static void doFile (const char * moduleName)
{
assert (moduleName);
printBeginGuard(moduleName, cout);
printCopyright (cout);
cout << endl;
cout << "#include \"AAFTypes.h\"" << endl;
cout << endl;
cout << "// AAF extensible enumeration member UIDs." << endl
<< "//" << endl << endl;
size_t i = 0;
for (i = 0; i < sizeof(members)/sizeof(members[0]); i++) {
if (members[i].kind == 1) {
if ((i > 0) && (members[i-1].kind == 1)) {
cout << "// None currently defined" << endl;
cout << endl;
}
cout << "// Members of " << members[i].name << endl;
cout << "//" << endl;
} else if (members[i].kind == 2) {
printDefinition("const aafUID_t",
prefix,
members[i].name,
0,
members[i].identifier,
cout);
}
}
printEndGuard(moduleName, cout);
}
static void doFile(const char* moduleName)
{
assert(moduleName);
printBeginGuard(moduleName, cout);
printCopyright(cout);
cout << endl;
cout << "#include \"AAFTypes.h\"" << endl;
cout << endl;
cout << "// AAF type definition UIDs." << endl
<< "//" << endl << endl;
size_t i = 0;
for (i = 0; i < sizeof(types)/sizeof(types[0]); i++){
printDefinition("const aafUID_t",
prefix,
types[i].name,
0,
types[i].identifier,
cout);
}
cout << endl;
printEndGuard(moduleName, cout);
}
void printBinaryInformation(FILE *fp,
const ProgramContextInterface &programContext,
const BinaryInformationSettings &settings)
{
const char *prefix = settings.prefix_;
const char *suffix = settings.suffix_;
const char *precisionString = "";
#ifdef GMX_DOUBLE
precisionString = " (double precision)";
#endif
const char *const name = programContext.displayName();
if (settings.bGeneratedByHeader_)
{
fprintf(fp, "%sCreated by:%s\n", prefix, suffix);
}
if (settings.bCopyright_)
{
GMX_RELEASE_ASSERT(prefix[0] == '\0' && suffix[0] == '\0',
"Prefix/suffix not supported with copyright");
// This line is printed again after the copyright notice to make it
// appear together with all the other information, so that it is not
// necessary to read stuff above the copyright notice.
// The line above the copyright notice puts the copyright notice is
// context, though.
// TODO: It would be nice to know here whether we are really running a
// Gromacs binary or some other binary that is calling Gromacs; we
// could then print "%s is part of GROMACS" or some alternative text.
fprintf(fp, "%sGROMACS: %s, %s%s%s\n", prefix, name,
gmx_version(), precisionString, suffix);
fprintf(fp, "\n");
printCopyright(fp);
fprintf(fp, "\n");
}
fprintf(fp, "%sGROMACS: %s, %s%s%s\n", prefix, name,
gmx_version(), precisionString, suffix);
const char *const binaryPath = programContext.fullBinaryPath();
if (binaryPath != NULL && binaryPath[0] != '\0')
{
fprintf(fp, "%sExecutable: %s%s\n", prefix, binaryPath, suffix);
}
const char *const libraryPath = programContext.defaultLibraryDataPath();
if (libraryPath != NULL && libraryPath[0] != '\0')
{
fprintf(fp, "%sLibrary dir: %s%s\n", prefix, libraryPath, suffix);
}
const char *const commandLine = programContext.commandLine();
if (commandLine != NULL && commandLine[0] != '\0')
{
fprintf(fp, "%sCommand line:%s\n%s %s%s\n",
prefix, suffix, prefix, commandLine, suffix);
}
if (settings.bExtendedInfo_)
{
GMX_RELEASE_ASSERT(prefix[0] == '\0' && suffix[0] == '\0',
"Prefix/suffix not supported with extended info");
fprintf(fp, "\n");
gmx_print_version_info(fp);
}
}
static void doFile (const char * moduleName)
{
assert(moduleName);
printBeginGuard(moduleName, cout);
printCopyright(cout);
cout << endl;
