_csv_filename;
hrrinfo->times_csv=NULL;
hrrinfo->times=NULL;
hrrinfo->timeslist=NULL;
hrrinfo->hrrval_csv=NULL;
hrrinfo->hrrval=NULL;
hrrinfo->ntimes_csv=0;
hrrinfo->loaded=1;
hrrinfo->display=display;
hrrinfo->itime=0;
HRRFILE=fopen(hrrinfo->file,"r");
if(HRRFILE==NULL){
readhrr(UNLOAD,errorcode);
return;
}
// size data
ntimeshrr=0;
nfirst=-1;
while(!feof(HRRFILE)){
if(fgets(buffer,LENBUFFER,HRRFILE)==NULL)break;
if(nfirst==-1&&strstr(buffer,".")!=NULL)nfirst=ntimeshrr;
ntimeshrr++;
}
ntimes_saved=ntimeshrr;
ntimeshrr-=nfirst;
rewind(HRRFILE);
NewMemory((void **)&hrrinfo->times_csv,ntimeshrr*sizeof(float));
NewMemory((void **)&hrrinfo->hrrval_csv,ntimeshrr*sizeof(float));
// read data
hrrtime=hrrinfo->times_csv;
hrrval=hrrinfo->hrrval_csv;
ntimeshrr=0;
// read no more than the number of lines found during first pass
while(ntimeshrr<ntimes_saved&&!feof(HRRFILE)){
if(fgets(buffer,LENBUFFER,HRRFILE)==NULL)break;
if(ntimeshrr<nfirst){
ntimeshrr++;
continue;
}
stripcommas(buffer);
sscanf(buffer,"%f %f",hrrtime,hrrval);
hrrtime++;
hrrval++;
ntimeshrr++;
}
hrrinfo->ntimes_csv=ntimeshrr-nfirst;
fclose(HRRFILE);
}
int
allscores (void *space, Matchtype *m, IntSequence **s, Uint len, Uint match,
void *info)
{
char *pic;
float rmsd = -1;
double explambda, E;
FILE* fp;
imbissinfo *imbiss;
struct salami_info *salami;
stringset_t *query;
imbiss = (imbissinfo*) info;
if (m->count <= imbiss->minseeds) return 0;
if (match > imbiss->noofhits) return -1;
/*report score stuff*/
printf("[%d]: score: %f, count: %d\n", match, m->score, m->count);
printf("%d\t%s\t%d\t", m->id, s[m->id]->url, m->count);
pic= depictSequence(space, len, 20, m->pos, m->count,'*');
printf("[%s]\n", pic);
printf("%s\n", s[m->id]->description);
if (imbiss->wurst) {
salami = doWurstAlignment(space, m, s, len, imbiss->query);
printf("sequence identity: %f\n", salami->id);
printf("scr: %f (%f), scr_tot: %f, cvr: %f (raw: %d)\n",
salami->sw_score, salami->sw_smpl_score, salami->sw_score_tot,
salami->sw_cvr, salami->sw_raw);
printf("frac_dme: %f, z_scr: %f, rmsd: %f, andrew_scr %f\n",
salami->frac_dme, salami->z_scr, salami->rmsd, salami->andrew_scr);
printf("tm_scr %f\n", salami->tmscore);
FREEMEMORY(space, salami);
}
printf("gapless sw score: %f\n", m->swscore);
if (imbiss->reportfile) {
query = tokensToStringset(space, "/.",
s[m->id]->url, strlen(s[m->id]->url));
fp = fopen(imbiss->reportfile,"a+");
fprintf(fp, "%s\t%f\t%d\n", query->strings[query->noofstrings-1].str,
rmsd, s[m->id]->length);
fclose(fp);
destructStringset(space, query);
}
/*report blast stuff*/
printf("highest seed score (HSS): %f\n", m->blast);
/*printf("lambda*S %19.16e\n", m->blast *((imbissinfo*)info)->lambda);*/
explambda = exp(- imbiss->lambda * m->blast );
/*printf("exp(-lambda*S): %19.16e\n", explambda); */
E = ((imbissinfo*)info)->K*2500000*imbiss->substrlen*explambda;
/*printf("E=Kmn * exp(-lambda*S): %19.16e\n", E);*/
printf("log(HSS): %f\n", log10(E));
printf("1-exp(-HSS): %19.16e\n", 1-exp(-E));
FREEMEMORY(space, pic);
return 1;
}
int
main (int argc, char** argv)
{
Sint optindex, c;
unsigned char depictsw=0;
unsigned char wurst=1;
unsigned char gnuplot=0;
Uint i, j, noofseqs=0, nooffreqs=0, noofqueries=0;
Uint noofhits=100;
Uint substrlen = 10;
Uint minseeds = 5;
Uint maxmatches = 10000;
char *seq, *vec, *bin;
imbissinfo *imbiss;
void *space = NULL;
double *scores = NULL;
int swscores[2]={3,-2};
char *pveclistfile=NULL;
char *alphabetfile=NULL;
char *inputfile=NULL;
char *batchfile = NULL;
char *subfile=NULL;
char *reportfile = NULL;
int (*handler)
(void *, Matchtype *, IntSequence **, Uint,
Uint, void *) = allscores;
double (*filter)
(void *, Matchtype *, IntSequence *, IntSequence *,
Uint *, Uint, Uint, void *) = swconstfilter;
Matchtype* (*select)
(void *, Matchtype *, Uint k,
IntSequence *, IntSequence **, void *) = selectSW;
stringset_t **fn, **freq, *queryurl, **queries=NULL;
Suffixarray *arr = NULL;
IntSequence **sequences = NULL;
IntSequence *input = NULL;
FAlphabet *alphabet = NULL;
PairSint *matches=NULL;
Uint percent=0;
time_t startsuf, endsuf;
double difsuf, difmatch, difrank;
#ifdef MEMMAN_H
Spacetable spacetab;
initmemoryblocks(&spacetab, 100000);
space = &spacetab;
#endif
while(1)
{
c=getopt_long(argc, argv, "SAghFGBLM:D:r:m:x:n:p:b:s:a:q:l:c:dvw",
long_options, &optindex);
if (c==-1) break;
switch(c) {
case 'r':
reportfile=optarg;
break;
case 'v':
verbose_flag=1;
break;
case 'd':
depictsw = 1;
break;
case 's':
pveclistfile = optarg;
break;
case 'a':
alphabetfile = optarg;
break;
case 'q':
inputfile = optarg;
noofqueries = 1;
break;
case 'l':
substrlen = atoi(optarg);
break;
case 'c':
minseeds = atoi(optarg);
break;
