try {
+ pDataArray->outputFName = pDataArray->m->getFullPathName(pDataArray->outputFName);
+ pDataArray->filename = pDataArray->m->getFullPathName(pDataArray->filename);
+ pDataArray->alns = pDataArray->m->getFullPathName(pDataArray->alns);
+
//clears files
ofstream out, out1, out2;
pDataArray->m->openOutputFile(pDataArray->outputFName, out); out.close();
string path = pDataArray->m->argv;
string tempPath = path;
- for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+ for (int j = 0; j < path.length(); j++) { tempPath[j] = tolower(path[j]); }
path = path.substr(0, (tempPath.find_last_of('m')));
string uchimeCommand = path;
cPara.push_back(tempIdsmoothwindow);
}
- /*if (useMinsmoothid) {
- char* tempminsmoothid = new char[14];
- //strcpy(tempminsmoothid, "--minsmoothid");
- *tempminsmoothid = '\0'; strncat(tempminsmoothid, "--minsmoothid", 13);
- cPara.push_back(tempminsmoothid);
- char* tempMinsmoothid = new char[minsmoothid.length()+1];
- *tempMinsmoothid = '\0'; strncat(tempMinsmoothid, minsmoothid.c_str(), minsmoothid.length());
- //strcpy(tempMinsmoothid, minsmoothid.c_str());
- cPara.push_back(tempMinsmoothid);
- }*/
-
if (pDataArray->useMaxp) {
char* tempmaxp = new char[7];
//strcpy(tempmaxp, "--maxp");
try {
+ pDataArray->outputFName = pDataArray->m->getFullPathName(pDataArray->outputFName);
+ pDataArray->filename = pDataArray->m->getFullPathName(pDataArray->filename);
+ pDataArray->alns = pDataArray->m->getFullPathName(pDataArray->alns);
+
int totalSeqs = 0;
int numChimeras = 0;