strcpy(tempUchime, "./uchime ");
cPara.push_back(tempUchime);
- char* tempIn = new char[7];
- strcpy(tempIn, "--input");
+ char* tempIn = new char[8];
+ *tempIn = '\0'; strncat(tempIn, "--input", 7);
+ //strcpy(tempIn, "--input");
cPara.push_back(tempIn);
- char* temp = new char[filename.length()];
- strcpy(temp, filename.c_str());
+ char* temp = new char[filename.length()+1];
+ *temp = '\0'; strncat(temp, filename.c_str(), filename.length());
+ //strcpy(temp, filename.c_str());
cPara.push_back(temp);
//are you using a reference file
if (templatefile != "self") {
-
//add reference file
- char* tempRef = new char[4];
- strcpy(tempRef, "--db");
+ char* tempRef = new char[5];
+ //strcpy(tempRef, "--db");
+ *tempRef = '\0'; strncat(tempRef, "--db", 4);
cPara.push_back(tempRef);
- char* tempR = new char[templatefile.length()];
- strcpy(tempR, templatefile.c_str());
+ char* tempR = new char[templatefile.length()+1];
+ //strcpy(tempR, templatefile.c_str());
+ *tempR = '\0'; strncat(tempR, templatefile.c_str(), templatefile.length());
cPara.push_back(tempR);
}
- char* tempO = new char[11];
- strcpy(tempO, "--uchimeout");
+ char* tempO = new char[12];
+ *tempO = '\0'; strncat(tempO, "--uchimeout", 11);
+ //strcpy(tempO, "--uchimeout");
cPara.push_back(tempO);
- char* tempout = new char[outputFName.length()];
- strcpy(tempout, outputFName.c_str());
+ char* tempout = new char[outputFName.length()+1];
+ //strcpy(tempout, outputFName.c_str());
+ *tempout = '\0'; strncat(tempout, outputFName.c_str(), outputFName.length());
cPara.push_back(tempout);
if (chimealns) {
- char* tempA = new char[12];
- strcpy(tempA, "--uchimealns");
+ char* tempA = new char[13];
+ *tempA = '\0'; strncat(tempA, "--uchimealns", 12);
+ //strcpy(tempA, "--uchimealns");
cPara.push_back(tempA);
- char* tempa = new char[alns.length()];
- strcpy(tempa, alns.c_str());
+ char* tempa = new char[alns.length()+1];
+ //strcpy(tempa, alns.c_str());
+ *tempa = '\0'; strncat(tempa, alns.c_str(), alns.length());
cPara.push_back(tempa);
}
if (useAbskew) {
- char* tempskew = new char[8];
- strcpy(tempskew, "--abskew");
+ char* tempskew = new char[9];
+ *tempskew = '\0'; strncat(tempskew, "--abskew", 8);
+ //strcpy(tempskew, "--abskew");
cPara.push_back(tempskew);
- char* tempSkew = new char[abskew.length()];
- strcpy(tempSkew, abskew.c_str());
+ char* tempSkew = new char[abskew.length()+1];
+ //strcpy(tempSkew, abskew.c_str());
+ *tempSkew = '\0'; strncat(tempSkew, abskew.c_str(), abskew.length());
cPara.push_back(tempSkew);
}
if (useMinH) {
- char* tempminh = new char[6];
- strcpy(tempminh, "--minh");
+ char* tempminh = new char[7];
+ *tempminh = '\0'; strncat(tempminh, "--minh", 6);
+ //strcpy(tempminh, "--minh");
cPara.push_back(tempminh);
- char* tempMinH = new char[minh.length()];
- strcpy(tempMinH, minh.c_str());
+ char* tempMinH = new char[minh.length()+1];
+ *tempMinH = '\0'; strncat(tempMinH, minh.c_str(), minh.length());
+ //strcpy(tempMinH, minh.c_str());
cPara.push_back(tempMinH);
}
if (useMindiv) {
- char* tempmindiv = new char[8];
- strcpy(tempmindiv, "--mindiv");
+ char* tempmindiv = new char[9];
+ *tempmindiv = '\0'; strncat(tempmindiv, "--mindiv", 8);
+ //strcpy(tempmindiv, "--mindiv");
cPara.push_back(tempmindiv);
- char* tempMindiv = new char[mindiv.length()];