case 'b':
batchfile = optarg;
break;
case 'p':
percent = atoi(optarg);
break;
case 'x':
subfile = optarg;
break;
case 'n':
noofhits = atoi(optarg);
break;
case 'w':
wurst = 0;
break;
case 'B':
filter = scorefilter;
select = selectBlastScore;
break;
case 'S':
filter = scorefilter;
select = selectScore;
break;
case 'A':
filter = swconstfilter;
select = selectSW;
break;
case 'F':
filter = scorefilter;
select = selectScoreSWconst;
break;
case 'G':
filter = scorefilter;
select = selectBlastScoreSWconst;
break;
case 'M':
swscores[0]=atoi(optarg);
break;
case 'L':
handler = latexscores;
break;
case 'D':
swscores[1]=atoi(optarg);
break;
case 'g':
gnuplot = 1;
break;
case 'm':
maxmatches=atoi(optarg);
break;
case 'h':
default:
usage(argv[0]);
exit (EXIT_FAILURE);
}
}
if (pveclistfile==NULL || (inputfile == NULL && batchfile==NULL)
|| alphabetfile == NULL) {
usage(argv[0]);
exit (EXIT_FAILURE);
}
imbiss = ALLOCMEMORY(space, NULL, imbissinfo, 1);
imbiss->reportfile = reportfile;
imbiss->swscores = swscores;
imbiss->noofhits = noofhits;
imbiss->minseeds = minseeds;
imbiss->wurst = wurst;
/*read batch file*/
if (batchfile) {
queries = readcsv(space, batchfile, "", &noofqueries);
}
/*read substitution matrix*/
if (subfile) {
freq=readcsv(space, subfile,",", &nooffreqs);
scores = ALLOCMEMORY(space, NULL, double, ((nooffreqs-1)*(nooffreqs-1)) );
for(i=1; i < nooffreqs; i++) {
for(j=1; j < nooffreqs; j++) {
if(strcmp(SETSTR(freq[i],j),"inf")==0){
MATRIX2D(scores, nooffreqs-1, i, j)=0;
}else{
MATRIX2D(scores, nooffreqs-1, i, j)=atof(SETSTR(freq[i],j));
}
}
}
}
/*read alphabet*/
if (alphabetfile != NULL) {
alphabet = loadCSValphabet(space, alphabetfile);
sortMapdomain(space, alphabet);
}
/*load sequence database*/
fn=readcsv(space, pveclistfile, "", &noofseqs);
sequences = ALLOCMEMORY(space, NULL, IntSequence *, noofseqs);
for(i=0; i < noofseqs; i++)
{
sequences[i] = loadSequence(space, SETSTR(fn[i],0));
}
for (i=0; i < noofseqs; i++) {
destructStringset(space, fn[i]);
}
FREEMEMORY(space, fn);
/*construct the suffix array*/
time (&startsuf);
arr = constructSufArr(space, sequences, noofseqs, NULL);
constructLcp(space, arr);
time (&endsuf);
difsuf = difftime (endsuf, startsuf);
/*do search*/
for (i=0; i < noofqueries; i++) {
/*get query form batchfile*/
if (queries) {
inputfile = SETSTR(queries[i],0);
}
/*typically only used with batchfile*/
if (percent != 0) {
substrlen =
((double)((double)input->length/100)*(double) percent);
}
input = loadSequence(space, inputfile);
//seq = printSequence (space, input, 60);
printf(">IMBISS order delivered\n");
//printf("%s\n",seq);
printf("%s\n", input->url);
//FREEMEMORY(space, seq);
time (&startsuf);
matches=sufSubstring(space, arr, input->sequence, input->length, substrlen);
time (&endsuf);
difmatch = difftime (endsuf, startsuf);
/*get prob vector url for salami/wurst*/
//printf("%.*s\n", 5, input->url + 58);
vec = malloc(sizeof(char)*66);
sprintf(vec, "/smallfiles/public/no_backup/bm/pdb_all_vec_6mer_struct/%5s.vec\0", input->url+56);
bin = malloc(sizeof(char)*54);
sprintf(bin, "/smallfiles/public/no_backup/bm/pdb_all_bin/%5s.bin\0", input->url+56);
queryurl = initStringset(space);
addString(space, queryurl, bin, strlen(bin));
addString(space, queryurl, vec, strlen(vec));
getimbissblast(space, input, sequences, noofseqs, alphabet, imbiss);
imbiss->query = queryurl;
imbiss->substrlen = substrlen;
imbiss->alphabet = alphabet;
/*if a substition file was given ...*/
if (subfile) {
imbiss->sub = createsubmatrix(scores, imbiss->score, nooffreqs-1);
}
/*match 'n' report*/
time (&startsuf);
imbiss->consensus = ALLOCMEMORY(space, NULL, Uint, (input->length-substrlen));
memset(imbiss->consensus, 0, (sizeof(Uint)*(input->length-substrlen)));
rankSufmatch(space, arr, matches, input->length-substrlen,
maxmatches, substrlen,
sequences, noofseqs, filter, select, handler,
input, imbiss, scores, depictsw);
if (gnuplot) {
consensus (space, imbiss->consensus, input->length-substrlen,
input, substrlen, imbiss);
}
time (&endsuf);
difrank = difftime (endsuf, startsuf);
printf ("Building the suffixtree has taken %f seconds.\n", difsuf);
printf ("Match the suffixtree has taken %f seconds.\n", difmatch);
printf ("Rank the suffixtree has taken %f seconds.\n", difrank);
/*partial cleanup*/
//destructStringset(space, queryurl);
destructSequence(space, input);
if(subfile) {
FREEMEMORY(space, imbiss->sub);
}
FREEMEMORY(space, imbiss->consensus);
FREEMEMORY(space, imbiss->score);
FREEMEMORY(space, matches);
free(bin);
free(vec);
}
/*final cleanup*/
for (i=0; i < noofseqs; i++) {
destructSequence(space, sequences[i]);
}
FREEMEMORY(space, sequences);
destructSufArr(space, arr);
