#include "mothurout.h"
+
/******************************************************/
MothurOut* MothurOut::getInstance() {
if( _uniqueInstance == 0) {
}
/***********************************************************************/
+#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 defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
#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);
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")) {
}
}
#endif
-
+#endif
fileHandle.open(completeFileName.c_str());
if(!fileHandle) {
//mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
//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")) {
}
}
#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")) {
}
}
#endif
-
+#endif
fileHandle.open(completeFileName.c_str(), ios::trunc);
if(!fileHandle) {
mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
}
//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; }