int main (int argc, char **argv) {
void *argtable[] = {
help = arg_lit0("h","help","print this screen"),
verbose = arg_lit0("v","verbose","tell me everything"),
fsyslog = arg_lit0(NULL,"syslog","use syslog"),
cachepath = arg_file1(NULL,NULL,"cachepath","directory or .cdb database file"),
netaddress0 = arg_file1(NULL,NULL,"read_address","zmq read network address"),
netaddress1 = arg_file1(NULL,NULL,"write_address","zmq write network address"),
end = arg_end(20),
};
int32_t nerrors = arg_parse(argc,argv,argtable);
if (help->count) {
fprintf(stdout,"tmpcache %s - version 0\n",__FUNCTION__);
arg_print_syntaxv(stdout,argtable,"\n\n");
arg_print_glossary (stdout,argtable,"%-25s %s\n");
goto finish;
}
if (verbose->count) {
fprintf(stdout,"tmpcache host - version 0\n");
int32_t major,minor,patch;
zmq_version (&major,&minor,&patch);
fprintf(stdout,"compiled with zmq support %d.%d.%d\n",major,minor,patch);
goto finish;
}
if (nerrors) {
arg_print_errors (stdout,end,"");
arg_print_syntaxv(stdout,argtable,"\n\n");
goto finish;
}
u_term = 0;
signal (SIGINT,signalhandler);
signal (SIGTERM,signalhandler);
if (fsyslog->count)
openlog (NULL,LOG_PID|LOG_NDELAY,LOG_USER);
void *read (void *arg) {
tc_readconfig_t *config = (tc_readconfig_t *)arg;
if (fsyslog->count)
syslog (LOG_INFO,"reading cache from %s @ %s",btocstr(config->cachepath),btocstr(config->address));
tc_readfromcache (config);
if (fsyslog->count)
syslog (LOG_INFO,"closing cache %s @ %s for reading",btocstr(config->cachepath),btocstr(config->address));
}
int main(int argc, char* argv[])
{
// Setup.
AppLib::Logging::setApplicationName(std::string("apputil"));
struct arg_file *script = arg_file1(NULL, NULL, "script", "the path of the script to execute");
struct arg_end *end = arg_end(20);
void *argtable[] = { script, end };
script->filename[0] = NULL;
// Check to see if the argument definitions were allocated
// correctly.
if (arg_nullcheck(argtable))
{
AppLib::Logging::showErrorW("Insufficient memory.");
return 1;
}
// Now parse the arguments.
int nerrors = arg_parse(argc, argv, argtable);
// Check to see if there were errors.
if (nerrors > 0 && script->filename[0] == NULL)
{
printf("Usage: apputil");
arg_print_syntax(stdout, argtable, "\n");
arg_print_errors(stdout, end, "apputil");
printf("AppUtil - The application scripting utility.\n\n");
arg_print_glossary(stdout, argtable, " %-25s %s\n");
return 1;
}
// Execute.
return runPython(script->filename[0], argc, argv);
}
/*
* All code below is "unimportant", it's only argument and file handling
*/
int main(int argc, char *argv[]) {
struct arg_file *ifile = arg_file1("i", "input-file", "INPUT_FILE", "Set Input File");
struct arg_file *ofile = arg_file0("o", "output-file", "OUTPUT_FILE", "Set Output File");
struct arg_str *pass = arg_str0("p", "password", "PASSWORD", "Set Encryption Password");
struct arg_int *pas = arg_int0("c", "passes", "PASSES", "Set number of passes (To decrypt you'll need the same number of passes)");
struct arg_int *buf = arg_int0("b", "buffer-size", "BUFFER_SIZE", "Set Buffer Size");
struct arg_end *end = arg_end(20);
void *argtable[] = {
ifile, ofile, pass, pas, buf, end};
int nerrors = arg_parse(argc, argv, argtable);
if (nerrors > 0) {
arg_print_errors(stdout, end, "rxe");
printf("\nUsage: rxe");
arg_print_syntax(stdout, argtable, "\n");
arg_print_glossary(stdout, argtable, " %-10s %s\n");
} else {
if (buf->count > 0) {
BUFFER_SIZE = buf->ival[0];
}
FILE *outfile, *infile = fopen(ifile->filename[0], "rb");
if (ofile->count > 0) outfile = fopen(ofile->filename[0], "wb");
else {
char farr[2048];
char *ptr;
strcpy(farr, ifile->filename[0]);
if ((ptr = strstr(farr, ".rxe")) != NULL) {
farr[0] = '\0';
farr[1] = '\0';
farr[2] = '\0';
farr[3] = '\0';
} else strcat(farr, ".rxe");
outfile = fopen(farr, "wb");
}
if(pas->count > 0) PASSES = pas->ival[0];
if(pass->count > 0) RXE_Main(infile, outfile, (char *)pass->sval[0]);
else RXE_Main(infile, outfile, "DEFAULT");
fclose(outfile);
fclose(infile);
}
return 0;
}
void test_argfile_basic_003(CuTest* tc) {
struct arg_file* a = arg_file1(NULL, NULL, "<file>", "filename to test");
struct arg_end* end = arg_end(20);
void* argtable[] = {a, end};
int nerrors;
char* argv[] = {"program", "./foo.bar", NULL};
int argc = sizeof(argv) / sizeof(char*) - 1;
CuAssertTrue(tc, arg_nullcheck(argtable) == 0);
nerrors = arg_parse(argc, argv, argtable);
CuAssertTrue(tc, nerrors == 0);
CuAssertTrue(tc, a->count == 1);
CuAssertStrEquals(tc, a->filename[0], "./foo.bar");
CuAssertStrEquals(tc, a->basename[0], "foo.bar");
CuAssertStrEquals(tc, a->extension[0], ".bar");
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
}
int _tmain(int argc, char* argv[])
{
// determine my process name
_splitpath(argv[0],NULL,NULL,gszProcName,NULL);
#else
int
main(int argc, const char** argv)
{
// determine my process name
CUtility::splitpath((char *)argv[0],NULL,gszProcName);
#endif
int iScreenLogLevel; // level of screen diagnostics
int iFileLogLevel; // level of file diagnostics
char szLogFile[_MAX_PATH]; // write diagnostics to this file
int Rslt;
bool bSkipFirst; // true if first line contains header and should be skipped
int iMinLength; // core elements must be of at least this length
int iMaxLength; // and no longer than this length
char szInLociFile[_MAX_PATH]; // input element loci from this file
char szInSeqFile[_MAX_PATH]; // input bioseq file containing assembly
char szRsltsFile[_MAX_PATH]; // output stats to this file
// command line args
struct arg_lit *help = arg_lit0("hH","help", "print this help and exit");
struct arg_lit *version = arg_lit0("v","version,ver", "print version information and exit");
struct arg_int *FileLogLevel=arg_int0("f", "FileLogLevel", "<int>","Level of diagnostics written to logfile 0=fatal,1=errors,2=info,3=diagnostics,4=debug");
struct arg_int *ScreenLogLevel=arg_int0("S", "ScreenLogLevel", "<int>","Level of diagnostics written to logfile 0=fatal,1=errors,2=info,3=diagnostics,4=debug");
struct arg_file *LogFile = arg_file0("F","log","<file>", "diagnostics log file");
struct arg_file *InLociFile = arg_file1("i","inloci","<file>", "element loci CSV file");
struct arg_file *InSeqFile = arg_file1("I","assembly","<file>", "genome assembly bioseq file");
struct arg_file *RsltsFile = arg_file1("o","output","<file>", "output file");
struct arg_lit *SkipFirst = arg_lit0("x","skipfirst", "skip first line of CSV - header line");
struct arg_int *MinLength = arg_int0("l","minlength","<int>", "minimum element length (default 10)");
struct arg_int *MaxLength = arg_int0("L","maxlength","<int>", "maximum element length (default 1000000000)");
struct arg_end *end = arg_end(20);
void *argtable[] = {help,version,FileLogLevel,ScreenLogLevel,LogFile,
InLociFile,InSeqFile,RsltsFile,SkipFirst,MinLength,MaxLength,
end};
char **pAllArgs;
int argerrors;
argerrors = CUtility::arg_parsefromfile(argc,(char **)argv,&pAllArgs);
if(argerrors >= 0)
argerrors = arg_parse(argerrors,pAllArgs,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0)
{
printf("\n%s csv2stats, Version %s\nOptions ---\n", gszProcName,cpszProgVer);
arg_print_syntax(stdout,argtable,"\n");
arg_print_glossary(stdout,argtable," %-25s %s\n");
printf("\nNote: Parameters can be entered into a parameter file, one parameter per line.");
printf("\n To invoke this parameter file then precede its name with '@'");
printf("\n e.g. %s @myparams.txt\n\n",gszProcName);
exit(1);
}
/* special case: '--version' takes precedence error reporting */
if (version->count > 0)
{
printf("\n%s Version %s\n",gszProcName,cpszProgVer);
exit(1);
}
if (!argerrors)
{
if(FileLogLevel->count && !LogFile->count)
{
printf("\nError: FileLogLevel '-f%d' specified but no logfile '-F<logfile>'",FileLogLevel->ival[0]);
exit(1);
}
iScreenLogLevel = iFileLogLevel = FileLogLevel->count ? FileLogLevel->ival[0] : eDLInfo;
if(iFileLogLevel < eDLNone || iFileLogLevel > eDLDebug)
{
printf("\nError: FileLogLevel '-l%d' specified outside of range %d..%d",iFileLogLevel,eDLNone,eDLDebug);
exit(1);
}
if(LogFile->count)
{
strncpy(szLogFile,LogFile->filename[0],_MAX_PATH);
szLogFile[_MAX_PATH-1] = '\0';
}
else
{
iFileLogLevel = eDLNone;
szLogFile[0] = '\0';
}
bSkipFirst = SkipFirst->count ? true : false;
iMinLength = MinLength->count ? MinLength->ival[0] : cDfltMinLengthRange;
if(iMinLength < 1 || iMinLength > cMaxLengthRange)
{
printf("Error: Mininum element length '-l%d' is not in range 1..%d",iMinLength,cMaxLengthRange);
exit(1);
}
iMaxLength = MaxLength->count ? MaxLength->ival[0] : cMaxLengthRange;
if(iMaxLength < iMinLength || iMaxLength > cMaxLengthRange)
{
printf("Error: Maximum element length '-L%d' is not in range %d..%d",iMaxLength,iMinLength,cMaxLengthRange);
exit(1);
}
strncpy(szInLociFile,InLociFile->filename[0],_MAX_PATH);
szInLociFile[_MAX_PATH-1] = '\0';
strncpy(szInSeqFile,InSeqFile->filename[0],_MAX_PATH);
szInSeqFile[_MAX_PATH-1] = '\0';
strncpy(szRsltsFile,RsltsFile->filename[0],_MAX_PATH);
szRsltsFile[_MAX_PATH-1] = '\0';
// now that command parameters have been parsed then initialise diagnostics log system
if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
{
printf("\nError: Unable to start diagnostics subsystem.");
if(szLogFile[0] != '\0')
printf(" Most likely cause is that logfile '%s' can't be opened/created",szLogFile);
exit(1);
}
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Version: %s Processing parameters:",cpszProgVer);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Input CSV element loci file: '%s'",szInLociFile);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Input bioseq genome assembly file: '%s'",szInSeqFile);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output to file: '%s'",szRsltsFile);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"First line contains header: %s",bSkipFirst ? "yes" : "no");
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Minimum element length: %d",iMinLength);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Maximum element length: %d",iMaxLength);
#ifdef _WIN32
SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif
// processing here...
Rslt = Process(bSkipFirst,iMinLength,iMaxLength,szInLociFile,szInSeqFile,szRsltsFile);
gStopWatch.Stop();
Rslt = Rslt >=0 ? 0 : 1;
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
exit(Rslt);
}
else
{
printf("\n%s csv2stats, Version %s\n",gszProcName,cpszProgVer);
arg_print_errors(stdout,end,gszProcName);
arg_print_syntax(stdout,argtable,"\nUse '-h' to view option and parameter usage\n");
exit(1);
}
}
int genkmarkers(int argc, char* argv[])
{
// determine my process name
_splitpath(argv[0],NULL,NULL,gszProcName,NULL);
#else
int
genkmarkers(int argc, char** argv)
{
// determine my process name
CUtility::splitpath((char *)argv[0],NULL,gszProcName);
#endif
int iScreenLogLevel; // level of screen diagnostics
int iFileLogLevel; // level of file diagnostics
char szLogFile[_MAX_PATH]; // write diagnostics to this file
int Rslt = 0; // function result code >= 0 represents success, < 0 on failure
int NumberOfProcessors; // number of installed CPUs
int NumThreads; // number of threads (0 defaults to number of CPUs)
int PMode; // processing mode
int KMerLen; // this length K-mers
int PrefixLen; // inter-cultivar shared prefix length
int SuffixLen; // cultivar specific suffix length
int MinWithPrefix; // minimum number of cultivars required to have the shared prefix
int MinHamming; // must be at least this Hamming away from any other K-mer in other species
char szCultivarName[cMaxDatasetSpeciesChrom+1]; // cultivar name
char szPartialCultivarsList[(cMaxDatasetSpeciesChrom + 10) * cMaxTargCultivarChroms]; // individual species parsed from this comma/tab/space separated list
int NumPartialCultivars; // there are this many pseudo chromosomes for targeted cultivar for which K-mer markers are required
char *pszPartialCultivars[cMaxTargCultivarChroms+1]; // pseudo chromosome names which identify targeted cultivar
char szSfxPseudoGenome[_MAX_PATH]; // contains assembly + suffix array over all psuedo-chromosomes for all cultivars
char szMarkerFile[_MAX_PATH]; // output potential markers to this file
char szMarkerReadsFile[_MAX_PATH]; // output reads containing potential markers to this file
char szSQLiteDatabase[_MAX_PATH]; // results summaries to this SQLite file
char szExperimentName[cMaxDatasetSpeciesChrom+1]; // experiment name
char szExperimentDescr[1000]; // describes experiment
// command line args
struct arg_lit *help = arg_lit0("h","help", "Print this help and exit");
struct arg_lit *version = arg_lit0("v","version,ver", "Print version information and exit");
struct arg_int *FileLogLevel=arg_int0("f", "FileLogLevel", "<int>","Level of diagnostics written to screen and logfile 0=fatal,1=errors,2=info,3=diagnostics,4=debug");
struct arg_file *LogFile = arg_file0("F","log","<file>", "Diagnostics log file");
struct arg_int *pmode = arg_int0("m","mode","<int>", "Processing mode : 0 - default with K-mer extension, 1 - no K-mer extension, 2 - inter-cultivar shared prefix sequences ");
struct arg_int *kmerlen = arg_int0("k","kmer","<int>", "Cultivar specific K-mers of this length (default 50, range 25..100)");
struct arg_int *prefixlen = arg_int0("p","prefixlen","<int>", "Cultivar specific K-mers to contain inter-cultivar shared prefix sequences of this length (Mode 2 only");
struct arg_int *minwithprefix = arg_int0("s","minshared","<int>","Inter-cultivar shared prefix sequences must be present in this many cultivars (Mode 2 only, default all)");
struct arg_int *minhamming = arg_int0("K","minhamming","<int>", "Minimum Hamming separation distance in other non-target cultivars (default 2, range 1..5)");
struct arg_str *cultivar = arg_str1("c","cultivar","<str>", "Cultivar name to associate with identified marker K-mers");
struct arg_str *chromnames = arg_str1("C","chromnames","<str>", "Comma/space separated list of pseudo-chrom names specific to cultivar for which markers are required");
struct arg_file *infile = arg_file1("i","in","<file>", "Use this suffix indexed pseudo-chromosomes file");
struct arg_file *outfile = arg_file1("o","markers","<file>", "Output accepted marker K-mer sequences to this multifasta file");
struct arg_file *outreadsfile = arg_file0("O","markerreads","<file>", "Output reads containing accepted marker K-mers to this multifasta file");
struct arg_int *numthreads = arg_int0("T","threads","<int>", "number of processing threads 0..128 (defaults to 0 which sets threads to number of CPU cores)");
struct arg_file *summrslts = arg_file0("q","sumrslts","<file>", "Output results summary to this SQLite3 database file");
struct arg_str *experimentname = arg_str0("w","experimentname","<str>", "experiment name SQLite3 database file");
struct arg_str *experimentdescr = arg_str0("W","experimentdescr","<str>", "experiment description SQLite3 database file");
struct arg_end *end = arg_end(200);
void *argtable[] = {help,version,FileLogLevel,LogFile,
summrslts,experimentname,experimentdescr,
pmode,kmerlen,prefixlen,minwithprefix,minhamming,cultivar,chromnames,infile,outfile,outreadsfile,
numthreads,
end};
char **pAllArgs;
int argerrors;
argerrors = CUtility::arg_parsefromfile(argc,(char **)argv,&pAllArgs);
if(argerrors >= 0)
argerrors = arg_parse(argerrors,pAllArgs,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0)
{
printf("\n%s %s %s, Version %s\nOptions ---\n", gszProcName,gpszSubProcess->pszName,gpszSubProcess->pszFullDescr,cpszProgVer);
arg_print_syntax(stdout,argtable,"\n");
arg_print_glossary(stdout,argtable," %-25s %s\n");
printf("\nNote: Parameters can be entered into a parameter file, one parameter per line.");
printf("\n To invoke this parameter file then precede its name with '@'");
printf("\n e.g. %s %s @myparams.txt\n",gszProcName,gpszSubProcess->pszName);
printf("\nPlease report any issues regarding usage of %s at https://github.com/csiro-crop-informatics/biokanga/issues\n\n",gszProcName);
return(1);
}
/* special case: '--version' takes precedence error reporting */
if (version->count > 0)
{
printf("\n%s %s Version %s\n",gszProcName,gpszSubProcess->pszName,cpszProgVer);
return(1);
}
if (!argerrors)
{
if(FileLogLevel->count && !LogFile->count)
{
printf("\nError: FileLogLevel '-f%d' specified but no logfile '-F<logfile>\n'",FileLogLevel->ival[0]);
return(1);
}
iScreenLogLevel = iFileLogLevel = FileLogLevel->count ? FileLogLevel->ival[0] : eDLInfo;
if(iFileLogLevel < eDLNone || iFileLogLevel > eDLDebug)
{
printf("\nError: FileLogLevel '-l%d' specified outside of range %d..%d\n",iFileLogLevel,eDLNone,eDLDebug);
return(1);
}
if(LogFile->count)
{
strncpy(szLogFile,LogFile->filename[0],_MAX_PATH);
szLogFile[_MAX_PATH-1] = '\0';
}
else
{
iFileLogLevel = eDLNone;
szLogFile[0] = '\0';
}
// now that log parameters have been parsed then initialise diagnostics log system
if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
{
printf("\nError: Unable to start diagnostics subsystem\n");
if(szLogFile[0] != '\0')
printf(" Most likely cause is that logfile '%s' can't be opened/created\n",szLogFile);
return(1);
}
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Subprocess %s Version %s starting",gpszSubProcess->pszName,cpszProgVer);
gExperimentID = 0;
gProcessID = 0;
gProcessingID = 0;
szSQLiteDatabase[0] = '\0';
szExperimentName[0] = '\0';
szExperimentDescr[0] = '\0';
if(experimentname->count)
{
strncpy(szExperimentName,experimentname->sval[0],sizeof(szExperimentName));
szExperimentName[sizeof(szExperimentName)-1] = '\0';
CUtility::TrimQuotedWhitespcExtd(szExperimentName);
CUtility::ReduceWhitespace(szExperimentName);
}
else
szExperimentName[0] = '\0';
gExperimentID = 0;
gProcessID = 0;
gProcessingID = 0;
szSQLiteDatabase[0] = '\0';
szExperimentDescr[0] = '\0';
if(summrslts->count)
{
strncpy(szSQLiteDatabase,summrslts->filename[0],sizeof(szSQLiteDatabase)-1);
szSQLiteDatabase[sizeof(szSQLiteDatabase)-1] = '\0';
CUtility::TrimQuotedWhitespcExtd(szSQLiteDatabase);
if(strlen(szSQLiteDatabase) < 1)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: After removal of whitespace, no SQLite database specified with '-q<filespec>' option");
return(1);
}
if(strlen(szExperimentName) < 1)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: After removal of whitespace, no SQLite experiment name specified with '-w<str>' option");
return(1);
}
if(experimentdescr->count)
{
strncpy(szExperimentDescr,experimentdescr->sval[0],sizeof(szExperimentDescr)-1);
szExperimentDescr[sizeof(szExperimentDescr)-1] = '\0';
CUtility::TrimQuotedWhitespcExtd(szExperimentDescr);
}
if(strlen(szExperimentDescr) < 1)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: After removal of whitespace, no SQLite experiment description specified with '-W<str>' option");
return(1);
}
gExperimentID = gSQLiteSummaries.StartExperiment(szSQLiteDatabase,false,true,szExperimentName,szExperimentName,szExperimentDescr);
if(gExperimentID < 1)
return(1);
gProcessID = gSQLiteSummaries.AddProcess((char *)gpszSubProcess->pszName,(char *)gpszSubProcess->pszName,(char *)gpszSubProcess->pszFullDescr);
if(gProcessID < 1)
return(1);
gProcessingID = gSQLiteSummaries.StartProcessing(gExperimentID,gProcessID,(char *)cpszProgVer);
if(gProcessingID < 1)
return(1);
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Initialised SQLite database '%s' for results summary collection",szSQLiteDatabase);
gDiagnostics.DiagOut(eDLInfo,gszProcName,"SQLite database experiment identifier for '%s' is %d",szExperimentName,gExperimentID);
gDiagnostics.DiagOut(eDLInfo,gszProcName,"SQLite database process identifier for '%s' is %d",(char *)gpszSubProcess->pszName,gProcessID);
gDiagnostics.DiagOut(eDLInfo,gszProcName,"SQLite database processing instance identifier is %d",gProcessingID);
}
else
{
szSQLiteDatabase[0] = '\0';
szExperimentDescr[0] = '\0';
}
// show user current resource limits
#ifndef _WIN32
gDiagnostics.DiagOut(eDLInfo, gszProcName, "Resources: %s",CUtility::ReportResourceLimits());
#endif
#ifdef _WIN32
SYSTEM_INFO SystemInfo;
GetSystemInfo(&SystemInfo);
NumberOfProcessors = SystemInfo.dwNumberOfProcessors;
#else
NumberOfProcessors = sysconf(_SC_NPROCESSORS_CONF);
#endif
int MaxAllowedThreads = min(cMaxWorkerThreads,NumberOfProcessors); // limit to be at most cMaxWorkerThreads
if((NumThreads = numthreads->count ? numthreads->ival[0] : MaxAllowedThreads)==0)
NumThreads = MaxAllowedThreads;
if(NumThreads < 0 || NumThreads > MaxAllowedThreads)
{
gDiagnostics.DiagOut(eDLWarn,gszProcName,"Warning: Number of threads '-T%d' specified was outside of range %d..%d",NumThreads,1,MaxAllowedThreads);
gDiagnostics.DiagOut(eDLWarn,gszProcName,"Warning: Defaulting number of threads to %d",MaxAllowedThreads);
NumThreads = MaxAllowedThreads;
}
