PhyloSummary::PhyloSummary(string refTfile, GroupMap* g, bool r, int p){
try {
m = MothurOut::getInstance();
maxLevel = 0;
ignore = false;
numSeqs = 0;
relabund = r;
printlevel = p;
groupmap = g;
ct = NULL;
//check for necessary files
string taxFileNameTest = m->getFullPathName((refTfile.substr(0,refTfile.find_last_of(".")+1) + "tree.sum"));
ifstream FileTest(taxFileNameTest.c_str());
if (!FileTest) {
m->mothurOut("Error: can't find " + taxFileNameTest + "."); m->mothurOutEndLine(); exit(1);
}else{
readTreeStruct(FileTest);
}
tree[0].rank = "0";
assignRank(0);
}
catch(exception& e) {
m->errorOut(e, "PhyloSummary", "PhyloSummary");
exit(1);
}
}
PhyloSummary::PhyloSummary(string refTfile, CountTable* c){
try {
m = MothurOut::getInstance();
maxLevel = 0;
ignore = false;
numSeqs = 0;
ct = c;
groupmap = NULL;
//check for necessary files
if (refTfile == "saved") { ReferenceDB* rdb = ReferenceDB::getInstance(); refTfile = rdb->getSavedTaxonomy(); }
string taxFileNameTest = m->getFullPathName((refTfile.substr(0,refTfile.find_last_of(".")+1) + "tree.sum"));
ifstream FileTest(taxFileNameTest.c_str());
if (!FileTest) {
m->mothurOut("Error: can't find " + taxFileNameTest + "."); m->mothurOutEndLine(); exit(1);
}else{
readTreeStruct(FileTest);
}
tree[0].rank = "0";
assignRank(0);
}
catch(exception& e) {
m->errorOut(e, "PhyloSummary", "PhyloSummary");
exit(1);
}
}
/** Diese Funktion prueft ob die Datei mit gewuenschten Namen bereits existiert.
* Wenn der Name bereits vergeben wurde, so hat der Nutzer die Moeglichkeit einen neuen Namen zu vergeben
* oder die bereits bestehende Datei zu ueberschreiben.
* @param name Der Dateiname.
*/
string Magische_Quadrate::ueberpruefe_ob_file_existiert(string name)
{
string file_name = name;
bool ok = false;
do
{
ifstream FileTest(file_name.c_str());
if (FileTest && ok == false)
{
int eingabe = 0;
cout << "\nDie Datei " + file_name + " existiert bereits!\n";
cout << "Soll die Datei ueberschrieben werden [0] oder moechten Sie eine neue angeben[1]?\n";
cout << "Ihre Wahl: ";
eingabe = erfasse_int(0,1);
if (eingabe == 1)
{
cout << "\nBitte geben Sie den Namen Ihrer neuen Datei an: ";
erfasse_zeichenkette(file_name);
}
else
ok = true;
}
else
{
ok = true;
FileTest.close();
}
} while (!ok);
return file_name;
}
bool pruefe_ob_datei_vorhanden(char *dateiname) {
bool datei_vorhanden = true;
std::ifstream FileTest(dateiname);
if(!FileTest) {
std::cout << "FEHLER: Datei existiert nicht." << std::endl;
datei_vorhanden = false;
}
return datei_vorhanden;
}
static void Handle_FileTest
(
le_msg_MessageRef_t _msgRef
)
{
// Get the message buffer pointer
__attribute__((unused)) uint8_t* _msgBufPtr = ((_Message_t*)le_msg_GetPayloadPtr(_msgRef))->buffer;
// Unpack the input parameters from the message
