/* Write all FONT records. */
void wbook_store_all_fonts(struct wbookctx *wbook)
{
int i;
struct pkt *font;
struct htbl *fonts;
int key;
int index;
font = fmt_get_font(wbook->tmp_format);
for (i = 1; i < 6; i++) {
bw_append(wbook->biff, font->data, font->len);
}
pkt_free(font);
fonts = hashtbl_new(wbook->formatcount + 1); /* For tmp_format */
index = 6; /* First user defined FONT */
key = fmt_gethash(wbook->tmp_format);
hashtbl_insert(fonts, key, 0); /* Index of the default font */
/* User defined fonts */
for (i = 0; i < wbook->formatcount; i++) {
int data;
key = fmt_gethash(wbook->formats[i]);
data = hashtbl_get(fonts, key);
if (data >= 0) {
/* FONT has already been used */
wbook->formats[i]->font_index = data;
} else {
/* Add a new FONT record */
hashtbl_insert(fonts, key, index);
wbook->formats[i]->font_index = index;
index++;
font = fmt_get_font(wbook->formats[i]);
bw_append(wbook->biff, font->data, font->len);
pkt_free(font);
}
}
hashtbl_destroy(fonts);
}
//checks whether edge exists and inserts if not
//ie insert if profile -> origprof doesn't exist yet
void check_insert_edge(FILE *fp,char *profile,char *origprof) {
int k1=0,k2=0; //*f1,*f2;
//double ratio;
char *diff,*copy,*brac;
HASHTBL *hash = NULL;
/*
hash = graph[k1-1];
f1 = hashtbl_get(hash,profile);
hash = graph[k2-1];
f2 = hashtbl_get(hash,origprof);
ratio = ((double)*f2)/((double)*f1);
// printf("ratio for %s and %s is %d/%d = %.2f\n",origprof,profile,*f2,*f1,ratio);
*/
copy = malloc(sizeof(char)*(strlen(profile)+strlen(origprof)+4));
// if (strlen(profile)+strlen(origprof) > (ARRAYSIZE*size-4))
//copy = resize(&size,strlen(profile)+strlen(origprof)+4,copy);
sprintf(copy,"%s-> %s",profile,origprof);
if (hashtbl_get(edges,copy)) return;
hashtbl_insert(edges,copy,"1");
if (!(hash = hashtbl_create(HASHSIZE,NULL))) {
fprintf(stderr, "ERROR: hashtbl_create() failed");
exit(EXIT_FAILURE);
}
diff = find_diff(hash,profile,origprof,&k1,&k2);
brac = edge_label(hash,profile,origprof,k2);
//color=gray%.0f,100-(ratio*100);
if (strlen(brac) > 1)
fprintf(fp,"\"%s\"-> \"%s\" [label=\" %s\\n%s \",fontsize=8];\n",profile,origprof,brac,diff);
//if (VERBOSE)
//printf("inserting edge %s\n",copy);
free(copy);
free(diff);
free(brac);
hashtbl_destroy(hash);
}
//input first the fasta file, then the sample_1000.out file run on the fasta, then options
int main(int argc, char *argv[]) {
int i,total,notcommon,most;
char **mostfreq;
FILE *fp;
OUTPUT = DEF_OUTPUT;
INPUT = NULL;
NATIVE = NULL;
FILTER = 0;
NOISE = DEF_NOISE;
MIN_HEL_LEN = DEF_MIN_HEL_LEN;
// THRESH_FREQ = DEF_THRESH_FREQ;
THRESH_FREQ = 0;
THRESH_COMMON = DEF_THRESH_COMMON;
VERBOSE = 0;
NUMFREQ = 0;
NUMPROF = 0;
PROF_FREQ = 0;
// PROF_FREQ = DEF_PROF_FREQ;
NUMSTRUCTS = 0;
THRESH_STRUCT = DEF_THRESH_STRUCT;
LENGTH = 0;
STATS = 0;
GRAPH = 1;
REP_STRUCT = 0;
if (argc < 3) {
fprintf(stderr,"Not enough arguments\n");
exit(EXIT_FAILURE);
}
//OUTPUT = malloc(strlen(argv[1])+5);
//sprintf(OUTPUT,"%s.dot",argv[1]);
for (i = 3; i < argc; i++) {
//printf("argv[%d] is %s\n",i,argv[i]);
if (!strcmp(argv[i],"-f")) {
FILTER = 1;
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%d",&NUMFREQ)) {
// sscanf(argv[i+1],"%s",val);
//printf("val is %s and argv %s\n",val,argv[i+1]);
NUMFREQ = atoi(argv[i+1]);
i++;
}
else
NUMFREQ = DEF_NUMFREQ;
}
else if (!strcmp(argv[i],"-z")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%d",&NOISE)) {
NOISE = atoi(argv[i+1]);
i++;
}
}
else if (!strcmp(argv[i],"-h")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%f",&THRESH_FREQ)) {
THRESH_FREQ = atof(argv[i+1]);
if (THRESH_FREQ < 0 || THRESH_FREQ > 100) {
fprintf(stderr,"Error: invalid input %f for frequency threshold\n",THRESH_FREQ);
THRESH_FREQ = DEF_THRESH_FREQ;
}
i++;
}
}
else if (!strcmp(argv[i],"-c")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%f",&THRESH_COMMON)) {
THRESH_COMMON = atof(argv[i+1]);
if (THRESH_COMMON < 0.0 || THRESH_COMMON > 100.0) {
fprintf(stderr,"Error: invalid input %f for common threshold\n",THRESH_COMMON);
THRESH_COMMON = DEF_THRESH_COMMON;
}
i++;
}
}
else if (!strcmp(argv[i],"-q")) {