PMode = (etPMode)(pmode->count ? pmode->ival[0] : ePMExtdKMers);
if(PMode < ePMExtdKMers || PMode >= ePMplaceholder)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Processing mode '-m%d' specified outside of range %d..%d\n",PMode,ePMExtdKMers,(int)ePMplaceholder-1);
exit(1);
}
KMerLen = kmerlen->count ? kmerlen->ival[0] : cDfltKMerLen;
if(KMerLen < cMinKMerLen || KMerLen > cMaxKMerLen)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: K-mer core length '-k%d' must be in range %d..%d",KMerLen,cMinKMerLen,cMaxKMerLen);
return(1);
}
if(PMode == 2)
{
PrefixLen = prefixlen->count ? prefixlen->ival[0] : KMerLen/2;
if(PrefixLen < cMinKMerLen/2 || PrefixLen > KMerLen-(cMinKMerLen/2))
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Prefix length '-p%d' must be in range %d..%d",KMerLen,cMinKMerLen/2,KMerLen-(cMinKMerLen/2));
return(1);
}
SuffixLen = KMerLen - PrefixLen;
MinWithPrefix = minwithprefix->count ? minwithprefix->ival[0] : 0;
if(MinWithPrefix != 0 && MinWithPrefix < 1)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Minimum cultivars sharing prefix sequence '-s%d' must be either 0 (all) or at least 1",MinWithPrefix);
return(1);
}
}
MinHamming = minhamming->count ? minhamming->ival[0] : cDfltHamming;
if(MinHamming < cMinHamming || MinHamming > cMaxHamming)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Minimum Hamming separation '-K%d' must be in range %d..%d",MinHamming,cMinHamming,cMaxHamming);
return(1);
}
strncpy(szCultivarName,cultivar->sval[0],cMaxDatasetSpeciesChrom);
szCultivarName[cMaxDatasetSpeciesChrom]= '\0';
CUtility::TrimQuotedWhitespcExtd(szCultivarName);
if(strlen(szCultivarName) < 1)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Expected cultivar name '-c<name>' is empty");
return(1);
}
strncpy(szPartialCultivarsList,chromnames->sval[0],sizeof(szPartialCultivarsList));
szPartialCultivarsList[sizeof(szPartialCultivarsList)-1] = '\0';
CUtility::TrimQuotedWhitespcExtd(szPartialCultivarsList);
CUtility::ReduceWhitespace(szPartialCultivarsList);
char *pChr = szPartialCultivarsList;
char *pStartChr;
char Chr;
int CurSpeciesLen;
NumPartialCultivars=0;
CurSpeciesLen = 0;
pStartChr = pChr;
while((Chr = *pChr++) != '\0')
{
if(Chr == ' ' || Chr == '\t' || Chr == ',') // treat any of these as delimiters
{
pChr[-1] = '\0';
if(CurSpeciesLen != 0)
{
pszPartialCultivars[NumPartialCultivars++] = pStartChr;
CurSpeciesLen = 0;
}
pStartChr = pChr;
continue;
}
CurSpeciesLen += 1;
}
if(CurSpeciesLen)
pszPartialCultivars[NumPartialCultivars++] = pStartChr;
if(!NumPartialCultivars)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Expected at least one ('-C<names>') targeted cultivar chromosme name");
return(1);
}
strcpy(szSfxPseudoGenome,infile->filename[0]);
CUtility::TrimQuotedWhitespcExtd(szSfxPseudoGenome);
if(strlen(szSfxPseudoGenome) < 1)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Expected input pseudo-genome suffix array filename '-i<name>' is empty");
return(1);
}
strcpy(szMarkerFile,outfile->filename[0]);
CUtility::TrimQuotedWhitespcExtd(szMarkerFile);
if(strlen(szMarkerFile) < 1)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Expected marker file to generate filename '-o<name>' is empty");
return(1);
}
if(outreadsfile->count)
{
strcpy(szMarkerReadsFile,outreadsfile->filename[0]);
CUtility::TrimQuotedWhitespcExtd(szMarkerReadsFile);
if(strlen(szMarkerReadsFile) < 1)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Reads containing markers filename '-O<name>' is empty");
return(1);
}
}
else
szMarkerReadsFile[0] = '\0';
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Processing parameters:");
const char *pszDescr;
switch(PMode) {
case ePMExtdKMers:
pszDescr = "Extended K-mer markers";
break;
case ePMNoExtdKMers:
pszDescr = "Non-extended K-mer markers";
break;
case ePMPrefixKMers:
pszDescr = "K-mers to share prefix sequence with other cultivars";
break;
}
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Processing mode is : '%s'",pszDescr);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Targeted cultivar name : '%s'",szCultivarName);
for(int Idx = 0; Idx < NumPartialCultivars; Idx++)
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Targeted cultivar chromosome name (%d) : '%s'", Idx + 1,pszPartialCultivars[Idx]);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Core K-mer length : %d",KMerLen);
if(PMode == ePMPrefixKMers)
{
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Inter-cultivar shared prefix sequence length : %d",PrefixLen);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Cultivar specific suffix sequence length : %d",SuffixLen);
if(MinWithPrefix)
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Min number cultivars sharing prefix : %d",MinWithPrefix);
else
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Min number cultivars sharing prefix : 'All'");
}
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Minimum Hamming separation : %d",MinHamming);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Input indexed pseudo-genome file: '%s'",szSfxPseudoGenome);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Write marker K-mers to file: '%s'",szMarkerFile);
if(szMarkerReadsFile[0] != '\0')
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Write marker containing reads to file: '%s'",szMarkerReadsFile);
if(szExperimentName[0] != '\0')
gDiagnostics.DiagOutMsgOnly(eDLInfo,"This processing reference: %s",szExperimentName);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Number of processing threads: %d",NumThreads);
if(gExperimentID > 0)
{
int ParamID;
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTText,(int)strlen(szLogFile),"log",szLogFile);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTInt32,sizeof(PMode),"mode",&PMode);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTInt32,sizeof(KMerLen),"kmer",&KMerLen);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTInt32,sizeof(PrefixLen),"prefixlen",&PrefixLen);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTInt32,sizeof(SuffixLen),"suffixlen",&SuffixLen);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTInt32,sizeof(MinWithPrefix),"minwithprefix",&MinWithPrefix);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTInt32,sizeof(MinHamming),"minhamming",&MinHamming);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTInt32,sizeof(NumThreads),"threads",&NumThreads);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTInt32,sizeof(NumberOfProcessors),"cpus",&NumberOfProcessors);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTText,(int)strlen(szCultivarName),"cultivar",szCultivarName);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTInt32,sizeof(NumPartialCultivars),"NumPartialCultivars",&NumPartialCultivars);
for(int Idx = 0; Idx < NumPartialCultivars; Idx++)
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTText,(int)strlen(pszPartialCultivars[Idx]),"chromnames",pszPartialCultivars[Idx]);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTText,(int)strlen(szSfxPseudoGenome),"in",szSfxPseudoGenome);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTText,(int)strlen(szMarkerFile),"markers",szMarkerFile);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTText,(int)strlen(szMarkerReadsFile),"markerreads",szMarkerReadsFile);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTText,(int)strlen(szSQLiteDatabase),"sumrslts",szSQLiteDatabase);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTText,(int)strlen(szExperimentName),"experimentname",szExperimentName);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTText,(int)strlen(szExperimentDescr),"experimentdescr",szExperimentDescr);
}
#ifdef _WIN32
SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif
gStopWatch.Start();
Rslt = LocMarkers((etPMode)PMode,KMerLen,PrefixLen,SuffixLen,MinWithPrefix,MinHamming,szCultivarName,NumPartialCultivars,pszPartialCultivars,szSfxPseudoGenome,szMarkerFile,szMarkerReadsFile,NumThreads);
Rslt = Rslt >=0 ? 0 : 1;
if(gExperimentID > 0)
{
if(gProcessingID)
gSQLiteSummaries.EndProcessing(gProcessingID,Rslt);
gSQLiteSummaries.EndExperiment(gExperimentID);
}
gStopWatch.Stop();
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
return(Rslt);
}
else
{
printf("\n%s %s %s, Version %s\n", gszProcName,gpszSubProcess->pszName,gpszSubProcess->pszFullDescr,cpszProgVer);
arg_print_errors(stdout,end,gszProcName);
arg_print_syntax(stdout,argtable,"\nUse '-h' to view option and parameter usage\n");
return(1);
}
return 0;
}
int main(int argc, char *argv[]) {
int retcode = 1;
int nerrors = 0;
streamer_t streamer;
memset(&streamer, 0, sizeof(streamer_t));
// Signal handlers
signal(SIGINT, sig_fn);
signal(SIGTERM, sig_fn);
// Initialize SDL2
if (SDL_Init(SDL_INIT_AUDIO) != 0) {
fprintf(stderr, "%s\n", SDL_GetError());
return 1;
}
// Defaults
streamer.freq = 44100;
streamer.n_channels = 2;
streamer.bits = 16;
streamer.volume = 1.0f;
streamer.quality = DUMB_RQ_CUBIC;
// commandline argument parser options
struct arg_lit *arg_help =
arg_lit0("h", "help", "print this help and exits");
struct arg_dbl *arg_volume =
arg_dbl0("v", "volume", "<volume",
"sets the output volume (-8.0 to +8.0, default 1.0)");
struct arg_int *arg_samplerate = arg_int0(
"s", "samplerate", "<freq>", "sets the sampling rate (default 44100)");
struct arg_int *arg_quality = arg_int0(
"r", "quality", "<quality>", "specify the resampling quality to use");
struct arg_lit *arg_mono =
arg_lit0("m", "mono", "generate mono output instead of stereo");
struct arg_lit *arg_eight =
arg_lit0("8", "eight", "generate 8-bit instead of 16-bit");
struct arg_lit *arg_noprogress =
arg_lit0("n", "noprogress", "hide progress bar");
struct arg_file *arg_output =
arg_file0("o", "output", "<file>", "output file");
struct arg_file *arg_input =
arg_file1(NULL, NULL, "<file>", "input module file");
struct arg_end *arg_fend = arg_end(20);
void *argtable[] = {arg_help, arg_input, arg_volume,
arg_samplerate, arg_quality, arg_mono,
arg_eight, arg_noprogress, arg_fend};
const char *progname = "dumbplay";
// Make sure everything got allocated
if (arg_nullcheck(argtable) != 0) {
fprintf(stderr, "%s: insufficient memory\n", progname);
goto exit_0;
}
// Parse inputs
nerrors = arg_parse(argc, argv, argtable);
// Handle help
if (arg_help->count > 0) {
fprintf(stderr, "Usage: %s", progname);
arg_print_syntax(stderr, argtable, "\n");
fprintf(stderr, "\nArguments:\n");
arg_print_glossary(stderr, argtable, "%-25s %s\n");
goto exit_0;
}
// Handle libargtable errors
if (nerrors > 0) {
arg_print_errors(stderr, arg_fend, progname);
fprintf(stderr, "Try '%s --help' for more information.\n", progname);
goto exit_0;
}
// Handle the switch options
streamer.input = arg_input->filename[0];
if (arg_eight->count > 0) {
streamer.bits = 8;
}
if (arg_mono->count > 0) {
streamer.n_channels = 1;
}
if (arg_noprogress->count > 0) {
streamer.no_progress = true;
}
if (arg_volume->count > 0) {
streamer.volume = arg_volume->dval[0];
if (streamer.volume < -8.0f || streamer.volume > 8.0f) {
fprintf(stderr, "Volume must be between -8.0f and 8.0f.\n");
goto exit_0;
}
}
if (arg_samplerate->count > 0) {
streamer.freq = arg_samplerate->ival[0];
if (streamer.freq < 1 || streamer.freq > 96000) {
fprintf(stderr, "Sampling rate must be between 1 and 96000.\n");
goto exit_0;
}
}
if (arg_quality->count > 0) {
streamer.quality = arg_quality->ival[0];
if (streamer.quality < 0 || streamer.quality >= DUMB_RQ_N_LEVELS) {
fprintf(stderr, "Quality must be between %d and %d.\n", 0,
DUMB_RQ_N_LEVELS - 1);
goto exit_0;
}
}
// Load source file.
dumb_register_stdfiles();
streamer.src = dumb_load_any(streamer.input, 0, 0);
if (!streamer.src) {
fprintf(stderr, "Unable to load file %s for playback!\n",
streamer.input);
goto exit_0;
}
// Set up playback
streamer.renderer =
duh_start_sigrenderer(streamer.src, 0, streamer.n_channels, 0);
streamer.delta = 65536.0f / streamer.freq;
streamer.sbytes = (streamer.bits / 8) * streamer.n_channels;
streamer.ssize = duh_get_length(streamer.src);
// Stop producing samples on module end
DUMB_IT_SIGRENDERER *itsr = duh_get_it_sigrenderer(streamer.renderer);
dumb_it_set_loop_callback(itsr, &dumb_it_callback_terminate, NULL);
dumb_it_set_xm_speed_zero_callback(itsr, &dumb_it_callback_terminate, NULL);
dumb_it_set_resampling_quality(itsr, streamer.quality);
// Set up the SDL2 format we want for playback.
SDL_AudioSpec want;
SDL_zero(want);
want.freq = streamer.freq;
want.format = (streamer.bits == 16) ? AUDIO_S16 : AUDIO_S8;
want.channels = streamer.n_channels;
want.samples = SAMPLES;
want.callback = stream_audio;
want.userdata = &streamer;
// Find SDL2 audio device, and request the format we just set up.
// SDL2 will tell us what we got in the "have" struct.
SDL_AudioSpec have;
streamer.dev = SDL_OpenAudioDevice(NULL, 0, &want, &have, 0);
if (streamer.dev == 0) {
fprintf(stderr, "%s\n", SDL_GetError());
goto exit_1;
}
// Make sure we got the format we wanted. If not, stop here.
if (have.format != want.format) {
fprintf(stderr, "Could not get correct playback format.\n");
goto exit_2;
}
// Play file
SDL_PauseAudioDevice(streamer.dev, 0);
// Show initial state of the progress bar (if it is enabled)
int time_start = SDL_GetTicks();
float seek = 0.0f;
int ms_played = 0;
if (!streamer.no_progress) {
show_progress(PROGRESSBAR_LENGTH, seek, ms_played);
}
// Loop while dumb is still giving data. Update progressbar if enabled.
while (!stop_signal && !streamer.ended) {
if (!streamer.no_progress) {
seek = ((float)streamer.spos) / ((float)streamer.ssize);
ms_played = SDL_GetTicks() - time_start;
show_progress(PROGRESSBAR_LENGTH, seek, ms_played);
}
SDL_Delay(100);
}
// We made it this far without crashing, so let's just exit with no error :)
retcode = 0;
// Free up resources and exit.
if (streamer.sig_samples) {
destroy_sample_buffer(streamer.sig_samples);
}
exit_2:
SDL_CloseAudioDevice(streamer.dev);
exit_1:
if (streamer.renderer) {
duh_end_sigrenderer(streamer.renderer);
}
if (streamer.src) {
unload_duh(streamer.src);
}
exit_0:
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
SDL_Quit();
return retcode;
}
int main(int argc, char* argv[]) {
// commandline argument parser options
struct arg_lit *help = arg_lit0("h", "help", "print this help and exit");
struct arg_lit *vers = arg_lit0("v", "version", "print version information and exit");
struct arg_file *file = arg_file1("f", "file", "<file>", "font file");
struct arg_int *fh = arg_int1("g", "height", "<value>", "font height in pixels (6 or 8)");
struct arg_str *text = arg_str0("t", "text", "<value>", "text to show");
struct arg_int *scale = arg_int0("s", "scale", "<value>", "scaling for the window");
struct arg_file *export = arg_file0("e", "export", "<file>", "Export the full font to a PNG file");
struct arg_lit *split = arg_lit0(NULL, "split", "Split to separate PNG files (set path in -e).");
struct arg_end *end = arg_end(20);
void* argtable[] = {help,vers,file,fh,text,scale,export,split,end};
const char* progname = "fonttool";
// Make sure everything got allocated
if(arg_nullcheck(argtable) != 0) {
printf("%s: insufficient memory\n", progname);
goto exit_0;
}
// Parse arguments
int nerrors = arg_parse(argc, argv, argtable);
// Handle help
if(help->count > 0) {
printf("Usage: %s", progname);
arg_print_syntax(stdout, argtable, "\n");
printf("\nArguments:\n");
arg_print_glossary(stdout, argtable, "%-25s %s\n");
goto exit_0;
}
// Handle version
if(vers->count > 0) {
printf("%s v0.1\n", progname);
printf("Command line One Must Fall 2097 Font file editor.\n");
printf("Source code is available at https://github.com/omf2097 under MIT license.\n");
printf("(C) 2013 Tuomas Virtanen\n");
goto exit_0;
}
// Handle errors
if(nerrors > 0) {
arg_print_errors(stdout, end, progname);
printf("Try '%s --help' for more information.\n", progname);
goto exit_0;
}
// Requite either export or text
if(export->count <= 0 && text->count <= 0) {
printf("Use either --export or --text arguments!\n");
goto exit_0;
}
// Font size
int _fs = fh->ival[0];
if(_fs < 6 || _fs > 8 || _fs == 7) {
printf("Only valid values for fontsize are 6 and 8.\n");
goto exit_0;
}
// Load fonts
sd_font font;
sd_font_create(&font);
int ret = sd_font_load(&font, file->filename[0], _fs);
if(ret != SD_SUCCESS) {
printf("Couldn't load small font file! Error [%d] %s.\n", ret, sd_get_error(ret));
goto exit_1;
}
// Export or display
if(export->count > 0) {
export_to(&font, export->filename[0], (split->count > 0));
} else {
int main(int argc, char **argv)
{
/* SYNTAX 1: insert [-nvR] <file> [file]... -o <file> */
struct arg_rex *cmd1 = arg_rex1(NULL, NULL, "insert", NULL, REG_ICASE, NULL);
struct arg_lit *noact1 = arg_lit0("n", NULL, "take no action");
struct arg_lit *verbose1 = arg_lit0("v", "verbose", "verbose messages");
struct arg_lit *recurse1 = arg_lit0("R", NULL, "recurse through subdirectories");
struct arg_file *infiles1 = arg_filen(NULL, NULL, NULL, 1,argc+2, "input file(s)");
struct arg_file *outfile1 = arg_file0("o", NULL, "<output>", "output file (default is \"-\")");
struct arg_end *end1 = arg_end(20);
void* argtable1[] = {cmd1,noact1,verbose1,recurse1,infiles1,outfile1,end1};
int nerrors1;
/* SYNTAX 2: remove [-nv] <file> */
struct arg_rex *cmd2 = arg_rex1(NULL, NULL, "remove", NULL, REG_ICASE, NULL);
struct arg_lit *noact2 = arg_lit0("n", NULL, NULL);
struct arg_lit *verbose2 = arg_lit0("v", "verbose", NULL);
struct arg_file *infiles2 = arg_file1(NULL, NULL, NULL, NULL);
struct arg_end *end2 = arg_end(20);
void* argtable2[] = {cmd2,noact2,verbose2,infiles2,end2};
int nerrors2;
/* SYNTAX 3: search [-v] <pattern> [-o <file>] [--help] [--version] */
struct arg_rex *cmd3 = arg_rex1(NULL, NULL, "search", NULL, REG_ICASE, NULL);
struct arg_lit *verbose3 = arg_lit0("v", "verbose", NULL);
struct arg_str *pattern3 = arg_str1(NULL, NULL, "<pattern>", "search string");
struct arg_file *outfile3 = arg_file0("o", NULL, "<output>", NULL);
struct arg_end *end3 = arg_end(20);
void* argtable3[] = {cmd3,verbose3,pattern3,outfile3,end3};
int nerrors3;
/* SYNTAX 4: [-help] [-version] */
struct arg_lit *help4 = arg_lit0(NULL,"help", "print this help and exit");
struct arg_lit *version4 = arg_lit0(NULL,"version", "print version information and exit");
struct arg_end *end4 = arg_end(20);
void* argtable4[] = {help4,version4,end4};
int nerrors4;
const char* progname = "multisyntax";
int exitcode=0;
/* verify all argtable[] entries were allocated sucessfully */
if (arg_nullcheck(argtable1)!=0 ||
arg_nullcheck(argtable2)!=0 ||
arg_nullcheck(argtable3)!=0 ||
arg_nullcheck(argtable4)!=0 )
{
/* NULL entries were detected, some allocations must have failed */
printf("%s: insufficient memory\n",progname);
exitcode=1;
goto exit;
}
/* set any command line default values prior to parsing */
outfile1->filename[0]="-";
outfile3->filename[0]="-";
/* Above we defined a separate argtable for each possible command line syntax */
/* and here we parse each one in turn to see if any of them are successful */
nerrors1 = arg_parse(argc,argv,argtable1);
nerrors2 = arg_parse(argc,argv,argtable2);
nerrors3 = arg_parse(argc,argv,argtable3);
nerrors4 = arg_parse(argc,argv,argtable4);
/* Execute the appropriate main<n> routine for the matching command line syntax */
/* In this example program our alternate command line syntaxes are mutually */
/* exclusive, so we know in advance that only one of them can be successful. */
if (nerrors1==0)
exitcode = mymain1(noact1->count, verbose1->count, recurse1->count,
outfile1->filename[0], infiles1->filename, infiles1->count);
else if (nerrors2==0)
exitcode = mymain2(noact2->count, verbose2->count, infiles2->filename[0]);
else if (nerrors3==0)
exitcode = mymain3(verbose3->count, pattern3->sval[0], outfile3->filename[0]);
else if (nerrors4==0)
exitcode = mymain4(help4->count, version4->count, progname,
argtable1, argtable2, argtable3, argtable4);
else
{
/* We get here if the command line matched none of the possible syntaxes */
if (cmd1->count > 0)
{
/* here the cmd1 argument was correct, so presume syntax 1 was intended target */
arg_print_errors(stdout,end1,progname);
printf("usage: %s ", progname);
arg_print_syntax(stdout,argtable1,"\n");
}
else if (cmd2->count > 0)
{
/* here the cmd2 argument was correct, so presume syntax 2 was intended target */
arg_print_errors(stdout,end2,progname);
printf("usage: %s ", progname);
arg_print_syntax(stdout,argtable2,"\n");
}
else if (cmd3->count > 0)
{
/* here the cmd3 argument was correct, so presume syntax 3 was intended target */
arg_print_errors(stdout,end3,progname);
printf("usage: %s ", progname);
arg_print_syntax(stdout,argtable3,"\n");
}
else
{
/* no correct cmd literals were given, so we cant presume which syntax was intended */
printf("%s: missing <insert|remove|search> command.\n",progname);
