Int2 Main(void)
{
CharPtr filename = NULL;
Char daytime[100];
Int4 success = 0;
DayTimeStr(daytime, TRUE, TRUE);
printf("import starts. [%s]\n", daytime);
/* check command line arguments (see NCBI toolkit corelib) */
if (!GetArgs("dbxref", NUMARGS, myargs))
{
printf("Main: can not get command line arguments\n");
return 1;
}
else printf("Finished getting arguments\n");
/*initialize codeBase*/
if (!InitCodeBaseForDBXREF())
{
printf( "Main: InitCodeBaseForPreBIND failed.");
error4exitTest(&codeBase); /*quits program */
return 1;
}
else
{
/* setCodeBaseFlagsExclNoidx */
codeBase.accessMode=OPEN4DENY_RW;
codeBase.autoOpen=0;
printf("Finished init codebase with ExclNoindex.\n");
}
if ((Boolean) myargs[0].intvalue== TRUE)
{
if(!MyOpenLL_GO("LL_GO", TRUE)){
printf("OpenTables: OpenLL_GO failed.");
success=1;
}
else{
printf("LL_GO table created successfully!\n");
if(d4close(pD4LL_GO) != r4success) success=1;
}
}
/*import RESULT table from text file and then quit*/
if (success==0 && myargs[4].strvalue != NULL)
{
filename = myargs[4].strvalue;
printf("Import RESULT from %s.\n", filename);
/*cycle through the RESULT file and place info in the RESULT database*/
if (ImportLL_GOTable(filename) != 0)
{
printf( "Import RESULT failed.");
success=1;
}
/*diagnostic line*/
printf("Import Finished.\n");
}
/* close codebase */
code4close(&codeBase);
code4initUndo(&codeBase);
return success;
}
void InitBSPLog(Int4 randseed,CharPtr sequence,Int4 tstruc)
{
CharPtr decsequence;
static Char pcUname[PATH_MAX]="";
Char timedate[25];
#ifdef OS_UNIX
struct utsname utsbuf;
#endif
bspTempLog=BSNew(0);
/* compute log file name */
if (generation==0)
sprintf(LogOutName,"%sfold_%ld_%s_%ld_%s",CFG_local_datafilepath,(long)experiment,handle,(long)tstruc,fnamtrj);
else
sprintf(LogOutName,"%sfold_%ld_%s_%ld_%s_%s_%d",CFG_local_datafilepath,(long)experiment,handle,(long)tstruc,handle,fnamtrj,generation);
BSprintf(bspTempLog,"\nFoldtraj v%s log report",FOLDTRAJ_VERSION);
BSprintf(bspTempLog,"\nTrajectory File: %s%s_%d",CFG_local_datafilepath,fnamtrj,generation);
BSprintf(bspTempLog,"\tStructure File Base Name: %s_%s_%d",handle,fnamtrj,generation);
BSprintf(bspTempLog,"\tRandom Seed: %ld\t# Generated: %ld\tStart Numbering at: %ld",randseed,STRUCS_PER_RUN,1);
BSprintf(bspTempLog,"\tCompared to Native Structure: 1CDZ");
decsequence=DecodeSequence(sequence,EXTAA_PARENT);
BSprintf(bspTempLog,"\nSequence: %s",decsequence);
decsequence=MemFree(decsequence);
BSprintf(bspTempLog,"\nFolding Conditions:\t%ldx%ld Trajectory Distributions\t%s Random Walk\tAverage Timeout: %ld\tBackbone Error Tolerance: %4.2f\tBackbone Precision: %6.4f\tBackbone Atom Bounciness: %5.2f%%\tSidechain Atom Bounciness: %5.2f %%\tHydrogen Bumpchecking: %s\t# Rotamer Tries: %d/chi angle\tMarkov Scale Factor: %4.2f",
