if (taxonomyfile != "") { mothurOut("taxonomy=" + taxonomyfile); mothurOutEndLine(); }
if (treefile != "") { mothurOut("tree=" + treefile); mothurOutEndLine(); }
if (flowfile != "") { mothurOut("flow=" + flowfile); mothurOutEndLine(); }
+ if (biomfile != "") { mothurOut("biom=" + biomfile); mothurOutEndLine(); }
if (processors != "1") { mothurOut("processors=" + processors); mothurOutEndLine(); }
}
if (taxonomyfile != "") { return true; }
if (treefile != "") { return true; }
if (flowfile != "") { return true; }
+ if (biomfile != "") { return true; }
if (processors != "1") { return true; }
return hasCurrent;
accnosfile = "";
taxonomyfile = "";
flowfile = "";
+ biomfile = "";
processors = "1";
}
catch(exception& e) {
exit(1);
}
}
+/***********************************************************************/
+string MothurOut::findProgramPath(string programName){
+ try {
+
+ string envPath = getenv("PATH");
+ string pPath = "";
+
+ //delimiting path char
+ char delim;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ delim = ':';
+#else
+ delim = ';';
+#endif
+
+ //break apart path variable by ':'
+ vector<string> dirs;
+ splitAtChar(envPath, dirs, delim);
+
+ if (debug) { mothurOut("[DEBUG]: dir's in path: \n"); }
+
+ //get path related to mothur
+ for (int i = 0; i < dirs.size(); i++) {
+
+ if (debug) { mothurOut("[DEBUG]: " + dirs[i] + "\n"); }
+
+ //to lower so we can find it
+ string tempLower = "";
+ for (int j = 0; j < dirs[i].length(); j++) { tempLower += tolower(dirs[i][j]); }
+
+ //is this mothurs path?
+ if (tempLower.find(programName) != -1) { pPath = dirs[i]; break; }
+ }
+
+ if (debug) { mothurOut("[DEBUG]: programPath = " + pPath + "\n"); }
+
+ if (pPath != "") {
+ //add programName so it looks like what argv would look like
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ pPath += "/" + programName;
+#else
+ pPath += "\\" + programName;
+#endif
+ }else {
+ //okay programName is not in the path, so the folder programName is in must be in the path
+ //lets find out which one
+
+ //get path related to the program
+ for (int i = 0; i < dirs.size(); i++) {
+
+ if (debug) { mothurOut("[DEBUG]: looking in " + dirs[i] + " for " + programName + " \n"); }
+
+ //is this the programs path?
+ ifstream in;
+ string tempIn = dirs[i];
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ tempIn += "/" + programName;
+#else
+ tempIn += "\\" + programName;
+#endif
+ openInputFile(tempIn, in, "");
+
+ //if this file exists
+ if (in) { in.close(); pPath = tempIn; if (debug) { mothurOut("[DEBUG]: found it, programPath = " + pPath + "\n"); } break; }
+ }
+ }
+
+ return pPath;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "findProgramPath");
+ exit(1);
+ }
+}
/*********************************************************************************************/
void MothurOut::setFileName(string filename) {
try {
//add / to name if needed
string lastChar = pathname.substr(pathname.length()-1);
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
if (lastChar != "/") { pathname += "/"; }
#else
if (lastChar != "\\") { pathname += "\\"; }
if (pid == 0) { //only one process should output to screen
#endif
- cout << output;
out << output;
+ logger() << output;
#ifdef USE_MPI
}
if (pid == 0) { //only one process should output to screen
#endif
- cout << endl;
out << endl;
+ logger() << endl;
#ifdef USE_MPI
}
if (pid == 0) { //only one process should output to screen
#endif
- cout << output;
+
out << output;
outputFile << output;
+ logger() << output;
#ifdef USE_MPI
}
#endif
+
}
catch(exception& e) {
errorOut(e, "MothurOut", "MothurOut");
if (pid == 0) { //only one process should output to screen
#endif
- cout << endl;
out << endl;
outputFile << endl;
+ logger() << endl;
#ifdef USE_MPI
}
//
// On failure, returns 0.0, 0.0
int MothurOut::mem_usage(double& vm_usage, double& resident_set) {
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
