if (sharedfile != "") { mothurOut("shared=" + sharedfile); mothurOutEndLine(); }
if (taxonomyfile != "") { mothurOut("taxonomy=" + taxonomyfile); mothurOutEndLine(); }
if (treefile != "") { mothurOut("tree=" + treefile); mothurOutEndLine(); }
+ if (flowfile != "") { mothurOut("flow=" + flowfile); mothurOutEndLine(); }
+ if (processors != "1") { mothurOut("processors=" + processors); mothurOutEndLine(); }
}
catch(exception& e) {
if (sharedfile != "") { return true; }
if (taxonomyfile != "") { return true; }
if (treefile != "") { return true; }
+ if (flowfile != "") { return true; }
+ if (processors != "1") { return true; }
return hasCurrent;
sfffile = "";
oligosfile = "";
accnosfile = "";
- taxonomyfile = "";
+ taxonomyfile = "";
+ flowfile = "";
+ processors = "1";
}
catch(exception& e) {
errorOut(e, "MothurOut", "clearCurrentFiles");
}
}
/*********************************************************************************************/
+void MothurOut::mothurOut(string output, ofstream& outputFile) {
+ try {
+
+#ifdef USE_MPI
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+
+ if (pid == 0) { //only one process should output to screen
+#endif
+
+ cout << output;
+ out << output;
+ outputFile << output;
+
+#ifdef USE_MPI
+ }
+#endif
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "MothurOut");
+ exit(1);
+ }
+}
+/*********************************************************************************************/
+void MothurOut::mothurOutEndLine(ofstream& outputFile) {
+ try {
+#ifdef USE_MPI
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+
+ if (pid == 0) { //only one process should output to screen
+#endif
+
+ cout << endl;
+ out << endl;
+ outputFile << endl;
+
+#ifdef USE_MPI
+ }
+#endif
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "MothurOutEndLine");
+ exit(1);
+ }
+}
+/*********************************************************************************************/
void MothurOut::mothurOutJustToLog(string output) {
try {
#ifdef USE_MPI
char d;
while(isspace(d=f.get())) { ;}
- f.putback(d);
+ if(!f.eof()) { f.putback(d); }
}
catch(exception& e) {
errorOut(e, "MothurOut", "gobble");
try {
char d;
while(isspace(d=f.get())) {;}
- f.putback(d);
+ if(!f.eof()) { f.putback(d); }
}
catch(exception& e) {
errorOut(e, "MothurOut", "gobble");
string line = "";
- while (!fileHandle.eof()) {
+ while (fileHandle) {
//get next character
char c = fileHandle.get();
//are you at the end of the line
- if ((c == '\n') || (c == '\r') || (c == '\f')){ break; }
+ if ((c == '\n') || (c == '\r') || (c == '\f') || (c == EOF)){ break; }
else { line += c; }
}
/***********************************************************************/
+int MothurOut::getRandomIndex(int highest){
+ try {
+
+ int random = (int) ((float)(highest+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
+
+ return random;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "getRandomIndex");
+ exit(1);
+ }
+
+}
+/**********************************************************************/
+
string MothurOut::getPathName(string longName){
try {
string rootPathName = longName;
cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
system(command.c_str());
cerr << "Done decompressing " << completeFileName << "\n";
- remove(tempName.c_str());
+ mothurRemove(tempName);
exit(EXIT_SUCCESS);
} else {
cerr << "waiting on child process " << fork_result << "\n";
cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
system(command.c_str());
cerr << "Done decompressing " << completeFileName << "\n";
- remove(tempName.c_str());
+ mothurRemove(tempName);
exit(EXIT_SUCCESS);
} else {
cerr << "waiting on child process " << fork_result << "\n";
try {
ifstream inTest;
int exist = openInputFile(newName, inTest, "");
+ inTest.close();
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
if (exist == 0) { //you could open it so you want to delete it
- inTest.close();
string command = "rm " + newName;
system(command.c_str());
}
string command = "mv " + oldName + " " + newName;
system(command.c_str());
#else
- remove(newName.c_str());
+ mothurRemove(newName);
int renameOk = rename(oldName.c_str(), newName.c_str());
#endif
return 0;
}
/**************************************************************************************************/
-void MothurOut::appendFiles(string temp, string filename) {
+int MothurOut::appendFiles(string temp, string filename) {
