DBConnection *DBConnection_new(char *host, char *user, char *pass,
char *dbname, unsigned int port) {
DBConnection *dbc;
MYSQL *mysql;
if ((dbc = (DBConnection *)calloc(1,sizeof(DBConnection))) == NULL) {
Error_write(ECALLERR,"DBConnection_new",ERR_SEVERE,"dbc");
return NULL;
}
if ((mysql = mysql_init(NULL)) == NULL) {
Error_write(EMYSQLCONN, "DBConnection_new", ERR_SEVERE,
" failed creating mysql object in mysql_init, mysql error %s",mysql_error(mysql));
return NULL;
}
/* on unix, localhost will connect via a local socket by default and ignore the port. If the
* user has specified a port then force mysql to use it by setting the protocol to TCP (this is
* necessary if using ssh tunnels). */
if (mysql && host && port && !strcmp(host, "localhost")) {
const enum mysql_protocol_type arg = MYSQL_PROTOCOL_TCP ;
mysql_options(mysql, MYSQL_OPT_PROTOCOL, &arg) ;
}
if ((mysql_real_connect(mysql,host, user, pass, dbname, port, NULL, 0)) == NULL) {
Error_write(EMYSQLCONN, "DBConnection_new", ERR_SEVERE,
" dbname %s (host %s user %s pass %s port %d), mysql error %s",
dbname,host,user,pass,port,mysql_error(mysql));
return NULL;
}
EcoString_copyStr(ecoSTable, &(dbc->host), host, 0);
EcoString_copyStr(ecoSTable, &(dbc->user), user, 0);
if (pass) EcoString_copyStr(ecoSTable, &(dbc->pass), pass, 0);
EcoString_copyStr(ecoSTable, &(dbc->dbName), dbname, 0);
dbc->port = port;
dbc->mysql = mysql;
dbc->prepare = DBConnection_prepare;
if (!dbc->host ||
!dbc->user ||
!dbc->dbName ||
(pass && !dbc->pass)) {
Error_trace("DBConnnection_new",NULL);
return NULL;
}
return dbc;
}
ECOSTRING RawContig_setName(RawContig *rc, char *name) {
if (!EcoString_copyStr(ecoSTable,&(rc->name),name,0)) {
fprintf(stderr,"ERROR: Failed allocating space for contig name\n");
return NULL;
}
return rc->name;
}
ECOSTRING Sequence_setName(Sequence *seq, char *name) {
if (EcoString_copyStr(ecoSTable,&(seq->name),name,0)) {
fprintf(stderr,"ERROR: Failed allocating space for seq name\n");
return NULL;
}
return seq->name;
}
ECOSTRING PredictionExon_setDisplayLabel(PredictionExon *pe, char *label) {
EcoString_copyStr(ecoSTable, &(pe->displayLabel), label, 0);
return pe->displayLabel;
}
ECOSTRING SyntenyRegion_setSeqType(SyntenyRegion *sr, char *seqType) {
EcoString_copyStr(ecoSTable, &(sr->seqType), seqType, 0);
return sr->seqType;
}
ECOSTRING SyntenyRegion_setHitChrName(SyntenyRegion *sr, char *hitChrName) {
EcoString_copyStr(ecoSTable, &(sr->hitChrName), hitChrName, 0);
return sr->hitChrName;
}
ECOSTRING PredictionTranscript_setType(PredictionTranscript *t, char *type) {
EcoString_copyStr(ecoSTable,&(t->type),type,0);
return t->type;
}
ECOSTRING PredictionTranscript_setDisplayLabel(PredictionTranscript *pt, char *label) {
EcoString_copyStr(ecoSTable, &(pt->displayLabel), label, 0);
return pt->displayLabel;
}
ECOSTRING SimpleFeature_setDisplayLabel(SimpleFeature *sf, char *label) {
EcoString_copyStr(ecoSTable, &(sf->displayLabel), label, 0);
return sf->displayLabel;
}
CoordSystem *CoordSystem_new(char *name, char *version, int rank, IDType dbID, CoordSystemAdaptor *csa, int isDefault, int isSeqLevel, int isTopLevel) {
if (version == NULL) {
version = emptyString;
}
isTopLevel = isTopLevel ? 1 : 0;
isSeqLevel = isSeqLevel ? 1 : 0;
isDefault = isDefault ? 1 : 0;
if ( isTopLevel == 1 ) {
if ( rank != 0 ) {
fprintf(stderr,"RANK argument must be 0 if TOP_LEVEL is 1");
exit(1);
}
if ( name != NULL ) {
if ( strcmp(name,"toplevel")) {
fprintf(stderr,"The NAME argument must be 'toplevel' if TOP_LEVEL is 1");
exit(1);
}
} else {
name="toplevel";
}
if ( isSeqLevel == 1 ) {
fprintf(stderr,"SEQUENCE_LEVEL argument must be 0 if TOP_LEVEL is 1");
exit(1);
}
isDefault = 0;
} else {
if ( rank == 0 ) {
fprintf(stderr,"RANK argument must be non-zero unless TOP_LEVEL is 1");
exit(1);
}
if ( name == NULL ) {
fprintf(stderr,"The NAME argument is required");
exit(1);
} else if ( !strcmp(name,"toplevel")) {
fprintf( stderr, "Cannot name coord system 'toplevel unless TOP_LEVEL is 1" );
exit(1);
}
}
if ( rank < 0 ) {
fprintf(stderr, "The RANK argument must be a non negative integer");
exit(1);
}
CoordSystem *cs;
if ((cs = (CoordSystem *)calloc(1,sizeof(CoordSystem))) == NULL) {
fprintf(stderr,"ERROR: Failed allocating space for cs\n");
return NULL;
}
cs->objectType = CLASS_COORDSYSTEM;
cs->funcs = &coordSystemFuncs;
EcoString_copyStr(ecoSTable,&(cs->version),version,0);
EcoString_copyStr(ecoSTable,&(cs->name),name,0);
cs->isTopLevel = isTopLevel;
cs->isSeqLevel = isSeqLevel;
cs->isDefaultVersion = isDefault;
cs->rank = rank;
CoordSystem_setAdaptor(cs, (BaseAdaptor *)csa);
CoordSystem_setDbID(cs, dbID);
return cs;
}