vm_usage = 0.0;
resident_set = 0.0;
}
/***********************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
#ifdef USE_COMPRESSION
inline bool endsWith(string s, const char * suffix){
size_t suffixLength = strlen(suffix);
string rootName = longName;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
#ifdef USE_COMPRESSION
if (endsWith(rootName, ".gz") || endsWith(rootName, ".bz2")) {
int pos = rootName.find_last_of('.');
}
/***********************************************************************/
+bool MothurOut::dirCheck(string& dirName){
+ try {
+
+ string tag = "";
+ #ifdef USE_MPI
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+
+ tag = toString(pid);
+ #endif
+
+ //add / to name if needed
+ string lastChar = dirName.substr(dirName.length()-1);
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ if (lastChar != "/") { dirName += "/"; }
+ #else
+ if (lastChar != "\\") { dirName += "\\"; }
+ #endif
+
+ //test to make sure directory exists
+ dirName = getFullPathName(dirName);
+ string outTemp = dirName + tag + "temp";
+ ofstream out;
+ out.open(outTemp.c_str(), ios::trunc);
+ if(!out) {
+ mothurOut(dirName + " directory does not exist or is not writable."); mothurOutEndLine();
+ }else{
+ out.close();
+ mothurRemove(outTemp);
+ return true;
+ }
+
+ return false;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "dirCheck");
+ exit(1);
+ }
+
+}
+/***********************************************************************/
+
string MothurOut::hasPath(string longName){
try {
string path = "";
string MothurOut::getExtension(string longName){
try {
- string extension = longName;
+ string extension = "";
if(longName.find_last_of('.') != longName.npos){
int pos = longName.find_last_of('.');
string cwd;
//get current working directory
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
if (path.find("~") != -1) { //go to home directory
string homeDir;
}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; }
+ }else { mothurOut("cannot resolve path for " + fileName + "\n"); return fileName; }
}
for (int i = index; i >= 0; i--) {
}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; }
+ }else { mothurOut("cannot resolve path for " + fileName + "\n"); return fileName; }
}
for (int i = index; i >= 0; i--) {
try {
//get full path name
string completeFileName = getFullPathName(fileName);
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
#ifdef USE_COMPRESSION
// check for gzipped or bzipped file
if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
//get full path name
string completeFileName = getFullPathName(fileName);
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
#ifdef USE_COMPRESSION
// check for gzipped or bzipped file
if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
int exist = openInputFile(newName, inTest, "");
inTest.close();
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
if (exist == 0) { //you could open it so you want to delete it
string command = "rm " + newName;
system(command.c_str());
try {
string completeFileName = getFullPathName(fileName);
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
#ifdef USE_COMPRESSION
// check for gzipped file
if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
int numLines = 0;
if (ableToOpen == 0) { //you opened it
- while(char c = input.get()){
- if(input.eof()) { break; }
- else { output << c; if (c == '\n') {numLines++;} }
- }
+
+ char buffer[4096];
+ while (!input.eof()) {
+ input.read(buffer, 4096);
+ output.write(buffer, input.gcount());
+ //count number of lines
+ for (int i = 0; i < input.gcount(); i++) { if (buffer[i] == '\n') {numLines++;} }
+ }
input.close();
}
//if you can, use the unix sort since its been optimized for years
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
string command = "sort -n -k +3 " + distFile + " -o " + outfile;
system(command.c_str());
#else //you are stuck with my best attempt...