try{
ofstream output;
ifstream input;
int ableToOpen = openInputFile(temp, input, "no error");
//int ableToOpen = openInputFile(temp, input);
+ int numLines = 0;
if (ableToOpen == 0) { //you opened it
while(char c = input.get()){
if(input.eof()) { break; }
- else { output << c; }
+ else { output << c; if (c == '\n') {numLines++;} }
}
input.close();
}
output.close();
+
+ return numLines;
}
catch(exception& e) {
errorOut(e, "MothurOut", "appendFiles");
output.close();
//remove temp files
- remove(tempDistFile.c_str());
- remove(tempOutfile.c_str());
+ mothurRemove(tempDistFile);
+ mothurRemove(tempOutfile);
#endif
return outfile;
}
}
/**************************************************************************************************/
-vector<unsigned long int> MothurOut::setFilePosFasta(string filename, int& num) {
+vector<unsigned long long> MothurOut::setFilePosFasta(string filename, int& num) {
try {
- vector<unsigned long int> positions;
+ vector<unsigned long long> positions;
ifstream inFASTA;
- openInputFile(filename, inFASTA);
+ //openInputFile(filename, inFASTA);
+ inFASTA.open(filename.c_str(), ios::binary);
string input;
+ unsigned long long count = 0;
while(!inFASTA.eof()){
- input = getline(inFASTA);
- if (input.length() != 0) {
- if(input[0] == '>'){ unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
+ //input = getline(inFASTA);
+ //cout << input << '\t' << inFASTA.tellg() << endl;
+ //if (input.length() != 0) {
+ // if(input[0] == '>'){ unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); cout << (pos - input.length() - 1) << endl; }
+ //}
+ //gobble(inFASTA); //has to be here since windows line endings are 2 characters and mess up the positions
+ char c = inFASTA.get(); count++;
+ if (c == '>') {
+ positions.push_back(count-1);
+ //cout << count << endl;
}
- gobble(inFASTA); //has to be here since windows line endings are 2 characters and mess up the positions
}
inFASTA.close();
fclose (pFile);
}*/
- unsigned long int size = positions[(positions.size()-1)];
+ unsigned long long size = positions[(positions.size()-1)];
ifstream in;
openInputFile(filename, in);
in.close();
positions.push_back(size);
+ positions[0] = 0;
return positions;
}
}
}
/**************************************************************************************************/
-vector<unsigned long int> MothurOut::setFilePosEachLine(string filename, int& num) {
+vector<unsigned long long> MothurOut::setFilePosEachLine(string filename, int& num) {
try {
filename = getFullPathName(filename);
- vector<unsigned long int> positions;
+ vector<unsigned long long> positions;
ifstream in;
- openInputFile(filename, in);
-
+ //openInputFile(filename, in);
+ in.open(filename.c_str(), ios::binary);
+
string input;
+ unsigned long long count = 0;
+ positions.push_back(0);
+
while(!in.eof()){
- unsigned long int lastpos = in.tellg();
- input = getline(in);
- if (input.length() != 0) {
- unsigned long int pos = in.tellg();
- if (pos != -1) { positions.push_back(pos - input.length() - 1); }
- else { positions.push_back(lastpos); }
+ //unsigned long long lastpos = in.tellg();
+ //input = getline(in);
+ //if (input.length() != 0) {
+ //unsigned long long pos = in.tellg();
+ //if (pos != -1) { positions.push_back(pos - input.length() - 1); }
+ //else { positions.push_back(lastpos); }
+ //}
+ //gobble(in); //has to be here since windows line endings are 2 characters and mess up the positions
+
+
+ //getline counting reads
+ char d = in.get(); count++;
+ while ((d != '\n') && (d != '\r') && (d != '\f') && (d != in.eof())) {
+ //get next character
+ d = in.get();
+ count++;
+ }
+
+ if (!in.eof()) {
+ d=in.get(); count++;
+ while(isspace(d) && (d != in.eof())) { d=in.get(); count++;}
}
- gobble(in); //has to be here since windows line endings are 2 characters and mess up the positions
+ positions.push_back(count-1);
+ cout << count-1 << endl;
}
in.close();
- num = positions.size();
+ num = positions.size()-1;
FILE * pFile;
- unsigned long int size;
+ unsigned long long size;
//get num bytes in file
pFile = fopen (filename.c_str(),"rb");
fclose (pFile);
}
- positions.push_back(size);
+ positions[(positions.size()-1)] = size;
return positions;
}
}
/**************************************************************************************************/
-vector<unsigned long int> MothurOut::divideFile(string filename, int& proc) {