printf("usage 1: %s ", progname); arg_print_syntax(stdout,argtable1,"\n");
printf("usage 2: %s ", progname); arg_print_syntax(stdout,argtable2,"\n");
printf("usage 3: %s ", progname); arg_print_syntax(stdout,argtable3,"\n");
printf("usage 4: %s", progname); arg_print_syntax(stdout,argtable4,"\n");
}
}
exit:
/* deallocate each non-null entry in each argtable */
arg_freetable(argtable1,sizeof(argtable1)/sizeof(argtable1[0]));
arg_freetable(argtable2,sizeof(argtable2)/sizeof(argtable2[0]));
arg_freetable(argtable3,sizeof(argtable3)/sizeof(argtable3[0]));
arg_freetable(argtable4,sizeof(argtable4)/sizeof(argtable4[0]));
return exitcode;
}
int _tmain(int argc, char* argv[])
{
// determine my process name
_splitpath(argv[0],NULL,NULL,gszProcName,NULL);
#else
int
main(int argc, const char** argv)
{
// determine my process name
CUtility::splitpath((char *)argv[0],NULL,gszProcName);
#endif
int iScreenLogLevel; // level of screen diagnostics
int iFileLogLevel; // level of file diagnostics
char szLogFile[_MAX_PATH]; // write diagnostics to this file
int Rslt;
int iProcMode;
int iMinLength;
int iMaxLength;
int iMinMergeLength;
int iMaxMergeLength;
char szRefFile[_MAX_PATH]; // process ref hypers from this file
char szRelFile[_MAX_PATH]; // process rel hypers from this file
char szOutLociFile[_MAX_PATH]; // write loci to this file
char szRefSpecies[cMaxDatasetSpeciesChrom]; // use this species as the ref species in generated szOutLociFile
char szRelSpecies[cMaxDatasetSpeciesChrom]; // use this species/list as the rel species in generated szOutLociFile
char szElType[cMaxDatasetSpeciesChrom]; // use this as the element type in generated szOutLociFile
int iRefExtend; // extend ref element lengths left+right by this many bases
int iRelExtend; // extend rel element lengths left+right by this many bases
int iJoinDistance; // if > 0 then join elements which only differ by at most this distance beween end of element i and start of element i+1
// command line args
struct arg_lit *help = arg_lit0("h","help", "print this help and exit");
struct arg_lit *version = arg_lit0("v","version,ver", "print version information and exit");
struct arg_int *FileLogLevel=arg_int0("f", "FileLogLevel", "<int>","Level of diagnostics written to screen and logfile 0=fatal,1=errors,2=info,3=diagnostics,4=debug");
struct arg_file *LogFile = arg_file0("F","log","<file>", "diagnostics log file");
struct arg_file *RefFile = arg_file1("i","reffile","<file>", "reference hyper element CSV file");
struct arg_file *RelFile = arg_file0("I","relfile","<file>", "relative hyper element CSV file");
struct arg_file *OutLociFile = arg_file1("o",NULL,"<file>", "output loci to file as CSV");
struct arg_str *RefSpecies = arg_str1("r","refspecies","<string>","output loci file ref species");
struct arg_str *RelSpecies = arg_str1("R","relspecies","<string>","output loci file rel species");
struct arg_str *ElType = arg_str0("t","eltype","<string>","output loci file element type");
struct arg_int *ProcMode = arg_int0("p","mode","<int>", "processing mode: 0:Intersect (Ref & Rel)\n\t\t1:Ref exclusive (Ref & !Rel)\n\t\t2:Rel exclusive (!Ref & Rel)\n\t\t3:Union (Ref | Rel)\n\t\t4:Neither (!(Ref | Rel))");
struct arg_int *MinLength = arg_int0("l","minlength","<int>", "minimum input ref/rel element length (default 4)");
struct arg_int *MaxLength = arg_int0("L","maxlength","<int>", "maximum input ref/rel element length (default 1000000)");
struct arg_int *MinMergeLength = arg_int0("m","minmergelength","<int>","minimum merged output element length (default 4)");
struct arg_int *MaxMergeLength = arg_int0("M","maxmergelength","<int>","maximum merged output element length (default 1000000)");
struct arg_int *RefExtend = arg_int0("e","refextend","<int>", "extend ref element flanks left+right by this many bases (default 0)");
struct arg_int *RelExtend = arg_int0("E","relextend","<int>", "extend rel element flanks left+right by this many bases (default 0)");
struct arg_int *JoinDistance = arg_int0("j","join","<int>", "merge output elements which are only separated by this number of bases (default 0)");
struct arg_end *end = arg_end(20);
void *argtable[] = {help,version,FileLogLevel,LogFile,
ProcMode,
RefFile,RelFile,OutLociFile,
MinLength,MaxLength,RefExtend,RelExtend,JoinDistance,MinMergeLength,MaxMergeLength,
RefSpecies,RelSpecies,ElType,
end};
char **pAllArgs;
int argerrors;
argerrors = CUtility::arg_parsefromfile(argc,(char **)argv,&pAllArgs);
if(argerrors >= 0)
argerrors = arg_parse(argerrors,pAllArgs,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0)
{
printf("\n%s CSV Merge Elements, Version %s\nOptions ---\n", gszProcName,cpszProgVer);
arg_print_syntax(stdout,argtable,"\n");
arg_print_glossary(stdout,argtable," %-25s %s\n");
printf("\nNote: Parameters can be entered into a parameter file, one parameter per line.");
printf("\n To invoke this parameter file then precede its name with '@'");
printf("\n e.g. %s @myparams.txt\n",gszProcName);
printf("\nPlease report any issues regarding usage of %s at https://github.com/csiro-crop-informatics/biokanga/issues\n\n",gszProcName);
exit(1);
}
/* special case: '--version' takes precedence error reporting */
if (version->count > 0)
{
printf("\n%s Version %s\n",gszProcName,cpszProgVer);
exit(1);
}
if (!argerrors)
{
if(FileLogLevel->count && !LogFile->count)
{
printf("\nError: FileLogLevel '-f%d' specified but no logfile '-F<logfile>'",FileLogLevel->ival[0]);
exit(1);
}
iScreenLogLevel = iFileLogLevel = FileLogLevel->count ? FileLogLevel->ival[0] : eDLInfo;
if(iFileLogLevel < eDLNone || iFileLogLevel > eDLDebug)
{
printf("\nError: FileLogLevel '-l%d' specified outside of range %d..%d",iFileLogLevel,eDLNone,eDLDebug);
exit(1);
}
if(LogFile->count)
{
strncpy(szLogFile,LogFile->filename[0],_MAX_PATH);
szLogFile[_MAX_PATH-1] = '\0';
}
else
{
iFileLogLevel = eDLNone;
szLogFile[0] = '\0';
}
iProcMode = ProcMode->count ? ProcMode->ival[0] : ePMElIntersect;
if(iProcMode < ePMElIntersect || iProcMode > ePMElRefNotRefRel)
{
printf("Error: Processing mode '-p%d' is not in range 0..4",iProcMode);
exit(1);
}
strncpy(szOutLociFile,OutLociFile->filename[0],_MAX_PATH);
szOutLociFile[_MAX_PATH-1] = '\0';
strncpy(szRefSpecies,RefSpecies->sval[0],sizeof(szRefSpecies));
szRefSpecies[sizeof(szRefSpecies)-1] = '\0';
strncpy(szRelSpecies,RelSpecies->sval[0],sizeof(szRelSpecies));
szRelSpecies[sizeof(szRelSpecies)-1] = '\0';
if(ElType->count)
{
strncpy(szElType,ElType->sval[0],sizeof(szElType));
szElType[sizeof(szElType)-1] = '\0';
}
else
strcpy(szElType,"merged");
iMinLength = MinLength->count ? MinLength->ival[0] : cDfltMinLength;
if(iMinLength < 0 || iMinLength > cMaxLengthRange)
{
printf("Error: Minimum element length '-l%d' is not in range 0..%d",iMinLength,cMaxLengthRange);
exit(1);
}
iMaxLength = MaxLength->count ? MaxLength->ival[0] : cDfltMaxLength;
if(iMaxLength < iMinLength || iMaxLength > cMaxLengthRange)
{
printf("Error: Maximum element length '-L%d' is not in range %d..%d",iMaxLength,iMinLength,cMaxLengthRange);
exit(1);
}
iMinMergeLength = MinMergeLength->count ? MinMergeLength->ival[0] : cDfltMinLength;
if(iMinMergeLength < 0 || iMinMergeLength > cMaxLengthRange)
{
printf("Error: Minimum output merged element length '-m%d' is not in range 0..%d",iMinMergeLength,cMaxLengthRange);
exit(1);
}
iMaxMergeLength = MaxMergeLength->count ? MaxMergeLength->ival[0] : cDfltMaxLength;
if(iMaxMergeLength < iMinMergeLength || iMaxMergeLength > cMaxLengthRange)
{
printf("Error: Maximum element length '-M%d' is not in range %d..%d",iMaxMergeLength,iMinMergeLength,cMaxLengthRange);
exit(1);
}
iJoinDistance = JoinDistance->count ? JoinDistance->ival[0] : cDfltJoinOverlap;
if(iJoinDistance < 0 || iJoinDistance > cMaxJoinOverlap)
{
printf("Error: Join separation length '-j%d' is not in range %d..%d",iJoinDistance,0,cMaxJoinOverlap);
exit(1);
}
iRefExtend = RefExtend->count ? RefExtend->ival[0] : 0;
if(iRefExtend < (-1 * cMaxExtendLength) || iRefExtend > cMaxExtendLength)
{
printf("Error: Ref Extension length '-e%d' is not in range %d..%d",iRefExtend,(-1 * cMaxExtendLength),cMaxExtendLength);
exit(1);
}
iRelExtend = RelExtend->count ? RelExtend->ival[0] : 0;
if(iRelExtend < (-1 * cMaxExtendLength) || iRelExtend > cMaxExtendLength)
{
printf("Error: Rel Extension length '-E%d' is not in range %d..%d",iRelExtend,(-1 * cMaxExtendLength),cMaxExtendLength);
exit(1);
}
strncpy(szRefFile,RefFile->filename[0],_MAX_PATH);
szRefFile[_MAX_PATH-1] = '\0';
if(RelFile->count)
{
strncpy(szRelFile,RelFile->filename[0],_MAX_PATH);
szRelFile[_MAX_PATH-1] = '\0';
}
else
{
if(iProcMode == ePMElRefExclusive || iProcMode == ePMElRefRelUnion)
szRelFile[0] = '\0';
else
{
printf("Error: Rel loci file must be specified in processing mode '-p%d' (%s)",iProcMode,ProcMode2Txt((etProcMode)iProcMode));
exit(1);
}
}
// now that command parameters have been parsed then initialise diagnostics log system
if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
{
printf("\nError: Unable to start diagnostics subsystem.");
if(szLogFile[0] != '\0')
printf(" Most likely cause is that logfile '%s' can't be opened/created",szLogFile);
exit(1);
}
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Version: %s Processing parameters:",cpszProgVer);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Processing Mode: %d (%s)",iProcMode,ProcMode2Txt((etProcMode)iProcMode));
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Reference CSV file: '%s'",szRefFile);
if(szRelFile[0] != '\0')
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Relative CSV file: '%s'",szRelFile);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output processed loci into CSV file: '%s'",szOutLociFile);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output loci file ref species: '%s'",szRefSpecies);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output loci file rel species: '%s'",szRelSpecies);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output loci file element type: '%s'",szElType);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Minimum input element length: %d",iMinLength);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Maximum input element length: %d",iMaxLength);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Ref element flank extension length: %d",iRefExtend);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Rel element flank extension length: %d",iRelExtend);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Merge output elements separated by at most this many bases: %d",iJoinDistance);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Minimum output merged element length: %d",iMinMergeLength);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Maximum output merged element length: %d",iMaxMergeLength);
// processing here...
gStopWatch.Start();
#ifdef _WIN32
SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif
Rslt = Process((etProcMode)iProcMode,iMinLength,iMaxLength,iRefExtend,iRelExtend,iJoinDistance,iMinMergeLength,iMaxMergeLength,szRefFile,szRelFile,szOutLociFile,
szRefSpecies,szRelSpecies,szElType);
gStopWatch.Stop();
Rslt = Rslt >=0 ? 0 : 1;
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
exit(Rslt);
}
else
{
printf("\n%s CSV Merge Elements, Version %s\n",gszProcName,cpszProgVer);
arg_print_errors(stdout,end,gszProcName);
arg_print_syntax(stdout,argtable,"\nUse '-h' to view option and parameter usage\n");
exit(1);
}
}
int main(int argc, char* argv[])
{
// Define arguments.
struct arg_lit* show_help = arg_lit0("h", "help", "Show this help.");
struct arg_str* type_assembler = arg_str0("t", NULL, "<type>", "The type of assembler to output for.");
struct arg_file* input_file = arg_file1(NULL, NULL, "<file>", "The input file (or - to read from standard input).");
struct arg_file* output_file = arg_file1("o", "output", "<file>", "The output file (or - to send to standard output).");
struct arg_end *end = arg_end(20);
void *argtable[] = { output_file, show_help, type_assembler, input_file, end };
// Parse arguments.
int nerrors = arg_parse(argc,argv,argtable);
if (nerrors != 0 || show_help->count != 0)
{
if (show_help->count != 0)
arg_print_errors(stdout, end, "compiler");
fprintf(stderr, "syntax:\n compiler");
arg_print_syntax(stdout, argtable, "\n");
fprintf(stderr, "options:\n");
arg_print_glossary(stdout, argtable, " %-25s %s\n");
return 1;
}
// Parse C.
pp_add_search_path(".");
pp_add_search_path("include");
pp_add_search_path(dirname<std::string>(input_file->filename[0]).c_str());
yyout = stderr;
yyin = pp_do(input_file->filename[0]);
if (yyin == NULL)
{
pp_cleanup();
return 1;
}
yyparse();
if (yyin != stdin)
fclose(yyin);
pp_cleanup();
if (program == NULL)
{
std::cerr << "An error occurred while compiling." << std::endl;
return 1;
}
// Assembler type.
const char* asmtype = "dcpu16toolchain";
if (type_assembler->count > 0)
asmtype = type_assembler->sval[0];
// Spacing.
std::cerr << std::endl;
// Generate assembly using the AST.
try
{
AsmGenerator generator(asmtype);
AsmBlock* block = program->compile(generator);
if (strcmp(output_file->filename[0], "-") == 0)
{
std::cout << generator.m_Preassembly << std::endl;
std::cout << *block << std::endl;
std::cout << generator.m_Postassembly << std::endl;
}
else
{
std::ofstream output(output_file->filename[0], std::ios::out | std::ios::trunc);
output << generator.m_Preassembly << std::endl;
output << *block << std::endl;
output << generator.m_Postassembly << std::endl;
output.close();
}
delete block;
}
catch (CompilerException* ex)
{
std::string msg = ex->getMessage();
std::cerr << "An error occurred while compiling." << std::endl;
std::cerr << msg << std::endl;
return 1;
}
return 0;
}
int main(int argc, char* argv[]) {
double discountFactor = 0.9;
FILE* initFileFd = NULL;
FILE** combinedFd = NULL;
FILE* optimalFd = NULL;
optimistic_instance* optimistic = NULL;
random_search_instance* random_search = NULL;
uct_instance* uct = NULL;
uniform_instance* uniform = NULL;
unsigned int maxDepth = 0;
unsigned int i = 0;
unsigned int n = 0;
state** initialStates = NULL;
unsigned int timestamp = time(NULL);
double* optimalValues = NULL;
int readFscanf = -1;
struct arg_file* initFile = arg_file1(NULL, "init", "<file>", "File containing the inital state");
struct arg_int* d = arg_int1("d", NULL, "<n>", "Maximum depth of an uniform tree which the number of call per step");
struct arg_int* k = arg_int1("k", NULL, "<n>", "Branching factor of the problem");
struct arg_file* where = arg_file1(NULL, "where", "<file>", "Directory where we save the outputs");
struct arg_file* optimal = arg_file1(NULL, "optimal", "<file>", "File containing the optimal values");
struct arg_end* end = arg_end(6);
void* argtable[6];
int nerrors = 0;
argtable[0] = initFile;
argtable[1] = where;
argtable[2] = d;
argtable[3] = k;
argtable[4] = optimal;
argtable[5] = end;
if(arg_nullcheck(argtable) != 0) {
printf("error: insufficient memory\n");
arg_freetable(argtable, 6);
return EXIT_FAILURE;
}
nerrors = arg_parse(argc, argv, argtable);
if(nerrors > 0) {
printf("%s:", argv[0]);
arg_print_syntax(stdout, argtable, "\n");
arg_print_errors(stdout, end, argv[0]);
arg_freetable(argtable, 6);
return EXIT_FAILURE;
}
initGenerativeModelParameters();
K = k->ival[0];
initGenerativeModel();
optimalFd = fopen(optimal->filename[0], "r");
initFileFd = fopen(initFile->filename[0], "r");
readFscanf = fscanf(initFileFd, "%u\n", &n);
initialStates = (state**)malloc(sizeof(state*) * n);
for(i = 0; i < n; i++) {
char str[1024];
readFscanf = fscanf(initFileFd, "%s\n", str);
initialStates[i] = makeState(str);
}
maxDepth = d->ival[0];
combinedFd = (FILE**)malloc(sizeof(FILE*) * maxDepth);
for(i = 1; i <= maxDepth; i++) {
char str[1024];
sprintf(str, "%s/%u_combined_%u_%u.csv", where->filename[0], timestamp, K, i);
combinedFd[i - 1] = fopen(str, "w");
fprintf(combinedFd[i - 1], "n,optimistic,random search,uct,uniform\n");
}
arg_freetable(argtable, 6);
optimalValues = (double*)malloc(sizeof(double) * K);
optimistic = optimistic_initInstance(initialStates[0], discountFactor);
random_search = random_search_initInstance(initialStates[0], discountFactor);
uct = uct_initInstance(initialStates[0], discountFactor);
uniform = uniform_initInstance(initialStates[0], discountFactor);
for(i = 0; i < n; i++) {
unsigned int j = 1;
unsigned int maxNbIterations = K;
unsigned int optimalAction = 0;
char str[1024];
readFscanf = fscanf(optimalFd, "%s\n", str);
optimalValues[0] = strtod(strtok(str, ","), NULL);
printf("%.15f,",optimalValues[0]);
for(; j < K; j++) {
optimalValues[j] = strtod(strtok(NULL, ","), NULL);
printf("%.15f,",optimalValues[j]);
}
optimalAction = atol(strtok(NULL, ","));
printf("%u\n",optimalAction);
for(j = 1; j <= maxDepth; j++) {
unsigned int crtOptimalAction = getActionId(optimistic_planning(optimistic, maxNbIterations));
fprintf(combinedFd[j - 1], "%u,", maxNbIterations);
fprintf(combinedFd[j - 1], "%.15f,", crtOptimalAction == optimalAction ? 0.0 : optimalValues[optimalAction] - optimalValues[crtOptimalAction]);
maxNbIterations += pow(K, j+1);
}
if(i < (n - 1))
optimistic_resetInstance(optimistic, initialStates[i+1]);
printf("optimistic: %uth initial state processed\n", i+1);
fflush(NULL);
maxNbIterations = K;
for(j = 1; j <= maxDepth; j++) {
unsigned int crtOptimalAction = getActionId(random_search_planning(random_search, maxNbIterations));
fprintf(combinedFd[j - 1], "%.15f,", crtOptimalAction == optimalAction ? 0.0 : optimalValues[optimalAction] - optimalValues[crtOptimalAction]);
maxNbIterations += pow(K, j+1);
}
if(i < (n - 1))
random_search_resetInstance(random_search, initialStates[i + 1]);
printf("random_search: %uth initial state processed\n", i+1);
fflush(NULL);
maxNbIterations = K;
for(j = 1; j <= maxDepth; j++) {
unsigned int crtOptimalAction = getActionId(uct_planning(uct, maxNbIterations));
fprintf(combinedFd[j - 1], "%.15f,", crtOptimalAction == optimalAction ? 0.0 : optimalValues[optimalAction] - optimalValues[crtOptimalAction]);
maxNbIterations += pow(K, j+1);
}
if(i < (n - 1))
uct_resetInstance(uct, initialStates[i + 1]);
printf("uct: %uth initial state processed\n", i+1);
fflush(NULL);
maxNbIterations = K;
for(j = 1; j <= maxDepth; j++) {
unsigned int crtOptimalAction = getActionId(uniform_planning(uniform, maxNbIterations));
fprintf(combinedFd[j - 1], "%.15f\n", crtOptimalAction == optimalAction ? 0.0 : optimalValues[optimalAction] - optimalValues[crtOptimalAction]);
maxNbIterations += pow(K, j+1);
}
if(i < (n - 1))
uniform_resetInstance(uniform, initialStates[i + 1]);
printf("uniform: %uth initial state processed\n", i+1);
printf("%uth initial state processed\n", i+1);
fflush(NULL);
}
for(i = 0; i < maxDepth; i++) {
fclose(combinedFd[i]);
}
for(i = 0; i < n; i++)
freeState(initialStates[i]);
free(initialStates);
free(combinedFd);
optimistic_uninitInstance(&optimistic);
random_search_uninitInstance(&random_search);
uct_uninitInstance(&uct);
uniform_uninitInstance(&uniform);
freeGenerativeModel();
freeGenerativeModelParameters();
return EXIT_SUCCESS;
}
int main(int argc, char *argv[]) {
SDL_AudioSpec want, have;
SDL_AudioDeviceID dev;
Streamer streamer;
int retcode = 0;
// Init SDL Audio
if(SDL_Init(SDL_INIT_AUDIO) != 0) {
fprintf(stderr, "Error: %s\n", SDL_GetError());
return 1;
}
// commandline argument parser options
struct arg_lit *help = arg_lit0("h", "help", "print this help and exit");
struct arg_lit *vers = arg_lit0("v", "version", "print version information and exit");
struct arg_file *file = arg_file1("f", "file", "<file>", "SOUNDS.DAT file");
struct arg_file *output = arg_file0("o", "output", "<file>", "Output sounds file");
struct arg_int *sid = arg_int0("s", "sound", "<int>", "Sound ID");
struct arg_int *sampleprint = arg_int0(NULL, "print", "<int>", "Print first n bytes from selected sound");
struct arg_lit *play = arg_lit0("p", "play", "Play selected sound");
struct arg_file *export = arg_file0("e", "export", "<file>", "Export selected sound to AU file");
struct arg_file *import = arg_file0("i", "import", "<file>", "Import selected sound from AU file");
struct arg_end *end = arg_end(20);
void* argtable[] = {help,vers,file,output,sid,sampleprint,play,export,import,end};
const char* progname = "soundtool";
// Make sure everything got allocated
if(arg_nullcheck(argtable) != 0) {
printf("%s: insufficient memory\n", progname);
goto exit_0;
}
// Parse arguments
int nerrors = arg_parse(argc, argv, argtable);
// Handle help
if(help->count > 0) {
printf("Usage: %s", progname);
arg_print_syntax(stdout, argtable, "\n");
printf("\nArguments:\n");
arg_print_glossary(stdout, argtable, "%-25s %s\n");
goto exit_0;
}
// Handle version
if(vers->count > 0) {
printf("%s v0.1\n", progname);
