int
subscr (symtype a, symtype b, void *info )
{
double* M;
FAlphabet *alphabet;
imbissinfo *p;
int val;
p = (imbissinfo*) info;
alphabet = p->alphabet;
M = (double*) p->sub;
/* ad = alphabet->mapdomain[(Uint)a];
bd = alphabet->mapdomain[(Uint)b];
printf("decoding %d and %d", ad, bd);
tupela = decodeCantor(NULL, ad, 2);
tupelb = decodeCantor(NULL, bd, 2);
printf("... ended ... to %d and %d \n", VECTOR(tupela,0), VECTOR(tupelb,0));
val = MATRIX2D(M, 309, VECTOR(tupela, 0), VECTOR(tupelb,0));
*/
val = MATRIX2D(M, 308, a ,b);
if (val < -10) val = -10;
return val;
}
double*
createsubmatrix (double *matrix, double *scr, Uint noofscores)
{
Uint i,j;
for(i=0; i < noofscores; i++) {
for (j=0; j < noofscores; j++) {
MATRIX2D(matrix, noofscores, i, j) =
MATRIX2D(matrix, noofscores, i, j) * scr[i];
if(i==j) {
MATRIX2D(matrix, noofscores, i, j) = scr[i];
}
}
}
return matrix;
}
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;
}