//PRUNE = 1;
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%d",&NUMPROF)) {
NUMPROF = atoi(argv[i+1]);
i++;
}
}
else if (!strcmp(argv[i],"-p")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%f",&PROF_FREQ)) {
PROF_FREQ = atof(argv[i+1]);
i++;
}
}
else if (!strcmp(argv[i],"-l")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%d",&MIN_HEL_LEN)) {
MIN_HEL_LEN = atoi(argv[i+1]);
i++;
}
}
else if (!strcmp(argv[i],"-s")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%d",&NUMSTRUCTS)) {
NUMSTRUCTS = atoi(argv[i+1]);
i++;
}
}
else if (!strcmp(argv[i],"-t")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%f",&THRESH_STRUCT)) {
THRESH_STRUCT = atof(argv[i+1]);
i++;
}
}
else if (!strcmp(argv[i],"-o")) {
if (i + 1 <= argc - 1) {
OUTPUT = argv[i+1];
i++;
}
}
else if (!strcmp(argv[i],"-i")) {
if (i + 1 <= argc - 1) {
INPUT = argv[i+1];
i++;
}
}
else if (!strcmp(argv[i],"-n")) {
if (i + 1 <= argc - 1) {
NATIVE = argv[i+1];
i++;
}
}
else if (!strcmp(argv[i],"-v"))
VERBOSE = 1;
else if (!strcmp(argv[i],"-a"))
STATS = 1;
else if (!strcmp(argv[i],"-g"))
GRAPH = 0;
else if (!strcmp(argv[i],"-r"))
REP_STRUCT = 1;
}
if (!(bp = hashtbl_create(HASHSIZE,NULL))) {
fprintf(stderr, "ERROR: hashtbl_create() for bp failed");
exit(EXIT_FAILURE);
}
if (!(marginals = hashtbl_create(HASHSIZE,NULL))) {
fprintf(stderr, "ERROR: hashtbl_create() for marginals failed");
exit(EXIT_FAILURE);
}
if (!(idhash = hashtbl_create(HASHSIZE,NULL))) {
fprintf(stderr, "ERROR: hashtbl_create() for idhash failed");
exit(EXIT_FAILURE);
}
if (!(binary = hashtbl_create(HASHSIZE,NULL))) {
fprintf(stderr, "ERROR: hashtbl_create() for binary failed");
exit(EXIT_FAILURE);
}
total = process_structs(argv[1],argv[2]);
if (THRESH_FREQ==0)
THRESH_FREQ = set_h_dropoff(marginals, H_START);
if (VERBOSE) {
printf("Threshold to find frequent helices: %.1f\%\n",THRESH_FREQ);
printf("Maximum number of frequent helices: ");
if (NUMFREQ == 0)
puts("no limit");
else
printf("%d\n",NUMFREQ);
/*
printf("Threshold to select frequent profiles: %.1f\%\n",PROF_FREQ);
printf("Maximum number of profiles: ");
if (NUMPROF == 0)
puts("no limit");
else
printf("%d\n",NUMPROF);
*/
printf("Number of structures processed: %d\n",NUMSTRUCTS);
}
printf("Total number of equivalence helix classes: %d\n",total-1);
if (VERBOSE)
print_all_helices(total);
// make_graph(marginals,max,id,total,argv[1],fp);
mostfreq = find_freq(total);
printf("Total number of selected helices: %d\n",hashtbl_numkeys(freq));
notcommon = make_profiles(argv[2]);
printf("Total number of profiles: %d\n",hashtbl_numkeys(cluster));
print_profiles();
if (PROF_FREQ == 0) {
PROF_FREQ = set_h_dropoff(cluster,P_START);
if (VERBOSE)
printf("setting p to %.1f\n",PROF_FREQ);
}
most = select_profiles(mostfreq,notcommon)-1;
printf("Total number of selected profiles: %d\n",hashtbl_numkeys(cluster));
if (hashtbl_numkeys(cluster) == 0)
GRAPH = 0;
if (hashtbl_numkeys(cluster) > 23 && GRAPH) {
GRAPH = 0;
printf("Total number of profiles above threshold %.1f is %d: disabling graph\n",PROF_FREQ,hashtbl_numkeys(cluster));
}
if (REP_STRUCT) {
//fp = fopen("structures.out","w");
//fprintf(fp,"Processing %s\n",argv[2]);
find_consensus();
print_consensus(argv[1]);
//print_cluster(argv[1]);
//fclose(fp);
}
if (GRAPH) {
fp = fopen(OUTPUT,"w");
insert_graph(fp,argv[1],most);
fputs("}",fp);
fclose(fp);
}
hashtbl_destroy(bp);
hashtbl_destroy(marginals);
hashtbl_destroy(idhash);
hashtbl_destroy(binary);
hashtbl_destroy(freq);
hashtbl_destroy(cluster);
hashtbl_destroy(bracket);
hashtbl_destroy(infreq);
return 0;
}
//takes input profile and checks if in graph
//if so, changes node shape to hexagon
//if not, insert new vertex
HASHTBL* process_input_profile(FILE *fp,HASHTBL *brac,char *fullprofile, int fullnum,char *profile,int numhelix, char *diff, int prob) {
HASHTBL *hash, *temp=NULL;
char *diff1,*bracket,*difftrip;
int *val,k1=0,k2=0;
KEY *parent,*next;
if (!(temp = hashtbl_create(HASHSIZE,NULL))) {
fprintf(stderr, "ERROR: hashtbl_create() failed");
exit(EXIT_FAILURE);
}
make_bracket_rep(brac,fullprofile);
hashtbl_destroy(brac);