#ifdef MEMMAN_H
activeblocks(space);
#endif
printf("Goodbye.\n");
return EXIT_SUCCESS;
}
void
constructsuflinks(void *space, Suffixarray *s) {
Uint i,
j,
a,
b,
k,
nooflists,
lcp,
pos;
Stack istack;
Stack jstack;
List *children,
**lists;
PairUint **data,
slinkinterval;
nooflists = maxlcp(s) +1;
lists = ALLOCMEMORY(space, NULL, List*, nooflists);
memset(lists, 0, sizeof(List*)*nooflists);
initStack(space, &istack, 1000);
initStack(space, &jstack, 1000);
stackpush(space, &istack, 0);
stackpush(space, &jstack, s->numofsuffixes-1);
while(!stackisempty(&istack)) {
i = stackpop(&istack);
j = stackpop(&jstack);
lcp = getlcpval(s, i, j);
/*printf("adding list %d\n", lcp);*/
if (lists[lcp] == NULL) {
lists[lcp] = initList(space, 10);
}
addinterval(space, lists[lcp], i, j);
/*printf("lcp: %d-[%d,%d]\n", lcp, i, j);*/
children = getChildintervals(space, s, i, j);
data = (PairUint**) dataList(space, children);
for(k=children->length; k > 0; k--) {
a = data[k-1]->a;
b = data[k-1]->b;
FREEMEMORY(space, data[k-1]);
if(a != b) {
stackpush(space, &istack, a);
stackpush(space, &jstack, b);
}
}
FREEMEMORY(space, data);
wrapList(space, children, NULL);
}
destructStack(space, &istack);
destructStack(space, &jstack);
s->suflink_l = ALLOCMEMORY(space, NULL, Uint, s->numofsuffixes);
s->suflink_r = ALLOCMEMORY(space, NULL, Uint, s->numofsuffixes);
memset(s->suflink_l, 0, sizeof(Uint)*s->numofsuffixes);
memset(s->suflink_r, 0, sizeof(Uint)*s->numofsuffixes);
for(i=1; i < nooflists; i++) {
if(lists[i] != NULL && lists[i-1] !=NULL) {
for(j=0; j < lists[i]->length; j++) {
/*printf("looking at interval [%d,%d], list %d\n", ((PairUint*)lists[i]->nodes[j].data)->a, ((PairUint*)lists[i]->nodes[j].data)->b, i);*/
slinkinterval = findslinkinterval(space, s, lists, i, j);
pos = getfirstlindex(s, ((PairUint*)lists[i]->nodes[j].data)->a, ((PairUint*)lists[i]->nodes[j].data)->b);
/*printf("store at %d: [%d,%d]\n", pos, slinkinterval.a, slinkinterval.b);*/
s->suflink_l[pos]=slinkinterval.a;
s->suflink_r[pos]=slinkinterval.b;
}
}
wrapList(space, lists[i-1], destructinterval);
}
FREEMEMORY(space, lists);
return;
}
int convert_slice(slice *slicei, int *thread_index) {
char slicefile_svz[1024], slicesizefile_svz[1024];
int fileversion, one, zero;
char *slice_file;
int version_local;
char filetype[1024];
char *shortlabel, *unit;
char units[256];
int ijkbar[6];
uLong framesize;
float *sliceframe_data=NULL;
unsigned char *sliceframe_compressed=NULL, *sliceframe_uncompressed=NULL;
unsigned char *sliceframe_compressed_rle=NULL, *sliceframe_uncompressed_rle=NULL;
char cval[256];
int sizebefore, sizeafter;
int returncode;
float minmax[2];
float time_local;
LINT data_loc;
int percent_done;
int percent_next=10;
float valmin, valmax, denom;
int chop_min, chop_max;
uLongf ncompressed_zlib;
int ncompressed_save;
#ifndef pp_THREAD
int count=0;
#endif
int ncol, nrow, idir;
float time_max;
int itime;
LINT file_loc;
FILE *SLICEFILE;
FILE *slicestream,*slicesizestream;
#ifdef pp_THREAD
if(GLOBcleanfiles==0) {
int fileindex;
fileindex = slicei + 1 - sliceinfo;
sprintf(threadinfo[*thread_index].label,"sf %i",fileindex);
}
#endif
slice_file=slicei->file;
version_local=slicei->version;
fileversion = 1;
one = 1;
zero=0;
// check if slice file is accessible
strcpy(filetype,"");
shortlabel=slicei->label.shortlabel;
if(strlen(shortlabel)>0)strcat(filetype,shortlabel);
trim(filetype);
if(getfileinfo(slice_file,NULL,NULL)!=0) {
fprintf(stderr,"*** Warning: The file %s does not exist\n",slice_file);
return 0;
}
SLICEFILE=fopen(slice_file,"rb");
if(SLICEFILE==NULL) {
fprintf(stderr,"*** Warning: The file %s could not be opened\n",slice_file);
return 0;
}
// set up slice compressed file
if(GLOBdestdir!=NULL) {
strcpy(slicefile_svz,GLOBdestdir);
strcat(slicefile_svz,slicei->filebase);
}
else {
strcpy(slicefile_svz,slicei->file);
}
{
char *ext;
int lensvz;
lensvz = strlen(slicefile_svz);
if(lensvz>4) {
ext = slicefile_svz + lensvz - 4;
if(strcmp(ext,".rle")==0) {
slicefile_svz[lensvz-4]=0;
}
strcat(slicefile_svz,".svz");
}
}
if(GLOBdestdir!=NULL) {
strcpy(slicesizefile_svz,GLOBdestdir);
strcat(slicesizefile_svz,slicei->filebase);
}
else {
strcpy(slicesizefile_svz,slicei->file);
}
{
char *ext;
int lensvz;
lensvz = strlen(slicesizefile_svz);
if(lensvz>4) {
ext = slicesizefile_svz + lensvz - 4;
if(strcmp(ext,".rle")==0) {
slicesizefile_svz[lensvz-4]=0;
}
strcat(slicesizefile_svz,".sz");
}
}
if(GLOBcleanfiles==1) {
slicestream=fopen(slicefile_svz,"rb");
if(slicestream!=NULL) {
fclose(slicestream);
PRINTF(" Removing %s\n",slicefile_svz);
UNLINK(slicefile_svz);
LOCK_COMPRESS;
GLOBfilesremoved++;
UNLOCK_COMPRESS;
}
slicesizestream=fopen(slicesizefile_svz,"rb");
