#include "mothurout.h"
+
/******************************************************/
MothurOut* MothurOut::getInstance() {
if( _uniqueInstance == 0) {
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("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 (fastafile != "") { mothurOut("fasta=" + fastafile); mothurOutEndLine(); }
+ if (groupfile != "") { mothurOut("group=" + groupfile); mothurOutEndLine(); }
+ if (listfile != "") { mothurOut("list=" + listfile); mothurOutEndLine(); }
+ if (namefile != "") { mothurOut("name=" + namefile); mothurOutEndLine(); }
+ if (oligosfile != "") { mothurOut("oligos=" + oligosfile); mothurOutEndLine(); }
+ if (orderfile != "") { mothurOut("order=" + orderfile); mothurOutEndLine(); }
+ if (ordergroupfile != "") { mothurOut("ordergroup=" + ordergroupfile); mothurOutEndLine(); }
+ if (phylipfile != "") { mothurOut("phylip=" + phylipfile); mothurOutEndLine(); }
+ if (qualfile != "") { mothurOut("qfile=" + qualfile); mothurOutEndLine(); }
+ if (rabundfile != "") { mothurOut("rabund=" + rabundfile); mothurOutEndLine(); }
+ if (relabundfile != "") { mothurOut("relabund=" + relabundfile); mothurOutEndLine(); }
+ if (sabundfile != "") { mothurOut("sabund=" + sabundfile); mothurOutEndLine(); }
+ if (sfffile != "") { mothurOut("sff=" + sfffile); mothurOutEndLine(); }
+ if (sharedfile != "") { mothurOut("shared=" + sharedfile); mothurOutEndLine(); }
+ 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(); }
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "printCurrentFiles");
+ exit(1);
+ }
+}
+/*********************************************************************************************/
+bool MothurOut::hasCurrentFiles() {
+ try {
+ bool hasCurrent = false;
+
+ if (accnosfile != "") { return true; }
+ if (columnfile != "") { return true; }
+ if (designfile != "") { return true; }
+ if (fastafile != "") { return true; }
+ if (groupfile != "") { return true; }
+ if (listfile != "") { return true; }
+ if (namefile != "") { return true; }
+ if (oligosfile != "") { return true; }
+ if (orderfile != "") { return true; }
+ if (ordergroupfile != "") { return true; }
+ if (phylipfile != "") { return true; }
+ if (qualfile != "") { return true; }
+ if (rabundfile != "") { return true; }
+ if (relabundfile != "") { return true; }
+ if (sabundfile != "") { return true; }
+ if (sfffile != "") { return true; }
+ if (sharedfile != "") { return true; }
+ if (taxonomyfile != "") { return true; }
+ if (treefile != "") { return true; }
+ if (flowfile != "") { return true; }
+ if (biomfile != "") { return true; }
+ if (processors != "1") { return true; }
+
+ return hasCurrent;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "hasCurrentFiles");
+ exit(1);
+ }
+}
+
+/*********************************************************************************************/
+void MothurOut::clearCurrentFiles() {
+ try {
+ phylipfile = "";
+ columnfile = "";
+ listfile = "";
+ rabundfile = "";
+ sabundfile = "";
+ namefile = "";
+ groupfile = "";
+ designfile = "";
+ orderfile = "";
+ treefile = "";
+ sharedfile = "";
+ ordergroupfile = "";
+ relabundfile = "";
+ fastafile = "";
+ qualfile = "";
+ sfffile = "";
+ oligosfile = "";
+ accnosfile = "";
+ taxonomyfile = "";
+ flowfile = "";
+ biomfile = "";
+ processors = "1";
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "clearCurrentFiles");
+ 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 {
logFileName = filename;
//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
}
}
}
/*********************************************************************************************/
+void MothurOut::mothurOut(string output, ofstream& outputFile) {
+ try {
+
+#ifdef USE_MPI
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+
+ if (pid == 0) { //only one process should output to screen
+#endif
+
+
+ out << output;
+ outputFile << output;
+ logger() << output;
+
+#ifdef USE_MPI
+ }
+#endif
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "MothurOut");
+ exit(1);
+ }
+}
+/*********************************************************************************************/