profile = sort_input(profile,numhelix);
//printf("(sorted) profile is %s with fullprofile %s and diff %s\n",profile,fullprofile,diff);
if ((hash = graph[numhelix-1]) && (hashtbl_get(hash,profile))) {
if (numhelix == fullnum) {
//printf("case 1: full profile found in graph\n");
fullprofile = sort_input(fullprofile,numhelix);
} else {
//cannot use find_diff because fullprofile has helices not in table[]
//puts("case 2: profile found in graph");
diff = insert_diff(temp,diff);
bracket = edge_label(temp,profile,fullprofile,fullnum);
fprintf(fp,"\"%s\"-> \"%s\" [label =\" %s\\n%s \",fontsize=8,style = dotted];\n",profile,fullprofile,diff,bracket);
}
}
else {
/*
if (numhelix == fullnum)
puts("case 3: full profile not found");
else
puts("case 4: profile not found");
*/
for (parent = find_parents(profile); parent; parent = next) {
diff1 = find_diff(temp,parent->data,profile,&k1,&k2);
if (numhelix != fullnum) {
difftrip = insert_diff(temp,diff);
diff1 = realloc(diff1,strlen(diff1)+strlen(difftrip)+4);
//printf("for parent %s, diff1 is now %s, diff is %s and difftrip is %s\n",parent->data,diff1,diff,difftrip);
sprintf(diff1,"%s\\n%s",diff1,difftrip);
//printf("Diff is %s for parent %s of profile %s; diff %s for %s\n",diff1,parent->data,profile,difftrip,fullprofile);
}
bracket = edge_label(temp,parent->data,fullprofile,fullnum);
fprintf(fp,"\"%s\"-> \"%s\" [label =\" %s\\n%s \",fontsize=8,style = dotted];\n",parent->data,fullprofile,bracket,diff1);
next = parent->next;
free(parent);
}
}
//printf("%s has size %d and prob %d\n",fullprofile,fullnum,prob);
fprintf(fp,"\"%s\" [shape = hexagon];\n",fullprofile);
val = malloc(sizeof(int)*2);
val[0] = fullnum;
val[1] = prob;
hashtbl_insert(input,fullprofile,val);
hashtbl_destroy(temp);
if (!(brac = hashtbl_create(HASHSIZE,NULL))) {
fprintf(stderr, "ERROR: hashtbl_create() failed");
exit(EXIT_FAILURE);
}
return brac;
}
//processes input file containing structures of interest, in triplet form
//similar code to make_cluster: converts triplet to profile,
void process_input(FILE *fp) {
HASHTBL *halfbrac;
FILE *file;
char temp[100],tmp[ARRAYSIZE],*profile,*fullprofile,*diff;
int i,j,k,*id,last=0,lastprob;
int numhelix = 0,fullnum = 0,size = INIT_SIZE,size2 = INIT_SIZE,size3 = INIT_SIZE;
if (!(halfbrac = hashtbl_create(HASHSIZE,NULL))) {
fprintf(stderr, "ERROR: hashtbl_create() for halfbrac failed");
exit(EXIT_FAILURE);
}
if (!(input = hashtbl_create(HASHSIZE,NULL))) {
fprintf(stderr, "ERROR: hashtbl_create() for input failed");
exit(EXIT_FAILURE);
}
//longest = hashtbl_get(max,"longest");
profile = malloc(sizeof(char)*ARRAYSIZE*size);
fullprofile = malloc(sizeof(char)*ARRAYSIZE*size2);
diff = malloc(sizeof(char)*ARRAYSIZE*size3);
profile[0] = '\0';
fullprofile[0] = '\0';
diff[0] = '\0';
if (!(file = fopen(INPUT,"r")))
fprintf(stderr,"Cannot open %s\n",INPUT);
while (fgets(temp,100,file)) {
if (sscanf(temp,"%d %d %d",&i,&j,&k) == 3) {
sprintf(tmp,"%d %d",i,j);
id = hashtbl_get(bp,tmp);
//printf("id is %d for %d %d %d\n",id,i,j,k);
if (!id)
id = process_native(i,j,k);
if (*id != last) {
sprintf(tmp,"%d",*id);
if (hashtbl_get(freq,tmp)) { //is a freq helix, save to profile
numhelix++;
if (strlen(profile)+strlen(tmp) > (ARRAYSIZE*size-2))
profile = resize(&size,strlen(profile)+strlen(tmp)+1,profile);
//printf("adding %d to profile\n",*id);
sprintf(profile,"%s%s ",profile,tmp);
}
else {
if (strlen(diff)+strlen(tmp)+2 > ARRAYSIZE*size3)
diff = resize(&size3,strlen(diff)+strlen(tmp)+2,diff);
sprintf(diff,"%s%s ",diff,tmp);
//printf("printing diff %s\n",diff);
}
fullnum++;
if (strlen(fullprofile)+strlen(tmp) > (ARRAYSIZE*size-2))
fullprofile = resize(&size2,strlen(fullprofile)+strlen(tmp)+2,fullprofile);
sprintf(fullprofile,"%s%s ",fullprofile,tmp);
//printf("helix %d added is %s\n",fullnum,tmp);
last = *id;
make_brackets(halfbrac,i,j,*id);
}
else //if id == last
printf("helix %d %d %d is duplicate with id %d: process_input()\n",i,j,k,*id);
}
else if (sscanf(temp,"Structure %d (%d)",&i,&j) == 2) {
if (strlen(fullprofile) == 0) {
lastprob = j;
continue;
}
