//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('.');
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")) {
//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;
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
}
}