- strcpy(tempMindiv, mindiv.c_str());
+ char* tempMindiv = new char[mindiv.length()+1];
+ *tempMindiv = '\0'; strncat(tempMindiv, mindiv.c_str(), mindiv.length());
+ //strcpy(tempMindiv, mindiv.c_str());
cPara.push_back(tempMindiv);
}
if (useXn) {
- char* tempxn = new char[4];
- strcpy(tempxn, "--xn");
+ char* tempxn = new char[5];
+ //strcpy(tempxn, "--xn");
+ *tempxn = '\0'; strncat(tempxn, "--xn", 4);
cPara.push_back(tempxn);
- char* tempXn = new char[xn.length()];
- strcpy(tempXn, xn.c_str());
+ char* tempXn = new char[xn.length()+1];
+ //strcpy(tempXn, xn.c_str());
+ *tempXn = '\0'; strncat(tempXn, xn.c_str(), xn.length());
cPara.push_back(tempXn);
}
if (useDn) {
- char* tempdn = new char[4];
- strcpy(tempdn, "--dn");
+ char* tempdn = new char[5];
+ //strcpy(tempdn, "--dn");
+ *tempdn = '\0'; strncat(tempdn, "--dn", 4);
cPara.push_back(tempdn);
- char* tempDn = new char[dn.length()];
- strcpy(tempDn, dn.c_str());
+ char* tempDn = new char[dn.length()+1];
+ *tempDn = '\0'; strncat(tempDn, dn.c_str(), dn.length());
+ //strcpy(tempDn, dn.c_str());
cPara.push_back(tempDn);
}
if (useXa) {
- char* tempxa = new char[4];
- strcpy(tempxa, "--xa");
+ char* tempxa = new char[5];
+ //strcpy(tempxa, "--xa");
+ *tempxa = '\0'; strncat(tempxa, "--xa", 4);
cPara.push_back(tempxa);
- char* tempXa = new char[xa.length()];
- strcpy(tempXa, xa.c_str());
+ char* tempXa = new char[xa.length()+1];
+ *tempXa = '\0'; strncat(tempXa, xa.c_str(), xa.length());
+ //strcpy(tempXa, xa.c_str());
cPara.push_back(tempXa);
}
if (useChunks) {
- char* tempchunks = new char[8];
- strcpy(tempchunks, "--chunks");
+ char* tempchunks = new char[9];
+ //strcpy(tempchunks, "--chunks");
+ *tempchunks = '\0'; strncat(tempchunks, "--chunks", 8);
cPara.push_back(tempchunks);
- char* tempChunks = new char[chunks.length()];
- strcpy(tempChunks, chunks.c_str());
+ char* tempChunks = new char[chunks.length()+1];
+ *tempChunks = '\0'; strncat(tempChunks, chunks.c_str(), chunks.length());
+ //strcpy(tempChunks, chunks.c_str());
cPara.push_back(tempChunks);
}
if (useMinchunk) {
- char* tempminchunk = new char[10];
- strcpy(tempminchunk, "--minchunk");
+ char* tempminchunk = new char[11];
+ //strcpy(tempminchunk, "--minchunk");
+ *tempminchunk = '\0'; strncat(tempminchunk, "--minchunk", 10);
cPara.push_back(tempminchunk);
- char* tempMinchunk = new char[minchunk.length()];
- strcpy(tempMinchunk, minchunk.c_str());
+ char* tempMinchunk = new char[minchunk.length()+1];
+ *tempMinchunk = '\0'; strncat(tempMinchunk, minchunk.c_str(), minchunk.length());
+ //strcpy(tempMinchunk, minchunk.c_str());
cPara.push_back(tempMinchunk);
}
if (useIdsmoothwindow) {
- char* tempidsmoothwindow = new char[16];
- strcpy(tempidsmoothwindow, "--idsmoothwindow");
+ char* tempidsmoothwindow = new char[17];
+ *tempidsmoothwindow = '\0'; strncat(tempidsmoothwindow, "--idsmoothwindow", 16);
+ //strcpy(tempidsmoothwindow, "--idsmoothwindow");
cPara.push_back(tempidsmoothwindow);
- char* tempIdsmoothwindow = new char[idsmoothwindow.length()];
- strcpy(tempIdsmoothwindow, idsmoothwindow.c_str());
+ char* tempIdsmoothwindow = new char[idsmoothwindow.length()+1];
+ *tempIdsmoothwindow = '\0'; strncat(tempIdsmoothwindow, idsmoothwindow.c_str(), idsmoothwindow.length());
+ //strcpy(tempIdsmoothwindow, idsmoothwindow.c_str());