TRAJDIV,TRAJDIV,WALKTYPE==WALK_CA?"C-Alpha":"Phi-Psi",TIMEOUT,BACKBONE_ERROR_TOLERANCE,
BACKBONE_PRECISION,ATOM_BOUNCINESS_BB*100.0,ATOM_BOUNCINESS_SC*100.0,
BUMPCHECK_HYDROGEN?"On":"Off",NUM_ROT_TRIES,MARKOV_SCALE_FACTOR);
if (WALKTYPE!=WALK_CA && MARKOV_SCALE_FACTOR>0.0)
ErrPostEx(SEV_ERROR,2,2,"Markov Scale Factor should be zero for non-Ca walk -- ignored");
if (TRAJTYPE!=TRAJ_NA) {
BSprintf(bspTempLog,"\tTrajectory Distribution: ");
switch (TRAJTYPE) {
case TRAJ_UNIFORM:
BSprintf(bspTempLog,"Uniform");
break;
case TRAJ_STANDARD:
BSprintf(bspTempLog,"Amino-Acid Based");
break;
case TRAJ_SSTRU:
BSprintf(bspTempLog,"1-State Secondary Structure Prediction");
break;
case TRAJ_GOR:
BSprintf(bspTempLog,"3-State Secondary Structure Prediction");
break;
default:
BSprintf(bspTempLog,"Unknown");
}
}
if (StringCmp(CONSTRAINT_FILE,""))
BSprintf(bspTempLog,"\tConstraint file: %s",CONSTRAINT_FILE);
BSprintf(bspTempLog,"\nSystem Information: ");
if (StringLen(pcUname)==0) {
StringCpy(pcUname,"Not Available\n");
#ifdef OS_UNIX
/* use uname to get sysinfo */
if (uname(&utsbuf)>=0) {
sprintf(pcUname,"%s %s %s %s %s\n",utsbuf.sysname,utsbuf.nodename,utsbuf.release,utsbuf.version,utsbuf.machine);
}
#else
#ifdef OS_MSWIN
/* assume ver is available */
if (GetMSWinVerInfo(pcUname)!=ERR_SUCCESS) {
StringCpy(pcUname,"Not Available\n");
}
#endif
#endif
}
BSWrite(bspTempLog,pcUname,StringLen(pcUname));
DayTimeStr(timedate,TRUE,TRUE);
BSprintf(bspTempLog,"Job started: %s\n",timedate);
BSprintf(bspTempLog,"\nStructure\tTime(s)\tTries\tBad Backbone Tries\tCrashes\tDistant Constraint Tries (# Violations)\tChain Length\tRadius of Gyration(A)\tHydrophobics Radius of Gyration(A)\tEnd-to-end Distance(A)\tRn\tCn");
BSprintf(bspTempLog,"\tSurface Accessibility (A^2)\tExposed Hydrophobics (A^2)");
BSprintf(bspTempLog,"\t# Helical Residues (DSSP)\t# Extended Residues (DSSP)");
BSprintf(bspTempLog,"\t# Extended Residues (CA-CA dist.)");
BSprintf(bspTempLog,"\tRMSD from Native(A)");
BSprintf(bspTempLog,"\tZhang Potential(Exclusive Window Size %d)\tBryant-Lawrence Potential(Exclusive Window Size %d)\tCrease Energy\n",ZHANG_WINDOWSIZE,BRYANT_WINDOWSIZE);
}
Int2 ImportLL_GOTable(CharPtr filename)
{
/*declarations and initializations*/
FILE *pFile = NULL;
Char line_buffer[MAXLINE];
CharPtr cur_line_ptr = NULL;
CharPtr gi_ptr=NULL;
CharPtr go_ptr=NULL;
CharPtr pmid_ptr=NULL;
Int4 gi = 0;
Int4 go =0;
Int4 pmid = 0;
CharPtr evicode= NULL;
Int2 append_status = 0;
Int4 results_appended=0;
Int4 result_already_found=0;
Int4 append_error=0;
Char daytime[100];
Int4 count=0;
Int4 percent=0;
Int4 step =0;
Int4 z=0;
Int4 max=0;
Int4 i ;
if(!OpenLL_GONoidx("LL_GO")){