cout << "#include \"AAFTypes.h\"" << endl;
cout << endl;
cout << "// AAF class definition UIDs." << endl
<< "//" << endl << endl;
cout << "// The AAF reference implementation uses shorter names than" << endl
<< "// SMPTE. The names are shortened by the following aliases." << endl
<< "//" << endl;
size_t maxNameLength = 0;
size_t i = 0;
for (i = 0; i < sizeof(aliases)/sizeof(aliases[0]); i++){
size_t length = strlen(aliases[i].alias);
if (length > maxNameLength) {
maxNameLength = length;
}
}
size_t width = maxNameLength;
for (i = 0; i < sizeof(aliases)/sizeof(aliases[0]); i++){
cout << "#define " << prefix;
printName(aliases[i].alias, width, cout);
cout << " " << prefix;
printName(aliases[i].name, 0, cout);
cout << endl;
}
cout << endl;
for (i = 0; i < sizeof(classes)/sizeof(classes[0]); i++){
printDefinition("const aafUID_t",
prefix,
classes[i].name,
0,
classes[i].identifier,
cout);
}
printEndGuard(moduleName, cout);
}
static void doFile(const char* moduleName)
{
assert(moduleName);
printBeginGuard(moduleName, cout);
printCopyright(cout);
cout << endl;
cout << "#include \"AAFTypes.h\"" << endl;
cout << endl;
cout << "// AAF property definition UIDs." << endl
<< "//" << endl << endl;
size_t i = 0;
for (i = 0; i < sizeof(properties)/sizeof(properties[0]); i++){
printDefinition("const aafUID_t",
prefix,
properties[i].name,
0,
properties[i].identifier,
cout);
}
Property_t special[] = {
{"Root_MetaDictionary",
{0x0D010301, 0x0101, 0x0100,{0x06, 0x0E, 0x2B, 0x34, 0x01, 0x01, 0x01, 0x02}}},
{"Root_Header",
{0x0D010301, 0x0102, 0x0100, {0x06, 0x0E, 0x2B, 0x34, 0x01, 0x01, 0x01, 0x02}}}
};
cout << "// Special property definition ids used for specifying the" << endl;
cout << "// starting strong reference in the target list of a" << endl;
cout << "// weak reference." << endl;
cout << "//" << endl;
for (i = 0; i < sizeof(special)/sizeof(special[0]); i++){
printDefinition("const aafUID_t",
prefix,
special[i].name,
0,
special[i].identifier,
cout);
}
printEndGuard(moduleName, cout);
}
static void doFile(const char* moduleName)
{
assert(moduleName);
printBeginGuard(moduleName, cout);
printCopyright(cout);
cout << endl;
cout << "// AAF property identifiers (PIDs)." << endl
<< "//" << endl << endl;
cout << "// A property is identified by a globally unique 16-byte" << endl
<< "// identifier. To save space in an AAF file we store a" << endl
<< "// 2-byte file unique PID with each property." << endl
<< "// The mapping for a particular file is recorded in the" << endl
<< "// dictionary contained in that file." << endl
<< "// For the predefined properties we optimize by using a" << endl
<< "// fixed, compiled-in mapping." << endl
<< "// This file defines that mapping." << endl
<< "//" << endl;
size_t maxNameLength = 0;
size_t i = 0;
for (i = 0; i < sizeof(properties)/sizeof(properties[0]); i++) {
size_t length = strlen(properties[i].name);
if (length > maxNameLength) {
maxNameLength = length;
}
}
for (i = 0; i < sizeof(properties)/sizeof(properties[0]); i++) {
printDefinition("const int",
"PID_",
properties[i].name,
maxNameLength,
properties[i].identifier,
cout);
}
printEndGuard(moduleName, cout);
}
static void doFile (const char * moduleName)
{
assert(moduleName);
printBeginGuard(moduleName, cout);
printCopyright(cout);
cout << endl;
cout << "#include \"AAFTypes.h\"" << endl;
cout << endl;
cout << "// AAF stored object UIDs." << endl
<< "//" << endl << endl;
cout << "#if !defined(INIT_AUID)" << endl;
cout << "#define ";
