+ CommandParameter psearch("search", "Multiple", "kmer-blast-suffix-distance-align", "kmer", "", "", "","",false,false); parameters.push_back(psearch);
+ CommandParameter pksize("ksize", "Number", "", "8", "", "", "","",false,false); parameters.push_back(pksize);
+ CommandParameter pmethod("method", "Multiple", "wang-knn-zap", "wang", "", "", "","",false,false); parameters.push_back(pmethod);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pmatch("match", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pmatch);
+ CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pmismatch);
+ CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "","",false,false); parameters.push_back(pgapopen);
+ CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pgapextend);
+ CommandParameter pcutoff("cutoff", "Number", "", "0", "", "", "","",false,true); parameters.push_back(pcutoff);
+ CommandParameter pprobs("probs", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pprobs);
+ CommandParameter piters("iters", "Number", "", "100", "", "", "","",false,true); parameters.push_back(piters);
+ CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);
+ CommandParameter pshortcuts("shortcuts", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pshortcuts);
+ CommandParameter pnumwanted("numwanted", "Number", "", "10", "", "", "","",false,true); parameters.push_back(pnumwanted);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClassifySeqsCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ClassifySeqsCommand::getHelpString(){