// parse and combine JuggleMaster and JuggleSaver patterns
int ParseAllPatterns(FILE *jm_input, FILE* js_input,
struct groups_t *groups, struct styles_t *styles) {
int jm = ParsePatterns(jm_input, groups, styles);
if (!jm) return 0;
#ifdef JUGGLESAVER_SUPPORT
if (!js_input) return 1;
struct pattern_group_t* last = groups->first;
while (last->next != NULL) last = last->next;
struct groups_t *js_groups = new groups_t;
js_groups->first = NULL;
int js = ParseJSPatterns(js_input, js_groups);
if (!js) { delete js_groups; return 0; }
last->next = js_groups->first;
delete js_groups;
#endif
return 1;
}
int main(int argc, char *argv[]) {
FILE *f;
struct groups_t g;
struct styles_t s;
struct pattern_group_t *groups;
struct style_t *styles;
struct pattern_t *patterns;
int quiet = 0;
int current_arg;
s.first = NULL;
g.first = NULL;
if(argc < 2) {
printf("Format: %s [-q[uiet]] <filename1> [filename2 ...]\n", argv[0]);
return 1;
}
if(strncmp(argv[1],"-q",2) == 0) {
quiet = 1;
current_arg = 2;
} else {
current_arg = 1;
}
for(;current_arg<argc;current_arg++) {
if((f = fopen(argv[current_arg],"r")) == NULL) {
perror("Couldn't open file");
return 1;
}
ParsePatterns(f,&g,&s);
fclose(f);
if(!quiet) {
printf("File: %s\n", argv[current_arg]);
groups = FirstGroup(&g);
printf("Group Data\n");
while(groups) {
printf(" Group Name: %s\n",Group_GetName(groups));
patterns = Group_GetPatterns(groups);
while(patterns) {
printf(" Pattern Name: %s\n",Patt_GetName(patterns));
printf(" Style: %s\n",Patt_GetStyle(patterns));
printf(" Data: %s\n",Patt_GetData(patterns));
printf(" Height ratio: %1.2f\n",Patt_GetHR(patterns));
printf(" Dwell Ratio: %1.2f\n",Patt_GetDR(patterns));
printf(" Author: %s\n",Patt_GetAuthor(patterns));
patterns = NextPatt(patterns);
}
groups = NextGroup(groups);
printf("\n");
};
printf("\n\n");
printf("Style Data\n");
styles = FirstStyle(&s);
while(styles) {
int i;
printf(" Style Name: %s\n",Style_GetName(styles));
printf(" Length: %i\n",Style_GetLength(styles));
printf(" Data:\n");
for(i=0;i<(int)Style_GetLength(styles);i++) {
if((i%4) == 0) {
printf(" {");
} else if ((i%4) == 2) {
printf("}{");
}
printf(" %i",Style_GetData(styles)[i]);
if ((i%4) == 0 || (i%4) == 2) {
printf(", ");
} else if ((i%4) == 3) {
printf("}\n");
}
}
styles = NextStyle(styles);
printf("\n");
}
printf("\n\n");
}
FreeGroups(&g);
FreeStyles(&s);
}
return 0;
}
/* load a description from a file */
PMSDESCRIPTION LoadSiteDescription(const char *Filename)
{
int error; /* non-zero if error occurred */
int foundPattern; /* non-zero if pattern found */
int foundScoring; /* non-zero if scoring parameters found*/
int foundQuality; /* non-zero if quality filter found */
PMSDESCRIPTION pDescription; /* site description to be loaded */
xmlDocPtr pXMLDocument; /* the XML document in the file */
xmlNode *pNode; /* current node in XML document */
/* parse XML file */
xmlInitParser();
pXMLDocument=xmlParseFile(Filename);
if (!pXMLDocument) {
fprintf(stderr,"Could not parse site description file!\n");
return(NULL);
}
/* get memory for site description */
pDescription=(PMSDESCRIPTION)malloc(sizeof(MSDESCRIPTION));
if (!pDescription) {
fprintf(stderr,"Could not allocate memory for site description!\n");
xmlFreeDoc(pXMLDocument);
xmlCleanupParser();
return(NULL);
}
pDescription->Length=0;
pDescription->Sequence=NULL;
pDescription->RepeatBasePosition=-1;
pDescription->Minimal5Flank=5;
pDescription->Minimal3Flank=5;
pDescription->MaximalMismatch=10;
pDescription->MaxMismatch5Req=1;
pDescription->MaxMismatch3Req=1;
pDescription->CutoffForNs=20;
pDescription->MaximumNs=30;
error=0;
do { /* region of controlled exit */
for(pNode=xmlDocGetRootElement(pXMLDocument);pNode;pNode=pNode->next)
if (pNode->type==XML_ELEMENT_NODE &&
!strcmp((const char*)pNode->name,"SiteDescription"))
break;
if (!pNode) {
fprintf(stderr,"Could not find <SiteDescription> in description file!\n");
error=1;
break;
}
foundPattern=0;
foundScoring=0;
foundQuality=0;
for(pNode=pNode->children;pNode;pNode=pNode->next) {
if (pNode->type != XML_ELEMENT_NODE) continue;
if (!strcmp((const char*)pNode->name,"Pattern")) {
if (foundPattern) {
fprintf(stderr,"Site description contains two patterns!\n");
error=1;
break;
}
foundPattern=1;
error=ParsePatterns(pDescription,pNode);
}
if (!strcmp((const char*)pNode->name,"ScoringRules")) {
if (foundScoring) {
fprintf(stderr,"Site description contains two scoring parameter "
"sets!\n");
error=1;
break;
}
foundScoring=1;
error=ParseScoring(pDescription,pNode);
}
if (!strcmp((const char*)pNode->name,"QualityFilter")) {
if (foundQuality) {
fprintf(stderr,"Site description contains two quality filter "
"parameter sets!\n");
error=1;
break;
}
foundQuality=1;
error=ParseQuality(pDescription,pNode);
}
if (error) break;
}
if (!foundPattern) {
fprintf(stderr,"Site description does not contain a pattern!\n");
error=1;
break;
}
if (pDescription->RepeatBasePosition<pDescription->Minimal5Flank) {
fprintf(stderr,"5' flank is shorter than requested minimal 5' flank "
"length!\n");
error=1;
break;
}
if (pDescription->Length-pDescription->RepeatBasePosition-1
<pDescription->Minimal3Flank) {
fprintf(stderr,"3' flank is shorter than requested minimal 3' flank "
"length!\n");
error=1;
break;
}
} while(0); /* end of region of controlled exit */
xmlFreeDoc(pXMLDocument);
xmlCleanupParser();
if (error) DestroySiteDescription(&pDescription);
return(pDescription);
}