printf("Command line One Must Fall 2097 SOUNDS.DAT file editor.\n");
printf("Source code is available at https://github.com/omf2097 under MIT license.\n");
printf("(C) 2013 Tuomas Virtanen\n");
goto exit_0;
}
// Handle errors
if(nerrors > 0) {
arg_print_errors(stdout, end, progname);
printf("Try '%s --help' for more information.\n", progname);
goto exit_0;
}
// Open sounds.dat
sd_sound_file sf;
sd_sounds_create(&sf);
retcode = sd_sounds_load(&sf, file->filename[0]);
if(retcode) {
printf("Error %d: %s\n", retcode, sd_get_error(retcode));
goto exit_1;
}
if(sid->count > 0) {
// Sound ID to handle
int sound_id = sid->ival[0];
const sd_sound *sound = sd_sounds_get(&sf, sound_id-1);
if(sound == NULL) {
printf("Invalid sound ID");
goto exit_1;
}
if(sampleprint->count > 0) {
int count = (sampleprint->ival[0] > sound->len) ? sound->len : sampleprint->ival[0];
printf("Sample size = %d\n", sound->len);
printf("Unknown = %d\n", sound->unknown);
printf("Attempting to print %d first bytes.\n", count);
for(int i = 0; i < count; i++) {
unsigned int s = sound->data[i] & 0xFF;
printf("%2x ", s);
}
} else if(play->count > 0) {
printf("Attempting to play sample #%d.\n", sound_id);
// Make sure there is data at requested ID position
if(sound->len <= 0) {
printf("Sample does not contain data.\n");
goto exit_1;
}
// Streamer
streamer.size = sound->len;
streamer.pos = 0;
streamer.data = sound->data;
// Initialize required audio
SDL_zero(want);
want.freq = 8000;
want.format = AUDIO_U8;
want.channels = 1;
want.samples = 4096;
want.callback = stream;
want.userdata = &streamer;
// Open device, play file
dev = SDL_OpenAudioDevice(NULL, 0, &want, &have, 0);
if(dev == 0) {
printf("Failed to open audio dev: %s\n", SDL_GetError());
goto exit_0;
} else {
if(have.format != want.format) {
printf("Could not get correct playback format.\n");
} else {
printf("Starting playback ...\n");
SDL_PauseAudioDevice(dev, 0);
while(streamer.pos < streamer.size) {
SDL_Delay(100);
}
printf("All done.\n");
}
SDL_CloseAudioDevice(dev);
}
} else if(import->count > 0) {
if(sd_sound_from_au(&sf, sound_id, import->filename[0]) != SD_SUCCESS) {
printf("Importing sample %d from file %s failed.\n", sound_id, import->filename[0]);
} else {
printf("Importing sample %d from file %s succeeded.\n", sound_id, import->filename[0]);
}
} else if(export->count > 0) {
if(sd_sound_to_au(&sf, sound_id, export->filename[0]) != SD_SUCCESS) {
printf("Exporting sample %d to file %s failed.\n", sound_id, export->filename[0]);
} else {
printf("Exporting sample %d to file %s succeeded.\n", sound_id, export->filename[0]);
}
} else {
int _tmain(int argc, char* argv[])
{
// determine my process name
_splitpath(argv[0],NULL,NULL,gszProcName,NULL);
#else
int
main(int argc, const char** argv)
{
// determine my process name
CUtility::splitpath((char *)argv[0],NULL,gszProcName);
#endif
int iScreenLogLevel; // level of screen diagnostics
int iFileLogLevel; // level of file diagnostics
char szLogFile[_MAX_PATH]; // write diagnostics to this file
int Rslt;
int Idx;
int iMode = 0; // processing mode
int iRandSeed = 0; // random base seed to use (if < 0 then current time used to seed generator)
int KMerLen; // what length kmer to generate for 1..cMaxKMerLen
int NumInFileSpecs; // number of input file specs
char *pszInFiles[cMaxInFileSpecs]; // input control aligned reads files
char szOutputFile[_MAX_PATH];
// command line args
struct arg_lit *help = arg_lit0("hH","help", "print this help and exit");
struct arg_lit *version = arg_lit0("v","version,ver", "print version information and exit");
struct arg_int *FileLogLevel=arg_int0("f", "FileLogLevel", "<int>","Level of diagnostics written to screen and logfile 0=fatal,1=errors,2=info,3=diagnostics,4=debug");
struct arg_file *LogFile = arg_file0("F","log","<file>", "diagnostics log file");
struct arg_int *Mode = arg_int0("m","mode","<int>", "processing mode - 0 randomise genome");
struct arg_int *kmerlen = arg_int0("k","kmerlen","<int>", "maintain frequency composition of K-mer length (default = 1, range 1..15)");
struct arg_file *InFiles = arg_filen("i",NULL,"<file>",1,cMaxInFileSpecs, "input genome assembly multifasta files (s) to randomise");
struct arg_file *OutFile= arg_file1("o",NULL,"<file>", "output randomised assembly to this file as multifasta");
struct arg_int *RandSeed = arg_int0("s","randseed","<int>", "random seed to use (default is use system time)");
struct arg_end *end = arg_end(20);
void *argtable[] = {help,version,FileLogLevel,LogFile,Mode,kmerlen,InFiles,OutFile,RandSeed,end};
char **pAllArgs;
int argerrors;
argerrors = CUtility::arg_parsefromfile(argc,(char **)argv,&pAllArgs);
if(argerrors >= 0)
argerrors = arg_parse(argerrors,pAllArgs,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0)
{
printf("\n%s Kanga randomise genome K-mers, Version %s\nOptions ---\n", gszProcName,cpszProgVer);
arg_print_syntax(stdout,argtable,"\n");
arg_print_glossary(stdout,argtable," %-25s %s\n");
printf("\nNote: Parameters can be entered into a parameter file, one parameter per line.");
printf("\n To invoke this parameter file then precede its name with '@'");
printf("\n e.g. %s @myparams.txt\n",gszProcName);
printf("\nPlease report any issues regarding usage of %s at https://github.com/csiro-crop-informatics/biokanga/issues\n\n",gszProcName);
exit(1);
}
/* special case: '--version' takes precedence error reporting */
if (version->count > 0)
{
printf("\n%s Version %s\n",gszProcName,cpszProgVer);
exit(1);
}
if (!argerrors)
{
if(FileLogLevel->count && !LogFile->count)
{
printf("\nError: FileLogLevel '-f%d' specified but no logfile '-F<logfile>\n'",FileLogLevel->ival[0]);
exit(1);
}
iScreenLogLevel = iFileLogLevel = FileLogLevel->count ? FileLogLevel->ival[0] : eDLInfo;
if(iFileLogLevel < eDLNone || iFileLogLevel > eDLDebug)
{
printf("\nError: FileLogLevel '-l%d' specified outside of range %d..%d\n",iFileLogLevel,eDLNone,eDLDebug);
exit(1);
}
if(LogFile->count)
{
strncpy(szLogFile,LogFile->filename[0],_MAX_PATH);
szLogFile[_MAX_PATH-1] = '\0';
}
else
{
iFileLogLevel = eDLNone;
szLogFile[0] = '\0';
}
// now that log parameters have been parsed then initialise diagnostics log system
if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
{
printf("\nError: Unable to start diagnostics subsystem\n");
if(szLogFile[0] != '\0')
printf(" Most likely cause is that logfile '%s' can't be opened/created\n",szLogFile);
exit(1);
}
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Version: %s",cpszProgVer);
iMode = Mode->count ? Mode->ival[0] : 0;
if(iMode < 0 || iMode >= cMaxSupportedModes)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Unsupported Mode '-m%d' requested",iMode);
exit(1);
}
KMerLen = 0;
switch(iMode) {
case 0: // generate random species fasta sequence
for(NumInFileSpecs=Idx=0;NumInFileSpecs < cMaxInFileSpecs && Idx < InFiles->count; Idx++)
{
pszInFiles[Idx] = NULL;
if(pszInFiles[NumInFileSpecs] == NULL)
pszInFiles[NumInFileSpecs] = new char [_MAX_PATH];
strncpy(pszInFiles[NumInFileSpecs],InFiles->filename[Idx],_MAX_PATH);
pszInFiles[NumInFileSpecs][_MAX_PATH-1] = '\0';
CUtility::TrimQuotedWhitespcExtd(pszInFiles[NumInFileSpecs]);
if(pszInFiles[NumInFileSpecs][0] != '\0')
NumInFileSpecs++;
}
if(!NumInFileSpecs)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: After removal of whitespace, no input file(s) specified with '-i<filespec>' option)\n");
exit(1);
}
KMerLen = kmerlen->count ? kmerlen->ival[0] : cDfltKMerLen;
if(KMerLen < 1 || KMerLen > cMaxKMerLen)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: K-mer length specified with '-k%d' is outside of range 1..10",KMerLen);
exit(1);
}
if(!OutFile->count || OutFile->filename[0][0] == '\0')
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: No output fasta file specified with '-o<filename>'");
exit(1);
}
strncpy(szOutputFile,OutFile->filename[0],_MAX_PATH);
szOutputFile[_MAX_PATH] = '\0';
if(!RandSeed->count)
iRandSeed = -1;
else
{
iRandSeed = RandSeed->ival[0];
if(iRandSeed < 0 || iRandSeed > 32767)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Random seed specified as '-s%d' must be between 0 and 32767",iRandSeed);
exit(1);
}
}
break;
}
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Processing parameters:");
switch(iMode) {
case 0:
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Mode: 0 (randomise genome K-mers)");
for(Idx=0; Idx < NumInFileSpecs; Idx++)
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Use frequency compositions from these genome multifasta file(s) (%d): '%s'",Idx+1,pszInFiles[Idx]);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Maintain K-mer composition of length: %d",KMerLen);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Genome output file: '%s'",szOutputFile);
if(iRandSeed >= 0)
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Random seed: %d",iRandSeed);
else
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Random seed: will use current time as seed");
break;
}
gStopWatch.Start();
#ifdef _WIN32
SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif
Rslt = GenerateRandFasta(iMode,KMerLen,NumInFileSpecs,pszInFiles,szOutputFile,iRandSeed);
Rslt = Rslt >=0 ? 0 : 1;
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
exit(Rslt);
}
else
{
printf("\n%s Kanga randomise genome K-mers, Version %s\n",gszProcName,cpszProgVer);
arg_print_errors(stdout,end,gszProcName);
arg_print_syntax(stdout,argtable,"\nUse '-h' to view option and parameter usage\n");
exit(1);
}
return 0;
}
int main(int argc, char* argv[])
{
// Define our variables.
FILE* load;
uint16_t flash[0x10000];
char leading[0x100];
unsigned int i;
bool uread = true;
vm_t* vm;
int nerrors;
bstring ss, st;
// Define arguments.
struct arg_lit* show_help = arg_lit0("h", "help", "Show this help.");
struct arg_file* input_file = arg_file1(NULL, NULL, "<file>", "The input file, or - to read from standard input.");
struct arg_file* execution_dump_file = arg_file0("e", "execution-dump", "<file>", "Produce a very large execution dump file.");
struct arg_lit* debug_mode = arg_lit0("d", "debug", "Show each executed instruction.");
struct arg_lit* terminate_mode = arg_lit0("t", "show-on-terminate", "Show state of machine when program is terminated.");
struct arg_lit* legacy_mode = arg_lit0("l", "legacy", "Automatically initialize hardware to legacy values.");
struct arg_lit* little_endian_mode = arg_lit0(NULL, "little-endian", "Use little endian serialization (for compatibility with older versions).");
struct arg_lit* verbose = arg_litn("v", NULL, 0, LEVEL_EVERYTHING - LEVEL_DEFAULT, "Increase verbosity.");
struct arg_lit* quiet = arg_litn("q", NULL, 0, LEVEL_DEFAULT - LEVEL_SILENT, "Decrease verbosity.");
struct arg_end* end = arg_end(20);
void* argtable[] = { input_file, debug_mode, execution_dump_file, terminate_mode, legacy_mode, little_endian_mode, verbose, quiet, end };
// Parse arguments.
nerrors = arg_parse(argc, argv, argtable);
version_print(bautofree(bfromcstr("Emulator")));
if (nerrors != 0 || show_help->count != 0)
{
if (show_help->count != 0)
arg_print_errors(stdout, end, "emulator");
printd(LEVEL_DEFAULT, "syntax:\n dtemu");
arg_print_syntax(stderr, argtable, "\n");
printd(LEVEL_DEFAULT, "options:\n");
arg_print_glossary(stderr, argtable, " %-25s %s\n");
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
// Set verbosity level.
debug_setlevel(LEVEL_DEFAULT + verbose->count - quiet->count);
// Set global path variable.
osutil_setarg0(bautofree(bfromcstr(argv[0])));
// Set endianness.
isetmode(little_endian_mode->count == 0 ? IMODE_BIG : IMODE_LITTLE);
// Zero out the flash space.
for (i = 0; i < 0x10000; i++)
flash[i] = 0x0;
// Zero out the leading space.
for (i = 0; i < 0x100; i++)
leading[i] = 0x0;
// Load from either file or stdin.
if (strcmp(input_file->filename[0], "-") != 0)
{
// Open file.
load = fopen(input_file->filename[0], "rb");
if (load == NULL)
{
fprintf(stderr, "emulator: unable to load %s from disk.\n", argv[1]);
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
}
else
{
// Windows needs stdin in binary mode.
#ifdef _WIN32
_setmode(_fileno(stdin), _O_BINARY);
#endif
// Set load to stdin.
load = stdin;
}
// Read up to 0x10000 words.
for (i = 0; i < 0x10000 && !feof(load); i++)
iread(&flash[i], load);
fclose(load);
// Check to see if the first X bytes matches the header
// for intermediate code and stop if it does.
ss = bfromcstr("");
st = bfromcstr(ldata_objfmt);
for (i = 0; i < strlen(ldata_objfmt); i++)
bconchar(ss, leading[i]);
if (biseq(ss, st))
{
fprintf(stderr, "emulator: it appears you passed intermediate code for execution. link\n");
fprintf(stderr, " the input code with the toolchain linker to execute it.\n");
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
// And then use the VM.
vm = vm_create();
vm->debug = (debug_mode->count > 0);
vm_flash(vm, flash);
vm_hw_timer_init(vm);
vm_hw_io_init(vm);
vm_hw_lem1802_init(vm);
vm_hw_lua_init(vm);
if (legacy_mode->count > 0)
{
vm_hw_lem1802_mem_set_screen(vm, 0x8000);
vm_hw_io_set_legacy(true);
}
vm_execute(vm, execution_dump_file->count > 0 ? execution_dump_file->filename[0] : NULL);
#ifdef __EMSCRIPTEN__
printd(LEVEL_WARNING, "warning: not cleaning up resources in Emscripten.\n");
#else
if (terminate_mode->count > 0)
{
fprintf(stderr, "\n");
fprintf(stderr, "A: 0x%04X [A]: 0x%04X\n", vm->registers[REG_A], vm->ram[vm->registers[REG_A]]);
fprintf(stderr, "B: 0x%04X [B]: 0x%04X\n", vm->registers[REG_B], vm->ram[vm->registers[REG_B]]);
fprintf(stderr, "C: 0x%04X [C]: 0x%04X\n", vm->registers[REG_C], vm->ram[vm->registers[REG_C]]);
fprintf(stderr, "X: 0x%04X [X]: 0x%04X\n", vm->registers[REG_X], vm->ram[vm->registers[REG_X]]);
fprintf(stderr, "Y: 0x%04X [Y]: 0x%04X\n", vm->registers[REG_Y], vm->ram[vm->registers[REG_Y]]);
fprintf(stderr, "Z: 0x%04X [Z]: 0x%04X\n", vm->registers[REG_Z], vm->ram[vm->registers[REG_Z]]);
fprintf(stderr, "I: 0x%04X [I]: 0x%04X\n", vm->registers[REG_I], vm->ram[vm->registers[REG_I]]);
fprintf(stderr, "J: 0x%04X [J]: 0x%04X\n", vm->registers[REG_J], vm->ram[vm->registers[REG_J]]);
fprintf(stderr, "PC: 0x%04X SP: 0x%04X\n", vm->pc, vm->sp);
fprintf(stderr, "EX: 0x%04X IA: 0x%04X\n", vm->ex, vm->ia);
}
vm_hw_lua_free(vm);
vm_hw_timer_free(vm);
vm_hw_io_free(vm);
vm_hw_lem1802_free(vm);
vm_free(vm);
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 0;
#endif
}
int main(int argc, char *argv[]) {
// commandline argument parser options
struct arg_lit *help = arg_lit0("h", "help", "print this help and exit");
struct arg_lit *vers = arg_lit0("v", "version", "print version information and exit");
struct arg_file *file = arg_file1("f", "file", "<file>", "language file");
struct arg_int *str = arg_int1("s", "string", "<value>", "print language string # (-1 for all).");
struct arg_end *end = arg_end(20);
void* argtable[] = {help,vers,file,str,end};
const char* progname = "languagetool";
// Make sure everything got allocated
if(arg_nullcheck(argtable) != 0) {
printf("%s: insufficient memory\n", progname);
goto exit_0;
}
// Parse arguments
int nerrors = arg_parse(argc, argv, argtable);
// Handle help
if(help->count > 0) {
printf("Usage: %s", progname);
arg_print_syntax(stdout, argtable, "\n");
printf("\nArguments:\n");
arg_print_glossary(stdout, argtable, "%-25s %s\n");
goto exit_0;
}
// Handle version
if(vers->count > 0) {
printf("%s v0.1\n", progname);
printf("Command line One Must Fall 2097 Language file editor.\n");
printf("Source code is available at https://github.com/omf2097 under MIT license.\n");
printf("(C) 2013 Tuomas Virtanen\n");
goto exit_0;
}
// Handle errors
if(nerrors > 0) {
arg_print_errors(stdout, end, progname);
printf("Try '%s --help' for more information.\n", progname);
goto exit_0;
}
// Get strings
sd_language *language = sd_language_create();
if(sd_language_load(language, file->filename[0])) {
printf("Language file could not be loaded!\n");
goto exit_0;
}
// Print
int id = str->ival[0];
if(id < 0) {
for(int i = 0; i < language->count; i++) {
printf("Title: %s\n", language->strings[i].description);
printf("Data: %s\n", language->strings[i].data);
}
} else if(id >= 0 && id < language->count) {
printf("Title: %s\n", language->strings[id].description);
printf("Data: %s\n", language->strings[id].data);
} else {
printf("String not found!\n");
}
sd_language_delete(language);
exit_0:
arg_freetable(argtable, sizeof(argtable)/sizeof(argtable[0]));
return 0;
}
int main(int argc, char* argv[])
{
// Define our variables.
FILE* in;
FILE* out;
int nerrors, i;
char* test;
uint16_t offset, current, store, mem_index;
struct lprov_entry* required = NULL;
struct lprov_entry* provided = NULL;
struct lprov_entry* adjustment = NULL;
struct lprov_entry* temp = NULL;
// Define arguments.
struct arg_lit* show_help = arg_lit0("h", "help", "Show this help.");
struct arg_file* input_files = arg_filen(NULL, NULL, "<file>", 1, 100, "The input object files.");
struct arg_file* output_file = arg_file1("o", "output", "<file>", "The output file (or - to send to standard output).");
struct arg_end *end = arg_end(20);
void *argtable[] = { show_help, input_files, output_file, end };
// Parse arguments.
nerrors = arg_parse(argc,argv,argtable);
if (nerrors != 0 || show_help->count != 0)
{
if (show_help->count != 0)
arg_print_errors(stdout, end, "linker");
printf("syntax:\n linker");
arg_print_syntax(stdout, argtable, "\n");
printf("options:\n");
arg_print_glossary(stdout, argtable, " %-25s %s\n");
return 1;
}
// Open the output file for writing.
out = fopen(output_file->filename[0], "wb");
if (out == NULL)
{
// Handle the error.
fprintf(stderr, "linker: unable to write to output file.\n");
return 1;
}
// We initially need to get a list of ALL provided
// labels before we can start replacing them.
offset = 0;
for (i = 0; i < input_files->count; i++)
{
// Open the input file.
in = fopen(input_files->filename[i], "rb");
if (in == NULL)
{
// Handle the error.
fprintf(stderr, "linker: unable to read input file '%s'.\n", input_files->filename[i]);
fclose(out);
return 1;
}
// Is this the object format?
test = malloc(strlen(ldata_objfmt) + 1);
memset(test, 0, strlen(ldata_objfmt) + 1);
fread(test, 1, strlen(ldata_objfmt), in);
fseek(in, 1, SEEK_CUR);
if (strcmp(test, ldata_objfmt) != 0)
{
// Handle the error.
fprintf(stderr, "linker: input file '%s' is not in object format 1.0.\n", input_files->filename[i]);
fclose(in);
fclose(out);
return 1;
}
free(test);
// Load only the provided label entries into memory.
objfile_load(input_files->filename[i], in, &offset, &provided, NULL, NULL);
// Close the file.
fclose(in);
}
// Now we can start replacing the labels with the provided values
// since we have ALL of the provided labels available.
offset = 0;
for (i = 0; i < input_files->count; i++)
{
// Open the input file.
in = fopen(input_files->filename[i], "rb");
if (in == NULL)
{
// Handle the error.
fprintf(stderr, "linker: unable to read input file '%s'.\n", input_files->filename[i]);
fclose(out);
return 1;
}
// Skip over the object format label; we already tested
// for this in phase 1.
fseek(in, strlen(ldata_objfmt) + 1, SEEK_CUR);
// Load only the required and adjustment entries into memory.
current = offset;
objfile_load(input_files->filename[i], in, &offset, NULL, &required, &adjustment);
// Copy all of the input file's data into the output
// file, word by word.
mem_index = 0;
fprintf(stderr, "BEGIN %s\n", input_files->filename[i]);
while (!feof(in))
{
// Read a word.
fread(&store, sizeof(uint16_t), 1, in);
// For some strange reason, the last two bytes get
// written twice, as if it's only EOF after you
// attempt to read past the end again. I'm not sure
// why the semantics are like this, but checking again
// for EOF here prevents us writing double.
if (feof(in))
break;
// Check to see if we need to do something with this
// word, such as adjusting it.
if (lprov_find_by_address(adjustment, mem_index) != NULL)
{
// We need to adjust this word by the offset.
store += current;
fprintf(stderr, "ADJUSTED 0x%04X: 0x%04X -> 0x%04X\n", mem_index, store - current, store);
}
// Check to see if we need to resolve this word into
// an actual address because it was imported.
temp = lprov_find_by_address(required, mem_index);
if (temp != NULL)
{
// Find the position we should change this to.
temp = lprov_find_by_label(provided, temp->label);
// We need to set this word to the proper location.
fprintf(stderr, "RESOLVED 0x%04X: 0x%04X -> 0x%04X\n", mem_index, store, temp->address);
store = temp->address;
}
// Now write the (potentially modified) word to the
// output.
fprintf(stderr, " >> WRITE 0x%04X\n", store);
fwrite(&store, sizeof(uint16_t), 1, out);
// Increment memory position.
mem_index++;
}
// Close the file.
fclose(in);
// Reset and free the required and adjustment linked list.