//printf("profile is %s, fullprofile %s with diff %s\n\n",profile,fullprofile,diff);
halfbrac = process_input_profile(fp,halfbrac,fullprofile,fullnum,profile,numhelix,diff,lastprob);
numhelix = 0;
fullnum = 0;
profile[0] = '\0';
fullprofile[0] = '\0';
diff[0] = '\0';
lastprob = j;
}
}
//printf("input profile is %s with fullprofile %s and diff %s\n",profile,fullprofile,diff);
halfbrac = process_input_profile(fp,halfbrac,fullprofile,fullnum,profile,numhelix,diff,lastprob);
free(profile);
hashtbl_destroy(halfbrac);
//finds edges between centroids
find_centroid_edges(fp);
}
//process input into three profiles Hs,Hu,Hn
//s = selected profiles, u = unselected in sample,n=in native only
//connects them, puts Hs in cluster with freq = 0 if not already there
int process_one_input(FILE *fp) {
HASHTBL *halfbrac;
FILE *file;
char temp[100],tmp[ARRAYSIZE],*profile,*fullprofile,*diff,*native,*diffn,*dup;
int i,j,k,*id,last=0,insample;
int numhelix = 0,fullnum = 0,natnum = 0;
int size = INIT_SIZE,size2 = INIT_SIZE,size3 = INIT_SIZE,size4 = INIT_SIZE,size5 = INIT_SIZE;
if (!(halfbrac = hashtbl_create(HASHSIZE,NULL))) {
fprintf(stderr, "ERROR: hashtbl_create() for halfbrac failed");
exit(EXIT_FAILURE);
}
if (!(input = hashtbl_create(HASHSIZE,NULL))) {
fprintf(stderr, "ERROR: hashtbl_create() for input failed");
exit(EXIT_FAILURE);
}
//longest = hashtbl_get(max,"longest");
profile = malloc(sizeof(char)*ARRAYSIZE*size);
fullprofile = malloc(sizeof(char)*ARRAYSIZE*size2);
diff = malloc(sizeof(char)*ARRAYSIZE*size3);
native = malloc(sizeof(char)*ARRAYSIZE*size4);
diffn = malloc(sizeof(char)*ARRAYSIZE*size5);
profile[0] = '\0';
fullprofile[0] = '\0';
diff[0] = '\0';
native[0] = '\0';
diffn[0] = '\0';
if (!(file = fopen(INPUT,"r")))
fprintf(stderr,"Cannot open %s\n",INPUT);
while (fgets(temp,100,file)) {
// if (sscanf(temp,"Structure %d (%d)",&i,&prob) == 2)
if (sscanf(temp,"%d %d %d",&i,&j,&k) == 3) {
insample = 1;
sprintf(tmp,"%d %d",i,j);
id = hashtbl_get(bp,tmp);
if (!id) {
id = process_native(i,j,k);
//printf("number in marginals %d\n",hashtbl_numkeys(marginals));
if (*id > hashtbl_numkeys(marginals))
insample = 0;
}
if (*id != last) {
sprintf(tmp,"%d",*id);
if (strlen(native)+strlen(tmp) > (ARRAYSIZE*size4-2))
native = realloc(native,ARRAYSIZE*(++size4));
sprintf(native,"%s%s ",native,tmp);
natnum++;
if (insample) {
fullnum++;
if (strlen(fullprofile)+strlen(tmp) > (ARRAYSIZE*size2-2))
fullprofile = realloc(fullprofile,ARRAYSIZE*(++size2));
sprintf(fullprofile,"%s%s ",fullprofile,tmp);
if (hashtbl_get(freq,tmp)) { //is a freq helix, save to profile
numhelix++;
if (strlen(profile)+strlen(tmp) > (ARRAYSIZE*size-2))
profile = realloc(profile,ARRAYSIZE*(++size));
//printf("adding %d to profile\n",*id);
sprintf(profile,"%s%s ",profile,tmp);
}
else { //if not freq record diff
if (strlen(diff)+strlen(tmp)+2 > ARRAYSIZE*size3)
diff = realloc(diff,ARRAYSIZE*(++size3));
sprintf(diff,"%s%s ",diff,tmp);
//printf("printing diff %s\n",diff);
}
}
else {
if (strlen(diffn)+strlen(tmp)+2 > ARRAYSIZE*size5)
diffn = realloc(diffn,ARRAYSIZE*(++size5));
sprintf(diffn,"%s%s ",diffn,tmp);
}
last = *id;
make_brackets(halfbrac,i,j,*id);
}
else if (VERBOSE)
printf("helix %d %d %d is duplicate with id %d: process_input()\n",i,j,k,*id);
}
}
native = sort_input(native,natnum);
//printf("native is now %s\n",native);
make_bracket_rep(halfbrac,native);
hashtbl_destroy(halfbrac);
fullprofile = sort_input(fullprofile,fullnum);
profile = sort_input(profile,numhelix);
//printf("native %s, fullprofile %s, profile %s, diff %s, diffn %s\n",native,fullprofile,profile,diff,diffn);
if (fullnum != natnum)
make_edge_and_node(fp,fullprofile,native,diffn,natnum);
if (numhelix != fullnum)
make_edge_and_node(fp,profile,fullprofile,diff,fullnum);
fprintf(fp,"\"%s\" [style = filled, fillcolor = gray60];\n",profile);
sprintf(tmp,"%d ",numhelix);
if (strlen(tmp)+strlen(profile) > ARRAYSIZE*size+1)
profile = realloc(profile,ARRAYSIZE*(++size));
dup = mystrdup(profile);
sprintf(profile,"%s%s",tmp,dup);
id = hashtbl_get(cluster,profile);
free(dup);
if (!id) {
id = malloc(sizeof(int));