+void MothurOut::mothurOutEndLine(ofstream& outputFile) {
+ try {
+#ifdef USE_MPI
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+
+ if (pid == 0) { //only one process should output to screen
+#endif
+
+ out << endl;
+ outputFile << endl;
+ logger() << endl;
+
+#ifdef USE_MPI
+ }
+#endif
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "MothurOutEndLine");
+ exit(1);
+ }
+}
+/*********************************************************************************************/
void MothurOut::mothurOutJustToLog(string output) {
try {
#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;
char d;
while(isspace(d=f.get())) { ;}
- f.putback(d);
+ if(!f.eof()) { f.putback(d); }
}
catch(exception& e) {
errorOut(e, "MothurOut", "gobble");
try {
char d;
while(isspace(d=f.get())) {;}
- f.putback(d);
+ if(!f.eof()) { f.putback(d); }
}
catch(exception& e) {
errorOut(e, "MothurOut", "gobble");
string line = "";
- while (!fileHandle.eof()) {
+ while (fileHandle) {
//get next character
char c = fileHandle.get();
//are you at the end of the line
- if ((c == '\n') || (c == '\r') || (c == '\f')){ break; }
+ if ((c == '\n') || (c == '\r') || (c == '\f') || (c == EOF)){ break; }
else { line += c; }
}
}
/***********************************************************************/
+#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);
return s.size() >= suffixLength && s.substr(s.size() - suffixLength, suffixLength).compare(suffix) == 0;
}
#endif
+#endif
string MothurOut::getRootName(string longName){
try {
string rootName = longName;
+#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('.');
cerr << "shortening " << longName << " to " << rootName << "\n";
}
#endif
-
+#endif
if(rootName.find_last_of(".") != rootName.npos){
int pos = rootName.find_last_of('.')+1;
rootName = rootName.substr(0, pos);
/***********************************************************************/
+int MothurOut::getRandomIndex(int highest){
+ try {
+
+ int random = (int) ((float)(highest+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
+
+ return random;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "getRandomIndex");
+ exit(1);
+ }
+
+}
+/**********************************************************************/
+
string MothurOut::getPathName(string longName){
try {
string rootPathName = longName;
}
/***********************************************************************/
+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('.');
//check for blank file
gobble(fileHandle);
if (fileHandle.eof()) { fileHandle.close(); return true; }
+ fileHandle.close();
}
return false;
}
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;
newFileName = homeDir + fileName.substr(fileName.find("~")+1);
return newFileName;
}else { //find path
- if (path.rfind("./") == -1) { return fileName; } //already complete name
+ if (path.rfind("./") == string::npos) { return fileName; } //already complete name
else { newFileName = fileName.substr(fileName.rfind("./")+2); } //save the complete part of the name
//char* cwdpath = new char[1024];
//break apart the current working directory
vector<string> dirs;
- while (simpleCWD.find_first_of('/') != -1) {
+ while (simpleCWD.find_first_of('/') != string::npos) {
string dir = simpleCWD.substr(0,simpleCWD.find_first_of('/'));
simpleCWD = simpleCWD.substr(simpleCWD.find_first_of('/')+1, simpleCWD.length());
dirs.push_back(dir);
int index = dirs.size()-1;
- while((pos = path.rfind("./")) != -1) { //while you don't have a complete path
+ while((pos = path.rfind("./")) != string::npos) { //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);
}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--) {
return newFileName;
}
#else
- if (path.find("~") != -1) { //go to home directory
+ if (path.find("~") != string::npos) { //go to home directory
string homeDir = getenv ("HOMEPATH");
newFileName = homeDir + fileName.substr(fileName.find("~")+1);
return newFileName;
}else { //find path
- if (path.rfind(".\\") == -1) { return fileName; } //already complete name
+ if (path.rfind(".\\") == string::npos) { return fileName; } //already complete name