cout << "DEFINE_AUID(name, l, w1, w2, b1, b2, b3, b4, b5, b6, b7, b8) \\"
<< endl;
cout << " extern \"C\" const aafUID_t name"
<< endl;
cout << "#else" << endl;
cout << "#define ";
cout << "DEFINE_AUID(name, l, w1, w2, b1, b2, b3, b4, b5, b6, b7, b8) \\"
<< endl;
cout << " extern \"C\" const aafUID_t name = \\"
<< endl;
cout << " { l, w1, w2, { b1, b2, b3, b4, b5, b6, b7, b8 } }"
<< endl;
cout << "#endif" << endl;
cout << endl;
cout << "// The AAF reference implementation uses shorter names than" << endl
<< "// SMPTE. The names are shortened by the following aliases." << endl
<< "//" << endl;
size_t maxNameLength = 0;
size_t i = 0;
for (i = 0; i < sizeof(aliases)/sizeof(aliases[0]); i++){
size_t length = strlen(aliases[i].alias);
if (length > maxNameLength) {
maxNameLength = length;
}
}
size_t width = maxNameLength;
for (i = 0; i < sizeof(aliases)/sizeof(aliases[0]); i++){
cout << "#define " << prefix;
printName(aliases[i].alias, width, cout);
cout << " " << prefix;
printName(aliases[i].name, 0, cout);
cout << endl;
}
cout << endl;
for (i = 0; i < sizeof(classes)/sizeof(classes[0]); i++){
printMacroInvocation(prefix,
"DEFINE_AUID",
classes[i].name,
classes[i].identifier,
cout);
cout << endl;
}
printEndGuard(moduleName, cout);
}
/**
* Entry point for the rmsd program. This program calculates the RMSD of the passed in structures.
*
* @param argc The argument count.
* @param argv The argument values.
*/
int main(int argc, char** argv) {
int i;
//Print the copyright notice.
printCopyright(argc, argv);
//Parse the arguments.
if (!parseArgs(argc, argv)) {
//If the arguments were not valid, print the usage and exit
printUsage(argc, argv);
exit(1);
}
//Create an alphabet for reading the sequences.
//AlphabetBuilder* alphabetBuilder = new AlphabetBuilder();
Alphabet* alphabet;
char* backboneAtom;
if (dna) {
alphabet = AlphabetBuilder::createDnaAlphabet();
backboneAtom = (char*) "P";
} else if (rna) {
alphabet = AlphabetBuilder::createRnaAlphabet();
backboneAtom = (char*) "P";
} else {
alphabet = AlphabetBuilder::createProteinAlphabet();
backboneAtom = (char*) "CA";
}
//Create the reader.
StructureAlignmentReader* reader = new
StructureAlignmentReader(alphabet,backboneAtom);
reader->setAlignmentPath("");
if (reader->setAlignmentFilename(fastaFilename) == 0) {
printf("Error: file %s was not found.\n", fastaFilename);
exit(1);
}
reader->setStructurePath(pdbDir);
//Read the alignment.
StructureAlignment* alignment = reader->getStructureAlignment();
if (alignment == NULL) {
printf("Error: file %s was not a valid FASTA file.\n", fastaFilename);
exit(1);
}
printf("Read alignment from '%s': %d sequences of length %d\n", fastaFilename, alignment->getNumberStructures(), alignment->getNumberPositions());
//Make sure all of the sequences are of the same length.
int length = -1;
if (alignment->getNumberStructures() > 0) length = alignment->getStructure(0)->getSize();
for (i=1; i<alignment->getNumberStructures(); i++) {
if (alignment->getStructure(i)->getSize() != length) {
printf("Error: file %s did not contain a sequence alignment.\n", fastaFilename);
exit(1);
}
}
if (!perResidue) {
RmsdTools *rmsdTools = new RmsdTools(alignment);
rmsdTools->rmsd();
FILE *out = fopen(outputFilename,"w");
rmsdTools->printRmsd(out);
fclose(out);
} else {
RmsdTools *rmsdTools = new RmsdTools(alignment);
rmsdTools->rmsdPerResidue();
FILE *out = fopen(outputFilename,"w");
rmsdTools->printRmsdPerResidue(out);
fclose(out);
}
//Free any used memory.