*id = 0;
hashtbl_insert(cluster,profile,id);
//printf("inserting input %s into cluster\n",profile);
}
free(profile);
return numhelix;
}
//runs through nodes in cluster, finding their LCA's
int insert_graph(FILE *fp,char *file,int gsize) {
int i,*freq,k = 0,numkeys,total;
char *profile;
KEY *node;
struct hashnode_s *begin;
if (!(edges = hashtbl_create(HASHSIZE,NULL))) {
fprintf(stderr, "ERROR: hashtbl_create() failed");
exit(EXIT_FAILURE);
}
fputs("digraph G {\n",fp);
fprintf(fp,"\tlabel = \"%s\";\n",file);
fprintf(fp,"\tpad = 0.5;\n");
fprintf(fp,"\tnodesep = 0.5;\n");
fprintf(fp,"\"\" [label=\"(0/%d)\"]\n",NUMSTRUCTS);
//fputs("{ node [shape = plaintext]; ",fp);
graphsize = gsize;
if (INPUT) {
i = process_one_input(fp);
if (i > gsize)
graphsize = i;
}
//printf("graphsize is %d for %s\n",*count,node->data);
graph = malloc(sizeof(HASHTBL*)*(graphsize+1));
for (i = 0; i <= graphsize; i++) graph[i] = NULL;
/*print ranks
for (i = 0; i < *count; i++) {
fprintf(fp,"%d",i+1);
if (i == *count-1)
fprintf(fp,"; }\n");
else
fprintf(fp,"->");
}
*/
numkeys = hashtbl_numkeys(cluster);
sums = malloc(sizeof(long)*numkeys);
k = numkeys-1;
profileID = malloc(sizeof(char*)*numkeys);
modprofileID = malloc(sizeof(char*)*numkeys);
most = 0;
//for each profile, insert with freq
for (node = hashtbl_getkeys(cluster); node; node = node->next) {
//printf("node data is %s with k = %d\n",node->data,k);
freq = hashtbl_get(cluster,node->data);
//need to insert into graph
if (freq) {
if (most < *freq)
most = *freq;
profile = malloc(strlen(node->data)+1);
sums[k] = insert_and_binary(node->data,profile,*freq);
profileID[k] = node->data;
modprofileID[k--] = profile;
if (*freq > 0)
fprintf(fp,"\"%s\" [shape = box];\n",profile);
}
else
fprintf(stderr,"No entry for %s\n",node->data);
//printf("for profile %s binary rep is %d with ID %d\n",node->data,sums[k+1],k+1);
}
make_key();
begin = insert_LCAs(fp,numkeys);
//printf("inserted LCA's with numkeys %d\n",numkeys);
add_infreq(begin);
find_LCA_edges(fp,begin,numkeys);
total = print_vertices(fp);
printf("Total number of vertices: %d\n",total);
if (INPUT)
hashtbl_destroy(input);
for (i = 0; i < graphsize; i++) {
if (graph[i])
hashtbl_destroy(graph[i]);
}
free(sums);
free(table);
free(profileID);
free(modprofileID);
hashtbl_destroy(edges);
return 0;
}
int oph_server_conf_load(short unsigned int instance, HASHTBL **hashtbl)
{
if(!hashtbl){
pmesg(LOG_ERROR, __FILE__, __LINE__, "Null input parameter\n");
return OPH_SERVER_CONF_NULL_PARAM;
}
if( !(*hashtbl = hashtbl_create(OPH_SERVER_CONF_LOAD_SIZE, NULL)) ){
pmesg(LOG_ERROR, __FILE__, __LINE__, "Unable to create hash table\n");
return OPH_SERVER_CONF_ERROR;
}
FILE *file = fopen(OPH_SERVER_CONF_FILE_PATH, "r");
if(file == NULL)
{
pmesg(LOG_ERROR, __FILE__, __LINE__, "Configuration file not found\n");
hashtbl_destroy(*hashtbl);
*hashtbl = NULL;
return OPH_SERVER_CONF_ERROR;
}
else
{
char buffer[OPH_SERVER_CONF_LINE_LEN] = {0};
char tmp_buffer[OPH_SERVER_CONF_LINE_LEN] = {0};
char *value = NULL;
char *position = NULL, *position2 = NULL;
const char *param_iter = NULL;
int i = 0, j = 0;
short int instance_flag = 0;
char *instance_string = 0;
short unsigned int instance_number = 0;
while(!feof(file)) {
//Retrieve instance header
memset(tmp_buffer, 0, sizeof(buffer));
memset(buffer, 0, sizeof(buffer));
if (!fgets (buffer, sizeof(buffer), file))
{
if(feof(file)){
fclose (file);
return OPH_SERVER_CONF_SUCCESS;
}
else{
fclose (file);
pmesg(LOG_ERROR, __FILE__, __LINE__, "Error while reading configuration file\n");
hashtbl_destroy(*hashtbl);
return OPH_SERVER_CONF_ERROR;
}
}
//Check if row is a comment
j = 0;
while(buffer[j] == ' ') j++;
//Row is a comment
if(buffer[j] == OPH_SERVER_CONF_COMMENT) continue;
//Check if row is newline
j = 0;
while(buffer[j] == ' ') j++;
//Row is a newline
if(buffer[j] == '\n') continue;
sscanf (buffer, "[%[^]]", tmp_buffer);
if(instance_flag == 0){
//If row does not contain an instance ref then step to next row
if (!(instance_string = strstr (tmp_buffer, OPH_SERVER_CONF_INSTANCE))){
continue;
}
else{
//Check instance number
