bool SimulationConfiguration::Implementation::physicalLayerIs(
const string &testValue) const {
return (stringToUpper(testValue) == stringToUpper(getPhysicalLayerType()));
}
bool SimulationConfiguration::Implementation::outputManagerIs(
const string &testValue) const {
return (stringToUpper(testValue) == stringToUpper(getOutputManagerType()));
}
bool SimulationConfiguration::Implementation::simulationTypeIs(
const string &testValue) const {
return (stringToUpper(testValue) == stringToUpper(getSimulationType()));
}
bool SimulationConfiguration::Implementation::optFossilCollManagerTypeIs(
const string &testValue) const {
return (stringToUpper(testValue) == stringToUpper(
getOptFossilCollManagerType()));
}
bool SimulationConfiguration::Implementation::eventListOrganizationIs(
const string &testValue) const {
return (stringToUpper(testValue) == stringToUpper(
getEventListOrganization()));
}
void InputStructures::read_fasta(string chr_file, map<string, string> & chr_seq) {
//chr_seq.clear();
map<string,string>::iterator it;
string temp_chr_seq = "";
string line = "";
ifstream inFile(chr_file.c_str());
string chr_num = "";
int chrNumber = 0;
string chrName;
bool firstContigFound = false;
if (!inFile.is_open()) {
cout << "Error opening file: " << chr_file << endl;
return;
}
getline(inFile,line);
it = chr_seq.begin();
// Read and process records
while (!inFile.eof() && line.length() > 0) {
if (line.at(0) == '#' && !firstContigFound) {
getline(inFile,line);
} else
if (line.at(0) == '>' || line.at(0) == '<') {
firstContigFound = true;
if (chrNumber > 0) {
//chr_seq.push_back(temp_chr_seq);
chr_seq.insert(it, pair<string,string>(chrName,temp_chr_seq));
if (DEBUG)
cout << "Chromosome Name = " << chrName << endl;
if (temp_chr_seq.length() > 0) {
if (DEBUG)
cout << temp_chr_seq.length() << endl;
temp_chr_seq.clear();
}
//chrNumber++;
}
chrNumber++;
//find if there are more than contig name in the line
int firstspace = line.find(" ");
chrName = line.substr(1, firstspace-1);
if (chrName.length() == 0) {
cerr << " Reference csfasta file provided has no contig name : " << line << endl;
exit(-1);
}
if (DEBUG)
cout << " Chr Name found in Reference csfasta : " << chrName << endl;
refSequences.push_back(chrName);
getline(inFile, line);
} else {
// Convert reference sequence to upper case characters
stringToUpper(line);
temp_chr_seq.append(line);
getline(inFile,line);
}
}
if (temp_chr_seq.length() > 0) {
//cout << temp_chr_seq.length() << endl;cout << "Dima's seq : " << temp_chr_seq.substr(279750,100) << endl;
chr_seq.insert(it, pair<string,string>(chrName,temp_chr_seq));
}
inFile.close();
}
/**********************************************************************************
* AUTHOR : Vijayakumara M
* DATE : 23 Aug 2005
* NAME : main
* DESCRIPTION : Model Data viewer main function - Takes file name as its argument
* and checks the integrity of the file and displays the options user
* entered in the command prompt.
* ARGUMENTS : int argc, char *argv[] ( file name and user desired options)
* RETURNS : 0 on success and -1 on failure.
* NOTES :
* CHANGE HISTROY
* Author Date Description of change
************************************************************************************/
int main(int argc, char* argv[])
{
string m_strLipiRootPath = "";
string m_logFileName = DEFAULT_LOG_FILE;
string m_logLevelStr = "ERROR";
LTKLogger::EDebugLevel m_logLevel = DEFAULT_LOG_LEVEL;
int index = 1;
int tmp = 0;
int str = 0;
int filteredArgc = argc;
bool filFlag = false; // Flag to indicate the file name specified in the comman prompt.
bool allFlag = false; // Flag to indicate all options to be displayed or not.
bool helpFlag = false;
bool preprocFlag = false; // Flag to indicate preproc fields to be displayed.
stringStringMap headerSequence; // Get the maped header tokenized stings.
stringStructMap optMap; // Gets the options and corresponding values.
stringStructMap optPreProcMap; // Gets the Preprocessing options and corresponding values.
string fileName; // Model Data file Name.
string description; // Option description
LTKCheckSumGenerate chFile; // instance of checkSum class for checking file integrity.
//Display order
char optIndex[][20]={"-PROJNAME","-NUMSHAPES","-RECNAME","-RECVER","-CHECKSUM","-CREATETIME","-MODTIME","-HEADERLEN","-DATAOFFSET","-HEADERVER","-BYTEORDER", "-FEATEXTR"};
if (argc == 1)
{
helpDisplay();
return SUCCESS;
}
// Get the argument passed through command prompt.
while(index < argc)
{
// If argument is equal to "-a" or "-all" set allFlag for to display all the options.
if(LTKSTRCMP(argv[index], OPTION_ALL) == 0)
{
allFlag = true;
index++;
continue;
}
//Preproc
if(LTKSTRCMP(argv[index], OPTION_PREPROC) == 0)
{
preprocFlag = true;
index++;
continue;
}
if(LTKSTRCMP(argv[index], OPTION_HELP) == 0)
{
// Call helpDisplay function for displaying the help notice.