+vector<unsigned long long> MothurOut::divideFile(string filename, int& proc) {
try{
-
- vector<unsigned long int> filePos;
+ vector<unsigned long long> filePos;
filePos.push_back(0);
FILE * pFile;
- unsigned long int size;
+ unsigned long long size;
filename = getFullPathName(filename);
-
+
//get num bytes in file
pFile = fopen (filename.c_str(),"rb");
if (pFile==NULL) perror ("Error opening file");
size=ftell (pFile);
fclose (pFile);
}
-
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+
//estimate file breaks
- unsigned long int chunkSize = 0;
+ unsigned long long chunkSize = 0;
chunkSize = size / proc;
//file to small to divide by processors
//for each process seekg to closest file break and search for next '>' char. make that the filebreak
for (int i = 0; i < proc; i++) {
- unsigned long int spot = (i+1) * chunkSize;
+ unsigned long long spot = (i+1) * chunkSize;
ifstream in;
openInputFile(filename, in);
in.seekg(spot);
//look for next '>'
- unsigned long int newSpot = spot;
+ unsigned long long newSpot = spot;
while (!in.eof()) {
char c = in.get();
+
if (c == '>') { in.putback(c); newSpot = in.tellg(); break; }
+ else if (int(c) == -1) { break; }
+
}
//there was not another sequence before the end of the file
- unsigned long int sanityPos = in.tellg();
+ unsigned long long sanityPos = in.tellg();
if (sanityPos == -1) { break; }
else { filePos.push_back(newSpot); }
//save end pos
filePos.push_back(size);
-
+
//sanity check filePos
for (int i = 0; i < (filePos.size()-1); i++) {
if (filePos[(i+1)] <= filePos[i]) { filePos.erase(filePos.begin()+(i+1)); i--; }
}
proc = (filePos.size() - 1);
-
+#else
+ mothurOut("[ERROR]: Windows version should not be calling the divideFile function."); mothurOutEndLine();
+ proc=1;
+ filePos.push_back(size);
+#endif
return filePos;
}
catch(exception& e) {
exit(1);
}
}
-
+/**************************************************************************************************/
+int MothurOut::divideFile(string filename, int& proc, vector<string>& files) {
+ try{
+
+ vector<unsigned long long> filePos = divideFile(filename, proc);
+
+ for (int i = 0; i < (filePos.size()-1); i++) {
+
+ //read file chunk
+ ifstream in;
+ openInputFile(filename, in);
+ in.seekg(filePos[i]);
+ unsigned long long size = filePos[(i+1)] - filePos[i];
+ char* chunk = new char[size];
+ in.read(chunk, size);
+ in.close();
+
+ //open new file
+ string fileChunkName = filename + "." + toString(i) + ".tmp";
+ ofstream out;
+ openOutputFile(fileChunkName, out);
+
+ out << chunk << endl;
+ out.close();
+ delete[] chunk;
+
+ //save name
+ files.push_back(fileChunkName);
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "divideFile");
+ exit(1);
+ }
+}
/***********************************************************************/
bool MothurOut::isTrue(string f){
}
}
/**********************************************************************************************************************/
+int MothurOut::readNames(string namefile, map<string, string>& nameMap) {
+ try {
+
+ //open input file
+ ifstream in;
+ openInputFile(namefile, in);
+
+ while (!in.eof()) {
+ if (control_pressed) { break; }
+
+ string firstCol, secondCol;
+ in >> firstCol >> secondCol; gobble(in);
+
+ nameMap[firstCol] = secondCol;
+ }
+ in.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "readNames");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int MothurOut::readNames(string namefile, map<string, vector<string> >& nameMap) {
+ try {
+
+ //open input file
+ ifstream in;
+ openInputFile(namefile, in);
+
+ while (!in.eof()) {
+ if (control_pressed) { break; }
+
+ string firstCol, secondCol;
+ in >> firstCol >> secondCol; gobble(in);
+
+ vector<string> temp;
+ splitAtComma(secondCol, temp);
+
+ nameMap[firstCol] = temp;
+ }
+ in.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "readNames");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
map<string, int> MothurOut::readNames(string namefile) {
try {
exit(1);
}
}
+/**********************************************************************************************************************/
+int MothurOut::readNames(string namefile, vector<seqPriorityNode>& nameVector, map<string, string>& fastamap) {
+ try {
+ int error = 0;
+
+ //open input file
+ ifstream in;
+ openInputFile(namefile, in);
+
+ while (!in.eof()) {
+ if (control_pressed) { break; }
+
+ string firstCol, secondCol;