if(instance != 0){
instance_string += strlen(OPH_SERVER_CONF_INSTANCE);
instance_number = (short unsigned int)strtol(instance_string, NULL, 10);
if(instance_number == 0) continue;
if(instance_number != instance) continue;
}
//If instance header is found read all lines until next one
instance_flag = 1;
}
}
else{
if (!strstr (tmp_buffer, OPH_SERVER_CONF_INSTANCE)){
//Parse row
//Get param-value separator
value = NULL;
position = position2 = NULL;
position = strchr(buffer, '=');
if(position != NULL){
//Set = symbol to NULL
position[0] = 0;
position++;
//If new line char is read, then remove it
if((position2 = strchr(position, '\n')) != NULL){
position2[0] = 0;
}
//Check if param is allowed
i = 0;
param_iter = oph_server_conf_params[i++];
while(param_iter){
if(STRCMP(buffer, param_iter) == 0) break;
param_iter = oph_server_conf_params[i++];
}
if( param_iter == NULL ) {
pmesg(LOG_DEBUG, __FILE__, __LINE__, "Configuration param not allowed %s\n", buffer);
continue;
}
//Alloc value to be added to hash table
value = strndup(position, OPH_SERVER_CONF_LINE_LEN);
if(value == NULL){
pmesg(LOG_ERROR, __FILE__, __LINE__, "Error while copying param %s\n", buffer);
fclose(file);
hashtbl_destroy(*hashtbl);
*hashtbl = NULL;
return OPH_SERVER_CONF_ERROR;
}
if(hashtbl_insert(*hashtbl, buffer, value)){
pmesg(LOG_ERROR, __FILE__, __LINE__, "Error while loading param %s\n", buffer);
fclose(file);
free(value);
hashtbl_destroy(*hashtbl);
*hashtbl = NULL;
return OPH_SERVER_CONF_ERROR;
}
pmesg(LOG_DEBUG, __FILE__, __LINE__, "LOADED PARAM: %s = %s \n", buffer, position);
}
else{
pmesg(LOG_DEBUG, __FILE__, __LINE__, "Configuration param corrupted %s\n", buffer);
}
}
else{
//Found second instance ref, end cycle
break;
}
}
}
fclose(file);
}
return OPH_SERVER_CONF_SUCCESS;
}
/*
* Function:
* hash_create
* Arguments:
* (htbl) Pointer to a pointer to a hash_table structure.
* Purpose:
* This function is our most important function. From this
* hash table, all other searches depend. This function will
* grab all the definitions, parse them, also each functions
* description, AND what it returns. It will build a new
* 'chain_node' for each, and add it to it's proper 'bucket'
* in our hash table.
* Returns:
* -1 - On error, call err_GetLastError for more information.
* 0 - If everything went planned.
*/
int
hashtbl_create( hashtbl **htbl )
{
chain_node *tmp;
char definition[CORE_MAX_DEF] = {0};
char description[CORE_MAX_DESC] = {0};
char returns[CORE_MAX_RET] = {0};
/* If this is still 0 they didn't call: core_start(); big no-no!!! */
if( !core_startup )
{
err_setError( FUNC_HASHTBL_CREATE,
FILE_HASH_C,
ERR_CORE_STARTUP,
__LINE__ );
return -1;
}
if( !htbl )
{
err_setError( FUNC_HASHTBL_CREATE, FILE_HASH_C, ERR_NULL_PARAM, __LINE__ );
return -1;
}
*htbl = malloc( sizeof(**htbl) );
if( *htbl == NULL )
{
err_setError( FUNC_HASHTBL_CREATE, FILE_HASH_C, ERR_MALLOC, __LINE__ );
return -1;
}
memset( *htbl, 0, sizeof(**htbl) );
/* If you mess w/ my data files you'll f**k this all up. Leave 'em alone */
while( fgets(definition, sizeof definition, def) != NULL &&
fgets(description, sizeof description, desc) != NULL &&
fgets(returns, sizeof returns, ret) != NULL )
{
tmp = malloc( sizeof(*tmp) );
if( tmp == NULL )
goto error1;
memset( tmp, 0, sizeof(*tmp) );
core_convertNewLines( description );
core_convertNewLines( returns );
tmp->name = malloc( (strlen(definition) + 1) * sizeof(*tmp->name) );
if( tmp->name == NULL )
{
free( tmp );
goto error1;
}
tmp->description = malloc( (strlen(description) + 1) *
sizeof(*tmp->description) );
if( tmp->description == NULL )
goto error;
tmp->returns = malloc( (strlen(returns) + 1) * sizeof(*tmp->returns) );
if( tmp->returns == NULL )
goto error;
strncpy( tmp->name, definition, strlen(definition) + 1 );
strncpy( tmp->description, description, strlen(description) + 1 );
strncpy( tmp->returns, returns, strlen(returns) + 1 );
if( core_parseDefinition(tmp->name,
&tmp->name,
&tmp->section,
&tmp->prototype) )
goto error;
core_convertNewLines( tmp->prototype );
if( hashtbl_add(*htbl, tmp) )
goto error;
}