helpDisplay();
return SUCCESS;
}
if(LTKSTRCMP(argv[index], OPTION_LIPI_ROOT) == 0)
{
if (index+1 >= argc)
{
cout << "Please specify LIPI_ROOT " << endl;
return FAILURE;
}
m_strLipiRootPath = argv[index+1];
index++;
}
if(LTKSTRCMP(argv[index], OPTION_INPUT) == 0)
{
//set filFlag if the file Name is spcified
if(index+1 < argc)
{
filFlag = true;
fileName = argv[index+1];
index++;
}
}
if(LTKSTRCMP(argv[index], OPTION_VER) == 0)
{
cout << SUPPORTED_MIN_VERSION << endl;
return SUCCESS;
}
if(LTKSTRCMP(argv[index], OPTION_LOGFILE) == 0)
{
if (index+1 >= argc)
{
cout << "Please specify log file name " << endl;
return FAILURE;
}
m_logFileName = argv[index+1];
filteredArgc = argc-2;
index++;
}
if(LTKSTRCMP(argv[index], OPTION_LOGLEVEL) == 0)
{
if (index+1 >= argc)
{
cout << "Please specify log level " << endl;
return FAILURE;
}
m_logLevelStr = argv[index+1];
int errorCode = mapLogLevel(m_logLevelStr, m_logLevel);
if (errorCode != SUCCESS)
{
LTKReturnError(errorCode);
}
filteredArgc = argc-2;
index++;
}
index++;
}
// If nothing specified except the file, display all
if( (filteredArgc == 5 || filteredArgc == 3) && filFlag)
{
allFlag = true;
}
index = 1;
if (m_strLipiRootPath.empty())
{
char* envstring = NULL;
envstring = getenv(LIPIROOT_ENV_STRING);
if(envstring == NULL )
{
cout << "Error, Environment variable is not set LIPI_ROOT" << endl;
return FAILURE;
}
m_strLipiRootPath = envstring;
envstring = NULL;
}
// Configure logger
LTKLoggerUtil::createLogger(m_strLipiRootPath);
LTKLoggerUtil::configureLogger(m_logFileName, m_logLevel);
//if filFlag is set, display File name is not specified and display help
if(filFlag == false)
{
cout <<endl<<endl<<"Model data file Name is not given " <<endl;
cout <<"Please specify the file Name with \"-input\" option" << endl;
cout << endl;
//Display Help
helpDisplay();
cout << endl;
LTKLoggerUtil::destroyLogger();
return FAILURE;
}
// Check file integrity. If file has been altered then set the chflag.
if((tmp = chFile.readMDTHeader(fileName, headerSequence)) != SUCCESS)
{
if( tmp == EMODEL_DATA_FILE_OPEN)
{
cout << "Unable to open model data file" << endl;
LTKLoggerUtil::destroyLogger();
return FAILURE;
}
else if( tmp == EMODEL_DATA_FILE_FORMAT)
{
cout << "Incompatible model data file. The header is not in the desired format." << endl;
LTKLoggerUtil::destroyLogger();
return FAILURE;
}
else if( tmp == EINVALID_INPUT_FORMAT)
{
cout << endl << "Model data file is corrupted" << endl;
LTKLoggerUtil::destroyLogger();
return FAILURE;
}
}
else
{
cout << endl << "Checksum successfully verified"<<endl<<endl;
}
if(preprocFlag)
{
// Map preprocessing options with their values.
mapPreprocOptions(optPreProcMap, headerSequence);
DisplayPreProc(optPreProcMap);
LTKLoggerUtil::destroyLogger();
return 0;
}
// Map options with their values.
mapOptions(optMap, headerSequence);
// Iterator pointing at the begining of the option mapped address.
map<string, option>::iterator the_begiter = optMap.begin();
if(allFlag)
{
str = 0;
while (optIndex[str][0] != '\0')
{
if(!(optMap[optIndex[str]].description.empty()))
cout << optMap[optIndex[str]].description << optMap[optIndex[str]].value << endl;
str++;
}
// Map preprocessing options with their values.
mapPreprocOptions(optPreProcMap, headerSequence);
DisplayPreProc(optPreProcMap);
if( !(headerSequence[PLATFORM].empty()))
{
cout << "Platform - " << headerSequence[PLATFORM] << endl;
cout << " " << headerSequence[OSVERSION] << endl;
cout << " " << headerSequence[PROCESSOR_ARCHITEC] << endl;
}
if( !(headerSequence[COMMENT].empty()))
{
cout << "Comment - " << headerSequence[COMMENT] << endl;
cout << "Comment length - " << headerSequence[COMMENTLEN] << endl;
}
if( !(headerSequence[DATASET].empty()))
{
cout << "Dataset name - " << headerSequence[DATASET] << endl;
}
LTKLoggerUtil::destroyLogger();
return 0;
}
// Display the values if file is present and in the desired format
while((index < argc))
{
if( (LTKSTRCMP(argv[index], "-INPUT") == 0) ||
(LTKSTRCMP(fileName.c_str(), argv[index]) == 0) ||
(LTKSTRCMP(argv[index], "-LIPIROOT") == 0) ||
(LTKSTRCMP(m_strLipiRootPath.c_str(), argv[index]) == 0))
{
++index;
continue;
}
if( (LTKSTRCMP(argv[index], "-DATASET") == 0) ||
(LTKSTRCMP(argv[index], "-COMMENT") == 0) ||
(LTKSTRCMP(argv[index], "-COMMENTLEN") == 0))
{
++index;
continue;
}
if(LTKSTRCMP(argv[index], "-PLATFORM") == 0)
{
cout << "Platform - " << headerSequence[PLATFORM] << endl;
cout << " " << headerSequence[OSVERSION] << endl;
cout << " " << headerSequence[PROCESSOR_ARCHITEC] << endl;
++index;
continue;
}
description = optMap[stringToUpper(argv[index])].description;
if(description.empty())
cout << "UnKnown Option - "<< argv[index] << endl;
else
cout << optMap[argv[index]].description << optMap[argv[index]].value << endl;
++index;
}
LTKLoggerUtil::destroyLogger();
return SUCCESS;
}