else { newFileName = fileName.substr(fileName.rfind(".\\")+2); } //save the complete part of the name
char *cwdpath = NULL;
int index = dirs.size()-1;
- while((pos = path.rfind(".\\")) != -1) { //while you don't have a complete path
+ while((pos = path.rfind(".\\")) != string::npos) { //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);
}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) || (__linux__) || (__unix__) || (__unix)
#ifdef USE_COMPRESSION
// check for gzipped or bzipped file
if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
system(command.c_str());
cerr << "Done decompressing " << completeFileName << "\n";
- remove(tempName.c_str());
+ mothurRemove(tempName);
exit(EXIT_SUCCESS);
} else {
cerr << "waiting on child process " << fork_result << "\n";
}
}
#endif
-
+#endif
fileHandle.open(completeFileName.c_str());
if(!fileHandle) {
+ //mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
return 1;
}else {
//check for blank file
//get full path name
string completeFileName = getFullPathName(fileName);
-
+#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")) {
cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
system(command.c_str());
cerr << "Done decompressing " << completeFileName << "\n";
- remove(tempName.c_str());
+ mothurRemove(tempName);
exit(EXIT_SUCCESS);
} else {
cerr << "waiting on child process " << fork_result << "\n";
}
}
#endif
-
+#endif
fileHandle.open(completeFileName.c_str());
if(!fileHandle) {
try {
ifstream inTest;
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
- inTest.close();
string command = "rm " + newName;
system(command.c_str());
}
string command = "mv " + oldName + " " + newName;
system(command.c_str());
#else
- remove(newName.c_str());
+ mothurRemove(newName);
int renameOk = rename(oldName.c_str(), newName.c_str());
#endif
return 0;
try {
string completeFileName = getFullPathName(fileName);
-
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
#ifdef USE_COMPRESSION
// check for gzipped file
if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
}
}
#endif
-
+#endif
fileHandle.open(completeFileName.c_str(), ios::trunc);
if(!fileHandle) {
mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
}
/**************************************************************************************************/
-void MothurOut::appendFiles(string temp, string filename) {
+int MothurOut::appendFiles(string temp, string filename) {
try{
ofstream output;
ifstream input;
//open output file in append mode
openOutputFileAppend(filename, output);
int ableToOpen = openInputFile(temp, input, "no error");
+ //int ableToOpen = openInputFile(temp, input);
+ int numLines = 0;
if (ableToOpen == 0) { //you opened it
- while(char c = input.get()){
- if(input.eof()) { break; }
- else { output << c; }
- }
+
+ 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();
}
output.close();
+
+ return numLines;
}
catch(exception& e) {
errorOut(e, "MothurOut", "appendFiles");
//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...
output.close();
//remove temp files
- remove(tempDistFile.c_str());
- remove(tempOutfile.c_str());
+ mothurRemove(tempDistFile);
+ mothurRemove(tempOutfile);
#endif
return outfile;
}
}
/**************************************************************************************************/
-vector<unsigned long int> MothurOut::setFilePosFasta(string filename, int& num) {
+vector<unsigned long long> MothurOut::setFilePosFasta(string filename, int& num) {
try {
- vector<unsigned long int> positions;
+ vector<unsigned long long> positions;
ifstream inFASTA;
- openInputFile(filename, inFASTA);
+ //openInputFile(filename, inFASTA);
+ inFASTA.open(filename.c_str(), ios::binary);
string input;
+ unsigned long long count = 0;
while(!inFASTA.eof()){
- input = getline(inFASTA);
- if (input.length() != 0) {
- if(input[0] == '>'){ unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
+ //input = getline(inFASTA);
+ //cout << input << '\t' << inFASTA.tellg() << endl;
+ //if (input.length() != 0) {
