#include "mothurout.h"
+
/******************************************************/
MothurOut* MothurOut::getInstance() {
if( _uniqueInstance == 0) {
}
}
/*********************************************************************************************/
+void MothurOut::setOutputDir(string pathname) {
+ try {
+ outputDir = pathname;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "setOutputDir");
+ exit(1);
+ }
+}
+/*********************************************************************************************/
void MothurOut::closeLog() {
try {
/***********************************************************************/
int MothurOut::openOutputFileAppend(string fileName, ofstream& fileHandle){
try {
+ fileName = getFullPathName(fileName);
+
fileHandle.open(fileName.c_str(), ios::app);
if(!fileHandle) {
mothurOut("[ERROR]: Could not open " + fileName); mothurOutEndLine();
/***********************************************************************/
void MothurOut::gobble(istream& f){
try {
+
char d;
- while(isspace(d=f.get())) {;}
+ while(isspace(d=f.get())) { ;}
f.putback(d);
}
catch(exception& e) {
}
/***********************************************************************/
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#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(longName.find_last_of(".") != longName.npos){
- int pos = longName.find_last_of('.')+1;
- rootName = longName.substr(0, pos);
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#ifdef USE_COMPRESSION
+ if (endsWith(rootName, ".gz") || endsWith(rootName, ".bz2")) {
+ int pos = rootName.find_last_of('.');
+ rootName = rootName.substr(0, pos);
+ 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);
}
return rootName;
/***********************************************************************/
bool MothurOut::isBlank(string fileName){
try {
+
+ fileName = getFullPathName(fileName);
+
ifstream fileHandle;
fileHandle.open(fileName.c_str());
if(!fileHandle) {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
if (path.find("~") != -1) { //go to home directory
- string homeDir = getenv ("HOME");
+ string homeDir;
+
+ char *homepath = NULL;
+ homepath = getenv ("HOME");
+ if ( homepath != NULL) { homeDir = homepath; }
+ else { 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];
+ //char* cwdpath = new char[1024];
+ //size_t size;
+ //cwdpath=getcwd(cwdpath,size);
+ //cwd = cwdpath;
+
+ char *cwdpath = NULL;
+ cwdpath = getcwd(NULL, 0); // or _getcwd
+ if ( cwdpath != NULL) { cwd = cwdpath; }
+ else { cwd = ""; }
- size_t size;
- cwdpath=getcwd(cwdpath,size);
-
- cwd = cwdpath;
//rip off first '/'
string simpleCWD;
//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);
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);
try {
//get full path name
string completeFileName = getFullPathName(fileName);
-
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#ifdef USE_COMPRESSION
+ // check for gzipped or bzipped file
+ if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
+ string tempName = string(tmpnam(0));
+ mkfifo(tempName.c_str(), 0666);
+ int fork_result = fork();
+ if (fork_result < 0) {
+ cerr << "Error forking.\n";
+ exit(1);
+ } else if (fork_result == 0) {
+ string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName;
+ cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
+ system(command.c_str());
+ cerr << "Done decompressing " << completeFileName << "\n";
+ remove(tempName.c_str());
+ exit(EXIT_SUCCESS);
+ } else {
+ cerr << "waiting on child process " << fork_result << "\n";
+ completeFileName = tempName;
+ }
+ }
+#endif
+#endif
fileHandle.open(completeFileName.c_str());
if(!fileHandle) {
+ //mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
return 1;
}else {
//check for blank file
int MothurOut::openInputFile(string fileName, ifstream& fileHandle){
try {
+
//get full path name
string completeFileName = getFullPathName(fileName);
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#ifdef USE_COMPRESSION
+ // check for gzipped or bzipped file
+ if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
+ string tempName = string(tmpnam(0));
+ mkfifo(tempName.c_str(), 0666);
+ int fork_result = fork();
+ if (fork_result < 0) {
+ cerr << "Error forking.\n";
+ exit(1);
+ } else if (fork_result == 0) {
+ string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName;
+ cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
+ system(command.c_str());
+ cerr << "Done decompressing " << completeFileName << "\n";
+ remove(tempName.c_str());
+ exit(EXIT_SUCCESS);
+ } else {
+ cerr << "waiting on child process " << fork_result << "\n";
+ completeFileName = tempName;
+ }
+ }
+#endif
+#endif
fileHandle.open(completeFileName.c_str());
if(!fileHandle) {
try {
string completeFileName = getFullPathName(fileName);
-
