string fastafile, groupfile, templatefile, outputDir, namefile, abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract;
int processors;
+
vector<string> outputNames;
vector<string> fastaFileNames;
vector<string> nameFileNames;
vector<char*> cPara;
+ string path = pDataArray->m->argv;
+ string tempPath = path;
+ for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+ path = path.substr(0, (tempPath.find_last_of('m')));
+
+ string uchimeCommand = path;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ uchimeCommand += "uchime ";
+#else
+ uchimeCommand += "uchime";
+ uchimeCommand = "\"" + uchimeCommand + "\"";
+#endif
+
char* tempUchime;
- tempUchime= new char[8];
+ tempUchime= new char[uchimeCommand.length()+1];
*tempUchime = '\0';
- strncat(tempUchime, "uchime ", 7);
+ strncat(tempUchime, uchimeCommand.c_str(), uchimeCommand.length());
cPara.push_back(tempUchime);
char* tempIn = new char[8];
//uchime_main(numArgs, uchimeParameters);
//cout << "commandString = " << commandString << endl;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#else
+ commandString = "\"" + commandString + "\"";
+#endif
system(commandString.c_str());
//free memory