+ in >> firstCol >> secondCol; gobble(in);
+
+ int num = getNumNames(secondCol);
+
+ map<string, string>::iterator it = fastamap.find(firstCol);
+ if (it == fastamap.end()) {
+ error = 1;
+ mothurOut("[ERROR]: " + firstCol + " is not in your fastafile, but is in your namesfile, please correct."); mothurOutEndLine();
+ }else {
+ seqPriorityNode temp(num, it->second, firstCol);
+ nameVector.push_back(temp);
+ }
+ }
+ in.close();
+
+ return error;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "readNames");
+ exit(1);
+ }
+}
/***********************************************************************/
exit(1);
}
}
+/***********************************************************************/
+int MothurOut::getNumChar(string line, char c){
+ try {
+ int count = 0;
+
+ if(line != ""){
+ for(int i=0;i<line.size();i++){
+ if(line[i] == c){
+ count++;
+ }
+ }
+ }
+
+ return count;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "getNumChar");
+ exit(1);
+ }
+}
+/***********************************************************************/
+int MothurOut::mothurRemove(string filename){
+ try {
+ filename = getFullPathName(filename);
+ int error = remove(filename.c_str());
+ //if (error != 0) {
+ // if (errno != ENOENT) { //ENOENT == file does not exist
+ // string message = "Error deleting file " + filename;
+ // perror(message.c_str());
+ // }
+ //}
+ return error;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "mothurRemove");
+ exit(1);
+ }
+}
+/***********************************************************************/
+bool MothurOut::mothurConvert(string item, int& num){
+ try {
+ bool error = false;
+
+ if (isNumeric1(item)) {
+ convert(item, num);
+ }else {
+ num = 0;
+ error = true;
+ mothurOut("[ERROR]: cannot convert " + item + " to an integer."); mothurOutEndLine();
+ commandInputsConvertError = true;
+ }
+
+ return error;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "mothurConvert");
+ exit(1);
+ }
+}
+/***********************************************************************/
+bool MothurOut::isNumeric1(string stringToCheck){
+ try {
+ bool numeric = false;
+
+ if(stringToCheck.find_first_not_of("0123456789.-") == string::npos) { numeric = true; }
+
+ return numeric;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "isNumeric1");
+ exit(1);
+ }
+
+}
+/***********************************************************************/
+bool MothurOut::mothurConvert(string item, float& num){
+ try {
+ bool error = false;
+
+ if (isNumeric1(item)) {
+ convert(item, num);
+ }else {
+ num = 0;
+ error = true;
+ mothurOut("[ERROR]: cannot convert " + item + " to a float."); mothurOutEndLine();
+ commandInputsConvertError = true;
+ }
+
+ return error;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "mothurConvert");
+ exit(1);
+ }
+}
+/***********************************************************************/
+bool MothurOut::mothurConvert(string item, double& num){
+ try {
+ bool error = false;
+
+ if (isNumeric1(item)) {
+ convert(item, num);
+ }else {
+ num = 0;
+ error = true;
+ mothurOut("[ERROR]: cannot convert " + item + " to a double."); mothurOutEndLine();
+ commandInputsConvertError = true;
+ }
+
+ return error;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "mothurConvert");
+ exit(1);
+ }
+}
/**************************************************************************************************/
vector<vector<double> > MothurOut::binomial(int maxOrder){
}
}
/**************************************************************************************************/
+int MothurOut::removeConfidences(string& tax) {
+ try {
+
+ string taxon;
+ string newTax = "";
+
+ while (tax.find_first_of(';') != -1) {
+
+ if (control_pressed) { return 0; }
+
+ //get taxon
+ taxon = tax.substr(0,tax.find_first_of(';'));
+
+ int pos = taxon.find_last_of('(');
+ if (pos != -1) {
+ //is it a number?
+ int pos2 = taxon.find_last_of(')');
+ if (pos2 != -1) {
+ string confidenceScore = taxon.substr(pos+1, (pos2-(pos+1)));
+ if (isNumeric1(confidenceScore)) {
+ taxon = taxon.substr(0, pos); //rip off confidence
+ }
+ }
+ }
+ taxon += ";";
+
+ tax = tax.substr(tax.find_first_of(';')+1, tax.length());
+ newTax += taxon;
+ }
+
+ tax = newTax;
+
+ return 0;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "removeConfidences");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
projects / mothur.git / blobdiff