#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
#include <sys/wait.h>
+ #include <sys/time.h>
+ #include <sys/resource.h>
#include <unistd.h>
#ifdef USE_READLINE
}
/***********************************************************************/
-inline string getline(ifstream& fileHandle) {
+inline void gobble(istringstream& f){
+
+ char d;
+ while(isspace(d=f.get())) {;}
+ f.putback(d);
+
+}
+
+/***********************************************************************/
+
+inline string getline(istringstream& fileHandle) {
try {
string line = "";
exit(1);
}
}
+/***********************************************************************/
+inline string getline(ifstream& fileHandle) {
+ try {
+
+ string line = "";
+
+ while (!fileHandle.eof()) {
+ //get next character
+ char c = fileHandle.get();
+
+ //are you at the end of the line
+ if ((c == '\n') || (c == '\r') || (c == '\f')){ break; }
+ else { line += c; }
+ }
+
+ return line;
+
+ }
+ catch(exception& e) {
+ cout << "Error in mothur function getline" << endl;
+ exit(1);
+ }
+}
/***********************************************************************/
inline bool isTrue(string f){
}
/***********************************************************************/
+//This function parses the estimator options and puts them in a vector
+inline void splitAtChar(string& estim, vector<string>& container, char symbol) {
+ try {
+ string individual;
+
+ while (estim.find_first_of(symbol) != -1) {
+ individual = estim.substr(0,estim.find_first_of(symbol));
+ if ((estim.find_first_of(symbol)+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
+ estim = estim.substr(estim.find_first_of(symbol)+1, estim.length());
+ container.push_back(individual);
+ }
+ }
+ //get last one
+ container.push_back(estim);
+ }
+ catch(exception& e) {
+ 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 estimator options and puts them in a vector
inline void splitAtDash(string& estim, vector<string>& container) {
try {
exit(1);
}
}
+
/**************************************************************************************************/
inline bool inUsersGroups(string groupname, vector<string> Groups) {
}
}
/**************************************************************************************************/
-inline vector<long> setFilePosFasta(string filename, int& num) {
+inline vector<unsigned long int> setFilePosFasta(string filename, int& num) {
- vector<long> positions;
+ vector<unsigned long int> positions;
ifstream inFASTA;
openInputFile(filename, inFASTA);
-
+
string input;
while(!inFASTA.eof()){
- input = getline(inFASTA); gobble(inFASTA);
+ input = getline(inFASTA);
if (input.length() != 0) {
- if(input[0] == '>'){ long pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
+ if(input[0] == '>'){ unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
}
+ gobble(inFASTA); //has to be here since windows line endings are 2 characters and mess up the positions
}
inFASTA.close();
fclose (pFile);
}*/
- long size = positions[(positions.size()-1)];
+ unsigned long int size = positions[(positions.size()-1)];
ifstream in;
openInputFile(filename, in);
return positions;
}
/**************************************************************************************************/
-inline vector<long> setFilePosEachLine(string filename, int& num) {
+inline vector<unsigned long int> setFilePosEachLine(string filename, int& num) {
- vector<long> positions;
+ vector<unsigned long int> positions;
ifstream in;
openInputFile(filename, in);
string input;
while(!in.eof()){
- long lastpos = in.tellg();
- input = getline(in); gobble(in);
+ unsigned long int lastpos = in.tellg();
+ input = getline(in);
if (input.length() != 0) {
- long pos = in.tellg();
+ unsigned long int 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
}
in.close();
num = positions.size();
FILE * pFile;
- long size;
+ unsigned long int size;
//get num bytes in file
pFile = fopen (filename.c_str(),"rb");
return positions;
}
+/**************************************************************************************************/
+inline bool checkReleaseVersion(ifstream& file, string version) {
+ try {
+
+ bool good = true;
+
+ string line = getline(file);
+ //before we added this check
+ if (line[0] != '#') { good = false; }
+ else {
+ //rip off #
+ line = line.substr(1);
+
+ vector<string> versionVector;
+ splitAtChar(version, versionVector, '.');
+
+ //check file version
+ vector<string> linesVector;
+ splitAtChar(line, linesVector, '.');
+
+ if (versionVector.size() != linesVector.size()) { good = false; }
+ else {
+ for (int j = 0; j < versionVector.size(); j++) {
+ int num1, num2;
+ convert(versionVector[j], num1);
+ convert(linesVector[j], num2);
+
+ //if mothurs version is newer than this files version, then we want to remake it
+ if (num1 > num2) { good = false; break; }
+ }
+ }
+
+ }
+
+ if (!good) { file.close(); }
+ else { file.seekg(0); }
+
+ return good;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function checkReleaseVersion. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
+ exit(1);
+ }
+}
/**************************************************************************************************/
#endif
projects / mothur.git / blobdiff