#include <ctime>
#include <limits>
+#ifdef USE_MPI
+ #include "mpi.h"
+#endif
/***********************************************************************/
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
#include <readline/history.h>
#endif
- //#include <readline/readline.h>
- //#include <readline/history.h>
#else
#include <conio.h> //allows unbuffered screen capture from stdin
#include <direct.h> //get cwd
return output.str();
}
/***********************************************************************/
-
inline int openOutputFileAppend(string fileName, ofstream& fileHandle){
fileHandle.open(fileName.c_str(), ios::app);
if(!fileHandle) {
- cout << "Error: Could not open " << fileName << endl;
+ cout << "Error: Could not open " << fileName << endl;
return 1;
}
else {
}
}
-/**************************************************************************************************/
-
-inline void mothurOut(string message) {
- try{
- ofstream out;
- string logFileName = "mothur.logFile";
- openOutputFileAppend(logFileName, out);
-
- cout << message;
- out << message;
-
- out.close();
- }
- catch(exception& e) {
- cout << "Error in mothur class mothurOut" << endl;
- exit(1);
- }
-}
-/**************************************************************************************************/
-
-inline void mothurOut(string message, string precision) {
- try{
- ofstream out;
- string logFileName = "mothur.logFile";
- openOutputFileAppend(logFileName, out);
-
- cout << precision << message;
- out << precision << message;
-
- out.close();
- }
- catch(exception& e) {
- cout << "Error in mothur class mothurOut" << endl;
- exit(1);
- }
-}
-
-/**************************************************************************************************/
-
-inline void mothurOutEndLine() {
- try {
- ofstream out;
- string logFileName = "mothur.logFile";
- openOutputFileAppend(logFileName, out);
-
- cout << endl;
- out << endl;
-
- out.close();
- }
- catch(exception& e) {
- cout << "error in mothur mothurOutEndLine" << endl;
- exit(1);
- }
-}
-
-
-/**************************************************************************************************/
-
-inline void errorOut(exception& e, string object, string function) {
-
- mothurOut("Error: ");
- mothurOut(toString(e.what()));
- mothurOut(" has occurred in the " + object + " class function " + function + ". Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.");
- mothurOutEndLine();
-
-}
-
/***********************************************************************/
inline bool isTrue(string f){
string path = "";
size_t found;
- found=longName.find_last_of("/\\");
+ found=longName.find_last_of("~/\\");
if(found != longName.npos){
path = longName.substr(0, found+1);
ifstream fileHandle;
fileHandle.open(fileName.c_str());
if(!fileHandle) {
- mothurOut("Error: Could not open " + fileName); mothurOutEndLine();
+ cout << "Error: Could not open " << fileName << endl;
return false;
}else {
//check for blank file
/***********************************************************************/
inline string getFullPathName(string fileName){
+ try{
string path = hasPath(fileName);
string newFileName;
string cwd;
//get current working directory
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- if (path.rfind("./") == -1) { return fileName; } //already complete name
- else { newFileName = fileName.substr(fileName.rfind("./")+2); } //save the complete part of the name
- char* cwdpath;
- size_t size;
- cwdpath=getcwd(cwdpath,size);
- cwd = cwdpath;
-
- //rip off first '/'
- string simpleCWD;
- if (cwd.length() > 0) { simpleCWD = cwd.substr(1); }
+ if (path.find("~") != -1) { //go to home directory
+ string homeDir = getenv ("HOME");
+ newFileName = homeDir + fileName.substr(fileName.find("~")+1);