// FIXME: Actually free the lists!
required = NULL;
adjustment = NULL;
}
// Close file.
fprintf(stderr, "linker: completed successfully.\n", input_files->filename[i]);
fclose(out);
return 0;
}
int main(int argc, char *argv[]) {
// commandline argument parser options
struct arg_lit *help = arg_lit0("h", "help", "print this help and exit");
struct arg_lit *vers = arg_lit0("v", "version", "print version information and exit");
struct arg_file *file = arg_file1("f", "file", "<file>", "Score file");
struct arg_int *page = arg_int0("p", "page", "<int>", "Page ID");
struct arg_file *output = arg_file0("o", "output", "<file>", "Output file");
struct arg_end *end = arg_end(20);
void* argtable[] = {help,vers,file,page,output,end};
const char* progname = "scoretool";
// Make sure everything got allocated
if(arg_nullcheck(argtable) != 0) {
printf("%s: insufficient memory\n", progname);
goto exit_0;
}
// Parse arguments
int nerrors = arg_parse(argc, argv, argtable);
// Handle help
if(help->count > 0) {
printf("Usage: %s", progname);
arg_print_syntax(stdout, argtable, "\n");
printf("\nArguments:\n");
arg_print_glossary(stdout, argtable, "%-25s %s\n");
goto exit_0;
}
// Handle version
if(vers->count > 0) {
printf("%s v0.1\n", progname);
printf("Command line One Must Fall 2097 Score file editor.\n");
printf("Source code is available at https://github.com/omf2097 under MIT license.\n");
printf("(C) 2014 Tuomas Virtanen\n");
goto exit_0;
}
// Handle errors
if(nerrors > 0) {
arg_print_errors(stdout, end, progname);
printf("Try '%s --help' for more information.\n", progname);
goto exit_0;
}
// Get score information
sd_score score;
sd_score_create(&score);
int ret = sd_score_load(&score, file->filename[0]);
if(ret != SD_SUCCESS) {
printf("Score file %s could not be loaded: %s\n",
file->filename[0],
sd_get_error(ret));
goto exit_0;
}
// See if we want to print a single page or all pages
if(page->count > 0) {
int page_id = page->ival[0];
if(page_id < 0 || page_id >= SD_SCORE_PAGES) {
printf("Page must be between 0 and 3.\n");
goto exit_1;
}
// Print only this page
print_page(&score, page_id);
} else {
for(int i = 0; i < SD_SCORE_PAGES; i++) {
print_page(&score, i);
printf("\n");
}
}
// Save if necessary
if(output->count > 0) {
ret = sd_score_save(&score, output->filename[0]);
if(ret != SD_SUCCESS) {
printf("Failed to save scores file to %s: %s\n",
output->filename[0],
sd_get_error(ret));
}
}
exit_1:
sd_score_free(&score);
exit_0:
arg_freetable(argtable, sizeof(argtable)/sizeof(argtable[0]));
return 0;
}
int main(int argc, char* argv[])
{
// Define our variables.
FILE* load;
uint16_t flash[0x10000];
char leading[0x100];
unsigned int i;
bool uread = true;
vm_t* vm;
int nerrors;
bstring ss, st;
host_context_t* dtemu = malloc(sizeof(host_context_t));
const char* warnprefix = "no-";
// Define arguments.
struct arg_lit* show_help = arg_lit0("h", "help", "Show this help.");
struct arg_file* input_file = arg_file1(NULL, NULL, "<file>", "The input file, or - to read from standard input.");
struct arg_file* execution_dump_file = arg_file0("e", "execution-dump", "<file>", "Produce a very large execution dump file.");
struct arg_lit* debug_mode = arg_lit0("d", "debug", "Show each executed instruction.");
struct arg_lit* terminate_mode = arg_lit0("t", "show-on-terminate", "Show state of machine when program is terminated.");
struct arg_lit* headless_mode = arg_lit0("h", "headless", "Run machine witout displaying monitor and SPED output");
struct arg_lit* legacy_mode = arg_lit0("l", "legacy", "Automatically initialize hardware to legacy values.");
struct arg_str* warning_policies = arg_strn("W", NULL, "policy", 0, _WARN_COUNT * 2 + 10, "Modify warning policies.");
struct arg_lit* little_endian_mode = arg_lit0(NULL, "little-endian", "Use little endian serialization (for compatibility with older versions).");
struct arg_lit* verbose = arg_litn("v", NULL, 0, LEVEL_EVERYTHING - LEVEL_DEFAULT, "Increase verbosity.");
struct arg_lit* quiet = arg_litn("q", NULL, 0, LEVEL_DEFAULT - LEVEL_SILENT, "Decrease verbosity.");
struct arg_int* radiation = arg_intn("r", NULL, "<n>", 0, 1, "Radiation factor (higher is less radiation)");
struct arg_lit* catch_fire = arg_lit0("c", "catch-fire", "The virtual machine should catch fire instead of halting.");
struct arg_end* end = arg_end(20);
void* argtable[] = { input_file, warning_policies, debug_mode, execution_dump_file, terminate_mode, headless_mode, legacy_mode, little_endian_mode, radiation, catch_fire, verbose, quiet, end };
// Parse arguments.
nerrors = arg_parse(argc, argv, argtable);
if (nerrors != 0 || show_help->count != 0)
{
if (show_help->count != 0)
arg_print_errors(stdout, end, "emulator");
printd(LEVEL_DEFAULT, "syntax:\n dtemu");
arg_print_syntax(stderr, argtable, "\n");
printd(LEVEL_DEFAULT, "options:\n");
arg_print_glossary(stderr, argtable, " %-25s %s\n");
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
// Set verbosity level.
debug_setlevel(LEVEL_DEFAULT + verbose->count - quiet->count);
// Show version information.
version_print(bautofree(bfromcstr("Emulator")));
// Set global path variable.
osutil_setarg0(bautofree(bfromcstr(argv[0])));
// Set endianness.
isetmode(little_endian_mode->count == 0 ? IMODE_BIG : IMODE_LITTLE);
// Set up warning policies.
dsetwarnpolicy(warning_policies);
// Set up error handling.
if (dsethalt())
{
// Handle the error.
dautohandle();
printd(LEVEL_ERROR, "emulator: error occurred.\n");
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
// Zero out the flash space.
for (i = 0; i < 0x10000; i++)
flash[i] = 0x0;
// Zero out the leading space.
for (i = 0; i < 0x100; i++)
leading[i] = 0x0;
// Load from either file or stdin.
if (strcmp(input_file->filename[0], "-") != 0)
{
// Open file.
load = fopen(input_file->filename[0], "rb");
if (load == NULL)
dhalt(ERR_EMU_LOAD_FILE_FAILED, input_file->filename[0]);
}
else
{
// Windows needs stdin in binary mode.
#ifdef _WIN32
_setmode(_fileno(stdin), _O_BINARY);
#endif
// Set load to stdin.
load = stdin;
}
// Read leading component.
for (i = 0; i < strlen(ldata_objfmt); i++)
leading[i] = fgetc(load);
fseek(load, 0, SEEK_SET);
// Read up to 0x10000 words.
for (i = 0; i < 0x10000 && !feof(load); i++)
iread(&flash[i], load);
fclose(load);
// Check to see if the first X bytes matches the header
// for intermediate code and stop if it does.
ss = bfromcstr("");
st = bfromcstr(ldata_objfmt);
for (i = 0; i < strlen(ldata_objfmt); i++)
bconchar(ss, leading[i]);
if (biseq(ss, st))
dhalt(ERR_INTERMEDIATE_EXECUTION, NULL);
// Set up the host context.
glfwInit();
dtemu->create_context = &dtemu_create_context;
dtemu->activate_context = &dtemu_activate_context;
dtemu->swap_buffers = &dtemu_swap_buffers;
dtemu->destroy_context = &dtemu_destroy_context;
dtemu->get_ud = &dtemu_get_ud;
// And then use the VM.
vm = vm_create();
vm->debug = (debug_mode->count > 0);
vm_flash(vm, flash);
// Set radiation and catch fire settings.
if (radiation->count == 1)
vm->radiation_factor = radiation->ival[0];
if (catch_fire->count == 1)
vm->can_fire = true;
// Init hardware.
vm_hw_clock_init(vm);
if (headless_mode->count < 1)
vm->host = dtemu;
vm_hw_sped3_init(vm);
vm_hw_lem1802_init(vm);
vm_hw_m35fd_init(vm);
vm_hw_lua_init(vm);
if (legacy_mode->count > 0)
{
for (i = 0; i < vm_hw_count(vm); i++) {
hw_t* device = vm_hw_get_device(vm, i);
if (device == NULL)
continue;
if (device->id == 0x7349F615 && device->manufacturer == 0x1C6C8B36)
{
vm_hw_lem1802_mem_set_screen((struct lem1802_hardware*)device->userdata, 0x8000);
break;
}
}
}
vm_execute(vm, execution_dump_file->count > 0 ? execution_dump_file->filename[0] : NULL);
if (terminate_mode->count > 0)
{
fprintf(stderr, "\n");
fprintf(stderr, "A: 0x%04X [A]: 0x%04X\n", vm->registers[REG_A], vm->ram[vm->registers[REG_A]]);
fprintf(stderr, "B: 0x%04X [B]: 0x%04X\n", vm->registers[REG_B], vm->ram[vm->registers[REG_B]]);
fprintf(stderr, "C: 0x%04X [C]: 0x%04X\n", vm->registers[REG_C], vm->ram[vm->registers[REG_C]]);
fprintf(stderr, "X: 0x%04X [X]: 0x%04X\n", vm->registers[REG_X], vm->ram[vm->registers[REG_X]]);
fprintf(stderr, "Y: 0x%04X [Y]: 0x%04X\n", vm->registers[REG_Y], vm->ram[vm->registers[REG_Y]]);
fprintf(stderr, "Z: 0x%04X [Z]: 0x%04X\n", vm->registers[REG_Z], vm->ram[vm->registers[REG_Z]]);
fprintf(stderr, "I: 0x%04X [I]: 0x%04X\n", vm->registers[REG_I], vm->ram[vm->registers[REG_I]]);
fprintf(stderr, "J: 0x%04X [J]: 0x%04X\n", vm->registers[REG_J], vm->ram[vm->registers[REG_J]]);
fprintf(stderr, "PC: 0x%04X SP: 0x%04X\n", vm->pc, vm->sp);
fprintf(stderr, "EX: 0x%04X IA: 0x%04X\n", vm->ex, vm->ia);
}
vm_hw_lua_free(vm);
vm_free(vm);
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
glfwTerminate();
return 0;
}
int main(int argc, char* argv[])
{
// Define arguments.
struct arg_lit* show_help = arg_lit0("h", "help", "Show this help.");
struct arg_str* type_assembler = arg_str0("t", NULL, "<type>", "The type of assembler to output for.");
struct arg_file* input_file = arg_file1(NULL, NULL, "<file>", "The input file (or - to read from standard input).");
struct arg_file* output_file = arg_file1("o", "output", "<file>", "The output file (or - to send to standard output).");
// 20 is maxcount for include directories, this has to be set to some constant number.
struct arg_file* include_dirs = arg_filen("I", NULL, "<directory>", 0, 20, "Adds the directory <dir> to the directories to be searched for header files.");
struct arg_lit* verbose = arg_litn("v", NULL, 0, LEVEL_EVERYTHING - LEVEL_DEFAULT, "Increase verbosity.");
struct arg_lit* quiet = arg_litn("q", NULL, 0, LEVEL_DEFAULT - LEVEL_SILENT, "Decrease verbosity.");
struct arg_end* end = arg_end(20);
void* argtable[] = { output_file, show_help, type_assembler, include_dirs, input_file, verbose, quiet, end };
// Parse arguments.
int nerrors = arg_parse(argc, argv, argtable);
version_print(bautofree(bfromcstr("Compiler")));
if (nerrors != 0 || show_help->count != 0)
{
if (nerrors != 0)
arg_print_errors(stderr, end, "compiler");
fprintf(stderr, "syntax:\n dtcc");
arg_print_syntax(stderr, argtable, "\n");
fprintf(stderr, "options:\n");
arg_print_glossary(stderr, argtable, " %-25s %s\n");
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
// Set verbosity level.
debug_setlevel(LEVEL_DEFAULT + verbose->count - quiet->count);
// Set global path variable.
osutil_setarg0(bautofree(bfromcstr(argv[0])));
// Run the preprocessor.
ppfind_add_path(bautofree(bfromcstr(".")));
ppfind_add_path(bautofree(bfromcstr("include")));
ppfind_add_autopath(bautofree(bfromcstr(input_file->filename[0])));
for (int i = 0; i < include_dirs->count; ++i)
ppfind_add_path(bautofree(bfromcstr(include_dirs->filename[i])));
bstring pp_result_name = pp_do(bautofree(bfromcstr(input_file->filename[0])));
if (pp_result_name == NULL)
{
fprintf(stderr, "compiler: invalid result returned from preprocessor.\n");
pp_cleanup(bautofree(pp_result_name));
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
// Parse C.
yyout = stderr;
yyin = fopen((const char*)(pp_result_name->data), "r");
if (yyin == NULL)
{
pp_cleanup(bautofree(pp_result_name));
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
yyparse();
if (yyin != stdin)
fclose(yyin);
pp_cleanup(bautofree(pp_result_name));
if (program == NULL)
{
std::cerr << "An error occurred while compiling." << std::endl;
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
// Assembler type.
const char* asmtype = "toolchain";
if (type_assembler->count > 0)
asmtype = type_assembler->sval[0];
// Initially save to a temporary file.
std::string temp = std::string(tempnam(".", "cc."));
// Generate assembly using the AST.
try
{
AsmGenerator generator(asmtype);
AsmBlock* block = program->compile(generator);
std::ofstream output(temp.c_str(), std::ios::out | std::ios::trunc);
if (output.bad() || output.fail())
{
printd(LEVEL_ERROR, "compiler: temporary file not writable.\n");
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
output << *block << std::endl;
output.close();
delete block;
}
catch (CompilerException* ex)
{
std::string msg = ex->getMessage();
std::cerr << "An error occurred while compiling." << std::endl;
std::cerr << msg << std::endl;
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
// Re-open the temporary file for reading.
std::ifstream input(temp.c_str(), std::ios::in);
if (input.bad() || input.fail())
{
printd(LEVEL_ERROR, "compiler: temporary file not readable.\n");
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
// Open the output file.
std::ostream* output;
if (strcmp(output_file->filename[0], "-") != 0)
{
// Write to file.
output = new std::ofstream(output_file->filename[0], std::ios::out | std::ios::trunc);
if (output->bad() || output->fail())
{
printd(LEVEL_ERROR, "compiler: output file not readable.\n");
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
}
else
{
// Set output to cout.
output = &std::cout;
}
// Copy data.
std::copy(std::istreambuf_iterator<char>(input), std::istreambuf_iterator<char>(), std::ostreambuf_iterator<char>(*output));
// Close files and delete temporary.