printf("OpenTables: OpenLL_GO no indexing failed.");
return 1;
}
printf("LL_GO table opened without indexing. \n");
pFile = FileOpen(filename, "r");
if (pFile == NULL)
{
printf("ImportResult: Failed to open file: %s. ", filename);
return 1;
}
DayTimeStr(daytime, TRUE, TRUE);
printf("Start importing table. [%s].\n",daytime);
cur_line_ptr = fgets(line_buffer, (size_t)100, pFile);
if((Int4)myargs[1].intvalue >0 ) z = (Int4)myargs[1].intvalue;
if((Int4)myargs[2].intvalue >0 ) max = (Int4)myargs[2].intvalue;
step =(Int4) max/100.0;
printf("start from line [ %ld ]; import [ %ld ] lines; step = [ %ld ] \n", z+1, max, step);
for(i=0; i<z; i++)
{
fgets(line_buffer, (size_t)MAXLINE, pFile);
}
if(setvbuf(stdout, NULL, _IONBF, 0))
printf( "Couldn't turn off stdout buffer\n");
printf("%ld", percent);
while (cur_line_ptr && count < max)
{
/*line is split by tabs*/
gi_ptr = strtok(cur_line_ptr, "\t\n");
go_ptr =strtok(NULL, "\t\n");
pmid_ptr = strtok(NULL, "\t\n");
evicode = strtok(NULL, "\t\n");
gi = (Int4)atoi(gi_ptr);
go = (Int4)atoi(go_ptr);
pmid = (Int4)atoi(pmid_ptr);
if(gi <= 0){
printf( "line %d: Invalid gi %d. Record skipped.\n",count+z, gi);
continue;
}
if(go <= 0){
printf( "line %d: Invalid go id: %d.Record skipped.\n", count+z, go );
continue;
}
/*if(pmid <= 0){
ErrPostEx(SEV_ERROR, 0, 0, "LL_Append2GO: Invalid pmid on record with NPID: %d.\nRecord skipped.", NPid);
return LL_ERROR;
}*/
if(evicode == NULL){
printf( "line %d: Invalid E Code . Record skipped.\n", count+z);
continue;
}
/* insert record into RESULT.dbf */
d4appendStart(pD4LL_GO, 0);
d4blank(pD4LL_GO);
f4assignInt(pF4LL_NP_GO, gi);
f4assignInt(pF4LL_GOID, go);
f4assignInt(pF4LL_PMID, pmid);
f4assign(pF4LL_EVICODE, evicode);
append_status = d4append(pD4LL_GO);
switch(append_status){
case r4success:
results_appended++;
break;
case r4unique:
result_already_found++;
break;
default:
printf( "ImportResult failed to append record. append_status = %d", append_status);
append_error++;
}
count++;
if (count%step==0) {
percent++;
printf("\b\b%ld", percent);
}
/*get the next line*/
cur_line_ptr = fgets(line_buffer, (size_t)MAXLINE, pFile);
}
printf("\n==\nappended= %ld; \tpresent= %ld; error= %ld\n\n", (long) results_appended, (long) result_already_found, (long)append_error);
/*close the file*/
FileClose(pFile);
DayTimeStr(daytime, TRUE, TRUE);
printf("Finished importing RESULT table. [%s]\n", daytime);
if((Boolean)myargs[3].intvalue == TRUE) {
printf("Start rebuilding index ... [%s]\n", daytime);
if(ReindexLL_GO()==FALSE){
printf("reindex RESULT table error \n");
return 1;
};
DayTimeStr(daytime, TRUE, TRUE);
printf("Finished rebuilding index. [%s]\n", daytime);
}
/* close RESULT table */
if(d4close(pD4LL_GO) != r4success) return 1;
return 0;
}