+ return newFileName;
+ }else { //find path
+ if (path.rfind("./") == -1) { return fileName; } //already complete name
+ else { newFileName = fileName.substr(fileName.rfind("./")+2); } //save the complete part of the name
+
+ char* cwdpath = new char[1024];
+
+ size_t size;
+ cwdpath=getcwd(cwdpath,size);
- //break apart the current working directory
- vector<string> dirs;
- while (simpleCWD.find_first_of('/') != -1) {
- string dir = simpleCWD.substr(0,simpleCWD.find_first_of('/'));
- simpleCWD = simpleCWD.substr(simpleCWD.find_first_of('/')+1, simpleCWD.length());
- dirs.push_back(dir);
- }
- //get last one // ex. ../../../filename = /user/work/desktop/filename
- dirs.push_back(simpleCWD); //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
+ cwd = cwdpath;
- int index = dirs.size()-1;
+ //rip off first '/'
+ string simpleCWD;
+ if (cwd.length() > 0) { simpleCWD = cwd.substr(1); }
- while((pos = path.rfind("./")) != -1) { //while you don't have a complete path
- if (path[(pos-1)] == '.') { //you want your parent directory ../
- path = path.substr(0, pos-1);
- index--;
- if (index == 0) { break; }
- }else if (path[(pos-1)] == '/') { //you want the current working dir ./
- path = path.substr(0, pos);
- }else if (pos == 1) { break;
- }else { mothurOut("cannot resolve path for " + fileName); mothurOutEndLine(); return fileName; }
- }
+ //break apart the current working directory
+ vector<string> dirs;
+ while (simpleCWD.find_first_of('/') != -1) {
+ string dir = simpleCWD.substr(0,simpleCWD.find_first_of('/'));
+ simpleCWD = simpleCWD.substr(simpleCWD.find_first_of('/')+1, simpleCWD.length());
+ dirs.push_back(dir);
+ }
+ //get last one // ex. ../../../filename = /user/work/desktop/filename
+ dirs.push_back(simpleCWD); //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
+
+
+ int index = dirs.size()-1;
- for (int i = index; i >= 0; i--) {
- newFileName = dirs[i] + "/" + newFileName;
- }
+ while((pos = path.rfind("./")) != -1) { //while you don't have a complete path
+ if (pos == 0) { break; //you are at the end
+ }else if (path[(pos-1)] == '.') { //you want your parent directory ../
+ path = path.substr(0, pos-1);
+ index--;
+ if (index == 0) { break; }
+ }else if (path[(pos-1)] == '/') { //you want the current working dir ./
+ path = path.substr(0, pos);
+ }else if (pos == 1) { break; //you are at the end
+ }else { cout << "cannot resolve path for " << fileName << endl; return fileName; }
+ }
- newFileName = "/" + newFileName;
- return newFileName;
+ for (int i = index; i >= 0; i--) {
+ newFileName = dirs[i] + "/" + newFileName;
+ }
+ newFileName = "/" + newFileName;
+ return newFileName;
+ }
#else
- if (path.rfind(".\\") == -1) { return fileName; } //already complete name
- else { newFileName = fileName.substr(fileName.rfind(".\\")+2); } //save the complete part of the name
-
- char *cwdpath = NULL;
- cwdpath = getcwd(NULL, 0); // or _getcwd
- if ( cwdpath != NULL) { cwd = cwdpath; }
- else { cwd = ""; }
-
- //break apart the current working directory
- vector<string> dirs;
- while (cwd.find_first_of('\\') != -1) {
- string dir = cwd.substr(0,cwd.find_first_of('\\'));
- cwd = cwd.substr(cwd.find_first_of('\\')+1, cwd.length());
- dirs.push_back(dir);
-
- }
- //get last one
- dirs.push_back(cwd); //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
+ if (path.find("~") != -1) { //go to home directory
+ string homeDir = getenv ("HOME");
+ newFileName = homeDir + fileName.substr(fileName.find("~")+1);
+ return newFileName;
+ }else { //find path
+ if (path.rfind(".\\") == -1) { return fileName; } //already complete name
+ else { newFileName = fileName.substr(fileName.rfind(".\\")+2); } //save the complete part of the name
+