if (strcmp(output_file->filename[0], "-") != 0)
{
((std::ofstream*)output)->close();
delete output;
}
input.close();
unlink(temp.c_str());
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 0;
}
int main(int argc, char* argv[]) {
#ifdef BALL
double discountFactor = 0.9;
#else
#ifdef CART_POLE
double discountFactor = 0.95;
#else
#ifdef DOUBLE_CART_POLE
double discountFactor = 0.95;
#else
#ifdef MOUNTAIN_CAR
double discountFactor = 0.99;
#else
#ifdef ACROBOT
double discountFactor = 0.95;
#else
#ifdef BOAT
double discountFactor = 0.95;
#else
#ifdef SWIMMER
double discountFactor = 0.95;
#endif
#endif
#endif
#endif
#endif
#endif
#endif
FILE* initFileFd = NULL;
state** initialStates = NULL;
FILE* results = NULL;
char str[1024];
unsigned int i = 0;
unsigned int* ns = NULL;
unsigned int nbN = 0;
unsigned int* hs = NULL;
unsigned int nbH = 0;
unsigned int n = 0;
unsigned int nbSteps = 0;
unsigned int nbIterations = 1;
unsigned int timestamp = time(NULL);
int readFscanf = -1;
random_search_instance* random_search = NULL;
struct arg_file* initFile = arg_file1(NULL, "init", "<file>", "File containing the inital state");
struct arg_str* r = arg_str1("n", NULL, "<s>", "List of maximum numbers of evaluations");
struct arg_str* d = arg_str1("h", NULL, "<s>", "List of depth");
struct arg_int* s = arg_int1("s", NULL, "<n>", "Number of steps");
struct arg_int* it = arg_int1("i", NULL, "<n>", "Number of iteration");
struct arg_file* where = arg_file1(NULL, "where", "<file>", "Directory where we save the outputs");
struct arg_end* end = arg_end(7);
int nerrors = 0;
void* argtable[7];
argtable[0] = initFile;
argtable[1] = r;
argtable[2] = d;
argtable[3] = s;
argtable[4] = it;
argtable[5] = where;
argtable[6] = end;
if(arg_nullcheck(argtable) != 0) {
printf("error: insufficient memory\n");
arg_freetable(argtable, 7);
return EXIT_FAILURE;
}
nerrors = arg_parse(argc, argv, argtable);
if(nerrors > 0) {
printf("%s:", argv[0]);
arg_print_syntax(stdout, argtable, "\n");
arg_print_errors(stdout, end, argv[0]);
arg_freetable(argtable, 7);
return EXIT_FAILURE;
}
initGenerativeModelParameters();
initGenerativeModel();
initFileFd = fopen(initFile->filename[0], "r");
readFscanf = fscanf(initFileFd, "%u\n", &n);
initialStates = (state**)malloc(sizeof(state*) * n);
for(; i < n; i++) {
readFscanf = fscanf(initFileFd, "%s\n", str);
initialStates[i] = makeState(str);
}
fclose(initFileFd);
nbSteps = s->ival[0];
nbIterations = it->ival[0];
ns = parseUnsignedIntList((char*)r->sval[0], &nbN);
hs = parseUnsignedIntList((char*)d->sval[0], &nbH);
random_search = random_search_initInstance(NULL, discountFactor);
h_max = h_max_crt_depth;
sprintf(str, "%s/%u_results_random_search_%s.csv", where->filename[0], timestamp,(char*)r->sval[0]);
results = fopen(str, "w");
for(i = 0; i < nbIterations; i++) {
unsigned int j = 0;
for(;j < nbH; j++) {
unsigned int k = 0;
crtDepth = hs[j];
for(; k < nbN; k++) {
unsigned int l = 0;
double sumRewards = 0.0;
for(; l < n; l++) {
unsigned int m = 0;
state* crt = copyState(initialStates[l]);
for(; m < nbSteps; m++) {
char isTerminal = 0;
double reward = 0.0;
state* nextState = NULL;
double* optimalAction = NULL;
random_search_resetInstance(random_search, crt);
optimalAction = random_search_planning(random_search, ns[k]);
isTerminal = nextStateReward(crt, optimalAction, &nextState, &reward) < 0 ? 1 : 0;
freeState(crt);
free(optimalAction);
crt = nextState;
sumRewards += reward;
if(isTerminal)
break;
}
random_search_resetInstance(random_search, crt);
freeState(crt);
printf(">>>>>>>>>>>>>> %uth initial state processed with h=%u and n=%u of iteration %u\n", l + 1, hs[j], ns[k], i+1);
fflush(NULL);
}
fprintf(results, "%u,%u,%.15f\n", hs[j],ns[k], sumRewards / (double)n);
printf(">>>>>>>>>>>>>> n = %u done\n\n", ns[k]);
fflush(NULL);
}
printf(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> h = %u done \n\n", hs[j]);
fflush(NULL);
}
fprintf(results,"\n");
printf(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ITERATION %u DONE <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n\n\n", i+1);
fflush(NULL);
}
fclose(results);
arg_freetable(argtable, 7);
for(i = 0; i < n; i++)
freeState(initialStates[i]);
free(initialStates);
random_search_uninitInstance(&random_search);
freeGenerativeModel();
freeGenerativeModelParameters();
return EXIT_SUCCESS;
}
int main(int argc, char* argv[]) {
double discountFactor = 0.9;
FILE* initFileFd = NULL;
double* setPoints = NULL;
unsigned int nbSetPoints = 0;
unsigned int maxDepth = 0;
FILE* results = NULL;
char str[1024];
unsigned int i = 0;
unsigned int minDepth = 1;
unsigned int crtDepth = 0;
unsigned int maxNbIterations = 0;
unsigned int nbSteps = 0;
unsigned int timestamp = time(NULL);
int readFscanf = -1;
optimistic_instance* optimistic = NULL;
random_search_instance* random_search = NULL;
uct_instance* uct = NULL;
uniform_instance* uniform = NULL;
struct arg_file* initFile = arg_file1(NULL, "init", "<file>", "File containing the set points");
struct arg_int* d2 = arg_int0(NULL, "min", "<n>", "Minimum depth to start from (min>0)");
struct arg_int* d = arg_int1("d", NULL, "<n>", "Maximum depth of an uniform tree which the number of call per step");
struct arg_int* s = arg_int1("s", NULL, "<n>", "Number of steps");
struct arg_int* k = arg_int1("k", NULL, "<n>", "Branching factor of the problem");
struct arg_file* where = arg_file1(NULL, "where", "<file>", "Directory where we save the outputs");
struct arg_end* end = arg_end(7);
int nerrors = 0;
void* argtable[7];
argtable[0] = initFile;
argtable[1] = d2;
argtable[2] = d;
argtable[3] = s;
argtable[4] = k;
argtable[5] = where;
argtable[6] = end;
if(arg_nullcheck(argtable) != 0) {
printf("error: insufficient memory\n");
arg_freetable(argtable, 7);
return EXIT_FAILURE;
}
nerrors = arg_parse(argc, argv, argtable);
if(nerrors > 0) {
printf("%s:", argv[0]);
arg_print_syntax(stdout, argtable, "\n");
arg_print_errors(stdout, end, argv[0]);
arg_freetable(argtable, 7);
return EXIT_FAILURE;
}
initGenerativeModelParameters();
K = k->ival[0];
initGenerativeModel();
initFileFd = fopen(initFile->filename[0], "r");
readFscanf = fscanf(initFileFd, "%u\n", &nbSetPoints);
setPoints = (double*)malloc(sizeof(double) * nbSetPoints);
for(; i < nbSetPoints; i++) {
readFscanf = fscanf(initFileFd, "%s\n", str);
setPoints[i] = strtod(str, NULL);
}
fclose(initFileFd);
if(d2->count)
minDepth = d2->ival[0];
maxDepth = d->ival[0];
maxNbIterations = K;
nbSteps = s->ival[0];
optimistic = optimistic_initInstance(NULL, discountFactor);
random_search = random_search_initInstance(NULL, discountFactor);
uct = uct_initInstance(NULL, discountFactor);
uniform = uniform_initInstance(NULL, discountFactor);
sprintf(str, "%s/%u_results_%u_%u.csv", where->filename[0], timestamp, K, nbSteps);
results = fopen(str, "w");
for(crtDepth = 1; crtDepth < minDepth; crtDepth++)
maxNbIterations += pow(K, crtDepth+1);
for(crtDepth = minDepth; crtDepth <= maxDepth; crtDepth++) {
double averages[4] = {0.0, 0.0, 0.0, 0.0};
state* crt1 = initState();
state* crt2 = copyState(crt1);
state* crt3 = copyState(crt1);
state* crt4 = copyState(crt1);
optimistic_resetInstance(optimistic, crt1);
uct_resetInstance(uct, crt3);
uniform_resetInstance(uniform, crt4);
for(i = 0; i < nbSetPoints; i++) {
unsigned int j = 0;
parameters[10] = setPoints[i];
for(; j < nbSteps; j++) {
char isTerminal = 0;
double reward = 0.0;
state* nextState = NULL;
optimistic_keepSubtree(optimistic);
action* optimalAction = optimistic_planning(optimistic, maxNbIterations);
isTerminal = nextStateReward(crt1, optimalAction, &nextState, &reward);
freeState(crt1);
crt1 = nextState;
averages[0] += reward;
if(isTerminal < 0)
break;
}
optimistic_resetInstance(optimistic, crt1);
printf("Optimistic : %uth set point processed\n", i + 1);
for(j = 0; j < nbSteps; j++) {
char isTerminal = 0;
double reward = 0.0;
state* nextState = NULL;
random_search_resetInstance(random_search, crt2);
action* optimalAction = random_search_planning(random_search, maxNbIterations);
isTerminal = nextStateReward(crt2, optimalAction, &nextState, &reward);
freeState(crt2);
crt2 = nextState;
averages[1] += reward;
if(isTerminal < 0)
break;
}
random_search_resetInstance(random_search, crt1);
printf("Random search: %uth set point processed\n", i + 1);
for(j = 0; j < nbSteps; j++) {
char isTerminal = 0;
double reward = 0.0;
state* nextState = NULL;
uct_keepSubtree(uct);
action* optimalAction = uct_planning(uct, maxNbIterations);
isTerminal = nextStateReward(crt3, optimalAction, &nextState, &reward);
freeState(crt3);
crt3 = nextState;
averages[2] += reward;
if(isTerminal < 0)
break;
}
uct_resetInstance(uct, crt3);
printf("Uct : %uth set point processed\n", i + 1);
for(j = 0; j < nbSteps; j++) {
char isTerminal = 0;
double reward = 0.0;
state* nextState = NULL;
uniform_keepSubtree(uniform);
action* optimalAction = uniform_planning(uniform, maxNbIterations);
isTerminal = nextStateReward(crt4, optimalAction, &nextState, &reward);
freeState(crt4);
crt4 = nextState;
averages[3] += reward;
if(isTerminal < 0)
break;
}
uniform_resetInstance(uniform, crt4);
printf("Uniform : %uth set point processed\n", i + 1);
printf(">>>>>>>>>>>>>> %uth set point processed\n", i + 1);
}
fprintf(results, "%u,%.15f,%.15f,%.15f,%.15f\n", maxNbIterations, averages[0] / (double)nbSetPoints, averages[1] / (double)nbSetPoints, averages[2] / (double)nbSetPoints, averages[3] / (double)nbSetPoints);
fflush(results);
freeState(crt1);
freeState(crt2);
freeState(crt3);
freeState(crt4);
printf(">>>>>>>>>>>>>> %u depth done\n\n", crtDepth);
maxNbIterations += pow(K, crtDepth+1);
}
fclose(results);
arg_freetable(argtable, 7);
free(setPoints);
optimistic_uninitInstance(&optimistic);
random_search_uninitInstance(&random_search);
uct_uninitInstance(&uct);
uniform_uninitInstance(&uniform);
freeGenerativeModel();
freeGenerativeModelParameters();
return EXIT_SUCCESS;
}
int main(int argc, char* argv[]) {
// commandline argument parser options
struct arg_lit *help = arg_lit0("h", "help", "print this help and exit");
struct arg_lit *vers = arg_lit0("v", "version", "print version information and exit");
struct arg_file *file = arg_file1("f", "file", "<file>", "Input altpals file");
struct arg_int *pal = arg_int1("p", "palette", "<number>", "Select a palette");
struct arg_file *export = arg_file0("e", "export", "<file>", "Export selected palette to GPL file");
struct arg_file *import = arg_file0("i", "import", "<file>", "Import selected palette from GPL file");
struct arg_file *output = arg_file0("o", "output", "<file>", "Output altpals file");
struct arg_end *end = arg_end(20);
void* argtable[] = {help,vers,file,pal,output,import,export,end};
const char* progname = "altpaltool";
// Make sure everything got allocated
if(arg_nullcheck(argtable) != 0) {
printf("%s: insufficient memory\n", progname);
goto exit_0;
}
// Parse arguments
int nerrors = arg_parse(argc, argv, argtable);
// Handle help
if(help->count > 0) {
printf("Usage: %s", progname);
arg_print_syntax(stdout, argtable, "\n");
printf("\nArguments:\n");
arg_print_glossary(stdout, argtable, "%-25s %s\n");
goto exit_0;
}
// Handle version
if(vers->count > 0) {
printf("%s v0.1\n", progname);
printf("Command line One Must Fall 2097 Altpals file editor.\n");
printf("Source code is available at https://github.com/omf2097 under MIT license.\n");
printf("(C) 2014 Tuomas Virtanen\n");
goto exit_0;
}
// Handle errors
if(nerrors > 0) {
arg_print_errors(stdout, end, progname);
printf("Try '%s --help' for more information.\n", progname);
goto exit_0;
}
// Need import or export ...
if(pal->count > 0 && import->count == 0 && export->count == 0) {
printf("Define either --import or --export with --palette!\n");
goto exit_0;
}
// Make sure output is set
if(import->count > 0 && output->count <= 0) {
printf("Define --output with --import.\n");
goto exit_0;
}
// Load file
sd_altpal_file alt;
sd_altpal_create(&alt);
int ret = sd_altpals_load(&alt, file->filename[0]);
if(ret != SD_SUCCESS) {
printf("Unable to load altpals file %s: %s.\n",
file->filename[0],
sd_get_error(ret));
goto exit_1;
}
// Check ID
int pal_id = pal->ival[0];
if(pal_id < 0 || pal_id > SD_ALTPALS_PALETTES) {
printf("Palette index %d does not exist!\n", pal_id);
goto exit_1;
}
// Check what to do
if(export->count > 0) {
ret = sd_palette_to_gimp_palette(&alt.palettes[pal_id], export->filename[0]);
if(ret == SD_SUCCESS) {
printf("Palette %d exported to file %s succesfully.\n",
pal_id,
export->filename[0]);
} else {
int main(int argc, char *argv[]) {
#ifndef _OPENMP
fprintf(stderr, "\nERROR: Program built with compiler lacking OpenMP support.\n");
fprintf(stderr, "See SEAStAR README file for information about suitable compilers.\n");
exit(EXIT_FAILURE);
#endif
///////////////////////////
// Variable declarations
///////////////////////////
// Input filenames
UT_string *in_read1_fq_fn, *in_read2_fq_fn, *in_single1_fq_fn, *in_single2_fq_fn;
utstring_new(in_read1_fq_fn);
utstring_new(in_read2_fq_fn);
utstring_new(in_single1_fq_fn);
utstring_new(in_single2_fq_fn);
// Output filenames
UT_string *out_read1_fn, *out_read2_fn, *out_single1_fn, *out_single2_fn, *out_mates_fn, *out_filetype;
utstring_new(out_filetype);
utstring_new(out_read1_fn);
utstring_new(out_read2_fn);
utstring_new(out_single1_fn);
utstring_new(out_single2_fn);
utstring_new(out_mates_fn);
// Read name prefix
UT_string *out_read_prefix;
utstring_new(out_read_prefix);
// Flags
int singles_flag = 0; // 1 when two output singles files being written
int num_input_singles_files = 0;
// Read counters
unsigned long int mp_org = 0, R1_org = 0, R2_org = 0, singlet1_org = 0, singlet2_org = 0;
unsigned long int mp_cnt = 0, R1_cnt = 0, R2_cnt = 0, singlet1_cnt = 0, singlet2_cnt = 0, s1_cnt = 0, s2_cnt = 0;
unsigned long int comp_r1 = 0, comp_r2 = 0, comp_s1 = 0, comp_s2 = 0;
unsigned long int read1_singlet_cnt = 0, read2_singlet_cnt = 0;
////////////////////////////////////////////////////////////////////////
// All done with variable declarations!!
///////////////////////////////////
// Command line argtable settings
///////////////////////////////////
struct arg_lit *gzip = arg_lit0("z", "gzip", "Output converted files in gzip compressed format. [NULL]");
struct arg_lit *inv_singles = arg_lit0("v", "invert_singles", "Causes singles output to be the inverse of the input. 2->1 or 1->2 [NULL]");
struct arg_lit *num_singles = arg_lit0("s", "singles", "Write two singlet files, one for each mate-paired input file. [NULL]");
struct arg_rem *sing_rem = arg_rem(NULL, "Note! -v is only valid when there are input singlet reads. -s is only valid when there are NO input singlet reads.");
struct arg_str *pre_read_id = arg_str0(NULL, "prefix", "<string>", "Prefix to add to read identifiers. [out_prefix]");
struct arg_lit *no_pre = arg_lit0(NULL, "no_prefix", "Do not change the read names in any way. [NULL]");
struct arg_lit *pre_read_len = arg_lit0(NULL, "add_len", "Add the final trimmed length value to the read id prefix. [length not added]");
struct arg_dbl *prob = arg_dbl0("p","correct_prob","<d>","Probability that output reads are correct. 0.0 disables quality trimming. [0.5]");
struct arg_int *fixed_len = arg_int0("f","fixed_len","<u>","Trim all reads to a fixed length, still filtering on quality [no fixed length]");
struct arg_int *len = arg_int0("l","min_read_len","<u>","Minimum length of a singlet or longest-mate in nucleotides [24]");
struct arg_int *mate_len = arg_int0("m","min_mate_len","<u>","Minimum length of the shortest mate in nucleotides [min_read_len]");
struct arg_dbl *entropy = arg_dbl0("e","entropy_filter","<d>","Remove reads with per position information below given value (in bits per dinucleotide) [No filter]");
struct arg_lit *entropy_strict = arg_lit0(NULL, "entropy_strict", "Reject reads for low entropy overall, not just the retained part after trimming [NULL]");
struct arg_lit *mates = arg_lit0(NULL, "mates_file", "Produce a Velvet compatible interleaved paired read output file (e.g. <out_prefix>_mates.fastq). [NULL]");
struct arg_lit *no_rev = arg_lit0(NULL, "no_rev", "By default, the second read in each pair is reversed for colorspace --mate-file output. --no_rev disables reversing. [rev]");
struct arg_lit *only_mates = arg_lit0(NULL, "only_mates", "Supress writing .read1 and .read2 outputs. Requires --mates_file. [NULL]");
struct arg_lit *fasta = arg_lit0(NULL, "fasta", "Write FASTA format files instead of FASTQ for all outputs (e.g. <out_prefix>.<read_type>.fasta). [FASTQ]");
struct arg_file *input = arg_file1(NULL, NULL, "<in_prefix>", "Input file prefix: (e.g. <in_prefix>_single.fastq [<in_prefix>_read1.fastq <in_prefix>_read2.fastq]) ");
struct arg_file *output = arg_file1(NULL, NULL, "<out_prefix>", "Output file prefix: (e.g. <out_prefix>_single.fastq [<out_prefix>_read1.fastq <out_prefix>_read2.fastq]) ");
struct arg_lit *version = arg_lit0(NULL,"version","Print the build version and exit.");
struct arg_lit *h = arg_lit0("h", "help", "Request help.");
struct arg_end *end = arg_end(20);
void *argtable[] = {h,version,gzip,inv_singles,num_singles,sing_rem,prob,len,mate_len,fixed_len,pre_read_id,pre_read_len,no_pre,entropy,entropy_strict,mates,no_rev,only_mates,fasta,input,output,end};
int arg_errors = 0;
////////////////////////////////////////////////////////////////////////
// Handle command line processing (via argtable2 library)
////////////////////////////////////////////////////////////////////////
arg_errors = arg_parse(argc, argv, argtable);
if (version->count) {
fprintf(stderr, "%s version: %s\n", argv[0], SS_BUILD_VERSION);
exit(EXIT_SUCCESS);
}
if (h->count) {
fprintf(stderr,"\ntrim_fastq is a utility for performing quality and information-based\n");
fprintf(stderr,"trimming on paired or unpaired, nucleotide or SOLiD colorspace reads. \n\n");
arg_print_syntaxv(stderr, argtable, "\n\n");
arg_print_glossary(stderr, argtable, "%-25s %s\n");
fprintf(stderr, "\nInput and output \"prefixes\" are the part of the filename before:\n");
fprintf(stderr, "_single.fastq [_read1.fastq _read2.fastq] A singlets (single) file\n");
fprintf(stderr, "is required. Mate-paired read files are automatically used if present.\n");
fprintf(stderr, "Multiple output files only produced for mate-paired inputs.\n");
fprintf(stderr, "\nNote! Input and output files may be gzipped, and outputs can be written\n");
fprintf(stderr, "as either FASTQ or FASTA format files.\n");
exit(EXIT_FAILURE);
}
if (arg_errors) {
arg_print_errors(stderr, end, "trimfastq");
arg_print_syntaxv(stderr, argtable, "\n");
exit(EXIT_FAILURE);
}
// Validate entropy
if (entropy->count) {
entropy_cutoff = entropy->dval[0];
if ((entropy_cutoff < 0.0) || (entropy_cutoff > 4.0)) {
fprintf(stderr, "entropy_filter must be [0.0 - 4.0] \n");
exit(EXIT_FAILURE);
}
strict_ent = entropy_strict->count;
} else {
if (entropy_strict->count) {
fprintf(stderr, "Error: --entropy_strict requires --entropy_filter.\n");
exit(EXIT_FAILURE);
}
entropy_cutoff = -1.0;
}
// Validate error_prob
if (prob->count) {
err_prob = prob->dval[0];
if ((err_prob < 0.0) || (err_prob > 1.0)) {
fprintf(stderr, "--correct_prob (-p) must be 0.0 - 1.0 inclusive\n");
exit(EXIT_FAILURE);
}
} else {
err_prob = 0.5;
}
// Validate min read len
if (len->count) {
min_len = len->ival[0];
if (min_len <= 0) {
fprintf(stderr, "min_read_len must be > 0\n");
exit(EXIT_FAILURE);
}
} else {
min_len = 24;
}
// Validate min mate len
if (mate_len->count) {
min_mate_len = mate_len->ival[0];
if (min_mate_len <= 0) {
fprintf(stderr, "min_mate_len must be > 0\n");
exit(EXIT_FAILURE);
}
if (min_mate_len > min_len) {
fprintf(stderr, "min_mate_len must be <= min_len\n");
exit(EXIT_FAILURE);
}
} else {
min_mate_len = min_len;
}
if (fixed_len->count) {
fix_len = min_mate_len = min_len = fixed_len->ival[0];
if ((mate_len->count) || (len->count)) {
fprintf(stderr, "fixed_len cannot be used with min_read_len or min_mate_len\n");
exit(EXIT_FAILURE);
}
if (fix_len <= 0) {
fprintf(stderr, "fixed_len must be > 0\n");
exit(EXIT_FAILURE);
}
} else {
fix_len = 0;
}
if (pre_read_id->count) {
if (no_pre->count) {
fprintf(stderr, "Error: Both --prefix and --no_prefix were specified.\n");
exit(EXIT_FAILURE);
}
if (! strlen(pre_read_id->sval[0])) {
fprintf(stderr, "Read ID prefix may not be zero length.\n");
exit(EXIT_FAILURE);
}
if (strchr(pre_read_id->sval[0], ':') || strchr(pre_read_id->sval[0], '|') || strchr(pre_read_id->sval[0], '+') || strchr(pre_read_id->sval[0], '/')) {
fprintf(stderr, "Read ID prefix '%s' may not contain the characters ':', '|', '+' or '/'.\n", pre_read_id->sval[0]);
exit(EXIT_FAILURE);
}
// Build default read ID prefix
ss_strcat_utstring(out_read_prefix, pre_read_id->sval[0]);
} else {
if (!no_pre->count) {
if (strchr(output->filename[0], ':') || strchr(output->filename[0], '|') || strchr(output->filename[0], '+') || strchr(output->filename[0], '/')) {
fprintf(stderr, "Read ID prefix '%s' (from output prefix) may not contain the characters ':', '|', '+' or '/'.\n", output->filename[0]);
fprintf(stderr, "Hint: Use the --prefix parameter if the output file prefix contains path information.\n");
exit(EXIT_FAILURE);
}
// Build default read ID prefix
ss_strcat_utstring(out_read_prefix, output->filename[0]);
}
}
if ((only_mates->count) && (!mates->count)) {
fprintf(stderr, "--only_mates requires --mates.\n");
exit(EXIT_FAILURE);
}
if ((no_rev->count) && (!mates->count)) {
fprintf(stderr, "--no_rev requires --mates.\n");
exit(EXIT_FAILURE);
}
// Check for null string prefixes
if (!(strlen(input->filename[0]) && strlen(output->filename[0]))) {
fprintf(stderr, "Error: NULL prefix strings are not permitted.\n");
exit(EXIT_FAILURE);
}
// Construct input filenames
utstring_printf(in_read1_fq_fn, "%s.read1.fastq", input->filename[0]);
utstring_printf(in_read2_fq_fn, "%s.read2.fastq", input->filename[0]);
utstring_printf(in_single1_fq_fn, "%s.single.fastq", input->filename[0]);
FILE *in_read_file = NULL;
num_input_singles_files = 1;
// Try to open a singlet fastq file
// Check singlet output options -s and -v
// Set input singlet names to
// - *.single.fastq or
// - *.single1.fastq and *.single2.fastq
if (!(in_read_file = ss_get_gzFile(utstring_body(in_single1_fq_fn), "r"))) {
utstring_clear(in_single1_fq_fn);
utstring_printf(in_single1_fq_fn, "%s.single1.fastq", input->filename[0]);
utstring_printf(in_single2_fq_fn, "%s.single2.fastq", input->filename[0]);
num_input_singles_files = 2;
if ((in_read_file = ss_get_gzFile(utstring_body(in_single1_fq_fn), "r")) || (in_read_file = ss_get_gzFile(utstring_body(in_single2_fq_fn), "r"))) {
singles_flag = 1; // Two singlet outputs
} else {
singles_flag = num_singles->count; // Number of singlet outputs set by -s parm
if (inv_singles->count) {
fprintf(stderr, "Error: Invalid option -v, No input singlet file(s) found. Use -s to select multiple output singlet files.\n");
exit(EXIT_FAILURE);
}
}
}
if (in_read_file) {
gzclose(in_read_file);
if (num_singles->count) {
fprintf(stderr, "Error: Invalid option -s, Input singlet file(s) found, use -v to change the number of output singlet files.\n");
exit(EXIT_FAILURE);
}
}
// singles->count inverts the current singles file input scheme
singles_flag = (singles_flag ^ inv_singles->count);
// Check if input fastq is colorspace
// If some files are colorspace and some are basespace, throw an error
int fcount = 0;
int cscount = 0;
fcount += ss_is_fastq(utstring_body(in_read1_fq_fn));
fcount += ss_is_fastq(utstring_body(in_read2_fq_fn));
fcount += ss_is_fastq(utstring_body(in_single1_fq_fn));
fcount += ss_is_fastq(utstring_body(in_single2_fq_fn));
cscount += (ss_is_fastq(utstring_body(in_read1_fq_fn)) && ss_is_colorspace_fastq(utstring_body(in_read1_fq_fn)));
cscount += (ss_is_fastq(utstring_body(in_read2_fq_fn)) && ss_is_colorspace_fastq(utstring_body(in_read2_fq_fn)));
cscount += (ss_is_fastq(utstring_body(in_single1_fq_fn)) && ss_is_colorspace_fastq(utstring_body(in_single1_fq_fn)));
cscount += (ss_is_fastq(utstring_body(in_single2_fq_fn)) && ss_is_colorspace_fastq(utstring_body(in_single2_fq_fn)));
if (cscount && (cscount != fcount)) {
printf("Error: Mixed colorspace and basespace FASTQ files detected\n");
exit(EXIT_FAILURE);
}
colorspace_flag = cscount ? 1 : 0;
// Output filenames
if (fasta->count) {
ss_strcat_utstring(out_filetype, "fasta");
read_count_divisor = 2;
} else {
ss_strcat_utstring(out_filetype, "fastq");
read_count_divisor = 4;
}
if (!only_mates->count) {
utstring_printf(out_read1_fn, "%s.read1.%s", output->filename[0], utstring_body(out_filetype));
utstring_printf(out_read2_fn, "%s.read2.%s", output->filename[0], utstring_body(out_filetype));
}
if (singles_flag == 1) {
utstring_printf(out_single1_fn, "%s.single1.%s", output->filename[0], utstring_body(out_filetype));
utstring_printf(out_single2_fn, "%s.single2.%s", output->filename[0], utstring_body(out_filetype));
} else {
utstring_printf(out_single1_fn, "%s.single.%s", output->filename[0], utstring_body(out_filetype));
}
if (mates->count) {
utstring_printf(out_mates_fn, "%s.mates.%s", output->filename[0], utstring_body(out_filetype));
}
////////////////////////////////////////////////////////////////////////////////////////////////
// Begin processing!