int dataFile;
dataFile = le_msg_GetFd(_msgRef);
// Call the function
FileTest ( (ServerCmdRef_t)_msgRef, dataFile );
}
//*****************************************************************************
// MAIN FUNCTION
//*****************************************************************************
void main() {
//
// Board Initialization
//
BoardInit();
//
// configure the GPIO pins for LEDs,UART
//
PinMuxConfig();
//
// Configure the UART
//
#ifndef NOTERM
InitTerm();
#endif //NOTERM
//
// Display Application Banner
//
DisplayBanner(APPLICATION_NAME);
//
// Configure all 3 LEDs
//
GPIO_IF_LedConfigure(LED1 | LED2 | LED3);
// switch off all LEDs
GPIO_IF_LedOff(MCU_ALL_LED_IND);
FileTest();
/*//
// Start the SimpleLink Host
//
VStartSimpleLinkSpawnTask(SPAWN_TASK_PRIORITY);
//
// Start the WlanStationMode task
//
osi_TaskCreate( WlanStationMode, (const signed char*)"Wlan Station Task",
OSI_STACK_SIZE, NULL, 1, NULL );
//
// Start the task scheduler
//
osi_start();*/
}
int main()
{
// for timing how long tests take
{
boost::progress_timer timer;
CoreFSTest();
MakeKnoxCryptTest();
FileDeviceTest();
FileBlockTest();
FileBlockIteratorTest();
FileTest();
ContentFolderTest();
}
simpletest::showResults();
}
static void Handle_FileTest
(
le_msg_MessageRef_t _msgRef
)
{
// Get the message buffer pointer
uint8_t* _msgBufPtr = ((_Message_t*)le_msg_GetPayloadPtr(_msgRef))->buffer;
// Needed if we are returning a result or output values
uint8_t* _msgBufStartPtr = _msgBufPtr;
// Unpack the input parameters from the message
int dataFile;
dataFile = le_msg_GetFd(_msgRef);
// Define storage for output parameters
int dataOut;
// Call the function
FileTest ( dataFile, &dataOut );
// Re-use the message buffer for the response
_msgBufPtr = _msgBufStartPtr;
// Pack any "out" parameters
le_msg_SetFd(_msgRef, dataOut);
// Return the response
LE_DEBUG("Sending response to client session %p : %ti bytes sent",
le_msg_GetSession(_msgRef),
_msgBufPtr-_msgBufStartPtr);
le_msg_Respond(_msgRef);
}
void test1(void)
{
uint32_t value=10;
uint32_t data[] = {1, 2, 3, 4};
size_t length=10;
uint32_t output[length];
char response[21];
char more[21];
allParameters(COMMON_TWO,
&value,
data,
4,
output,
&length,
"input string",
response,
sizeof(response),
more,
sizeof(more));
LE_PRINT_VALUE("%i", value);
LE_PRINT_ARRAY("%i", length, output);
LE_PRINT_VALUE("%s", response);
LE_PRINT_VALUE("%s", more);
// Call again with a special value, so that nothing is returned for the 'output', 'response'
// and 'more' output parameters. This could happen in a typical function, if an error is
// detected.
// Make 'length' larger than actually defined for the 'output' parameter to verify that
// only the maximum defined value is used on the server.