+ char *cwdpath = NULL;
+ cwdpath = getcwd(NULL, 0); // or _getcwd
+ if ( cwdpath != NULL) { cwd = cwdpath; }
+ else { cwd = ""; }
- int index = dirs.size()-1;
-
- while((pos = path.rfind(".\\")) != -1) { //while you don't have a complete path
- if (path[(pos-1)] == '.') { //you want your parent directory ../
- path = path.substr(0, pos-1);
- index--;
- if (index == 0) { break; }
- }else if (path[(pos-1)] == '\\') { //you want the current working dir ./
- path = path.substr(0, pos);
- }else if (pos == 1) { break;
- }else { mothurOut("cannot resolve path for " + fileName); mothurOutEndLine(); return fileName; }
- }
+ //break apart the current working directory
+ vector<string> dirs;
+ while (cwd.find_first_of('\\') != -1) {
+ string dir = cwd.substr(0,cwd.find_first_of('\\'));
+ cwd = cwd.substr(cwd.find_first_of('\\')+1, cwd.length());
+ dirs.push_back(dir);
- for (int i = index; i >= 0; i--) {
- newFileName = dirs[i] + "\\" + newFileName;
- }
+ }
+ //get last one
+ dirs.push_back(cwd); //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
+
+ int index = dirs.size()-1;
+
+ while((pos = path.rfind(".\\")) != -1) { //while you don't have a complete path
+ if (pos == 0) { break; //you are at the end
+ }else if (path[(pos-1)] == '.') { //you want your parent directory ../
+ path = path.substr(0, pos-1);
+ index--;
+ if (index == 0) { break; }
+ }else if (path[(pos-1)] == '\\') { //you want the current working dir ./
+ path = path.substr(0, pos);
+ }else if (pos == 1) { break; //you are at the end
+ }else { cout << "cannot resolve path for " << fileName << endl; return fileName; }
+ }
- return newFileName;
+ for (int i = index; i >= 0; i--) {
+ newFileName = dirs[i] + "\\" + newFileName;
+ }
+
+ return newFileName;
+ }
#endif
}
-
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function getFullPathName. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
+ exit(1);
+ }
}
/***********************************************************************/
/***********************************************************************/
inline int openInputFile(string fileName, ifstream& fileHandle){
+
//get full path name
string completeFileName = getFullPathName(fileName);
-
+
fileHandle.open(completeFileName.c_str());
if(!fileHandle) {
- mothurOut("Error: Could not open " + completeFileName); mothurOutEndLine();
+ cout << "Error: Could not open " << completeFileName << endl;
return 1;
}
else {
//check for blank file
gobble(fileHandle);
- if (fileHandle.eof()) { mothurOut(completeFileName + " is blank. Please correct."); mothurOutEndLine(); return 1; }
+ if (fileHandle.eof()) { cout << completeFileName << " is blank. Please correct." << endl; return 1; }
return 0;
}
system(command.c_str());
#else
remove(newName.c_str());
- renameOk = rename(oldName.c_str(), newName.c_str());
+ int renameOk = rename(oldName.c_str(), newName.c_str());
#endif
return 0;
}
/***********************************************************************/
inline int openOutputFile(string fileName, ofstream& fileHandle){
-
+
string completeFileName = getFullPathName(fileName);
fileHandle.open(completeFileName.c_str(), ios::trunc);
if(!fileHandle) {
- mothurOut("Error: Could not open " + completeFileName); mothurOutEndLine();
+ cout << "Error: Could not open " << completeFileName << endl;
return 1;
}
else {
container.push_back(estim);
}
catch(exception& e) {
- errorOut(e, "mothur", "splitAtDash");
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function splitAtDash. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
exit(1);
- }
+ }
}
/***********************************************************************/
container.insert(estim);
}
catch(exception& e) {
- errorOut(e, "mothur", "splitAtDash");