cPara.push_back(tempIdsmoothwindow);
}
if (useMinsmoothid) {
- char* tempminsmoothid = new char[13];
- strcpy(tempminsmoothid, "--minsmoothid");
+ char* tempminsmoothid = new char[14];
+ //strcpy(tempminsmoothid, "--minsmoothid");
+ *tempminsmoothid = '\0'; strncat(tempminsmoothid, "--minsmoothid", 13);
cPara.push_back(tempminsmoothid);
- char* tempMinsmoothid = new char[minsmoothid.length()];
- strcpy(tempMinsmoothid, minsmoothid.c_str());
+ 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 (useMaxp) {
- char* tempmaxp = new char[6];
- strcpy(tempmaxp, "--maxp");
+ char* tempmaxp = new char[7];
+ //strcpy(tempmaxp, "--maxp");
+ *tempmaxp = '\0'; strncat(tempmaxp, "--maxp", 6);
cPara.push_back(tempmaxp);
- char* tempMaxp = new char[maxp.length()];
- strcpy(tempMaxp, maxp.c_str());
+ char* tempMaxp = new char[maxp.length()+1];
+ *tempMaxp = '\0'; strncat(tempMaxp, maxp.c_str(), maxp.length());
+ //strcpy(tempMaxp, maxp.c_str());
cPara.push_back(tempMaxp);
}
if (!skipgaps) {
- char* tempskipgaps = new char[14];
- strcpy(tempskipgaps, "--[no]skipgaps");
+ char* tempskipgaps = new char[15];
+ //strcpy(tempskipgaps, "--[no]skipgaps");
+ *tempskipgaps = '\0'; strncat(tempskipgaps, "--[no]skipgaps", 14);
cPara.push_back(tempskipgaps);
}
if (!skipgaps2) {
- char* tempskipgaps2 = new char[15];
- strcpy(tempskipgaps2, "--[no]skipgaps2");
+ char* tempskipgaps2 = new char[16];
+ //strcpy(tempskipgaps2, "--[no]skipgaps2");
+ *tempskipgaps2 = '\0'; strncat(tempskipgaps2, "--[no]skipgaps2", 15);
cPara.push_back(tempskipgaps2);
}
if (useMinlen) {
- char* tempminlen = new char[8];
- strcpy(tempminlen, "--minlen");
+ char* tempminlen = new char[9];
+ *tempminlen = '\0'; strncat(tempminlen, "--minlen", 8);
+ //strcpy(tempminlen, "--minlen");
cPara.push_back(tempminlen);
- char* tempMinlen = new char[minlen.length()];
- strcpy(tempMinlen, minlen.c_str());
+ char* tempMinlen = new char[minlen.length()+1];
+ //strcpy(tempMinlen, minlen.c_str());
+ *tempMinlen = '\0'; strncat(tempMinlen, minlen.c_str(), minlen.length());
cPara.push_back(tempMinlen);
}
if (useMaxlen) {
- char* tempmaxlen = new char[8];
- strcpy(tempmaxlen, "--maxlen");
+ char* tempmaxlen = new char[9];
+ //strcpy(tempmaxlen, "--maxlen");
+ *tempmaxlen = '\0'; strncat(tempmaxlen, "--maxlen", 8);
cPara.push_back(tempmaxlen);
- char* tempMaxlen = new char[maxlen.length()];
- strcpy(tempMaxlen, maxlen.c_str());
+ char* tempMaxlen = new char[maxlen.length()+1];
+ *tempMaxlen = '\0'; strncat(tempMaxlen, maxlen.c_str(), maxlen.length());
+ //strcpy(tempMaxlen, maxlen.c_str());
cPara.push_back(tempMaxlen);
}
}
if (useQueryfract) {
- char* tempqueryfract = new char[12];
- strcpy(tempqueryfract, "--queryfract");
+ char* tempqueryfract = new char[13];
+ *tempqueryfract = '\0'; strncat(tempqueryfract, "--queryfract", 12);
+ //strcpy(tempqueryfract, "--queryfract");
cPara.push_back(tempqueryfract);
- char* tempQueryfract = new char[queryfract.length()];
- strcpy(tempQueryfract, queryfract.c_str());
+ char* tempQueryfract = new char[queryfract.length()+1];
+ *tempQueryfract = '\0'; strncat(tempQueryfract, queryfract.c_str(), queryfract.length());
+ //strcpy(tempQueryfract, queryfract.c_str());
cPara.push_back(tempQueryfract);
}
projects / mothur.git / blobdiff