if(slicesizestream!=NULL) {
fclose(slicesizestream);
PRINTF(" Removing %s\n",slicesizefile_svz);
UNLINK(slicesizefile_svz);
LOCK_COMPRESS;
GLOBfilesremoved++;
UNLOCK_COMPRESS;
}
return 0;
}
if(GLOBoverwrite_slice==0) {
slicestream=fopen(slicefile_svz,"rb");
if(slicestream!=NULL) {
fclose(slicestream);
fprintf(stderr,"*** Warning: %s exists.\n",slicefile_svz);
fprintf(stderr," Use the -f option to overwrite smokezip compressed files\n");
return 0;
}
}
slicestream=fopen(slicefile_svz,"wb");
slicesizestream=fopen(slicesizefile_svz,"w");
if(slicestream==NULL||slicesizestream==NULL) {
if(slicestream==NULL) {
fprintf(stderr,"*** Warning: The file %s could not be opened for writing\n",slicefile_svz);
}
if(slicesizestream==NULL) {
fprintf(stderr," %s could not be opened for writing\n",slicesizefile_svz);
}
if(slicestream!=NULL)fclose(slicestream);
if(slicesizestream!=NULL)fclose(slicesizestream);
fclose(SLICEFILE);
return 0;
}
// read and write slice header
strcpy(units,"");
unit=slicei->label.unit;
if(strlen(unit)>0)strcat(units,unit);
trim(units);
sprintf(cval,"%f",slicei->valmin);
trimzeros(cval);
#ifndef pp_THREAD
if(GLOBcleanfiles==0) {
PRINTF("Compressing %s (%s)\n",slice_file,filetype);
PRINTF(" using min=%s %s",cval,units);
}
#endif
sprintf(cval,"%f",slicei->valmax);
trimzeros(cval);
#ifndef pp_THREAD
if(GLOBcleanfiles==0) {
PRINTF(" max=%s %s\n",cval,units);
PRINTF(" ");
}
#endif
valmin=slicei->valmin;
valmax=slicei->valmax;
denom = valmax-valmin;
if(denom==0.0)denom=1.0;
chop_min=0;
chop_max=255;
if(GLOBno_chop==0) {
if(slicei->setchopvalmax==1) {
chop_max = 255*(slicei->chopvalmax-valmin)/denom;
if(chop_max<0)chop_max=0;
if(chop_max>255)chop_max=255;
}
if(slicei->setchopvalmin==1) {
chop_min = 255*(slicei->chopvalmin-valmin)/denom;
if(chop_min<0)chop_min=0;
if(chop_min>255)chop_min=255;
}
}
fwrite(&one,4,1,slicestream); // write out a 1 to determine "endianness" when file is read in later
fwrite(&zero,4,1,slicestream); // write out a zero now, then a one just before file is closed
fwrite(&fileversion,4,1,slicestream); // write out compressed fileversion in case file format changes later
fwrite(&version_local,4,1,slicestream); // fds slice file version
sizeafter=16;
//*** SLICE FILE FORMATS
//*** FDS FORMAT (FORTRAN - each FORTRAN record has a 4 byte header and a 4 byte trailer surrounding the data)
// 30 byte long label
// 30 byte short label
// 30 byte unit
// i1,i2,j1,j2,k1,k2
// for each time step:
// time, compressed frame size
// qq(1,nbuffer) where nbuffer = (i2+1-i1)*(j2+1-j1)*(k2+1-k1)
//*** ZLIB format (C - no extra bytes surrounding data)
//*** header
// endian
// completion (0/1)
// fileversion (compressed format)
// version_local (slicef version)
// global min max (used to perform conversion)
// i1,i2,j1,j2,k1,k2
//*** frame
// time, compressed frame size for each frame
// compressed buffer
//*** RLE format (FORTRAN)
//*** header
// endian
// fileversion, slice version
// global min max (used to perform conversion)
// i1,i2,j1,j2,k1,k2
//*** frame
// time
// compressed frame size for each frame
// compressed buffer
{
int skip;
skip = 3*(4+30+4); // skip over 3 records each containing a 30 byte FORTRAN character string
returncode=FSEEK(SLICEFILE,skip,SEEK_CUR);
sizebefore=skip;
}
FORTSLICEREAD(ijkbar,6);
sizebefore+=8+6*4;
framesize = (ijkbar[1]+1-ijkbar[0]);
framesize *= (ijkbar[3]+1-ijkbar[2]);
framesize *= (ijkbar[5]+1-ijkbar[4]);
minmax[0]=slicei->valmin;
minmax[1]=slicei->valmax;
fwrite(minmax,4,2,slicestream); // min max vals
fwrite(ijkbar,4,6,slicestream);
sizeafter+=(8+24);
ncompressed_save=1.02*framesize+600;
if(NewMemory((void **)&sliceframe_data,ncompressed_save*sizeof(float))==0)goto wrapup;
if(NewMemory((void **)&sliceframe_compressed,ncompressed_save*sizeof(unsigned char))==0)goto wrapup;
if(NewMemory((void **)&sliceframe_uncompressed,ncompressed_save*sizeof(unsigned char))==0)goto wrapup;
fprintf(slicesizestream,"%i %i %i %i %i %i\n",ijkbar[0],ijkbar[1],ijkbar[2],ijkbar[3],ijkbar[4],ijkbar[5]);
fprintf(slicesizestream,"%f %f\n",minmax[0],minmax[1]);
idir=0;
if(ijkbar[0]==ijkbar[1]) {
idir=1;
ncol = ijkbar[3] + 1 - ijkbar[2];
nrow = ijkbar[5] + 1 - ijkbar[4];
}
else if(ijkbar[2]==ijkbar[3]) {
idir=2;
ncol = ijkbar[1] + 1 - ijkbar[0];
nrow = ijkbar[5] + 1 - ijkbar[4];
}
else if(ijkbar[4]==ijkbar[5]) {
idir=3;
ncol = ijkbar[1] + 1 - ijkbar[0];
nrow = ijkbar[3] + 1 - ijkbar[2];
}
if(idir==0) {
idir=1;
ncol = ijkbar[3] + 1 - ijkbar[2];
nrow = ijkbar[5] + 1 - ijkbar[4];
}
{
int ni, nj, nk;
ni = ijkbar[1]+1-ijkbar[0];
nj = ijkbar[3]+1-ijkbar[2];
nk = ijkbar[5]+1-ijkbar[4];
time_max=-1000000.0;
itime=-1;
for(;;) {
int i;