length = 20;
allParameters(COMMON_ZERO,
&value,
data,
4,
output,
&length,
"new string",
response,
sizeof(response),
more,
sizeof(more));
LE_PRINT_VALUE("%i", value);
LE_PRINT_ARRAY("%i", length, output);
LE_PRINT_VALUE("%s", response);
LE_PRINT_VALUE("%s", more);
// Test file descriptors
int fdToServer;
int fdFromServer;
// Open a file known to exist
fdToServer = open("/usr/include/stdio.h", O_RDONLY);
LE_PRINT_VALUE("%i", fdToServer);
FileTest(fdToServer, &fdFromServer);
LE_PRINT_VALUE("%i", fdFromServer);
// Read and print out whatever is read from the server fd
writeFdToLog(fdFromServer);
}
int ChimeraPintailCommand::execute(){
try{
if (abort == true) { if (calledHelp) { return 0; } return 2; }
for (int s = 0; s < fastaFileNames.size(); s++) {
m->mothurOut("Checking sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
int start = time(NULL);
//set user options
if (maskfile == "default") { m->mothurOut("I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013."); m->mothurOutEndLine(); }
//check for quantile to save the time
string baseName = templatefile;
if (templatefile == "saved") { baseName = rdb->getSavedReference(); }
string tempQuan = "";
if ((!filter) && (maskfile == "")) {
tempQuan = inputDir + m->getRootName(m->getSimpleName(baseName)) + "pintail.quan";
}else if ((!filter) && (maskfile != "")) {
tempQuan = inputDir + m->getRootName(m->getSimpleName(baseName)) + "pintail.masked.quan";
}else if ((filter) && (maskfile != "")) {
tempQuan = inputDir + m->getRootName(m->getSimpleName(baseName)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "masked.quan";
}else if ((filter) && (maskfile == "")) {
tempQuan = inputDir + m->getRootName(m->getSimpleName(baseName)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "quan";
}
ifstream FileTest(tempQuan.c_str());
if(FileTest){
bool GoodFile = m->checkReleaseVersion(FileTest, m->getVersion());
if (GoodFile) {
m->mothurOut("I found " + tempQuan + " in your input file directory. I will use it to save time."); m->mothurOutEndLine(); quanfile = tempQuan; FileTest.close();
}
}else {
string tryPath = m->getDefaultPath();
string tempQuan = "";
if ((!filter) && (maskfile == "")) {
tempQuan = tryPath + m->getRootName(m->getSimpleName(baseName)) + "pintail.quan";
}else if ((!filter) && (maskfile != "")) {
tempQuan = tryPath + m->getRootName(m->getSimpleName(baseName)) + "pintail.masked.quan";
}else if ((filter) && (maskfile != "")) {
tempQuan = tryPath + m->getRootName(m->getSimpleName(baseName)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "masked.quan";
}else if ((filter) && (maskfile == "")) {
tempQuan = tryPath + m->getRootName(m->getSimpleName(baseName)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "quan";
}
ifstream FileTest2(tempQuan.c_str());
if(FileTest2){
bool GoodFile = m->checkReleaseVersion(FileTest2, m->getVersion());
if (GoodFile) {
m->mothurOut("I found " + tempQuan + " in your input file directory. I will use it to save time."); m->mothurOutEndLine(); quanfile = tempQuan; FileTest2.close();
}
}
}
chimera = new Pintail(fastaFileNames[s], templatefile, filter, processors, maskfile, consfile, quanfile, window, increment, outputDir);
if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it
string outputFileName, accnosFileName;
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]));
if (maskfile != "") { variables["[tag]"] = m->getSimpleName(m->getRootName(maskfile)); }
outputFileName = getOutputFileName("chimera", variables);
accnosFileName = getOutputFileName("accnos", variables);
if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
if (chimera->getUnaligned()) {
m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine();
delete chimera;
return 0;
}
templateSeqsLength = chimera->getLength();
#ifdef USE_MPI
int pid, numSeqsPerProcessor;
int tag = 2001;
vector<unsigned long long> MPIPos;
MPI_Status status;
MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
MPI_Comm_size(MPI_COMM_WORLD, &processors);
MPI_File inMPI;
MPI_File outMPI;
MPI_File outMPIAccnos;
int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
int inMode=MPI_MODE_RDONLY;
char outFilename[1024];
strcpy(outFilename, outputFileName.c_str());
char outAccnosFilename[1024];
strcpy(outAccnosFilename, accnosFileName.c_str());
char inFileName[1024];
strcpy(inFileName, fastaFileNames[s].c_str());
MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } delete chimera; return 0; }
if (pid == 0) { //you are the root process
MPIPos = m->setFilePosFasta(fastaFileNames[s], numSeqs); //fills MPIPos, returns numSeqs
//send file positions to all processes
for(int i = 1; i < processors; i++) {
MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
}
//figure out how many sequences you have to align
numSeqsPerProcessor = numSeqs / processors;