+ // if(input[0] == '>'){ unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); cout << (pos - input.length() - 1) << endl; }
+ //}
+ //gobble(inFASTA); //has to be here since windows line endings are 2 characters and mess up the positions
+ char c = inFASTA.get(); count++;
+ if (c == '>') {
+ positions.push_back(count-1);
+ //cout << count << endl;
}
- gobble(inFASTA); //has to be here since windows line endings are 2 characters and mess up the positions
}
inFASTA.close();
fclose (pFile);
}*/
- unsigned long int size = positions[(positions.size()-1)];
+ unsigned long long size = positions[(positions.size()-1)];
ifstream in;
openInputFile(filename, in);
in.seekg(size);
- while(char c = in.get()){
+ while(in.get()){
if(in.eof()) { break; }
else { size++; }
}
in.close();
positions.push_back(size);
+ positions[0] = 0;
return positions;
}
}
}
/**************************************************************************************************/
-vector<unsigned long int> MothurOut::setFilePosEachLine(string filename, int& num) {
+vector<unsigned long long> MothurOut::setFilePosEachLine(string filename, int& num) {
try {
filename = getFullPathName(filename);
- vector<unsigned long int> positions;
+ vector<unsigned long long> positions;
ifstream in;
- openInputFile(filename, in);
-
+ //openInputFile(filename, in);
+ in.open(filename.c_str(), ios::binary);
+
string input;
+ unsigned long long count = 0;
+ positions.push_back(0);
+
while(!in.eof()){
- unsigned long int lastpos = in.tellg();
- 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); }
+ //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())) {
+ //get next character
+ d = in.get();
+ count++;
+ }
+
+ if (!in.eof()) {
+ d=in.get(); count++;
+ while(isspace(d) && (d != in.eof())) { d=in.get(); count++;}
}
- gobble(in); //has to be here since windows line endings are 2 characters and mess up the positions
+ positions.push_back(count-1);
+ //cout << count-1 << endl;
}
in.close();
- num = positions.size();
+ num = positions.size()-1;
FILE * pFile;
- unsigned long int size;
+ unsigned long long size;
//get num bytes in file
pFile = fopen (filename.c_str(),"rb");
fclose (pFile);
}
- positions.push_back(size);
+ positions[(positions.size()-1)] = size;
return positions;
}
}
/**************************************************************************************************/
-vector<unsigned long int> MothurOut::divideFile(string filename, int& proc) {
+vector<unsigned long long> MothurOut::divideFile(string filename, int& proc) {
try{
-
- vector<unsigned long int> filePos;
+ vector<unsigned long long> filePos;
filePos.push_back(0);
FILE * pFile;
- unsigned long int size;
+ unsigned long long size;
filename = getFullPathName(filename);
-
+
//get num bytes in file
pFile = fopen (filename.c_str(),"rb");
if (pFile==NULL) perror ("Error opening file");
size=ftell (pFile);
fclose (pFile);
}
-
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+
//estimate file breaks
- unsigned long int chunkSize = 0;
+ unsigned long long chunkSize = 0;
chunkSize = size / proc;
//file to small to divide by processors
//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;
+ unsigned long long spot = (i+1) * chunkSize;
ifstream in;
openInputFile(filename, in);
in.seekg(spot);
//look for next '>'
- unsigned long int newSpot = spot;
+ unsigned long long newSpot = spot;
while (!in.eof()) {
char c = in.get();
+
if (c == '>') { in.putback(c); newSpot = in.tellg(); break; }
+ else if (int(c) == -1) { break; }
+
}
//there was not another sequence before the end of the file
- unsigned long int sanityPos = in.tellg();
+ unsigned long long sanityPos = in.tellg();
if (sanityPos == -1) { break; }
else { filePos.push_back(newSpot); }
//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]) { cout << "erasing " << (i+1) << endl; filePos.erase(filePos.begin()+(i+1)); i--; }
+ if (filePos[(i+1)] <= filePos[i]) { filePos.erase(filePos.begin()+(i+1)); i--; }
}
proc = (filePos.size() - 1);
-
+#else
+ mothurOut("[ERROR]: Windows version should not be calling the divideFile function."); mothurOutEndLine();
+ proc=1;
+ filePos.push_back(size);