FORTSLICEREAD(&time_local,1);
sizebefore+=12;
if(returncode==0)break;
FORTSLICEREAD(sliceframe_data,framesize); //---------------
if(returncode==0)break;
sizebefore+=(8+framesize*4);
if(time_local<time_max)continue;
time_max=time_local;
#ifndef pp_THREAD
count++;
#endif
data_loc=FTELL(SLICEFILE);
percent_done=100.0*(float)data_loc/(float)slicei->filesize;
#ifdef pp_THREAD
threadinfo[*thread_index].stat=percent_done;
if(percent_done>percent_next) {
LOCK_PRINT;
print_thread_stats();
UNLOCK_PRINT;
percent_next+=10;
}
#else
if(percent_done>percent_next) {
PRINTF(" %i%s",percent_next,GLOBpp);
FFLUSH();
percent_next+=10;
}
#endif
for(i=0; i<framesize; i++) {
int ival;
int icol, jrow, index2;
int ii,jj,kk;
// val_in(i,j,k) = i + j*ni + k*ni*nj
if(framesize<=ncol*nrow) { // only one slice plane
// i = jrow*ncol + icol;
icol = i%ncol;
jrow = i/ncol;
index2 = icol*nrow + jrow;
}
else {
ii = i%ni;
jj = (i/ni)%nj;
kk = i/(ni*nj);
index2 = ii*nj*nk + jj*nk + kk;
}
{
float val;
val = sliceframe_data[i];
if(val<valmin) {
ival=0;
}
else if(val>valmax) {
ival=255;
}
else {
ival = 1 + 253*(val-valmin)/denom;
}
if(ival<chop_min)ival=0;
if(ival>chop_max)ival=255;
sliceframe_uncompressed[index2] = ival;
}
}
itime++;
if(itime%GLOBslicezipstep!=0)continue;
//int compress (Bytef *dest, uLongf *destLen, const Bytef *source, uLong sourceLen);
ncompressed_zlib=ncompressed_save;
returncode=compress(sliceframe_compressed,&ncompressed_zlib,sliceframe_uncompressed,framesize);
file_loc=FTELL(slicestream);
fwrite(&time_local,4,1,slicestream);
fwrite(&ncompressed_zlib,4,1,slicestream);
fwrite(sliceframe_compressed,1,ncompressed_zlib,slicestream);
sizeafter+=(8+ncompressed_zlib);
fprintf(slicesizestream,"%f %i, %li\n",time_local,(int)ncompressed_zlib,(long)file_loc);
}
if(returncode!=0) {
fprintf(stderr,"*** Error: compress returncode=%i\n",returncode);
}
}
wrapup:
#ifndef pp_THREAD
PRINTF(" 100%s completed\n",GLOBpp);
#endif
FREEMEMORY(sliceframe_data);
FREEMEMORY(sliceframe_compressed);
FREEMEMORY(sliceframe_uncompressed);
FREEMEMORY(sliceframe_compressed_rle);
FREEMEMORY(sliceframe_uncompressed_rle);
fclose(SLICEFILE);
FSEEK(slicestream,4,SEEK_SET);
fwrite(&one,4,1,slicestream); // write completion code
fclose(slicestream);
fclose(slicesizestream);
{
char before_label[256],after_label[256];
getfilesizelabel(sizebefore,before_label);
getfilesizelabel(sizeafter,after_label);
#ifdef pp_THREAD
slicei->compressed=1;
sprintf(slicei->summary,"compressed from %s to %s (%4.1f%s reduction)",before_label,after_label,(float)sizebefore/(float)sizeafter,GLOBx);
threadinfo[*thread_index].stat=-1;
#else
PRINTF(" records=%i, ",count);
PRINTF("Sizes: original=%s, ",before_label);
PRINTF("compressed=%s (%4.1f%s reduction)\n\n",after_label,(float)sizebefore/(float)sizeafter,GLOBx);
#endif
}
return 1;
}
int convert_volslice(slice *slicei, int *thread_index) {
char slicefile_svz[1024];
char *slice_file;
char filetype[1024];
char *shortlabel;
int ijkbar[6];
uLong framesize;
float *sliceframe_data=NULL;
int sizebefore, sizeafter;
int returncode;
LINT data_loc;
int percent_done;
int percent_next=10;
#ifndef pp_THREAD
int count=0;
#endif
FILE *SLICEFILE;
FILE *slicestream;
#ifdef pp_THREAD
if(GLOBcleanfiles==0) {
int fileindex;
fileindex = slicei + 1 - sliceinfo;
sprintf(threadinfo[*thread_index].label,"vsf %i",fileindex);
}
#endif
slice_file=slicei->file;
// check if slice file is accessible
strcpy(filetype,"");
shortlabel=slicei->label.shortlabel;
if(strlen(shortlabel)>0)strcat(filetype,shortlabel);
trim(filetype);
if(getfileinfo(slice_file,NULL,NULL)!=0) {
fprintf(stderr,"*** Warning: The file %s does not exist\n",slice_file);
return 0;
}
SLICEFILE=fopen(slice_file,"rb");
if(SLICEFILE==NULL) {
fprintf(stderr,"*** Warning: The file %s could not be opened\n",slice_file);
return 0;
}
// set up slice compressed file
if(GLOBdestdir!=NULL) {
strcpy(slicefile_svz,GLOBdestdir);
strcat(slicefile_svz,slicei->filebase);
}
else {
strcpy(slicefile_svz,slicei->file);
}
if(strlen(slicefile_svz)>4)strcat(slicefile_svz,".svv");
if(GLOBcleanfiles==1) {
slicestream=fopen(slicefile_svz,"rb");
if(slicestream!=NULL) {
fclose(slicestream);
PRINTF(" Removing %s\n",slicefile_svz);
UNLINK(slicefile_svz);
LOCK_COMPRESS;
GLOBfilesremoved++;
UNLOCK_COMPRESS;
}
return 0;
}
if(GLOBoverwrite_slice==0) {
slicestream=fopen(slicefile_svz,"rb");
if(slicestream!=NULL) {
fclose(slicestream);
fprintf(stderr,"*** Warning: The file %s exists.\n",slicefile_svz);
fprintf(stderr," Use the -f option to overwrite smokezip compressed files\n");
return 0;
}
}
slicestream=fopen(slicefile_svz,"wb");
if(slicestream==NULL) {
fprintf(stderr,"*** Warning: The file %s could not be opened for writing\n",slicefile_svz);