#ifdef _OPENMP
omp_set_num_threads(10);
#endif
// This is the value of a non-valid pipe descriptor
#define NO_PIPE 0
int r1_pipe[2];
int r2_pipe[2];
int s1_pipe[2];
int s2_pipe[2];
pipe(r1_pipe);
pipe(r2_pipe);
pipe(s1_pipe);
pipe(s2_pipe);
int r1_out_pipe[2];
int r2_out_pipe[2];
int mates_out_pipe[2];
int s1_out_pipe[2];
int s2_out_pipe[2];
pipe(r1_out_pipe);
pipe(r2_out_pipe);
pipe(mates_out_pipe);
pipe(s1_out_pipe);
pipe(s2_out_pipe);
#pragma omp parallel sections default(shared)
{
#pragma omp section
{ // Read1 reader
fq_stream_trimmer(in_read1_fq_fn, r1_pipe[1], out_read_prefix, no_pre->count, pre_read_len->count, &comp_r1, &R1_org, '\0', fasta->count);
}
#pragma omp section
{ // Read1 writer
R1_cnt = ss_stream_writer(out_read1_fn, r1_out_pipe[0], gzip->count) / read_count_divisor;
}
#pragma omp section
{ // Read2 reader
fq_stream_trimmer(in_read2_fq_fn, r2_pipe[1], out_read_prefix, no_pre->count, pre_read_len->count, &comp_r2, &R2_org, '\0', fasta->count);
}
#pragma omp section
{ // Read2 writer
R2_cnt = ss_stream_writer(out_read2_fn, r2_out_pipe[0], gzip->count) / read_count_divisor;
}
#pragma omp section
{ // Single1 reader
// When there is only one input singles file, but two output singles files, then supply which mate to use for this stream in the split parameter
if ((singles_flag) && (num_input_singles_files == 1)) {
singlet1_cnt = fq_stream_trimmer(in_single1_fq_fn, s1_pipe[1], out_read_prefix, no_pre->count, pre_read_len->count, &comp_s1, &singlet1_org, '1', fasta->count);
} else {
singlet1_cnt = fq_stream_trimmer(in_single1_fq_fn, s1_pipe[1], out_read_prefix, no_pre->count, pre_read_len->count, &comp_s1, &singlet1_org, '\0', fasta->count);
}
}
#pragma omp section
{ // Single1 writer
s1_cnt = ss_stream_writer(out_single1_fn, s1_out_pipe[0], gzip->count) / read_count_divisor;
}
#pragma omp section
{ // Single2 reader
// When there is only one input singles file, but two output singles files, then supply which mate to use for this stream in the split parameter
if ((singles_flag) && (num_input_singles_files == 1)) {
singlet2_cnt = fq_stream_trimmer(in_single1_fq_fn, s2_pipe[1], out_read_prefix, no_pre->count, pre_read_len->count, &comp_s2, &singlet2_org, '2', fasta->count);
} else {
singlet2_cnt = fq_stream_trimmer(in_single2_fq_fn, s2_pipe[1], out_read_prefix, no_pre->count, pre_read_len->count, &comp_s2, &singlet2_org, '\0', fasta->count);
}
}
#pragma omp section
{ // Single2 writer
s2_cnt = ss_stream_writer(out_single2_fn, s2_out_pipe[0], gzip->count) / read_count_divisor;
}
#pragma omp section
{ // Velvet mates writer
// Divide count by 2 because both R1 and R2 reads go through this writer
mp_cnt = ss_stream_writer(out_mates_fn, mates_out_pipe[0], gzip->count) / 2 / read_count_divisor;
}
#pragma omp section
{ // Dispatcher
// Allocate data buffer strings
UT_string *r1_data;
utstring_new(r1_data);
UT_string *r2_data;
utstring_new(r2_data);
UT_string *s1_data;
utstring_new(s1_data);
UT_string *s2_data;
utstring_new(s2_data);
UT_string *rev_tmp;
utstring_new(rev_tmp);
UT_string *rev_data;
utstring_new(rev_data);
// Pipes
FILE *r1_in = fdopen(r1_pipe[0],"r");
FILE *r2_in = fdopen(r2_pipe[0],"r");
FILE *s1_in = fdopen(s1_pipe[0],"r");
FILE *s2_in = fdopen(s2_pipe[0],"r");
FILE *mates_out = fdopen(mates_out_pipe[1],"w");
FILE *r1_out = fdopen(r1_out_pipe[1],"w");
FILE *r2_out = fdopen(r2_out_pipe[1],"w");
FILE *s1_out = fdopen(s1_out_pipe[1],"w");
FILE *s2_out = fdopen(s2_out_pipe[1],"w");
if (!singles_flag) {
fclose(s2_out);
s2_out = s1_out;
}
// Flags for data left in single files
int single1_hungry = 1;
int single2_hungry = 1;
// Handle read1 and read2 files
while (ss_get_utstring(r1_in, r1_data)) {
if (!ss_get_utstring(r2_in, r2_data)) {
fprintf(stderr, "Error: Input read1 and read2 files are not synced\n");
exit(EXIT_FAILURE);
}
if (keep_read(r1_data)) {
if (keep_read(r2_data)) {
// Output both read1 and read2
if (mates->count) {
if (only_mates->count) {
// Interleaved velvet output only
output_read(r1_data, NULL, NULL, r1_in, NULL, mates_out, fasta->count);
if (no_rev->count || !colorspace_flag) {
output_read(r2_data, NULL, NULL, r2_in, NULL, mates_out, fasta->count);
} else {
output_read(r2_data, rev_data, rev_tmp, r2_in, NULL, mates_out, fasta->count);
}
} else {
// Interleaved velvet output and normal read file output
output_read(r1_data, NULL, NULL, r1_in, r1_out, mates_out, fasta->count);
if (no_rev->count || !colorspace_flag) {
output_read(r2_data, NULL, NULL, r2_in, r2_out, mates_out, fasta->count);
} else {
output_read(r2_data, rev_data, rev_tmp, r2_in, r2_out, mates_out, fasta->count);
}
}
} else {
// No interleaved velvet output
output_read(r1_data, NULL, NULL, r1_in, r1_out, NULL, fasta->count);
output_read(r2_data, NULL, NULL, r2_in, r2_out, NULL, fasta->count);
}
} else {
// Discard read2, output read1 as singlet
output_read(r1_data, NULL, NULL, r1_in, s1_out, NULL, fasta->count);
read1_singlet_cnt++;
}
} else {
if (keep_read(r2_data)) {
// Discard read1, output read2 as singlet
output_read(r2_data, NULL, NULL, r2_in, s2_out, NULL, fasta->count);
read2_singlet_cnt++;
}
}
// Process reads from singles here to take advantage of
// parallelism
if (single1_hungry || single2_hungry) {
if (single1_hungry) {
if (ss_get_utstring(s1_in, s1_data)) {
if (keep_read(s1_data)) {
output_read(s1_data, NULL, NULL, s1_in, s1_out, NULL, fasta->count);
}
} else {
single1_hungry = 0;
}
}
if (single2_hungry) {
if (ss_get_utstring(s2_in, s2_data)) {
if (keep_read(s2_data)) {
output_read(s2_data, NULL, NULL, s2_in, s2_out, NULL, fasta->count);
}
} else {
single2_hungry = 0;
}
}
}
}
while (single1_hungry || single2_hungry) {
if (single1_hungry) {
if (ss_get_utstring(s1_in, s1_data)) {
if (keep_read(s1_data)) {
output_read(s1_data, NULL, NULL, s1_in, s1_out, NULL, fasta->count);
}
} else {
single1_hungry = 0;
}
}
if (single2_hungry) {
if (ss_get_utstring(s2_in, s2_data)) {
if (keep_read(s2_data)) {
output_read(s2_data, NULL, NULL, s2_in, s2_out, NULL, fasta->count);
}
} else {
single2_hungry = 0;
}
}
}
fclose(r1_in);
fclose(r2_in);
fclose(s1_in);
fclose(s2_in);
fclose(mates_out);
fclose(r1_out);
fclose(r2_out);
fclose(s1_out);
if (singles_flag) {
fclose(s2_out);
}
// Free buffers
utstring_free(r1_data);
utstring_free(r2_data);
utstring_free(s1_data);
utstring_free(s2_data);
utstring_free(rev_tmp);
utstring_free(rev_data);
}
}
if (!(R1_org+singlet1_org+singlet2_org)) {
fprintf(stderr, "ERROR! No reads found in input files, or input(s) not found.\n");
exit(EXIT_FAILURE);
}
if (R1_org != R2_org) {
fprintf(stderr, "\nWarning! read1 and read2 fastq files did not contain an equal number of reads. %lu %lu\n", R1_org, R2_org);
}
if ((R1_org + R2_org) && !(singlet1_cnt + singlet2_cnt)) {
fprintf(stderr, "\nWarning! read1/read2 files were processed, but no corresponding input singlets were found.\n");
}
if (entropy->count) {
printf("\nLow complexity reads discarded: Read1: %lu, Read2: %lu, Singlets: %lu %lu\n", comp_r1, comp_r2, comp_s1, comp_s2);
}
mp_org = R1_org;
if (!only_mates->count) {
mp_cnt = R1_cnt;
}
printf("\nMatepairs: Before: %lu, After: %lu\n", mp_org, mp_cnt);
printf("Singlets: Before: %lu %lu After: %lu %lu\n", singlet1_org, singlet2_org, s1_cnt, s2_cnt);
printf("Read1 singlets: %lu, Read2 singlets: %lu, Original singlets: %lu %lu\n", read1_singlet_cnt, read2_singlet_cnt, singlet1_cnt, singlet2_cnt);
printf("Total Reads Processed: %lu, Reads retained: %lu\n", 2*mp_org+singlet1_org+singlet2_org, 2*mp_cnt+s1_cnt+s2_cnt);
utstring_free(in_read1_fq_fn);
utstring_free(in_read2_fq_fn);
utstring_free(in_single1_fq_fn);
utstring_free(in_single2_fq_fn);
utstring_free(out_read1_fn);
utstring_free(out_read2_fn);
utstring_free(out_single1_fn);
utstring_free(out_single2_fn);
utstring_free(out_mates_fn);
utstring_free(out_filetype);
utstring_free(out_read_prefix);
exit(EXIT_SUCCESS);
}
int main(int argc, char* argv[]) {
#ifdef BALL
double discountFactor = 0.9;
#else
#ifdef CART_POLE
double discountFactor = 0.95;
#else
#ifdef DOUBLE_CART_POLE
double discountFactor = 0.95;
#else
#ifdef MOUNTAIN_CAR
double discountFactor = 0.99;
#else
#ifdef ACROBOT
double discountFactor = 0.95;
#else
#ifdef BOAT
double discountFactor = 0.95;
#else
#ifdef CART_POLE_BINARY
double discountFactor = 0.95;
#else
#ifdef SWIMMER
double discountFactor = 0.95;
#endif
#endif
#endif
#endif
#endif
#endif
#endif
#endif
FILE* initFileFd = NULL;
state** initialStates = NULL;
FILE* results = NULL;
char str[1024];
unsigned int i = 0;
unsigned int h = 0;
unsigned int* ns = NULL;
unsigned int nbN = 0;
unsigned int n = 0;
unsigned int nbSteps = 0;
unsigned int timestamp = time(NULL);
int readFscanf = -1;
optimistic_instance* optimistic = NULL;
struct arg_file* initFile = arg_file1(NULL, "init", "<file>", "File containing the inital state");
struct arg_str* r = arg_str1("n", NULL, "<s>", "List of maximum numbers of evaluations");
struct arg_int* s = arg_int1("s", NULL, "<n>", "Number of steps");
struct arg_int* k = arg_int1("k", NULL, "<n>", "Branching factor of the problem");
struct arg_file* where = arg_file1(NULL, "where", "<file>", "Directory where we save the outputs");
struct arg_end* end = arg_end(6);
int nerrors = 0;
void* argtable[6];
argtable[0] = initFile;
argtable[1] = r;
argtable[2] = s;
argtable[3] = k;
argtable[4] = where;
argtable[5] = end;
if(arg_nullcheck(argtable) != 0) {
printf("error: insufficient memory\n");
arg_freetable(argtable, 6);
return EXIT_FAILURE;
}
nerrors = arg_parse(argc, argv, argtable);
if(nerrors > 0) {
printf("%s:", argv[0]);
arg_print_syntax(stdout, argtable, "\n");
arg_print_errors(stdout, end, argv[0]);
arg_freetable(argtable, 6);
return EXIT_FAILURE;
}
initGenerativeModelParameters();
K = k->ival[0];
initGenerativeModel();
initFileFd = fopen(initFile->filename[0], "r");
readFscanf = fscanf(initFileFd, "%u\n", &n);
initialStates = (state**)malloc(sizeof(state*) * n);
for(; i < n; i++) {
readFscanf = fscanf(initFileFd, "%s\n", str);
initialStates[i] = makeState(str);
}
fclose(initFileFd);
nbSteps = s->ival[0];
ns = parseUnsignedIntList((char*)r->sval[0], &nbN);
optimistic = optimistic_initInstance(NULL, discountFactor);
sprintf(str, "%s/%u_results_%u_%u.csv", where->filename[0], timestamp, K, nbSteps);
results = fopen(str, "w");
for(h = 0; h < nbN; h++) {
double sumRewards = 0.0;
for(i = 0; i < n; i++) {
unsigned int j = 0;
state* crt = copyState(initialStates[i]);
optimistic_resetInstance(optimistic, crt);
for(; j < nbSteps; j++) {
char isTerminal = 0;
double reward = 0.0;
state* nextState = NULL;
optimistic_keepSubtree(optimistic);
action* optimalAction = optimistic_planning(optimistic, ns[h]);
isTerminal = nextStateReward(crt, optimalAction, &nextState, &reward) < 0 ? 1 : 0;
freeState(crt);
crt = nextState;
sumRewards += reward;
if(isTerminal)
break;
}
optimistic_resetInstance(optimistic, crt);
freeState(crt);
printf(">>>>>>>>>>>>>> %uth initial state processed\n", i + 1);
fflush(NULL);
}
fprintf(results, "%u,%.15f\n", ns[h], sumRewards / (double)n);
printf(">>>>>>>>>>>>>> n = %u done\n\n", ns[h]);
fflush(NULL);
}
fclose(results);
arg_freetable(argtable, 6);
for(i = 0; i < n; i++)
freeState(initialStates[i]);
free(initialStates);
optimistic_uninitInstance(&optimistic);
freeGenerativeModel();
freeGenerativeModelParameters();
return EXIT_SUCCESS;
}
int main(int argc, char* argv[]) {
#ifdef BALL
double discountFactor = 0.9;
#else
#ifdef CART_POLE
double discountFactor = 0.95;
#else
#ifdef DOUBLE_CART_POLE
double discountFactor = 0.95;
#else
#ifdef MOUNTAIN_CAR
double discountFactor = 0.95;
#else
#ifdef ACROBOT
double discountFactor = 0.95;
#else
#ifdef BOAT
double discountFactor = 0.95;
#else
#ifdef CART_POLE_BINARY
double discountFactor = 0.95;
#else
#ifdef SWIMMER
double discountFactor = 0.95;
#endif
#endif
#endif
#endif
#endif
#endif
#endif
#endif
FILE* initFileFd = NULL;
state** initialStates = NULL;
unsigned int maxDepth = 0;
FILE* combinedFd = NULL;
FILE* results = NULL;
char str[1024];
unsigned int i = 0;
unsigned int minDepth = 1;
unsigned int crtDepth = 0;
unsigned int n = 0;
unsigned int maxNbIterations = 0;
unsigned int nbSteps = 0;
unsigned int timestamp = time(NULL);
int readFscanf = -1;
optimistic_instance* optimistic = NULL;
random_search_instance* random_search = NULL;
uct_instance* uct = NULL;
uniform_instance* uniform = NULL;
struct arg_file* initFile = arg_file1(NULL, "init", "<file>", "File containing the inital state");
struct arg_int* d = arg_int1("d", NULL, "<n>", "Maximum depth of an uniform tree which the number of call per step");
struct arg_int* d2 = arg_int0(NULL, "min", "<n>", "Minimun depth to start from (min > 0)");
struct arg_int* s = arg_int1("s", NULL, "<n>", "Number of steps");
struct arg_int* k = arg_int1("k", NULL, "<n>", "Branching factor of the problem");
struct arg_file* where = arg_file1(NULL, "where", "<file>", "Directory where we save the outputs");
struct arg_end* end = arg_end(7);
int nerrors = 0;
void* argtable[7];
argtable[0] = initFile;
argtable[1] = d2;
argtable[2] = d;
argtable[3] = s;
argtable[4] = k;
argtable[5] = where;
argtable[6] = end;
if(arg_nullcheck(argtable) != 0) {
printf("error: insufficient memory\n");
arg_freetable(argtable, 7);
return EXIT_FAILURE;
}
nerrors = arg_parse(argc, argv, argtable);
if(nerrors > 0) {
printf("%s:", argv[0]);
arg_print_syntax(stdout, argtable, "\n");
arg_print_errors(stdout, end, argv[0]);
arg_freetable(argtable, 7);
return EXIT_FAILURE;
}
initGenerativeModelParameters();
K = k->ival[0];
initGenerativeModel();
initFileFd = fopen(initFile->filename[0], "r");
readFscanf = fscanf(initFileFd, "%u\n", &n);
initialStates = (state**)malloc(sizeof(state*) * n);
for(; i < n; i++) {
readFscanf = fscanf(initFileFd, "%s\n", str);
initialStates[i] = makeState(str);
}
fclose(initFileFd);
if(d2->count)
minDepth = d2->ival[0];
maxDepth = d->ival[0];
maxNbIterations = K;
nbSteps = s->ival[0];
optimistic = optimistic_initInstance(NULL, discountFactor);
random_search = random_search_initInstance(NULL, discountFactor);
uct = uct_initInstance(NULL, discountFactor);
uniform = uniform_initInstance(NULL, discountFactor);
sprintf(str, "%s/%u_results_%u_%u.csv", where->filename[0], timestamp, K, nbSteps);
results = fopen(str, "w");
for(crtDepth = 1; crtDepth < minDepth; crtDepth++)
maxNbIterations += pow(K, crtDepth+1);
for(crtDepth = minDepth; crtDepth <= maxDepth; crtDepth++) {
double averages[4] = {0.0, 0.0, 0.0, 0.0};
sprintf(str, "%s/%u_combined_%u_%u(%u)_%u.csv", where->filename[0], timestamp, K, crtDepth, maxNbIterations, nbSteps);
combinedFd = fopen(str, "w");
fprintf(combinedFd, "nbIterations,optimistic,optimistic(discounted),optimistic depth,random search,random search(discounted),random search depth,uct,uct(discounted),uct depth,uniform,uniform(discounted),uniform depth\n");
for(i = 0; i < n; i++) {
unsigned int j = 0;
double sumRewards = 0.0;
double discountedSumRewards = 0.0;
unsigned int sumDepths = 0;
state* crt = copyState(initialStates[i]);
optimistic_resetInstance(optimistic, crt);
for(; j < nbSteps; j++) {
char isTerminal = 0;
double reward = 0.0;
state* nextState = NULL;
optimistic_keepSubtree(optimistic);
action* optimalAction = optimistic_planning(optimistic, maxNbIterations);
isTerminal = nextStateReward(crt, optimalAction, &nextState, &reward);
freeState(crt);
crt = nextState;
sumRewards += reward;
sumDepths += optimistic_getMaxDepth(optimistic);
discountedSumRewards += optimistic->gammaPowers[j] * reward;
if(isTerminal < 0)
break;
}
optimistic_resetInstance(optimistic, crt);
freeState(crt);
fprintf(combinedFd, "%u,%.15f,%.15f,%.15f,",maxNbIterations, sumRewards, discountedSumRewards, sumDepths / (double)((j == nbSteps) ? nbSteps : (j + 1)));
averages[0] += sumRewards;
printf("Optimistic : %uth initial state processed\n", i + 1);
sumRewards = 0.0;
discountedSumRewards = 0.0;
sumDepths = 0;
crt = copyState(initialStates[i]);
for(j = 0; j < nbSteps; j++) {
char isTerminal = 0;
double reward = 0.0;
state* nextState = NULL;
random_search_resetInstance(random_search, crt);
action* optimalAction = random_search_planning(random_search, maxNbIterations);
isTerminal = nextStateReward(crt, optimalAction, &nextState, &reward);
freeState(crt);
crt = nextState;
sumRewards += reward;
sumDepths += random_search_getMaxDepth(random_search);
discountedSumRewards += random_search->gammaPowers[j] * reward;
if(isTerminal < 0)
break;
}
random_search_resetInstance(random_search, crt);
freeState(crt);
fprintf(combinedFd, "%.15f,%.15f,%.15f,", sumRewards, discountedSumRewards, sumDepths / (double)((j == nbSteps) ? nbSteps : (j + 1)));
averages[1] += sumRewards;
printf("Random search: %uth initial state processed\n", i + 1);
sumRewards = 0.0;
discountedSumRewards = 0.0;
sumDepths = 0;
crt = copyState(initialStates[i]);
uct_resetInstance(uct, crt);
for(j = 0; j < nbSteps; j++) {
char isTerminal = 0;
double reward = 0.0;
state* nextState = NULL;
uct_keepSubtree(uct);
action* optimalAction = uct_planning(uct, maxNbIterations);
isTerminal = nextStateReward(crt, optimalAction, &nextState, &reward);
freeState(crt);
crt = nextState;
sumRewards += reward;
sumDepths += uct_getMaxDepth(uct);
discountedSumRewards += uct->gammaPowers[j] * reward;
if(isTerminal < 0)
break;
}
uct_resetInstance(uct, crt);
freeState(crt);
fprintf(combinedFd, "%.15f,%.15f,%.15f,", sumRewards, discountedSumRewards, sumDepths / (double)((j == nbSteps) ? nbSteps : (j + 1)));
averages[2] += sumRewards;
printf("Uct : %uth initial state processed\n", i + 1);
sumRewards = 0.0;
discountedSumRewards = 0.0;
crt = copyState(initialStates[i]);
uniform_resetInstance(uniform, crt);
for(j = 0; j < nbSteps; j++) {
char isTerminal = 0;
double reward = 0.0;
state* nextState = NULL;
uniform_keepSubtree(uniform);
action* optimalAction = uniform_planning(uniform, maxNbIterations);
isTerminal = nextStateReward(crt, optimalAction, &nextState, &reward);
freeState(crt);
crt = nextState;
sumRewards += reward;
discountedSumRewards += uniform->gammaPowers[j] * reward;
if(isTerminal < 0)
break;
}
uniform_resetInstance(uniform, crt);
freeState(crt);
fprintf(combinedFd, "%.15f,%.15f,%u\n", sumRewards, discountedSumRewards, crtDepth -1);
fflush(combinedFd);
averages[3] += sumRewards;
printf("Uniform : %uth initial state processed\n", i + 1);
printf(">>>>>>>>>>>>>> %uth initial state processed\n", i + 1);
}
fprintf(results, "%u,%.15f,%.15f,%.15f,%.15f\n", maxNbIterations, averages[0] / (double)n, averages[1] / (double)n, averages[2] / (double)n, averages[3] / (double)n);
fflush(results);
printf(">>>>>>>>>>>>>> %u depth done\n\n", crtDepth);
fclose(combinedFd);
maxNbIterations += pow(K, crtDepth+1);
}
fclose(results);
arg_freetable(argtable, 7);
for(i = 0; i < n; i++)
freeState(initialStates[i]);
free(initialStates);
optimistic_uninitInstance(&optimistic);
random_search_uninitInstance(&random_search);
uct_uninitInstance(&uct);
uniform_uninitInstance(&uniform);
freeGenerativeModel();
freeGenerativeModelParameters();
return EXIT_SUCCESS;
}
int main(int argc, char* argv[])
{
// Define our variables.