int startIndex = pid * numSeqsPerProcessor;
if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
//do your part
driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); m->mothurRemove(outputFileName); m->mothurRemove(accnosFileName); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } delete chimera; return 0; }
}else{ //you are a child process
MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
MPIPos.resize(numSeqs+1);
MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
//figure out how many sequences you have to align
numSeqsPerProcessor = numSeqs / processors;
int startIndex = pid * numSeqsPerProcessor;
if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
//do your part
driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } delete chimera; return 0; }
}
//close files
MPI_File_close(&inMPI);
MPI_File_close(&outMPI);
MPI_File_close(&outMPIAccnos);
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
//break up file
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
vector<unsigned long long> positions = m->divideFile(fastaFileNames[s], processors);
for (int i = 0; i < (positions.size()-1); i++) {
lines.push_back(new linePair(positions[i], positions[(i+1)]));
}
if(processors == 1){
numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); m->mothurRemove(accnosFileName); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; }
}else{
processIDS.resize(0);
numSeqs = createProcesses(outputFileName, fastaFileNames[s], accnosFileName);
rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
rename((accnosFileName + toString(processIDS[0]) + ".temp").c_str(), accnosFileName.c_str());
//append output files
for(int i=1;i<processors;i++){
m->appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
m->mothurRemove((outputFileName + toString(processIDS[i]) + ".temp"));
}
//append output files
for(int i=1;i<processors;i++){
m->appendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName);
m->mothurRemove((accnosFileName + toString(processIDS[i]) + ".temp"));
}
if (m->control_pressed) {
m->mothurRemove(outputFileName);
m->mothurRemove(accnosFileName);
for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } outputTypes.clear();
for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
delete chimera;
return 0;
}
}
#else
lines.push_back(new linePair(0, 1000));
numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); m->mothurRemove(accnosFileName); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; }
#endif
#endif
delete chimera;
for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName);
m->mothurOutEndLine();
m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
}
//set accnos file as new current accnosfile
string current = "";
itTypes = outputTypes.find("accnos");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
}
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "ChimeraPintailCommand", "execute");
exit(1);
}
}
//***************************************************************************************************************
ChimeraPintailCommand::ChimeraPintailCommand(string option) {
try {
abort = false; calledHelp = false;
rdb = ReferenceDB::getInstance();
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter("chimera.pintail");
map<string,string>::iterator it;
//check to make sure all parameters are valid for command
for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
vector<string> tempOutNames;
outputTypes["chimera"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
//if the user changes the input directory command factory will send this info to us in the output parameter
inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
else {
string path;
it = parameters.find("reference");
//user has given a template file
if(it != parameters.end()){
path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["reference"] = inputDir + it->second; }
}
it = parameters.find("conservation");
//user has given a template file
if(it != parameters.end()){
path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["conservation"] = inputDir + it->second; }
}
it = parameters.find("quantile");
//user has given a template file
if(it != parameters.end()){
path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["quantile"] = inputDir + it->second; }
}
}
//check for required parameters
fastafile = validParameter.validFile(parameters, "fasta", false);
if (fastafile == "not found") {
//if there is a current fasta file, use it
string filename = m->getFastaFile();
if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
}else {
m->splitAtDash(fastafile, fastaFileNames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < fastaFileNames.size(); i++) {
bool ignore = false;
if (fastaFileNames[i] == "current") {
fastaFileNames[i] = m->getFastaFile();