while(isspace(d) && (d != in.eof())) { d=in.get(); count++;}
}
positions.push_back(count-1);
- cout << count-1 << endl;
+ //cout << count-1 << endl;
}
in.close();
fclose (pFile);
}
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//estimate file breaks
unsigned long long chunkSize = 0;
exit(1);
}
}
+/***********************************************************************/
+
+vector<string> MothurOut::splitWhiteSpace(string& rest, char buffer[], int size){
+ try {
+ vector<string> pieces;
+
+ for (int i = 0; i < size; i++) {
+ if (!isspace(buffer[i])) { rest += buffer[i]; }
+ else {
+ pieces.push_back(rest); rest = "";
+ while (i < size) { //gobble white space
+ if (isspace(buffer[i])) { i++; }
+ else { rest = buffer[i]; break; } //cout << "next piece buffer = " << nextPiece << endl;
+ }
+ }
+ }
+
+ return pieces;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "parsePieces");
+ exit(1);
+ }
+}
/**********************************************************************************************************************/
int MothurOut::readNames(string namefile, map<string, string>& nameMap) {
try {
//open input file
ifstream in;
openInputFile(namefile, in);
-
+
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
+ string firstCol, secondCol;
+
while (!in.eof()) {
if (control_pressed) { break; }
- string firstCol, secondCol;
- in >> firstCol >> secondCol; gobble(in);
-
- nameMap[firstCol] = secondCol;
+ in.read(buffer, 4096);
+ vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) { nameMap[firstCol] = secondCol; pairDone = false; }
+ }
}
in.close();
- return 0;
+ return nameMap.size();
}
catch(exception& e) {
ifstream in;
openInputFile(namefile, in);
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
+ string firstCol, secondCol;
+
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.read(buffer, 4096);
+ vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ vector<string> temp;
+ splitAtComma(secondCol, temp);
+ nameMap[firstCol] = temp;
+ pairDone = false;
+ }
+ }
}
in.close();
-
- return 0;
-
+
+ return nameMap.size();
}
catch(exception& e) {
errorOut(e, "MothurOut", "readNames");
ifstream in;
openInputFile(namefile, in);
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
+ string firstCol, secondCol;
+
while (!in.eof()) {
if (control_pressed) { break; }
- string firstCol, secondCol;
- in >> firstCol >> secondCol; gobble(in);
-
- int num = getNumNames(secondCol);
-
- nameMap[firstCol] = num;
+ in.read(buffer, 4096);
+ vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ int num = getNumNames(secondCol);
+ nameMap[firstCol] = num;
+ pairDone = false;
+ }
+ }
}
- in.close();
+ in.close();
return nameMap;
ifstream in;
openInputFile(namefile, in);
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
+ string firstCol, secondCol;
+
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.read(buffer, 4096);
+ vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ 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);
+ }
+
+ pairDone = false;
+ }
+ }
}
- in.close();
-
+ in.close();
+
return error;
-
}
catch(exception& e) {
errorOut(e, "MothurOut", "readNames");
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){
exit(1);
}
}
+/***********************************************************************/
+string MothurOut::makeList(vector<string>& names) {
+ try {
+ string list = "";
+
+ if (names.size() == 0) { return list; }
+
+ for (int i = 0; i < names.size()-1; i++) { list += names[i] + ","; }
+
+ //get last name
+ list += names[names.size()-1];
+
+ return list;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "makeList");
+ exit(1);
+ }
+}
+
/***********************************************************************/
//This function parses the a string and puts peices in a vector
void MothurOut::splitAtComma(string& estim, vector<string>& container) {
exit(1);
}
}
+/***********************************************************************/
+//This function splits up the various option parameters
+void MothurOut::splitAtChar(string& prefix, string& suffix, char c){
+ try {
+ prefix = suffix.substr(0,suffix.find_first_of(c));
+ if ((suffix.find_first_of(c)+2) <= suffix.length()) { //checks to make sure you don't have comma at end of string
+ suffix = suffix.substr(suffix.find_first_of(c)+1, suffix.length());
+ string space = " ";
+ while(suffix.at(0) == ' ')
+ suffix = suffix.substr(1, suffix.length());
+ }
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "splitAtComma");
+ exit(1);
+ }
+}
+
/***********************************************************************/
//This function splits up the various option parameters
int pos2 = taxon.find_last_of(')');
if (pos2 != -1) {
string confidenceScore = taxon.substr(pos+1, (pos2-(pos+1)));
- if (isContainingOnlyDigits(confidenceScore)) {
+ if (isNumeric1(confidenceScore)) {
taxon = taxon.substr(0, pos); //rip off confidence
}
}
projects / mothur.git / blobdiff