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function splitAtDash. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
exit(1);
- }
+ }
}
/***********************************************************************/
//This function parses the line options and puts them in a set
container.insert(lineNum);
}
catch(exception& e) {
- errorOut(e, "mothur", "splitAtDash");
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function splitAtDash. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
exit(1);
- }
+ }
}
/***********************************************************************/
//This function parses the a string and puts peices in a vector
container.push_back(estim);
}
catch(exception& e) {
- errorOut(e, "mothur", "splitAtComma");
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function splitAtComma. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
exit(1);
- }
+ }
}
/***********************************************************************/
}
catch(exception& e) {
- errorOut(e, "mothur", "splitAtComma");
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function splitAtComma. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
exit(1);
- }
+ }
}
/***********************************************************************/
}
}
catch(exception& e) {
- errorOut(e, "mothur", "splitAtEquals");
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function splitAtEquals. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
exit(1);
- }
+ }
}
/**************************************************************************************************/
return false;
}
catch(exception& e) {
- errorOut(e, "mothur", "inUsersGroups");
- exit(1);
- }
-}
-
-/**************************************************************************************************/
-
-inline void mothurOutJustToLog(string message) {
- try {
- ofstream out;
- string logFileName = "mothur.logFile";
- openOutputFileAppend(logFileName, out);
-
- out << message;
-
- out.close();
- }
- catch(exception& e) {
- errorOut(e, "mothur", "mothurOutJustToLog");
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function inUsersGroups. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
exit(1);
- }
+ }
}
-
-
/**************************************************************************************************/
-
-inline void mothurOut(float num) {
- try {
- ofstream out;
- string logFileName = "mothur.logFile";
- openOutputFileAppend(logFileName, out);
-
- cout << num;
- out << num;
-
- out.close();
- }
- catch(exception& e) {
- cout << "Error in mothur class mothurOut float" << endl;
- exit(1);
- }
-}
-/***********************************************************************/
-inline void mothurOut(double value) {
+//returns true if any of the strings in first vector are in second vector
+inline bool inUsersGroups(vector<string> groupnames, vector<string> Groups) {
try {
- ofstream out;
- string logFileName = "mothur.logFile";
- openOutputFileAppend(logFileName, out);
-
- cout << value;
- out << value;
- out.close();
+ for (int i = 0; i < groupnames.size(); i++) {
+ if (inUsersGroups(groupnames[i], Groups)) { return true; }
+ }
+ return false;
}
catch(exception& e) {
- cout << "Error in mothur class mothurOut double" << endl;
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function inUsersGroups. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
exit(1);
- }
+ }
}
-
/***********************************************************************/
//this function determines if the user has given us labels that are smaller than the given label.
//if so then it returns true so that the calling function can run the previous valid distance.
//it's a "smart" distance function. It also checks for invalid labels.