int nerrors, i;
int32_t saved = 0; // The number of words saved during compression and optimization.
struct errinfo* errval;
const char* prepend = "error: ";
const char* warnprefix = "no-";
int msglen;
char* msg;
int target;
// Define arguments.
struct arg_lit* show_help = arg_lit0("h", "help", "Show this help.");
struct arg_str* target_arg = arg_str0("l", "link-as", "target", "Link as the specified object, can be 'image', 'static' or 'kernel'.");
struct arg_file* symbol_file = arg_file0("s", "symbols", "<file>", "Produce a combined symbol file (~triples memory usage!).");
struct arg_str* symbol_ext = arg_str0(NULL, "symbol-extension", "ext", "When -s is used, specifies the extension for symbol files. Defaults to \"dsym16\".");
struct arg_file* input_files = arg_filen(NULL, NULL, "<file>", 1, 100, "The input object files.");
struct arg_file* output_file = arg_file1("o", "output", "<file>", "The output file (or - to send to standard output).");
struct arg_file* kernel_file = arg_file0("k", "kernel", "<file>", "Directly link in the specified kernel.");
struct arg_file* jumplist_file = arg_file0("j", "jumplist", "<file>", "Link against the specified jumplist.");
struct arg_str* warning_policies = arg_strn("W", NULL, "policy", 0, _WARN_COUNT * 2 + 10, "Modify warning policies.");
struct arg_lit* keep_output_arg = arg_lit0(NULL, "keep-outputs", "Keep the .OUTPUT entries in the final static library (used for stdlib).");
struct arg_lit* little_endian_mode = arg_lit0(NULL, "little-endian", "Use little endian serialization (for compatibility with older versions).");
struct arg_lit* no_short_literals_arg = arg_lit0(NULL, "no-short-literals", "Do not compress literals to short literals.");
struct arg_int* opt_level = arg_int0("O", NULL, "<level>", "The optimization level.");
struct arg_lit* opt_mode = arg_lit0("S", NULL, "Favour runtime speed over size when optimizing.");
struct arg_lit* verbose = arg_litn("v", NULL, 0, LEVEL_EVERYTHING - LEVEL_DEFAULT, "Increase verbosity.");
struct arg_lit* quiet = arg_litn("q", NULL, 0, LEVEL_DEFAULT - LEVEL_SILENT, "Decrease verbosity.");
struct arg_end* end = arg_end(20);
void* argtable[] = { show_help, target_arg, keep_output_arg, little_endian_mode, opt_level, opt_mode, no_short_literals_arg,
symbol_ext, symbol_file, kernel_file, jumplist_file, warning_policies, output_file, input_files, verbose, quiet, end
};
// Parse arguments.
nerrors = arg_parse(argc, argv, argtable);
version_print(bautofree(bfromcstr("Linker")));
if (nerrors != 0 || show_help->count != 0)
{
if (show_help->count != 0)
arg_print_errors(stdout, end, "linker");
printd(LEVEL_DEFAULT, "syntax:\n dtld");
arg_print_syntax(stderr, argtable, "\n");
printd(LEVEL_DEFAULT, "options:\n");
arg_print_glossary(stderr, argtable, " %-25s %s\n");
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
// Set verbosity level.
debug_setlevel(LEVEL_DEFAULT + verbose->count - quiet->count);
// Set global path variable.
osutil_setarg0(bautofree(bfromcstr(argv[0])));
// Set endianness.
isetmode(little_endian_mode->count == 0 ? IMODE_BIG : IMODE_LITTLE);
// Set up warning policies.
dsetwarnpolicy(warning_policies);
// Set up error handling.
if (dsethalt())
{
errval = derrinfo();
// FIXME: Use bstrings here.
msglen = strlen(derrstr[errval->errid]) + strlen(prepend) + 1;
msg = malloc(msglen);
memset(msg, '\0', msglen);
strcat(msg, prepend);
strcat(msg, derrstr[errval->errid]);
printd(LEVEL_ERROR, msg, errval->errdata);
// Handle the error.
printd(LEVEL_ERROR, "linker: error occurred.\n");
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
// Check to make sure target is correct.
if (target_arg->count == 0)
target = IMAGE_APPLICATION;
else
{
if (strcmp(target_arg->sval[0], "image") == 0)
target = IMAGE_APPLICATION;
else if (strcmp(target_arg->sval[0], "static") == 0)
target = IMAGE_STATIC_LIBRARY;
else if (strcmp(target_arg->sval[0], "kernel") == 0)
target = IMAGE_KERNEL;
else
{
// Invalid option.
dhalt(ERR_INVALID_TARGET_NAME, NULL);
}
}
// Load all passed objects and use linker bin system to
// produce result.
bins_init();
for (i = 0; i < input_files->count; i++)
if (!bins_load(bautofree(bfromcstr(input_files->filename[i])), symbol_file->count > 0, (symbol_file->count > 0 && symbol_ext->count > 0) ? symbol_ext->sval[0] : "dsym16"))
// Failed to load one of the input files.
dhalt(ERR_BIN_LOAD_FAILED, input_files->filename[i]);
bins_associate();
bins_sectionize();
bins_flatten(bautofree(bfromcstr("output")));
if (target == IMAGE_KERNEL)
bins_write_jump();
saved = bins_optimize(
opt_mode->count == 0 ? OPTIMIZE_SIZE : OPTIMIZE_SPEED,
opt_level->count == 0 ? OPTIMIZE_NONE : opt_level->ival[0]);
if (no_short_literals_arg->count == 0 && target != IMAGE_STATIC_LIBRARY)
saved += bins_compress();
else if (no_short_literals_arg->count == 0)
dwarn(WARN_SKIPPING_SHORT_LITERALS_TYPE, NULL);
else
dwarn(WARN_SKIPPING_SHORT_LITERALS_REQUEST, NULL);
bins_resolve(
target == IMAGE_STATIC_LIBRARY,
target == IMAGE_STATIC_LIBRARY);
bins_save(
bautofree(bfromcstr("output")),
bautofree(bfromcstr(output_file->filename[0])),
target,
keep_output_arg->count > 0,
symbol_file->count > 0 ? symbol_file->filename[0] : NULL,
jumplist_file->count > 0 ? jumplist_file->filename[0] : NULL);
bins_free();
if (saved > 0)
printd(LEVEL_DEFAULT, "linker: saved %i words during optimization.\n", saved);
else if (saved < 0)
printd(LEVEL_DEFAULT, "linker: increased by %i words during optimization.\n", -saved);
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 0;
}
int _tmain(int argc, char* argv[])
{
// determine my process name
_splitpath(argv[0],NULL,NULL,gszProcName,NULL);
#else
int
main(int argc, const char** argv)
{
// determine my process name
CUtility::splitpath((char *)argv[0],NULL,gszProcName);
#endif
int iScreenLogLevel; // level of screen diagnostics
int iFileLogLevel; // level of file diagnostics
char szLogFile[_MAX_PATH]; // write diagnostics to this file
int Rslt;
etFMode FMode; // format output mode
char szOutputFileSpec[_MAX_PATH];
char szInputFileSpec[_MAX_PATH];
// command line args
struct arg_lit *help = arg_lit0("h","help", "print this help and exit");
struct arg_lit *version = arg_lit0("v","version,ver", "print version information and exit");
struct arg_int *FileLogLevel=arg_int0("f", "FileLogLevel", "<int>","Level of diagnostics written to screen and logfile 0=fatal,1=errors,2=info,3=diagnostics,4=debug");
struct arg_file *LogFile = arg_file0("F","log","<file>", "diagnostics log file");
struct arg_int *format = arg_int0("M","format","<int>", "output format: 0 - multifasta, 1 - CSV format only, 2 - BED format, 3 - XML entries only (default: 0)");
struct arg_file *InFile = arg_file1("i","input","<file>", "input from bioseq files");
struct arg_file *OutFile = arg_file1("o","result","<file>", "output entry dump file");
struct arg_end *end = arg_end(20);
void *argtable[] = {help,version,FileLogLevel,LogFile,LogFile,format,InFile,OutFile,end};
char **pAllArgs;
int argerrors;
argerrors = CUtility::arg_parsefromfile(argc,(char **)argv,&pAllArgs);
if(argerrors >= 0)
argerrors = arg_parse(argerrors,pAllArgs,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0)
{
printf("\n%s Dump biosequence (generated by genbioseq) file contents, Version %s\nOptions ---\n", gszProcName,cpszProgVer);
arg_print_syntax(stdout,argtable,"\n");
arg_print_glossary(stdout,argtable," %-25s %s\n");
printf("\nNote: Parameters can be entered into a parameter file, one parameter per line.");
printf("\n To invoke this parameter file then precede its name with '@'");
printf("\n e.g. %s @myparams.txt\n",gszProcName);
printf("\nPlease report any issues regarding usage of %s at https://github.com/csiro-crop-informatics/biokanga/issues\n\n",gszProcName);
exit(1);
}
/* special case: '--version' takes precedence error reporting */
if (version->count > 0)
{
printf("\n%s Version %s\n",gszProcName,cpszProgVer);
exit(1);
}
if (!argerrors)
{
if(FileLogLevel->count && !LogFile->count)
{
printf("\nError: FileLogLevel '-f%d' specified but no logfile '-F<logfile>'",FileLogLevel->ival[0]);
exit(1);
}
iScreenLogLevel = iFileLogLevel = FileLogLevel->count ? FileLogLevel->ival[0] : eDLInfo;
if(iFileLogLevel < eDLNone || iFileLogLevel > eDLDebug)
{
printf("\nError: FileLogLevel '-l%d' specified outside of range %d..%d",iFileLogLevel,eDLNone,eDLDebug);
exit(1);
}
if(LogFile->count)
{
strncpy(szLogFile,LogFile->filename[0],_MAX_PATH);
szLogFile[_MAX_PATH-1] = '\0';
}
else
{
iFileLogLevel = eDLNone;
szLogFile[0] = '\0';
}
FMode = (etFMode)(format->count ? format->ival[0] : eFMdefault);
if(FMode < eFMdefault || FMode >= eFMplaceholder)
{
printf("\nError: Requested output format '-M%d' not supported, must be in range %d..%d",FMode,eFMdefault,eFMplaceholder-1);
exit(1);
}
strcpy(szInputFileSpec,InFile->filename[0]);
strcpy(szOutputFileSpec,OutFile->filename[0]);
// now that command parameters have been parsed then initialise diagnostics log system
if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
{
printf("\nError: Unable to start diagnostics subsystem.");
if(szLogFile[0] != '\0')
printf(" Most likely cause is that logfile '%s' can't be opened/created",szLogFile);
exit(1);
}
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Version: %s Processing parameters:",cpszProgVer);
const char *pszDescr;
switch(FMode) {
case eFMdefault: // default is for multifasta
pszDescr = "Multifasta";
break;
case eFMcsv: // CSV entries
pszDescr = "CSV format";
break;
case eFMbed: // BED entries
pszDescr = "BED format";
break;
case eFMxml: // XML entries
pszDescr = "XML format";
break;
}
gDiagnostics.DiagOut(eDLInfo,gszProcName,"dump output format: %s",pszDescr);
gDiagnostics.DiagOut(eDLInfo,gszProcName,"input biosequence file: '%s'",szInputFileSpec);
gDiagnostics.DiagOut(eDLInfo,gszProcName,"output to file: '%s'",szOutputFileSpec);
gStopWatch.Start();
Rslt = Process(szInputFileSpec,szOutputFileSpec,FMode);
gStopWatch.Stop();
Rslt = Rslt >=0 ? 0 : 1;
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
exit(Rslt);
}
else
{
printf("\n%s Dump biosequence (generated by genbioseq) file contents, Version %s\n",gszProcName,cpszProgVer);
arg_print_errors(stdout,end,gszProcName);
arg_print_syntax(stdout,argtable,"\nUse '-h' to view option and parameter usage\n");
exit(1);
}
}
int main(int argc, char* argv[]) {
#ifdef BALL
double discountFactor = 0.9;
#else
#ifdef CART_POLE
double discountFactor = 0.95;
#else
#ifdef DOUBLE_CART_POLE
double discountFactor = 0.95;
#else
#ifdef MOUNTAIN_CAR
double discountFactor = 0.99;
#else
#ifdef ACROBOT
double discountFactor = 0.95;
#else
#ifdef BOAT
double discountFactor = 0.95;
#else
#ifdef SWIMMER
double discountFactor = 0.95;
#endif
#endif
#endif
#endif
#endif
#endif
#endif
FILE* initFileFd = NULL;
state** initialStates = NULL;
FILE* results = NULL;
char str[1024];
unsigned int i = 0;
unsigned int nbInitialStates = 0;
unsigned int* ns = NULL;
unsigned int nbN = 0;
double* Ls = NULL;
unsigned int nbL = 0;
unsigned int nbSteps = 0;
unsigned int timestamp = time(NULL);
int readFscanf = -1;
lipschitzian_instance* lipschitzian = NULL;
struct arg_file* initFile = arg_file1(NULL, "init", "<file>", "File containing the inital state");
struct arg_int* s = arg_int1("s", NULL, "<n>", "Number of steps");
struct arg_str* r = arg_str1("n", NULL, "<s>", "List of ressources");
struct arg_str* z = arg_str1("L", NULL, "<s>", "List of Lipschitz coefficients to try");
struct arg_file* where = arg_file1(NULL, "where", "<file>", "Directory where we save the outputs");
struct arg_end* end = arg_end(6);
int nerrors = 0;
void* argtable[6];
argtable[0] = initFile;
argtable[1] = r;
argtable[2] = s;
argtable[3] = z;
argtable[4] = where;
argtable[5] = end;
if(arg_nullcheck(argtable) != 0) {
printf("error: insufficient memory\n");
arg_freetable(argtable, 6);
return EXIT_FAILURE;
}
nerrors = arg_parse(argc, argv, argtable);
if(nerrors > 0) {
printf("%s:", argv[0]);
arg_print_syntax(stdout, argtable, "\n");
arg_print_errors(stdout, end, argv[0]);
arg_freetable(argtable, 6);
return EXIT_FAILURE;
}
initGenerativeModelParameters();
initGenerativeModel();
initFileFd = fopen(initFile->filename[0], "r");
readFscanf = fscanf(initFileFd, "%u\n", &nbInitialStates);
initialStates = (state**)malloc(sizeof(state*) * nbInitialStates);
for(; i < nbInitialStates; i++) {
readFscanf = fscanf(initFileFd, "%s\n", str);
initialStates[i] = makeState(str);
}
fclose(initFileFd);
nbSteps = s->ival[0];
Ls = parseDoubleList((char*)z->sval[0], &nbL);
ns = parseUnsignedIntList((char*)r->sval[0], &nbN);
sprintf(str, "%s/%u_results_%s_%s.csv", where->filename[0], timestamp, z->sval[0], r->sval[0]);
results = fopen(str, "w");
lipschitzian = lipschitzian_initInstance(NULL, discountFactor, 0.0);
for(i = 0; i < nbN; i++) { /* Loop on the computational ressources */
fprintf(results, "%u", ns[i]);
printf("Starting with %u computational ressources\n", ns[i]);
fflush(NULL);
unsigned int j = 0;
for(; j < nbL; j++) { /* Loop on the Lispchitz constant */
unsigned int k = 0;
double average = 0.0;
lipschitzian->L = Ls[j];
for(; k < nbInitialStates; k++) { /* Loop on the initial states */
unsigned int l = 0;
double sumRewards = 0.0;
state* crt = copyState(initialStates[k]);
lipschitzian_resetInstance(lipschitzian, crt);
for(; l < nbSteps; l++) { /* Loop on the step */
char isTerminal = 0;
double reward = 0.0;
state* nextState = NULL;
double* optimalAction = lipschitzian_planning(lipschitzian, ns[i]);
isTerminal = nextStateReward(crt, optimalAction, &nextState, &reward) < 0 ? 1 : 0;
free(optimalAction);
freeState(crt);
crt = nextState;
sumRewards += reward;
lipschitzian_resetInstance(lipschitzian,crt);
if(isTerminal)
break;
}
average += sumRewards;
freeState(crt);
printf("Computation of the %u initial state done with L=%f\n", k, Ls[j]);
fflush(NULL);
}
average = average /(double)nbInitialStates;
fprintf(results, ",%.15f", average);
printf("Computation with L=%f and n=%u done\n", Ls[j], ns[i]);
fflush(NULL);
}
fprintf(results,"\n");
printf("Computation with %u computational ressources done\n\n", ns[i]);
fflush(NULL);
}
fclose(results);
arg_freetable(argtable, 6);
for(i = 0; i < nbInitialStates; i++)
freeState(initialStates[i]);
free(initialStates);
lipschitzian_uninitInstance(&lipschitzian);
free(ns);
free(Ls);
freeGenerativeModel();
freeGenerativeModelParameters();
return EXIT_SUCCESS;
}
int main(int argc, char* argv[]) {
double discountFactor = 0.9;
unsigned int i = 0;
unsigned int n = 0;
FILE* initFileFd = NULL;
FILE* outputFileFd = NULL;
unsigned int nbIterations = 0;
int readFscanf = -1;
optimistic_instance* optimistic = NULL;
struct arg_file* initFile = arg_file1(NULL, "init", "<file>", "File containing the inital state");
struct arg_int* k = arg_int1("k", NULL, "<n>", "The branching factor of the problem");
struct arg_int* it = arg_int1("n", NULL, "<n>", "The number of iterations");
struct arg_file* outputFile = arg_file1("o", NULL, "<file>", "The output file");
struct arg_end* end = arg_end(5);
void* argtable[5];
int nerrors = 0;
argtable[0] = initFile;
argtable[1] = it;
argtable[2] = outputFile;
argtable[3] = k;
argtable[4] = end;
if(arg_nullcheck(argtable) != 0) {
printf("error: insufficient memory\n");
arg_freetable(argtable, 5);
return EXIT_FAILURE;
}
nerrors = arg_parse(argc, argv, argtable);
if(nerrors > 0) {
printf("%s:", argv[0]);
arg_print_syntax(stdout, argtable, "\n");
arg_print_errors(stdout, end, argv[0]);
arg_freetable(argtable, 5);
return EXIT_FAILURE;
}
nbIterations = it->ival[0];
initGenerativeModelParameters();
K = k->ival[0];
initGenerativeModel();
outputFileFd = fopen(outputFile->filename[0], "w");
initFileFd = fopen(initFile->filename[0], "r");
readFscanf = fscanf(initFileFd, "%u\n", &n);
arg_freetable(argtable, 5);
optimistic = optimistic_initInstance(NULL, discountFactor);
for(; i < n; i++) {
char str[1024];
unsigned int j = 0;
readFscanf = fscanf(initFileFd, "%s\n", str);
state* initial = makeState(str);
double crtOptimalValue = 0.0;
unsigned int crtOptimalAction = 0;
for(; j < K; j++) {
state* nextState = NULL;
double reward = 0.0;
char isTerminal = 0;
isTerminal = nextStateReward(initial, actions[j], &nextState, &reward);
optimistic_resetInstance(optimistic, nextState);
freeState(nextState);
optimistic_planning(optimistic, nbIterations);
if(optimistic->crtOptimalValue > crtOptimalValue) {
crtOptimalValue = optimistic->crtOptimalValue;
crtOptimalAction = j;
}
fprintf(outputFileFd, "%.15f,", optimistic->crtOptimalValue);
printf("%uth action done\n", j+1);
fflush(outputFileFd);
}
fprintf(outputFileFd, "%u\n", crtOptimalAction);
freeState(initial);
printf("%uth initial state processed\n", i+1);
fflush(outputFileFd);
}
fclose(outputFileFd);
fclose(initFileFd);
optimistic_uninitInstance(&optimistic);
freeGenerativeModel();
freeGenerativeModelParameters();
return EXIT_SUCCESS;
}