//delete alphabetBuilder;
delete alphabet;
delete reader;
return 0;
}
/* Read project preferences and command line arguments */
static int parseParameters(int argc, const char** argv, SeparationFlags* sfOut)
{
poptContext context;
int argRead;
static int version = FALSE;
static int copyright = FALSE;
static unsigned int numParams = 0;
static int serverParams = 0;
static const char** rest = NULL;
static SeparationFlags sf;
static const struct poptOption options[] =
{
{
"astronomy-parameter-file", 'a',
POPT_ARG_STRING, &sf.ap_file,
0, "Astronomy parameter file", NULL
},
{
"star-points-file", 's',
POPT_ARG_STRING, &sf.star_points_file,
0, "Star points files", NULL
},
{
"output", 'o',
POPT_ARG_STRING, &sf.separation_outfile,
0, "Output file for separation (enables separation)", NULL
},
{
"seed", 'e',
POPT_ARG_INT, &sf.separationSeed,
SEED_ARGUMENT, "Seed for random number generator", NULL
},
{
"modfit", 'f',
POPT_ARG_NONE, &sf.modfit,
0, "Modified fit from Newby 2011", NULL
},
{
"newbg", 'y',
POPT_ARG_NONE, &sf.background,
0, "Uses broken power law as background fit", NULL
},
{
"ignore-checkpoint", 'i',
POPT_ARG_NONE, &sf.ignoreCheckpoint,
0, "Ignore the checkpoint file", NULL
},
{
"cleanup-checkpoint", 'c',
POPT_ARG_NONE, &sf.cleanupCheckpoint,
0, "Delete checkpoint on successful", NULL
},
{
"print-likelihood-text", 't',
POPT_ARG_NONE, &sf.LikelihoodToText,
0, "Create text file with likelihood for use in local MLE", NULL
},
{
"debug-boinc", 'g',
POPT_ARG_NONE, &sf.debugBOINC,
0, "Init BOINC with debugging. No effect if not built with BOINC_APPLICATION", NULL
},
{
"process-priority", 'b',
POPT_ARG_INT, &sf.processPriority,
0, "Set process priority. Set priority 0 (lowest) to 4 (highest)", NULL
},
{
"device", 'd',
POPT_ARG_INT, &sf.useDevNumber,
0, "Device number passed by BOINC to use", NULL
},
{
"non-responsive", 'r',
POPT_ARG_NONE, &sf.nonResponsive,
0, "Do not care about display responsiveness (use with caution)", NULL
},
{
"gpu-target-frequency", 'q',
POPT_ARG_DOUBLE, &sf.targetFrequency,
0, "Target frequency for GPU tasks" , NULL
},
{
"gpu-wait-factor", 'w',
POPT_ARG_DOUBLE, &sf.waitFactor,
0, "Wait correction factor when using high CPU workarounds" , NULL
},
{
"gpu-polling-mode", 'm',
POPT_ARG_INT, &sf.pollingMode,
0, "Interval for polling GPU: (-2 (default): Use mode -1 unless working around high CPU driver issue. -1: use clWaitForEvents(). 0: Use clWaitForEvents() with initial wait, >= 1: sets manual interval polling in ms)" , NULL
},
{
"gpu-disable-checkpointing", 'k',
POPT_ARG_NONE, &sf.disableGPUCheckpointing,
0, "Disable checkpointing with GPUs" , NULL
},
{
"platform", 'l',
POPT_ARG_INT, &sf.usePlatform,
0, "CL platform index to use", NULL
