#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);
//check for blank file
gobble(fileHandle);
if (fileHandle.eof()) { fileHandle.close(); return true; }
+ fileHandle.close();
}
return false;
}
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();
in.seekg(size);
- while(char c = in.get()){
+ while(in.get()){
if(in.eof()) { break; }
else { size++; }
}
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");