+#endif
return filePos;
}
catch(exception& e) {
exit(1);
}
}
-
+/**************************************************************************************************/
+int MothurOut::divideFile(string filename, int& proc, vector<string>& files) {
+ try{
+
+ vector<unsigned long long> filePos = divideFile(filename, proc);
+
+ for (int i = 0; i < (filePos.size()-1); i++) {
+
+ //read file chunk
+ ifstream in;
+ openInputFile(filename, in);
+ in.seekg(filePos[i]);
+ unsigned long long size = filePos[(i+1)] - filePos[i];
+ char* chunk = new char[size];
+ in.read(chunk, size);
+ in.close();
+
+ //open new file
+ string fileChunkName = filename + "." + toString(i) + ".tmp";
+ ofstream out;
+ openOutputFile(fileChunkName, out);
+
+ out << chunk << endl;
+ out.close();
+ delete[] chunk;
+
+ //save name
+ files.push_back(fileChunkName);
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "divideFile");
+ exit(1);
+ }
+}
/***********************************************************************/
bool MothurOut::isTrue(string f){
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", "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 {
+ 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, 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; }
+
+ 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();
+
+ 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; }
+
+ 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; }
+
+ 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 nameMap.size();
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "readNames");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+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 {
+
+ map<string, int> nameMap;
+
+ //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) {
+ int num = getNumNames(secondCol);
+ nameMap[firstCol] = num;
+ pairDone = false;
+ }
+ }
+ }
+ in.close();
+
+ return nameMap;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "readNames");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int MothurOut::readNames(string namefile, vector<seqPriorityNode>& nameVector, map<string, string>& fastamap) {
+ try {
+ int error = 0;
+
+ //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) {
+ 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();
+
+ 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);
}
}
+/***********************************************************************/
+int MothurOut::getNumChar(string line, char c){
+ try {
+ int count = 0;
+
+ if(line != ""){
+ for(int i=0;i<line.size();i++){
+ if(line[i] == c){
+ count++;
+ }
+ }
+ }
+
+ return count;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "getNumChar");
+ exit(1);
+ }
+}
+/***********************************************************************/
+int MothurOut::mothurRemove(string filename){
+ try {
+ filename = getFullPathName(filename);
+ int error = remove(filename.c_str());
+ //if (error != 0) {
+ // if (errno != ENOENT) { //ENOENT == file does not exist
+ // string message = "Error deleting file " + filename;
+ // perror(message.c_str());
+ // }
+ //}
+ return error;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "mothurRemove");
+ 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);
}
}
-
+/**************************************************************************************************/
+unsigned int MothurOut::fromBase36(string base36){
+ try {
+ unsigned int num = 0;
+
+ map<char, int> converts;
+ converts['A'] = 0;
+ converts['a'] = 0;
+ converts['B'] = 1;
+ converts['b'] = 1;
+ converts['C'] = 2;
+ converts['c'] = 2;
+ converts['D'] = 3;
+ converts['d'] = 3;
+ converts['E'] = 4;
+ converts['e'] = 4;
+ converts['F'] = 5;
+ converts['f'] = 5;
+ converts['G'] = 6;
+ converts['g'] = 6;
+ converts['H'] = 7;
+ converts['h'] = 7;
+ converts['I'] = 8;
+ converts['i'] = 8;
+ converts['J'] = 9;
+ converts['j'] = 9;
+ converts['K'] = 10;
+ converts['k'] = 10;
+ converts['L'] = 11;
+ converts['l'] = 11;
+ converts['M'] = 12;
+ converts['m'] = 12;
+ converts['N'] = 13;
+ converts['n'] = 13;
+ converts['O'] = 14;