return 0;
}
// read and write slice header
#ifndef pp_THREAD
if(GLOBcleanfiles==0) {
PRINTF("Compressing %s (%s)\n",slice_file,filetype);
}
#endif
{
int skip;
skip = 3*(4+30+4); // skip over 3 records each containing a 30 byte FORTRAN character string
returncode=FSEEK(SLICEFILE,skip,SEEK_CUR);
sizebefore=skip;
}
FORTSLICEREAD(ijkbar,6);
sizebefore+=4+6*4+4;
sizeafter=0;
{
int one=1, version_local=0, completion=0;
fwrite(&one,4,1,slicestream);
fwrite(&version_local,4,1,slicestream);
fwrite(&completion,4,1,slicestream);
}
{
int ni, nj, nk;
ni = ijkbar[1]+1-ijkbar[0];
nj = ijkbar[3]+1-ijkbar[2];
nk = ijkbar[5]+1-ijkbar[4];
framesize = ni*nj*nk;
NewMemory((void **)&sliceframe_data,framesize*sizeof(float));
for(;;) {
float vmin, vmax;
float *valmin, *valmax;
unsigned char *compressed_data_out;
uLongf ncompressed_data_out;
float time_local;
FORTSLICEREAD(&time_local,1);
if(returncode==0)break;
CheckMemory;
sizebefore+=12;
FORTSLICEREAD(sliceframe_data,framesize); //---------------
if(returncode==0)break;
CheckMemory;
sizebefore+=(4+framesize*sizeof(float)+4);
valmin=NULL;
valmax=NULL;
if(slicei->voltype==1) {
vmin=0.0;
valmin=&vmin;
}
else if(slicei->voltype==2) {
vmin=20.0;
valmin=&vmin;
vmax=1400.0;
valmax=&vmax;
}
else {
ASSERT(0);
}
CheckMemory;
compress_volsliceframe(sliceframe_data, framesize, time_local, valmin, valmax,
&compressed_data_out, &ncompressed_data_out);
CheckMemory;
sizeafter+=ncompressed_data_out;
if(ncompressed_data_out>0) {
fwrite(compressed_data_out,1,ncompressed_data_out,slicestream);
}
CheckMemory;
FREEMEMORY(compressed_data_out);
#ifndef pp_THREAD
count++;
#endif
data_loc=FTELL(SLICEFILE);
percent_done=100.0*(float)data_loc/(float)slicei->filesize;
#ifdef pp_THREAD
threadinfo[*thread_index].stat=percent_done;
if(percent_done>percent_next) {
LOCK_PRINT;
print_thread_stats();
UNLOCK_PRINT;
percent_next+=10;
}
#else
if(percent_done>percent_next) {
PRINTF(" %i%s",percent_next,GLOBpp);
FFLUSH();
percent_next+=10;
}
#endif
}
if(returncode!=0) {
fprintf(stderr,"*** Error: compress returncode=%i\n",returncode);
}
FREEMEMORY(sliceframe_data);
}
#ifndef pp_THREAD
PRINTF(" 100%s completed\n",GLOBpp);
#endif
{
int completion=1;
FSEEK(slicestream,4,SEEK_SET);
fwrite(&completion,4,1,slicestream);
}
fclose(SLICEFILE);
fclose(slicestream);
{
char before_label[256],after_label[256];
getfilesizelabel(sizebefore,before_label);
getfilesizelabel(sizeafter,after_label);
#ifdef pp_THREAD
slicei->vol_compressed=1;
sprintf(slicei->volsummary,"compressed from %s to %s (%4.1f%s reduction)",before_label,after_label,(float)sizebefore/(float)sizeafter,GLOBx);
threadinfo[*thread_index].stat=-1;
#else
PRINTF(" records=%i, ",count);
PRINTF("Sizes: original=%s, ",before_label);
PRINTF("compressed=%s (%4.1f%s reduction)\n\n",after_label,(float)sizebefore/(float)sizeafter,GLOBx);
#endif
}
return 1;
}
int
main(int argc, char** argv)
{
Uint noofvecs, i;
Sint optindex, c;
vector_t info;
#ifdef MEMMAN_H
Spacetable spacetab;
#endif
void *space = NULL;
char *url = NULL;
char *outpath = NULL;
char *pveclistfile = NULL;
char *alphabetfile = NULL;
char *vecext="vec";
char *seqext="seq";
struct prob_vec *p_vec;
IntSequence *sequence;
FAlphabet *alphabet;
stringset_t *tok;
stringset_t **fn;
#ifdef MEMMAN_H
initmemoryblocks(&spacetab, 1000);
space = &spacetab;
#endif
while(1) {
c=getopt_long(argc, argv, "f:a:o:", long_options, &optindex);
if (c==-1) break;
switch(c) {
case 'f':
pveclistfile = optarg;
break;
case 'a':
alphabetfile = optarg;
break;
case 'o':
outpath = optarg;
break;
default:
usage(argv[0]);
exit (EXIT_FAILURE);
}
}
if (pveclistfile==NULL || alphabetfile == NULL) {
usage(argv[0]);
exit (EXIT_FAILURE);
}
fn=readcsv(space, pveclistfile, ".", &noofvecs);
alphabet = loadCSValphabet(space, alphabetfile);
sortMapdomain(space, alphabet);
for(i=0; i<noofvecs; i++)
{
INITVECTOR(&info);
SETSTR(fn[i],0) = concatdelim(space, SETSTR(fn[i],0), vecext,
SETSTRLEN(fn[i],0), 3, '.');
p_vec = prob_vec_read (SETSTR(fn[i],0));
if (p_vec->mship == NULL)
prob_vec_expand(p_vec);
sequence = encode_prob_vec(space, alphabet, p_vec, 0, 0,
cantorchar, &info);
sequence->info = (Uint*) info.elements;
sequence->namelen= strlen(alphabetfile);
COPYSTR(space, sequence->alphabetname, alphabetfile,
strlen(alphabetfile));
/*this is a potential security risk*/
if (p_vec->compnd_len > 0) {
sequence->descrlen = p_vec->compnd_len-1;
COPYSTR(space, sequence->description, p_vec->compnd,
p_vec->compnd_len-1);
} else {
sequence->descrlen = 14;
COPYSTR(space, sequence->description, "descriptor n/a", 14);
}
sequence->urllen = SETSTRLEN(fn[i],0);
COPYSTR(space, sequence->url, SETSTR(fn[i],0),
