+ if (chimealns) {
+ char* tempA = new char[12];
+ strcpy(tempA, "--uchimealns");
+ cPara.push_back(tempA);
+ char* tempa = new char[alns.length()];
+ strcpy(tempa, alns.c_str());
+ cPara.push_back(tempa);
+ }
+
+ if (useAbskew) {
+ char* tempskew = new char[8];
+ strcpy(tempskew, "--abskew");
+ cPara.push_back(tempskew);
+ char* tempSkew = new char[abskew.length()];
+ strcpy(tempSkew, abskew.c_str());
+ cPara.push_back(tempSkew);
+ }
+
+ if (useMinH) {
+ char* tempminh = new char[6];
+ strcpy(tempminh, "--minh");
+ cPara.push_back(tempminh);
+ char* tempMinH = new char[minh.length()];
+ strcpy(tempMinH, minh.c_str());
+ cPara.push_back(tempMinH);
+ }
+
+ if (useMindiv) {
+ char* tempmindiv = new char[8];
+ strcpy(tempmindiv, "--mindiv");
+ cPara.push_back(tempmindiv);
+ char* tempMindiv = new char[mindiv.length()];
+ strcpy(tempMindiv, mindiv.c_str());
+ cPara.push_back(tempMindiv);
+ }
+
+ if (useXn) {
+ char* tempxn = new char[4];
+ strcpy(tempxn, "--xn");
+ cPara.push_back(tempxn);
+ char* tempXn = new char[xn.length()];
+ strcpy(tempXn, xn.c_str());
+ cPara.push_back(tempXn);
+ }
+
+ if (useDn) {
+ char* tempdn = new char[4];
+ strcpy(tempdn, "--dn");
+ cPara.push_back(tempdn);
+ char* tempDn = new char[dn.length()];
+ strcpy(tempDn, dn.c_str());
+ cPara.push_back(tempDn);
+ }
+
+ if (useXa) {
+ char* tempxa = new char[4];
+ strcpy(tempxa, "--xa");
+ cPara.push_back(tempxa);
+ char* tempXa = new char[xa.length()];
+ strcpy(tempXa, xa.c_str());
+ cPara.push_back(tempXa);
+ }
+
+ if (useChunks) {
+ char* tempchunks = new char[8];
+ strcpy(tempchunks, "--chunks");
+ cPara.push_back(tempchunks);
+ char* tempChunks = new char[chunks.length()];
+ strcpy(tempChunks, chunks.c_str());
+ cPara.push_back(tempChunks);
+ }
+
+ if (useMinchunk) {
+ char* tempminchunk = new char[10];
+ strcpy(tempminchunk, "--minchunk");
+ cPara.push_back(tempminchunk);
+ char* tempMinchunk = new char[minchunk.length()];
+ strcpy(tempMinchunk, minchunk.c_str());
+ cPara.push_back(tempMinchunk);
+ }
+
+ if (useIdsmoothwindow) {
+ char* tempidsmoothwindow = new char[16];
+ strcpy(tempidsmoothwindow, "--idsmoothwindow");
+ cPara.push_back(tempidsmoothwindow);
+ char* tempIdsmoothwindow = new char[idsmoothwindow.length()];
+ strcpy(tempIdsmoothwindow, idsmoothwindow.c_str());
+ cPara.push_back(tempIdsmoothwindow);
+ }
+
+ if (useMinsmoothid) {
+ char* tempminsmoothid = new char[13];
+ strcpy(tempminsmoothid, "--minsmoothid");
+ cPara.push_back(tempminsmoothid);
+ char* tempMinsmoothid = new char[minsmoothid.length()];
+ strcpy(tempMinsmoothid, minsmoothid.c_str());
+ cPara.push_back(tempMinsmoothid);
+ }
+
+ if (useMaxp) {
+ char* tempmaxp = new char[6];
+ strcpy(tempmaxp, "--maxp");
+ cPara.push_back(tempmaxp);
+ char* tempMaxp = new char[maxp.length()];
+ strcpy(tempMaxp, maxp.c_str());
+ cPara.push_back(tempMaxp);
+ }
+
+ if (!skipgaps) {
+ char* tempskipgaps = new char[14];
+ strcpy(tempskipgaps, "--[no]skipgaps");
+ cPara.push_back(tempskipgaps);
+ }
+
+ if (!skipgaps2) {
+ char* tempskipgaps2 = new char[15];
+ strcpy(tempskipgaps2, "--[no]skipgaps2");
+ cPara.push_back(tempskipgaps2);
+ }
+
+ if (useMinlen) {
+ char* tempminlen = new char[8];
+ strcpy(tempminlen, "--minlen");
+ cPara.push_back(tempminlen);
+ char* tempMinlen = new char[minlen.length()];
+ strcpy(tempMinlen, minlen.c_str());
+ cPara.push_back(tempMinlen);
+ }
+
+ if (useMaxlen) {
+ char* tempmaxlen = new char[8];
+ strcpy(tempmaxlen, "--maxlen");
+ cPara.push_back(tempmaxlen);
+ char* tempMaxlen = new char[maxlen.length()];
+ strcpy(tempMaxlen, maxlen.c_str());
+ cPara.push_back(tempMaxlen);
+ }
+
+ if (ucl) {
+ char* tempucl = new char[5];
+ strcpy(tempucl, "--ucl");
+ cPara.push_back(tempucl);
+ }
+
+ if (useQueryfract) {
+ char* tempqueryfract = new char[12];
+ strcpy(tempqueryfract, "--queryfract");
+ cPara.push_back(tempqueryfract);
+ char* tempQueryfract = new char[queryfract.length()];
+ strcpy(tempQueryfract, queryfract.c_str());
+ cPara.push_back(tempQueryfract);
+ }
+
+