+//**********************************************************************************************************************
+vector<string> ChimeraBellerophonCommand::setParameters(){
+ try {
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none","none","none",false,true); parameters.push_back(pfasta);
+ CommandParameter pfilter("filter", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pfilter);
+ CommandParameter pcorrection("correction", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pcorrection);
+ CommandParameter pwindow("window", "Number", "", "0", "", "", "",false,false); parameters.push_back(pwindow);
+ CommandParameter pincrement("increment", "Number", "", "25", "", "", "",false,false); parameters.push_back(pincrement);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+ 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, "ChimeraBellerophonCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ChimeraBellerophonCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The chimera.bellerophon command reads a fastafile and creates list of potentially chimeric sequences.\n";
+ helpString += "The chimera.bellerophon command parameters are fasta, filter, correction, processors, window, increment. The fasta parameter is required, unless you have a valid current file.\n";
+ helpString += "The fasta parameter is required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n";
+ helpString += "The filter parameter allows you to specify if you would like to apply a vertical and 50% soft filter, default=false. \n";
+ helpString += "The correction parameter allows you to put more emphasis on the distance between highly similar sequences and less emphasis on the differences between remote homologs, default=true.\n";
+ helpString += "The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n";
+#ifdef USE_MPI
+ helpString += "When using MPI, the processors parameter is set to the number of MPI processes running. \n";
+#endif
+ helpString += "The window parameter allows you to specify the window size for searching for chimeras, default is 1/4 sequence length. \n";
+ helpString += "The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default is 25.\n";
+ helpString += "chimera.bellerophon(fasta=yourFastaFile, filter=yourFilter, correction=yourCorrection, processors=yourProcessors) \n";
+ helpString += "Example: chimera.bellerophon(fasta=AD.align, filter=True, correction=true, window=200) \n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraBellerophonCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ChimeraBellerophonCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "chimera") { outputFileName = "bellerophon.chimeras"; }
+ else if (type == "accnos") { outputFileName = "bellerophon.accnos"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraBellerophonCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ChimeraBellerophonCommand::ChimeraBellerophonCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["chimera"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraBellerophonCommand", "ChimeraBellerophonCommand");
+ exit(1);
+ }
+}