SETSTRLEN(fn[i],0));
SETSTR(fn[i],0) = concatdelim(space, SETSTR(fn[i],0), seqext,
SETSTRLEN(fn[i],0), 3, '.');
SETSTRLEN(fn[i],0) += 4;
if (outpath) {
tok = tokensToStringset(space, "/", SETSTR(fn[i],0),
SETSTRLEN(fn[i],0));
COPYSTR(space, url, outpath, strlen(outpath));
url = concat(space, url, SETSTR(tok, tok->noofstrings-1),
strlen(url), SETSTRLEN(tok, tok->noofstrings-1));
saveSequence(sequence, url);
destructStringset(space, tok);
FREEMEMORY(space, url);
url = NULL;
} else {
saveSequence(sequence, SETSTR(fn[i],0));
}
destructSequence (space, sequence);
prob_vec_destroy (p_vec);
destructStringset (space, fn[i]);
progressBarVT("probability vectors converted", noofvecs-1, i, 25);
}
printf("\nexit.\n");
FREEMEMORY(space, fn);
destructAlphabet(space, alphabet);
return EXIT_SUCCESS;
}
void
consensus (void *space, Uint *consensus, Uint len, IntSequence *query,
Uint seedlen, void* info) {
Uint i,j;
char *constr;
double sum, norm;
double *consensus_double;
double *seedprobability;
imbissinfo *imbiss;
IntSequence *consensusSequence;
gnuplot_ctrl *h;
imbiss = (imbissinfo*) info;
seedprobability = ALLOCMEMORY(space, NULL, double, len);
for (i=0; i < len; i++) {
for (sum=0.0, j=0; j < seedlen; j++) {
sum += imbiss->score[(Uint) query->sequence[i+j]];
}
seedprobability[i] = log10(imbiss->K*2500000*seedlen*
exp(-(double)imbiss->lambda*sum));
}
consensusSequence = initSequence(space);
consensusSequence->sequence = consensus;
consensusSequence->length = len;
constr = printSequence(space, consensusSequence, 60);
printf("%s\n", constr);
FREEMEMORY(space, constr);
consensus_double = ALLOCMEMORY(space, NULL, double, len);
h = gnuplot_init();
gnuplot_setstyle(h, "lines");
sum = 0;
for(i=0; i < len; i++) {
sum += consensus[i];
}
for(i=0; i < len; i++) {
norm = consensus[i];
norm = (norm > 0) ? norm : 1;
consensus_double[i] = log10(norm);
/* log10(imbiss->K*3000000*len*exp(-(double)consensus[i]));
if (consensus_double[i] < -400) consensus_double[i]=-400;*/
}
gnuplot_cmd(h, "set title 'IMBISS - seed statistics' -28,0 font'Helvetica,15'");
gnuplot_cmd(h, "set label '%s' at screen 0.12,0.92 font 'Helvetica,12'", imbiss->query->strings[0].str);
gnuplot_cmd(h, "set label 'seed length: %d' at graph 0.05,0.95 font 'Helvetica, 12'", seedlen);
gnuplot_set_xlabel(h, "query sequence residue");
gnuplot_set_ylabel(h, "log");
gnuplot_plot_x(h, consensus_double, len, "log(number of matches)");
gnuplot_plot_x(h, seedprobability, len, "log(Kmn*e^{lambda*score(seed)})");
FREEMEMORY(space, seedprobability);
FREEMEMORY(space, consensus_double);
FREEMEMORY(space, consensusSequence);
}
void adjustpart5bounds(partdata *parti){
int i,j,k,m;
part5data *datacopy;
int alpha05;
for(i=0;i<npart5prop;i++){
part5prop *propi;
int n;
int *buckets;
propi = part5propinfo + i;
if(propi->set_global_bounds==1){
propi->global_min = 1000000000.0;
propi->global_max = -1000000000.0;
}
NewMemory((void **)&propi->buckets,NBUCKETS*sizeof(int));
buckets = propi->buckets;
for (n=0;n<NBUCKETS;n++){
buckets[n]=0;
}
}
// compute global min and max
datacopy = parti->data5;
for(i=0;i<parti->ntimes;i++){
for(j=0;j<parti->nclasses;j++){
part5class *partclassi;
float *rvals;
partclassi=parti->partclassptr[j];
rvals = datacopy->rvals;
for(k=2;k<partclassi->ntypes;k++){
part5prop *prop_id;
float *valmin, *valmax;
prop_id = get_part5prop(partclassi->labels[k].longlabel);
if(prop_id==NULL)continue;
valmin = &prop_id->global_min;
valmax = &prop_id->global_max;
if(prop_id->set_global_bounds==1&&(valmin!=NULL||valmax!=NULL)){
for(m=0;m<datacopy->npoints;m++){
float val;
val=*rvals++;
if(valmin!=NULL)*valmin=MIN(*valmin,val);
if(valmax!=NULL)*valmax=MAX(*valmax,val);
}
}
}
datacopy++;
}
}
// generate data histogram (buckets) in order to determine percentile min and max
datacopy = parti->data5;
for(i=0;i<parti->ntimes;i++){
for(j=0;j<parti->nclasses;j++){
part5class *partclassi;
float *rvals;
partclassi = parti->partclassptr[j];
rvals = datacopy->rvals;
for(k=2;k<partclassi->ntypes;k++){
part5prop *prop_id;
float *valmin, *valmax, dg;
int *buckets;
prop_id = get_part5prop(partclassi->labels[k].longlabel);
if(prop_id==NULL)continue;
valmin = &prop_id->global_min;
valmax = &prop_id->global_max;
dg = (*valmax-*valmin)/(float)NBUCKETS;
if(dg==0.0)dg=1.0;
buckets=prop_id->buckets;
for(m=0;m<datacopy->npoints;m++){
float val;
int ival;
val=*rvals++;
ival = CLAMP((val-*valmin)/dg,0,NBUCKETS-1);
buckets[ival]++;
}
}
datacopy++;
}
}
// calculate percentile min and max
for(i=0;i<npart5prop;i++){
part5prop *propi;
int total;
int *buckets;
int nsmall, nbig;
int n;
float gmin, gmax, dg;
propi = part5propinfo + i;
buckets = propi->buckets;