return 0;
error:
if( tmp->description ) free( tmp->description );
if( tmp->returns ) free( tmp->returns );
if( tmp->name ) free( tmp->name );
free( tmp );
error1:
hashtbl_destroy( htbl );
return -1;
}
void activation_destroy(activation* act) {
assert(act != NULL);
hashtbl_destroy(act->env);
free(act->env);
}
//Procedure OPH_IO_SERVER_PROCEDURE_SUBSET
int oph_io_server_run_subset_procedure(oph_metadb_db_row ** meta_db, oph_iostore_handler * dev_handle, oph_io_server_thread_status * thread_status, oph_query_arg ** args, HASHTBL * query_args)
{
if (!query_args || !dev_handle || !thread_status || !meta_db) {
pmesg(LOG_ERROR, __FILE__, __LINE__, OPH_IO_SERVER_LOG_NULL_INPUT_PARAM);
logging(LOG_ERROR, __FILE__, __LINE__, OPH_IO_SERVER_LOG_NULL_INPUT_PARAM);
return OPH_IO_SERVER_NULL_PARAM;
}
//Check if current DB is setted
//TODO Improve how current DB is found
if (thread_status->current_db == NULL || thread_status->device == NULL) {
pmesg(LOG_ERROR, __FILE__, __LINE__, OPH_IO_SERVER_LOG_QUERY_NO_DB_SELECTED);
logging(LOG_ERROR, __FILE__, __LINE__, OPH_IO_SERVER_LOG_QUERY_NO_DB_SELECTED);
return OPH_IO_SERVER_METADB_ERROR;
}
//Fetch function arguments
char *function_args = hashtbl_get(query_args, OPH_QUERY_ENGINE_LANG_ARG_ARG);
if (function_args == NULL) {
pmesg(LOG_ERROR, __FILE__, __LINE__, OPH_IO_SERVER_LOG_MISSING_QUERY_ARGUMENT, OPH_QUERY_ENGINE_LANG_ARG_ARG);
logging(LOG_ERROR, __FILE__, __LINE__, OPH_IO_SERVER_LOG_MISSING_QUERY_ARGUMENT, OPH_QUERY_ENGINE_LANG_ARG_ARG);
return OPH_IO_SERVER_EXEC_ERROR;
}
//Length used for new query
unsigned int query_len = strlen(function_args) + 200;
char **func_args_list = NULL;
int func_args_num = 0;
if (oph_query_parse_multivalue_arg(function_args, &func_args_list, &func_args_num)) {
pmesg(LOG_ERROR, __FILE__, __LINE__, OPH_IO_SERVER_LOG_QUERY_MULTIVAL_PARSE_ERROR, OPH_QUERY_ENGINE_LANG_ARG_ARG);
logging(LOG_ERROR, __FILE__, __LINE__, OPH_IO_SERVER_LOG_QUERY_MULTIVAL_PARSE_ERROR, OPH_QUERY_ENGINE_LANG_ARG_ARG);
return OPH_IO_SERVER_EXEC_ERROR;
}
//Check number of arguments
if (func_args_num < 4 || func_args_num > 5) {
pmesg(LOG_ERROR, __FILE__, __LINE__, OPH_IO_SERVER_LOG_WRONG_PROCEDURE_ARG, OPH_IO_SERVER_PROCEDURE_SUBSET);
logging(LOG_ERROR, __FILE__, __LINE__, OPH_IO_SERVER_LOG_WRONG_PROCEDURE_ARG, OPH_IO_SERVER_PROCEDURE_SUBSET);
free(func_args_list);
return OPH_IO_SERVER_EXEC_ERROR;
}
//Argument 0 should be a string with optionally a hierarchical name (a.b)
//Remove leading/trailing spaces and match string
if (oph_query_check_procedure_string(&(func_args_list[0]))) {
pmesg(LOG_ERROR, __FILE__, __LINE__, OPH_IO_SERVER_LOG_ARG_NO_STRING, func_args_list[0]);
logging(LOG_ERROR, __FILE__, __LINE__, OPH_IO_SERVER_LOG_ARG_NO_STRING, func_args_list[0]);
free(func_args_list);
return OPH_IO_SERVER_EXEC_ERROR;
}
//Extract hierachical info
char **in_frag_components = NULL;
int in_frag_components_num = 0;
if (oph_query_parse_hierarchical_args(func_args_list[0], &in_frag_components, &in_frag_components_num)) {
pmesg(LOG_ERROR, __FILE__, __LINE__, OPH_IO_SERVER_LOG_QUERY_HIERARCHY_PARSE_ERROR, func_args_list[0]);
logging(LOG_ERROR, __FILE__, __LINE__, OPH_IO_SERVER_LOG_QUERY_HIERARCHY_PARSE_ERROR, func_args_list[0]);
free(func_args_list);
return OPH_IO_SERVER_PARSE_ERROR;
}
char *in_frag_name = NULL;
//If DB is setted in frag name
if (in_frag_components_num > 1) {
//Check if db is the one used by the query
if (STRCMP(thread_status->current_db, in_frag_components[0]) != 0) {
pmesg(LOG_ERROR, __FILE__, __LINE__, OPH_IO_SERVER_LOG_QUERY_WRONG_DB_SELECTED);
logging(LOG_ERROR, __FILE__, __LINE__, OPH_IO_SERVER_LOG_QUERY_WRONG_DB_SELECTED);
free(in_frag_components);
free(func_args_list);
return OPH_IO_SERVER_METADB_ERROR;
}
in_frag_name = in_frag_components[1];
} else {
in_frag_name = in_frag_components[0];
}
//Argument 1 should be a number
long long id_start = 0;
//Test number presence
char *end = NULL;
errno = 0;
id_start = strtoll((char *) func_args_list[1], &end, 10);
if ((errno != 0) || (end == (char *) func_args_list[1]) || (*end != 0)) {