},
{
"platform-vendor", '\0',
POPT_ARG_STRING, &sf.preferredPlatformVendor,
0, "CL Platform vendor name to try to use", NULL
},
{
"verbose", '\0',
POPT_ARG_NONE, &sf.verbose,
0, "Print some extra debugging information", NULL
},
{
"force-no-opencl", '\0',
POPT_ARG_NONE, &sf.forceNoOpenCL,
0, "Use regular CPU path instead of OpenCL if available", NULL
},
{
"force-no-il-kernel", '\0',
POPT_ARG_NONE, &sf.forceNoILKernel,
0, "Do not use AMD IL replacement kernels if available", NULL
},
{
"force-no-intrinsics", '\0',
POPT_ARG_NONE, &sf.forceNoIntrinsics,
0, "Use old default path", NULL
},
{
"force-x87", '\0',
POPT_ARG_NONE, &sf.forceX87,
0, "Force to use x87 path (ignored if x86_64)", NULL
},
{
"force-sse2", '\0',
POPT_ARG_NONE, &sf.forceSSE2,
0, "Force to use SSE2 path", NULL
},
{
"force-sse3", '\0',
POPT_ARG_NONE, &sf.forceSSE3,
0, "Force to use SSE3 path", NULL
},
{
"force-sse4.1", '\0',
POPT_ARG_NONE, &sf.forceSSE41,
0, "Force to use SSE4.1 path", NULL
},
{
"force-avx", '\0',
POPT_ARG_NONE, &sf.forceAVX,
0, "Force to use AVX path", NULL
},
{
"p", 'p',
POPT_ARG_NONE, &serverParams,
0, "Unused dummy argument to satisfy primitive arguments the server sends", NULL
},
{
"np", '\0',
POPT_ARG_INT | POPT_ARGFLAG_ONEDASH, &numParams,
0, "Unused dummy argument to satisfy primitive arguments the server sends", NULL
},
{
"version", 'v',
POPT_ARG_NONE, &version,
0, "Print version information", NULL
},
{
"copyright", '\0',
POPT_ARG_NONE, ©right,
0, "Print copyright information and exit", NULL
},
POPT_AUTOHELP
POPT_TABLEEND
};
setInitialFlags(&sf);
context = poptGetContext(argv[0], argc, argv, options, POPT_CONTEXT_POSIXMEHARDER);
if (!context)
{
mw_printf("Failed to get popt context\n");
exit(EXIT_FAILURE);
}
if (argc < 2)
{
poptPrintUsage(context, stderr, 0);
poptFreeContext(context);
exit(EXIT_FAILURE);
}
argRead = mwReadArguments(context);
if (argRead < 0)
{
poptFreeContext(context);
freeSeparationFlags(&sf);
exit(EXIT_FAILURE);
}
if (version)
{
printVersion(FALSE, sf.verbose);
}
if (copyright)
{
printCopyright();
}
if (version || copyright)
{
exit(EXIT_SUCCESS);
}
sf.setSeed = !!(argRead & SEED_ARGUMENT); /* Check if these flags were used */
sf.do_separation = (sf.separation_outfile && strcmp(sf.separation_outfile, ""));
if (sf.do_separation)
prob_ok_init(sf.separationSeed, sf.setSeed);
rest = poptGetArgs(context);
sf.forwardedArgs = mwGetForwardedArguments(rest, &sf.nForwardedArgs);
sf.numArgs = mwReadRestArgs(rest, sf.nForwardedArgs); /* Temporary */
poptFreeContext(context);
setDefaults(&sf);
*sfOut = sf;
return 0;
}
/**
* Entry point for the qpair program.
*
* @param argc The argument count.
* @param argv The argument values.
