return _uniqueInstance;
}
/*********************************************************************************************/
+set<string> MothurOut::getCurrentTypes() {
+ try {
+
+ set<string> types;
+ types.insert("fasta");
+ types.insert("accnos");
+ types.insert("column");
+ types.insert("design");
+ types.insert("group");
+ types.insert("list");
+ types.insert("name");
+ types.insert("oligos");
+ types.insert("order");
+ types.insert("ordergroup");
+ types.insert("phylip");
+ types.insert("qfile");
+ types.insert("relabund");
+ types.insert("sabund");
+ types.insert("rabund");
+ types.insert("sff");
+ types.insert("shared");
+ types.insert("taxonomy");
+ types.insert("tree");
+ types.insert("flow");
+ types.insert("biom");
+ types.insert("counttable");
+ types.insert("processors");
+
+ return types;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "getCurrentTypes");
+ exit(1);
+ }
+}
+/*********************************************************************************************/
void MothurOut::printCurrentFiles() {
try {
+
+
if (accnosfile != "") { mothurOut("accnos=" + accnosfile); mothurOutEndLine(); }
if (columnfile != "") { mothurOut("column=" + columnfile); mothurOutEndLine(); }
if (designfile != "") { mothurOut("design=" + designfile); mothurOutEndLine(); }
if (treefile != "") { mothurOut("tree=" + treefile); mothurOutEndLine(); }
if (flowfile != "") { mothurOut("flow=" + flowfile); mothurOutEndLine(); }
if (biomfile != "") { mothurOut("biom=" + biomfile); mothurOutEndLine(); }
+ if (counttablefile != "") { mothurOut("counttable=" + counttablefile); mothurOutEndLine(); }
if (processors != "1") { mothurOut("processors=" + processors); mothurOutEndLine(); }
}
if (treefile != "") { return true; }
if (flowfile != "") { return true; }
if (biomfile != "") { return true; }
+ if (counttablefile != "") { return true; }
if (processors != "1") { return true; }
return hasCurrent;
taxonomyfile = "";
flowfile = "";
biomfile = "";
+ counttablefile = "";
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 {
int numLines = 0;
if (ableToOpen == 0) { //you opened it
- while(!input.eof()){
- 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();
}
positions.push_back(0);
while(!in.eof()){
- //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())) {
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 {
+ if (rest != "") { 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", "splitWhiteSpace");
+ exit(1);
+ }
+}
+/***********************************************************************/
+vector<string> MothurOut::splitWhiteSpace(string input){
+ try {
+ vector<string> pieces;
+ string rest = "";
+
+ for (int i = 0; i < input.length(); i++) {
+ if (!isspace(input[i])) { rest += input[i]; }
+ else {
+ if (rest != "") { pieces.push_back(rest); rest = ""; }
+ while (i < input.length()) { //gobble white space
+ if (isspace(input[i])) { i++; }
+ else { rest = input[i]; break; } //cout << "next piece buffer = " << nextPiece << endl;
+ }
+ }
+ }
+
+ if (rest != "") { pieces.push_back(rest); }
+
+ return pieces;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "splitWhiteSpace");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int MothurOut::readTax(string namefile, map<string, string>& taxMap) {
+ 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; }
+
+ 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) {
+ //are there confidence scores, if so remove them
+ if (secondCol.find_first_of('(') != -1) { removeConfidences(secondCol); }
+ taxMap[firstCol] = secondCol;
+ if (debug) { mothurOut("[DEBUG]: name = '" + firstCol + "' tax = '" + secondCol + "'\n"); }
+ pairDone = false;
+ }
+ }
+ }
+ in.close();
+
+ return taxMap.size();
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "readTax");
+ exit(1);
+ }
+}
/**********************************************************************************************************************/
-int MothurOut::readNames(string namefile, map<string, string>& nameMap) {
+int MothurOut::readNames(string namefile, map<string, string>& nameMap, bool redund) {
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) {
+ //parse names into vector
+ vector<string> theseNames;
+ splitAtComma(secondCol, theseNames);
+ for (int i = 0; i < theseNames.size(); i++) { nameMap[theseNames[i]] = firstCol; }
+ pairDone = false;
+ }
+ }
}
in.close();
}
}
/**********************************************************************************************************************/
-int MothurOut::readNames(string namefile, map<string, vector<string> >& nameMap) {
+int MothurOut::readNames(string namefile, map<string, string>& nameMap, int flip) {
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);
+ 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[secondCol] = firstCol;
+ pairDone = false;
+ }
+ }
+ }
+ in.close();
+
+ return nameMap.size();
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "readNames");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int MothurOut::readNames(string namefile, map<string, string>& nameMap, map<string, int>& nameCount) {
+ try {
+ nameMap.clear(); nameCount.clear();
+ //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; }
- vector<string> temp;
- splitAtComma(secondCol, 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) {
+ //parse names into vector
+ vector<string> theseNames;
+ splitAtComma(secondCol, theseNames);
+ for (int i = 0; i < theseNames.size(); i++) { nameMap[theseNames[i]] = firstCol; }
+ nameCount[firstCol] = theseNames.size();
+ pairDone = false;
+ }
+ }
+ }
+ in.close();
+
+ return nameMap.size();
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "readNames");
+ 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; }
- 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) { nameMap[firstCol] = secondCol; pairDone = false; }
+ }
}
in.close();
}
}
/**********************************************************************************************************************/
+int MothurOut::readNames(string namefile, map<string, vector<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; }
+
+ 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 nameMap.size();
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "readNames");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
map<string, int> MothurOut::readNames(string namefile) {
try {
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; gobble(in);
- in >> 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);
}
}
-
+//**********************************************************************************************************************
+set<string> MothurOut::readAccnos(string accnosfile){
+ try {
+ set<string> names;
+ ifstream in;
+ openInputFile(accnosfile, in);
+ string name;
+
+ string rest = "";
+ char buffer[4096];
+
+ while (!in.eof()) {
+ if (control_pressed) { break; }
+
+ in.read(buffer, 4096);
+ vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) { names.insert(pieces[i]); }
+ }
+ in.close();
+
+ return names;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "readAccnos");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int MothurOut::readAccnos(string accnosfile, vector<string>& names){
+ try {
+ names.clear();
+ ifstream in;
+ openInputFile(accnosfile, in);
+ string name;
+
+ string rest = "";
+ char buffer[4096];
+
+ while (!in.eof()) {
+ if (control_pressed) { break; }
+
+ in.read(buffer, 4096);
+ vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) { names.push_back(pieces[i]); }
+ }
+ in.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "readAccnos");
+ exit(1);
+ }
+}
/***********************************************************************/
int MothurOut::getNumNames(string names){
exit(1);
}
}
+/***********************************************************************/
+bool MothurOut::mothurConvert(string item, intDist& 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 {
projects / mothur.git / blobdiff