inline bool anyLabelsToProcess(string label, set<string>& userLabels, string errorOff) {
try {
+
set<string>::iterator it;
vector<float> orderFloat;
map<string, float> userMap; //the conversion process removes trailing 0's which we need to put back
orderFloat.push_back(-1.0);
userMap["unique"] = -1.0;
}else {
- if (errorOff == "") { mothurOut(*it + " is not a valid label."); mothurOutEndLine(); }
+ if (errorOff == "") { cout << *it << " is not a valid label." << endl; }
userLabels.erase(*it);
it--;
}
if (orderFloat[i] < labelFloat) {
smaller = true;
if (orderFloat[i] == -1) {
- if (errorOff == "") { mothurOut("Your file does not include the label unique."); mothurOutEndLine(); }
+ if (errorOff == "") { cout << "Your file does not include the label unique." << endl; }
userLabels.erase("unique");
}
else {
- if (errorOff == "") { mothurOut("Your file does not include the label "); mothurOutEndLine(); }
+ if (errorOff == "") { cout << "Your file does not include the label " << endl; }
string s = "";
for (it2 = userMap.begin(); it2!= userMap.end(); it2++) {
if (it2->second == orderFloat[i]) {
break;
}
}
- if (errorOff == "") { mothurOut(s + ". I will use the next smallest distance. "); mothurOutEndLine(); }
+ if (errorOff == "") {cout << s << ". I will use the next smallest distance. " << endl; }
}
//since they are sorted once you find a bigger one stop looking
}else { break; }
}
catch(exception& e) {
- errorOut(e, "mothur", "anyLabelsToProcess");
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function anyLabelsToProcess. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
exit(1);
- }
+ }
}
/**************************************************************************************************/
//open output file in append mode
openOutputFileAppend(filename, output);
- openInputFile(temp, input);
+ int ableToOpen = openInputFile(temp, input, "no error");
- while(char c = input.get()){
- if(input.eof()) { break; }
- else { output << c; }
+ if (ableToOpen == 0) { //you opened it
+ while(char c = input.get()){
+ if(input.eof()) { break; }
+ else { output << c; }
+ }
+ input.close();
}
- input.close();
output.close();
}
catch(exception& e) {
- errorOut(e, "mothur", "appendFiles");
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function appendFiles. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
exit(1);
- }
+ }
}
/**************************************************************************************************/
-inline string sortFile(string distFile){
+inline string sortFile(string distFile, string outputDir){
try {
+
+ //if (outputDir == "") { outputDir += hasPath(distFile); }
string outfile = getRootName(distFile) + "sorted.dist";
+
//if you can, use the unix sort since its been optimized for years
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
return outfile;
}
catch(exception& e) {
- errorOut(e, "mothur", "sortFile");
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function sortfile. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
exit(1);
- }
+ }
}
+/**************************************************************************************************/
+inline vector<long> setFilePosFasta(string filename, int& num) {
+
+ vector<long> positions;
+ ifstream inFASTA;
+ openInputFile(filename, inFASTA);
+
+ string input;
+ while(!inFASTA.eof()){
+ input = getline(inFASTA); gobble(inFASTA);
+ if (input.length() != 0) {
+ if(input[0] == '>'){ long pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
+ }
+ }
+ inFASTA.close();
+
+ num = positions.size();
+
+ /*FILE * pFile;
+ long size;
+
+ //get num bytes in file
+ pFile = fopen (filename.c_str(),"rb");
+ if (pFile==NULL) perror ("Error opening file");
+ else{
+ fseek (pFile, 0, SEEK_END);
+ size=ftell (pFile);
+ fclose (pFile);
+ }*/
+
+ long size = positions[(positions.size()-1)];
+ ifstream in;
+ openInputFile(filename, in);
+
+ in.seekg(size);
+
+ while(char c = in.get()){
+ if(in.eof()) { break; }
+ else { size++; }
+ }
+ in.close();
+
+ positions.push_back(size);
+
+ return positions;
+}
+/**************************************************************************************************/
+inline vector<long> setFilePosEachLine(string filename, int& num) {
+
+ vector<long> positions;
+ ifstream in;
+ openInputFile(filename, in);
+
+ string input;
+ while(!in.eof()){
+ long lastpos = in.tellg();
+ input = getline(in); gobble(in);
+ if (input.length() != 0) {
+ long pos = in.tellg();
+ if (pos != -1) { positions.push_back(pos - input.length() - 1); }
+ else { positions.push_back(lastpos); }
+ }
+ }
+ in.close();
+
+ num = positions.size();
+
+ FILE * pFile;
+ long size;
+
+ //get num bytes in file
+ pFile = fopen (filename.c_str(),"rb");
+ if (pFile==NULL) perror ("Error opening file");
+ else{
+ fseek (pFile, 0, SEEK_END);
+ size=ftell (pFile);
+ fclose (pFile);
+ }
+
+ positions.push_back(size);
+
+ return positions;
+}
+
/**************************************************************************************************/
#endif
projects / mothur.git / blobdiff