+ converts['o'] = 14;
+ converts['P'] = 15;
+ converts['p'] = 15;
+ converts['Q'] = 16;
+ converts['q'] = 16;
+ converts['R'] = 17;
+ converts['r'] = 17;
+ converts['S'] = 18;
+ converts['s'] = 18;
+ converts['T'] = 19;
+ converts['t'] = 19;
+ converts['U'] = 20;
+ converts['u'] = 20;
+ converts['V'] = 21;
+ converts['v'] = 21;
+ converts['W'] = 22;
+ converts['w'] = 22;
+ converts['X'] = 23;
+ converts['x'] = 23;
+ converts['Y'] = 24;
+ converts['y'] = 24;
+ converts['Z'] = 25;
+ converts['z'] = 25;
+ converts['0'] = 26;
+ converts['1'] = 27;
+ converts['2'] = 28;
+ converts['3'] = 29;
+ converts['4'] = 30;
+ converts['5'] = 31;
+ converts['6'] = 32;
+ converts['7'] = 33;
+ converts['8'] = 34;
+ converts['9'] = 35;
+
+ int i = 0;
+ while (i < base36.length()) {
+ char c = base36[i];
+ num = 36 * num + converts[c];
+ i++;
+ }
+
+ return num;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "fromBase36");
+ exit(1);
+ }
+}
/***********************************************************************/
int MothurOut::factorial(int num){
}
container.push_back(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) {
errorOut(e, "MothurOut", "splitAtChar");
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
}
//go through users set and make them floats
- for(it = userLabels.begin(); it != userLabels.end(); ++it) {
+ for(it = userLabels.begin(); it != userLabels.end();) {
float temp;
if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){
convert(*it, temp);
orderFloat.push_back(temp);
userMap[*it] = temp;
+ it++;
}else if (*it == "unique") {
orderFloat.push_back(-1.0);
userMap["unique"] = -1.0;
+ it++;
}else {
- if (errorOff == "") { cout << *it << " is not a valid label." << endl; }
- userLabels.erase(*it);
- it--;
+ if (errorOff == "") { mothurOut(*it + " is not a valid label."); mothurOutEndLine(); }
+ userLabels.erase(it++);
}
}
if (orderFloat[i] < labelFloat) {
smaller = true;
if (orderFloat[i] == -1) {
- if (errorOff == "") { cout << "Your file does not include the label unique." << endl; }
+ if (errorOff == "") { mothurOut("Your file does not include the label unique."); mothurOutEndLine(); }
userLabels.erase("unique");
}
else {
- if (errorOff == "") { cout << "Your file does not include the label " << endl; }
+ if (errorOff == "") { mothurOut("Your file does not include the label "); mothurOutEndLine(); }
string s = "";
for (it2 = userMap.begin(); it2!= userMap.end(); it2++) {
if (it2->second == orderFloat[i]) {
break;
}
}
- if (errorOff == "") {cout << s << ". I will use the next smallest distance. " << endl; }
+ if (errorOff == "") {mothurOut( s + ". I will use the next smallest distance. "); mothurOutEndLine(); }
}
//since they are sorted once you find a bigger one stop looking
}else { break; }
}
}
/**************************************************************************************************/
+bool MothurOut::isContainingOnlyDigits(string input) {
+ try{
+
+ //are you a digit in ascii code
+ for (int i = 0;i < input.length(); i++){
+ if( input[i]>47 && input[i]<58){}
+ else { return false; }
+ }
+
+ return true;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "isContainingOnlyDigits");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int MothurOut::removeConfidences(string& tax) {
+ try {
+
+ string taxon;
+ string newTax = "";
+
+ while (tax.find_first_of(';') != -1) {
+
+ if (control_pressed) { return 0; }
+
+ //get taxon
+ taxon = tax.substr(0,tax.find_first_of(';'));
+
+ int pos = taxon.find_last_of('(');
+ if (pos != -1) {
+ //is it a number?
+ int pos2 = taxon.find_last_of(')');
+ if (pos2 != -1) {
+ string confidenceScore = taxon.substr(pos+1, (pos2-(pos+1)));
+ if (isNumeric1(confidenceScore)) {
+ taxon = taxon.substr(0, pos); //rip off confidence
+ }
+ }
+ }
+ taxon += ";";
+
+ tax = tax.substr(tax.find_first_of(';')+1, tax.length());
+ newTax += taxon;
+ }
+
+ tax = newTax;
+
+ return 0;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "removeConfidences");
+ exit(1);
+ }
+}
+/**************************************************************************************************/