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#ifdef USE_COMPRESSION
+ // check for gzipped file
+ if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
+ string tempName = string(tmpnam(0));
+ mkfifo(tempName.c_str(), 0666);
+ cerr << "Compressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
+ int fork_result = fork();
+ if (fork_result < 0) {
+ cerr << "Error forking.\n";
+ exit(1);
+ } else if (fork_result == 0) {
+ string command = string(endsWith(completeFileName, ".gz") ? "gzip" : "bzip2") + " -v > " + completeFileName + string(" < ") + tempName;
+ system(command.c_str());
+ exit(0);
+ } else {
+ completeFileName = tempName;
+ }
+ }
+#endif
+#endif
fileHandle.open(completeFileName.c_str(), ios::trunc);
if(!fileHandle) {
mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
//open output file in append mode
openOutputFileAppend(filename, output);
int ableToOpen = openInputFile(temp, input, "no error");
+ //int ableToOpen = openInputFile(temp, input);
if (ableToOpen == 0) { //you opened it
while(char c = input.get()){
/**************************************************************************************************/
vector<unsigned long int> MothurOut::setFilePosEachLine(string filename, int& num) {
try {
-
+ filename = getFullPathName(filename);
+
vector<unsigned long int> positions;
ifstream in;
openInputFile(filename, in);
FILE * pFile;
unsigned long int size;
-
+
//get num bytes in file
pFile = fopen (filename.c_str(),"rb");
if (pFile==NULL) perror ("Error opening file");
FILE * pFile;
unsigned long int size;
+ filename = getFullPathName(filename);
+
//get num bytes in file
pFile = fopen (filename.c_str(),"rb");
if (pFile==NULL) perror ("Error opening file");
//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; }
char c = in.get();
if (c == '>') { in.putback(c); newSpot = in.tellg(); break; }
}
-
+
//there was not another sequence before the end of the file
unsigned long int sanityPos = in.tellg();
- if (sanityPos = -1) { break; }
- else { filePos.push_back(newSpot); }
+
+ if (sanityPos == -1) { 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--; }
//This function parses the estimator options and puts them in a vector
void MothurOut::splitAtChar(string& estim, vector<string>& container, char symbol) {
try {
- string individual;
+ string individual = "";
+ int estimLength = estim.size();
+ for(int i=0;i<estimLength;i++){
+ if(estim[i] == symbol){
+ container.push_back(individual);
+ individual = "";
+ }
+ else{
+ individual += estim[i];
+ }
+ }
+ container.push_back(individual);
+
+ /*
while (estim.find_first_of(symbol) != -1) {
individual = estim.substr(0,estim.find_first_of(symbol));
}
}
//get last one
- container.push_back(estim);
+ container.push_back(estim); */
}
catch(exception& e) {
errorOut(e, "MothurOut", "splitAtChar");
//This function parses the estimator options and puts them in a vector
void MothurOut::splitAtDash(string& estim, vector<string>& container) {
try {
- string individual;
+ string individual = "";
+ int estimLength = estim.size();
+ for(int i=0;i<estimLength;i++){
+ if(estim[i] == '-'){
+ container.push_back(individual);
+ individual = "";
+ }
+ else{
+ individual += estim[i];
+ }
+ }
+ container.push_back(individual);
+
+
+ /* string individual;
while (estim.find_first_of('-') != -1) {
individual = estim.substr(0,estim.find_first_of('-'));
}
}
//get last one
- container.push_back(estim);
+ container.push_back(estim); */
}
catch(exception& e) {
errorOut(e, "MothurOut", "splitAtDash");
//This function parses the label options and puts them in a set
void MothurOut::splitAtDash(string& estim, set<string>& container) {
try {
- string individual;
-
- while (estim.find_first_of('-') != -1) {
- individual = estim.substr(0,estim.find_first_of('-'));
- if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
- estim = estim.substr(estim.find_first_of('-')+1, estim.length());
+ string individual = "";
+ int estimLength = estim.size();
+ for(int i=0;i<estimLength;i++){
+ if(estim[i] == '-'){
container.insert(individual);
+ individual = "";
+ }
+ else{
+ individual += estim[i];
}
}
+ container.insert(individual);
+
+ // string individual;
+
+ // while (estim.find_first_of('-') != -1) {
+ // individual = estim.substr(0,estim.find_first_of('-'));
+ // if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
+ // estim = estim.substr(estim.find_first_of('-')+1, estim.length());
+ // container.insert(individual);
+ // }
+ // }
//get last one
- container.insert(estim);
+ // container.insert(estim);
+
}
catch(exception& e) {
errorOut(e, "MothurOut", "splitAtDash");
}
//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; }
exit(1);
}
}
+
/**************************************************************************************************/
projects / mothur.git / blobdiff