pmesg(LOG_ERROR, __FILE__, __LINE__, OPH_IO_SERVER_LOG_ARG_NO_LONG, func_args_list[1]);
logging(LOG_ERROR, __FILE__, __LINE__, OPH_IO_SERVER_LOG_ARG_NO_LONG, func_args_list[1]);
free(in_frag_components);
free(func_args_list);
return OPH_IO_SERVER_EXEC_ERROR;
}
//Argument 2 should be a string
//Remove leading/trailing spaces and match string
if (oph_query_check_procedure_string(&(func_args_list[2]))) {
pmesg(LOG_ERROR, __FILE__, __LINE__, OPH_IO_SERVER_LOG_ARG_NO_STRING, func_args_list[2]);
logging(LOG_ERROR, __FILE__, __LINE__, OPH_IO_SERVER_LOG_ARG_NO_STRING, func_args_list[2]);
free(in_frag_components);
free(func_args_list);
return OPH_IO_SERVER_EXEC_ERROR;
}
//Argument 3 should be a string with optionally a hierarchical name (a.b)
//Remove leading/trailing spaces and match string
if (oph_query_check_procedure_string(&(func_args_list[3]))) {
pmesg(LOG_ERROR, __FILE__, __LINE__, OPH_IO_SERVER_LOG_ARG_NO_STRING, func_args_list[3]);
logging(LOG_ERROR, __FILE__, __LINE__, OPH_IO_SERVER_LOG_ARG_NO_STRING, func_args_list[3]);
free(in_frag_components);
free(func_args_list);
return OPH_IO_SERVER_EXEC_ERROR;
}
//Extract hierachical info
char **out_frag_components = NULL;
int out_frag_components_num = 0;
if (oph_query_parse_hierarchical_args(func_args_list[3], &out_frag_components, &out_frag_components_num)) {
pmesg(LOG_ERROR, __FILE__, __LINE__, OPH_IO_SERVER_LOG_QUERY_HIERARCHY_PARSE_ERROR, func_args_list[3]);
logging(LOG_ERROR, __FILE__, __LINE__, OPH_IO_SERVER_LOG_QUERY_HIERARCHY_PARSE_ERROR, func_args_list[3]);
free(in_frag_components);
free(func_args_list);
return OPH_IO_SERVER_PARSE_ERROR;
}
char *out_frag_name = NULL;
//If DB is setted in frag name
if (out_frag_components_num > 1) {
//Check if db is the one used by the query
if (STRCMP(thread_status->current_db, out_frag_components[0]) != 0) {
pmesg(LOG_ERROR, __FILE__, __LINE__, OPH_IO_SERVER_LOG_QUERY_WRONG_DB_SELECTED);
logging(LOG_ERROR, __FILE__, __LINE__, OPH_IO_SERVER_LOG_QUERY_WRONG_DB_SELECTED);
free(in_frag_components);
free(out_frag_components);
free(func_args_list);
return OPH_IO_SERVER_METADB_ERROR;
}
out_frag_name = out_frag_components[1];
} else {
out_frag_name = out_frag_components[0];
}
//Argument 4, if available, should be a string
char where_flag = 0;
if (func_args_num == 5) {
//Remove leading/trailing spaces and match string
if (oph_query_check_procedure_string(&(func_args_list[4]))) {
pmesg(LOG_ERROR, __FILE__, __LINE__, OPH_IO_SERVER_LOG_ARG_NO_STRING, func_args_list[4]);
logging(LOG_ERROR, __FILE__, __LINE__, OPH_IO_SERVER_LOG_ARG_NO_STRING, func_args_list[4]);
free(in_frag_components);
free(out_frag_components);
free(func_args_list);
return OPH_IO_SERVER_EXEC_ERROR;
}
//If arg list 4 is set, then activate where flag
where_flag = ((func_args_list[4])[0] != 0);
}
char new_query[query_len];
//Check if where is enabled
if (where_flag) {
snprintf(new_query, query_len - 1, "operation=create_frag_select;frag_name=%s;field=id_dim|%s;select_alias=|measure;from=%s;where=%s;sequential_id=%lld;", out_frag_name,
func_args_list[2], in_frag_name, func_args_list[4], id_start);
} else {
snprintf(new_query, query_len - 1, "operation=create_frag_select;frag_name=%s;field=id_dim|%s;select_alias=|measure;from=%s;", out_frag_name, func_args_list[2], in_frag_name);
}
free(in_frag_components);
free(out_frag_components);
free(func_args_list);
//Parse internal query
HASHTBL *procedure_query_args = NULL;
if (oph_query_parser(new_query, &procedure_query_args)) {
pmesg(LOG_WARNING, __FILE__, __LINE__, "Unable to run query\n");
logging(LOG_WARNING, __FILE__, __LINE__, "Unable to run query\n");
}
//Run create as select block
if (oph_io_server_run_create_as_select_table(meta_db, dev_handle, thread_status->current_db, args, procedure_query_args)) {
pmesg(LOG_ERROR, __FILE__, __LINE__, OPH_IO_SERVER_LOG_QUERY_DISPATCH_ERROR, "Create as Select");
logging(LOG_ERROR, __FILE__, __LINE__, OPH_IO_SERVER_LOG_QUERY_DISPATCH_ERROR, "Create as Select");
hashtbl_destroy(procedure_query_args);
return OPH_IO_SERVER_EXEC_ERROR;
}
hashtbl_destroy(procedure_query_args);
return OPH_IO_SERVER_SUCCESS;
}