}
/***********************************************************************/
-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){
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] == '>'){ 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();
string input;
while(!in.eof()){
unsigned long int lastpos = in.tellg();
- input = getline(in); gobble(in);
+ 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); }
}
+ gobble(in); //has to be here since windows line endings are 2 characters and mess up the positions
}
in.close();
return positions;
}
+/**************************************************************************************************/
+inline vector<unsigned long int> divideFile(string filename, int& proc) {
+ try{
+
+ vector<unsigned long int> filePos;
+ filePos.push_back(0);
+
+ FILE * pFile;
+ unsigned long int 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);
+ }
+
+ //estimate file breaks
+ unsigned long int chunkSize = 0;
+ chunkSize = size / proc;
+
+ //file to small to divide by processors
+ if (chunkSize == 0) { proc = 1; filePos.push_back(size); return filePos; }
+
+ //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;
+
+ ifstream in;
+ openInputFile(filename, in);
+ in.seekg(spot);
+
+ //look for next '>'
+ unsigned long int newSpot = spot;
+ while (!in.eof()) {
+ char c = in.get();
+ if (c == '>') { in.putback(c); newSpot = in.tellg(); break; }
+ }
+
+ //there was not another sequence before the end of the file
+ if (newSpot == spot) { break; }
+ else { filePos.push_back(newSpot); }
+
+ in.close();
+ }
+
+ //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);
+
+ return filePos;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function divideFile. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+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