if (fastaFileNames[i] != "") { m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
else {
m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
//erase from file list
fastaFileNames.erase(fastaFileNames.begin()+i);
i--;
}
}
if (!ignore) {
if (inputDir != "") {
string path = m->hasPath(fastaFileNames[i]);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
}
int ableToOpen;
ifstream in;
ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
//if you can't open it, try default location
if (ableToOpen == 1) {
if (m->getDefaultPath() != "") { //default path is set
string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
fastaFileNames[i] = tryPath;
}
}
if (ableToOpen == 1) {
if (m->getOutputDir() != "") { //default path is set
string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
fastaFileNames[i] = tryPath;
}
}
in.close();
if (ableToOpen == 1) {
m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
//erase from file list
fastaFileNames.erase(fastaFileNames.begin()+i);
i--;
}else {
m->setFastaFile(fastaFileNames[i]);
}
}
}
//make sure there is at least one valid file left
if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
}
string temp;
temp = validParameter.validFile(parameters, "filter", false); if (temp == "not found") { temp = "F"; }
filter = m->isTrue(temp);
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
m->mothurConvert(temp, processors);
temp = validParameter.validFile(parameters, "window", false); if (temp == "not found") { temp = "0"; }
m->mothurConvert(temp, window);
temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "25"; }
m->mothurConvert(temp, increment);
temp = validParameter.validFile(parameters, "save", false); if (temp == "not found"){ temp = "f"; }
save = m->isTrue(temp);
rdb->save = save;
if (save) { //clear out old references
rdb->clearMemory();
}
//this has to go after save so that if the user sets save=t and provides no reference we abort
templatefile = validParameter.validFile(parameters, "reference", true);
if (templatefile == "not found") {
//check for saved reference sequences
if (rdb->referenceSeqs.size() != 0) {
templatefile = "saved";
}else {
m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required.");
m->mothurOutEndLine();
abort = true;
}
}else if (templatefile == "not open") { abort = true; }
else { if (save) { rdb->setSavedReference(templatefile); } }
maskfile = validParameter.validFile(parameters, "mask", false);
if (maskfile == "not found") { maskfile = ""; }
else if (maskfile != "default") {
if (inputDir != "") {
string path = m->hasPath(maskfile);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { maskfile = inputDir + maskfile; }
}
ifstream in;
int ableToOpen = m->openInputFile(maskfile, in, "no error");
if (ableToOpen == 1) {
if (m->getDefaultPath() != "") { //default path is set
string tryPath = m->getDefaultPath() + m->getSimpleName(maskfile);
m->mothurOut("Unable to open " + maskfile + ". Trying default " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
maskfile = tryPath;
}
}
if (ableToOpen == 1) {
if (m->getOutputDir() != "") { //default path is set
string tryPath = m->getOutputDir() + m->getSimpleName(maskfile);
m->mothurOut("Unable to open " + maskfile + ". Trying output directory " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
maskfile = tryPath;
}
}
in.close();
if (ableToOpen == 1) {
m->mothurOut("Unable to open " + maskfile + "."); m->mothurOutEndLine();
abort = true;
}
}
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
consfile = validParameter.validFile(parameters, "conservation", true);
if (consfile == "not open") { abort = true; }
else if (consfile == "not found") {
consfile = "";
//check for consfile
string tempConsFile = m->getRootName(inputDir + m->getSimpleName(templatefile)) + "freq";
ifstream FileTest(tempConsFile.c_str());
if(FileTest){
bool GoodFile = m->checkReleaseVersion(FileTest, m->getVersion());
if (GoodFile) {
m->mothurOut("I found " + tempConsFile + " in your input file directory. I will use it to save time."); m->mothurOutEndLine(); consfile = tempConsFile; FileTest.close();
}
}else {
string tempConsFile = m->getDefaultPath() + m->getRootName(m->getSimpleName(templatefile)) + "freq";
ifstream FileTest2(tempConsFile.c_str());
if(FileTest2){
bool GoodFile = m->checkReleaseVersion(FileTest2, m->getVersion());
if (GoodFile) {
m->mothurOut("I found " + tempConsFile + " in your input file directory. I will use it to save time."); m->mothurOutEndLine(); consfile = tempConsFile; FileTest2.close();
}
}
}
}
quanfile = validParameter.validFile(parameters, "quantile", true);
if (quanfile == "not open") { abort = true; }
else if (quanfile == "not found") { quanfile = ""; }
}
}
catch(exception& e) {
m->errorOut(e, "ChimeraPintailCommand", "ChimeraPintailCommand");
exit(1);
}
}