if(propi->set_global_bounds==1){
total = 0;
for(n=0;n<NBUCKETS;n++){
total+=buckets[n];
}
alpha05 = (int)(percentile_level*total);
total = 0;
nsmall=0;
nbig = NBUCKETS-1;
for (n=0;n<NBUCKETS;n++){
total += buckets[n];
if(total>alpha05){
nsmall=n;
break;
}
}
total = 0;
for (n=NBUCKETS;n>0;n--){
total += buckets[n-1];
if(total>alpha05){
nbig=n-1;
break;
}
}
gmin = propi->global_min;
gmax = propi->global_max;
dg = (gmax-gmin)/(float)NBUCKETS;
propi->percentile_min = gmin + nsmall*dg;
propi->percentile_max = gmin + nbig*dg;
}
FREEMEMORY(propi->buckets);
}
for(i=0;i<npart5prop;i++){
part5prop *propi;
propi = part5propinfo + i;
switch(propi->setvalmin){
case PERCENTILE_MIN:
propi->valmin=propi->percentile_min;
break;
case GLOBAL_MIN:
propi->valmin=propi->global_min;
break;
case SET_MIN:
propi->valmin=propi->user_min;
break;
default:
ASSERT(FFALSE);
break;
}
switch(propi->setvalmax){
case PERCENTILE_MAX:
propi->valmax=propi->percentile_max;
break;
case GLOBAL_MAX:
propi->valmax=propi->global_max;
break;
case SET_MAX:
propi->valmax=propi->user_max;
break;
default:
ASSERT(FFALSE);
break;
}
}
adjustpart5chops(parti);
#ifdef _DEBUG
print_part5prop();
#endif
}
gmatch_t*
alignkdmatches(void *space,
Suffixarray *s,
matchstem_t *M,
CharSequence *query,
char *curseq,
Uint m,
Uint t,
Uint *enctab,
unsigned char bestonly,
Uint bedist,
double lambda,
double H,
double K,
double maxevalue,
int acc,
bitvector* D,
Uint dim,
Uint* nmatch,
int* bscr) {
Uint k,j,l,r,q,noofmatches=0, mat, mis, ins, del;
Lint pos, margin, schr, echr, sstart, slen, i ;
char *sseq;
unsigned int idx;
Alignment *al=NULL;
bitvector *peq;
PairSint result;
#ifdef ALIGNDBG
PairSint result2;
CharSequence *checkseq;
#endif
double E;
int scr;
int maxedist = 0;
int bestscr = 0;
gmatch_t *matches=NULL;
margin = bestscr = maxedist = m-ceil((acc*m)/100);
peq = getpeq(NULL, curseq, m, s->seq->map, s->seq->mapsize, enctab);
for(i=0; i < m; i++) {
for(q=0; q < M[i].noofbranches; q++) {
l = M[i].branches[q].l; r = M[i].branches[q].r;
scr = M[i].branches[q].mat - (M[i].branches[q].mis+M[i].branches[q].ins+M[i].branches[q].del);
E = evalue(lambda, K, spacemult(m, s->numofsuffixes, H, K), scr);
if(l <= r && E <= maxevalue && (r-l) <= t) {
for(j=l; j <= r; j++) {
pos = s->suftab[j];
/*skip marginal matches*/
for(k=0; k < noofmatches; k++)
if (abs((signed int)matches[k].p-(pos-(i+margin))) <= margin) break;
if (k == noofmatches) {
idx = getMultiCharSeqIndex(s->seq, &s->seq->sequences[pos]);
schr = (idx > 0) ? s->seq->markpos[idx-1]+1 : 0;
echr = s->seq->markpos[idx];
assert(echr >= pos);
sstart = MAX(schr, pos-(i+margin));
slen = (echr > sstart+m+2*(margin+1)) ? m+2*(margin+1) : (echr-sstart)+1;
sseq = &s->seq->sequences[sstart];
/*
if(echr == pos) {
fprintf(stderr, "\n\n sstart:%lld, slen:%lld, ssend:%lld, echr:%lld\n\n",
sstart, slen, sstart+slen-1, echr);
}
*/
myersbitmatrix(NULL, curseq, m, sseq, slen, s->seq->map,
s->seq->mapsize, enctab, m-bestscr, peq, &result, D, slen);
#ifdef ALIGNDBG
result2 = myersbitvector(NULL, curseq, m, sseq, slen,
s->seq->map, s->seq->mapsize, enctab, m-bestscr, peq);
assert(result.a == result2.a && result.b == result2.b);
#endif
if (result.a != -1 && result.b <= maxedist
&& result.b <= bestscr && result.a < slen) {
al = ALLOCMEMORY(space, NULL, Alignment, 1);
initAlignment(al, curseq, m, 0, sseq, slen, 0);
bitvectorbacktrack(al, D, slen, m, result.a);
#ifdef ALIGNDBG
assert(getEdist(al) == result.b);
checkseq = (CharSequence*) s->seq->ref[idx].ref;
assert(strncmp(& checkseq->sequence[pos-schr],
&s->seq->sequences[pos], slen) == 0);
#endif
countEops(al, &mat, &mis, &del, &ins);
/*skip identical matches*/
for(k=0; k < noofmatches; k++) {
if (matches[k].p == sstart+al->voff) break;
}
if (k == noofmatches) {
matches=realloc(matches, sizeof(gmatch_t)*(noofmatches+1));
matches[noofmatches].p = sstart+al->voff;
matches[noofmatches].q = sstart+result.a-1;
matches[noofmatches].edist = result.b;
matches[noofmatches].i = i;
matches[noofmatches].j = i+M[i].branches[q].mat+
M[i].branches[q].mis+M[i].branches[q].ins-1;
matches[noofmatches].scr = scr;
matches[noofmatches].evalue = E;
matches[noofmatches].mat = mat;
matches[noofmatches].mis = mis;
matches[noofmatches].ins = ins;
matches[noofmatches].del = del;
matches[noofmatches].subject = idx;
matches[noofmatches].checklen = matches[noofmatches].j;
matches[noofmatches].al = al;
noofmatches++;
if(bestonly) {
bestscr = MIN(maxedist, (result.b+bedist));
}
} else {
wrapAlignment(al);
FREEMEMORY(space, al);
}
}
}
}
}
}
}
for(i=0; i < s->seq->mapsize; i++) {
FREEMEMORY(space, peq[i]);
}
FREEMEMORY(space, peq);
(*bscr) = bestscr;
(*nmatch) = noofmatches;
return matches;
}