*/
int main(int argc, char** argv) {
//Print the copyright notice.
printCopyright(argc, argv);
//Parse the arguments.
if (!parseArgs(argc, argv)) {
//If the arguments were not valid, print the usage and exit.
printUsage(argc, argv);
exit(1);
}
// printf("Done parsing args. calcType: %d, alph: %d, fasta: %s, Dir: %s\n", calculationType, alphabetType, fastaFilename, pdbDir);
StructureAlignment* structAl1 = readStructureAlignment(fastaFilename, pdbDir);
// printf("Done creating structAl1\n");
if (structAl1 == NULL) {
printf("Error: couldn't read structure alignment\n");
exit(1);
}
//QTools* qTools = 0;
StructureQR* structQR = 0;
FILE* out = 0;
//char* kArgString = 0;
//int check = 0;
switch(calculationType) {
/* case QH:
qTools = new QTools(structAl1);
qTools->q(0);
out = fopen(outputFilename,"w");
qTools->printQ(out);
fclose(out);
break;
case QPERRESIDUE:
qTools = new QTools(structAl1);
qTools->qPerResidue();
out = fopen(outputFilename,"w");
qTools->printQPerResidue(out);
fclose(out);
break;
*/
case QR:
structQR = new StructureQR(structAl1);
// printf("Preparing to do structQR->qr()\n");
structQR->qr();
out = fopen(outputFilename,"w");
// printf("Preparing to print Columns\n");
structQR->printColumns(out);
fclose(out);
delete structQR;
break;
default:
printf("Error: invalid calculationType\n");
exit(1);
}
delete structAl1;
/******** if (qTools != 0) {
// XXX - SEGFAULT WHEN QTOOLS IS DELETED
delete qTools;
}
*/
return 0;
}
void printBinaryInformation(FILE *fp,
const ProgramContextInterface &programContext,
const BinaryInformationSettings &settings)
{
const char *prefix = settings.prefix_;
const char *suffix = settings.suffix_;
const char *precisionString = "";
#ifdef GMX_DOUBLE
precisionString = " (double precision)";
#endif
const char *const name = programContext.displayName();
if (settings.bGeneratedByHeader_)
{
fprintf(fp, "%sCreated by:%s\n", prefix, suffix);
}
// TODO: It would be nice to know here whether we are really running a
// Gromacs binary or some other binary that is calling Gromacs; we
// could then print "%s is part of GROMACS" or some alternative text.
std::string title
= formatString(":-) GROMACS - %s, %s%s (-:", name, gmx_version(), precisionString);
const int indent
= centeringOffset(78 - strlen(prefix) - strlen(suffix), title.length()) + 1;
fprintf(fp, "%s%*c%s%s\n", prefix, indent, ' ', title.c_str(), suffix);
fprintf(fp, "%s%s\n", prefix, suffix);
if (settings.bCopyright_)
{
GMX_RELEASE_ASSERT(prefix[0] == '\0' && suffix[0] == '\0',
"Prefix/suffix not supported with copyright");
printCopyright(fp);
fprintf(fp, "\n");
// This line is printed again after the copyright notice to make it
// appear together with all the other information, so that it is not
// necessary to read stuff above the copyright notice.
// The line above the copyright notice puts the copyright notice is
// context, though.
fprintf(fp, "%sGROMACS: %s, %s%s%s\n", prefix, name,
gmx_version(), precisionString, suffix);
}
const char *const binaryPath = programContext.fullBinaryPath();
if (!gmx::isNullOrEmpty(binaryPath))
{
fprintf(fp, "%sExecutable: %s%s\n", prefix, binaryPath, suffix);
}
const gmx::InstallationPrefixInfo installPrefix = programContext.installationPrefix();
if (!gmx::isNullOrEmpty(installPrefix.path))
{
fprintf(fp, "%sData prefix: %s%s%s\n", prefix, installPrefix.path,
installPrefix.bSourceLayout ? " (source tree)" : "", suffix);
}
const char *const commandLine = programContext.commandLine();
if (!gmx::isNullOrEmpty(commandLine))
{
fprintf(fp, "%sCommand line:%s\n%s %s%s\n",
prefix, suffix, prefix, commandLine, suffix);
}
if (settings.bExtendedInfo_)
{
GMX_RELEASE_ASSERT(prefix[0] == '\0' && suffix[0] == '\0',
"Prefix/suffix not supported with extended info");
fprintf(fp, "\n");
gmx_print_version_info(fp);
}
}