+ CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "OldFastaColumn",false,false); parameters.push_back(pcolumn);
+ CommandParameter poldfasta("oldfasta", "InputTypes", "", "", "none", "none", "OldFastaColumn",false,false); parameters.push_back(poldfasta);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+ CommandParameter poutput("output", "Multiple", "column-lt-square", "column", "", "", "",false,false); parameters.push_back(poutput);
+ CommandParameter pcalc("calc", "Multiple", "nogaps-eachgap-onegap", "onegap", "", "", "",false,false); parameters.push_back(pcalc);
+ CommandParameter pcountends("countends", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pcountends);
+ CommandParameter pcompress("compress", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pcompress);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+ CommandParameter pcutoff("cutoff", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pcutoff);
+ 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, "DistanceCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string DistanceCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The dist.seqs command reads a file containing sequences and creates a distance file.\n";
+ helpString += "The dist.seqs command parameters are fasta, oldfasta, column, calc, countends, output, compress, cutoff and processors. \n";
+ helpString += "The fasta parameter is required, unless you have a valid current fasta file.\n";
+ helpString += "The oldfasta and column parameters allow you to append the distances calculated to the column file.\n";
+ helpString += "The calc parameter allows you to specify the method of calculating the distances. Your options are: nogaps, onegap or eachgap. The default is onegap.\n";
+ helpString += "The countends parameter allows you to specify whether to include terminal gaps in distance. Your options are: T or F. The default is T.\n";
+ helpString += "The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0.\n";
+ helpString += "The output parameter allows you to specify format of your distance matrix. Options are column, lt, and square. The default is column.\n";
+ helpString += "The processors parameter allows you to specify number of processors to use. The default is 1.\n";
+ helpString += "The compress parameter allows you to indicate that you want the resulting distance file compressed. The default is false.\n";
+ helpString += "The dist.seqs command should be in the following format: \n";
+ helpString += "dist.seqs(fasta=yourFastaFile, calc=yourCalc, countends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) \n";
+ helpString += "Example dist.seqs(fasta=amazon.fasta, calc=eachgap, countends=F, cutoff= 2.0, processors=3).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. calc), '=' and parameters (i.e.yourCalc).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DistanceCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string DistanceCommand::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 == "phylip") { outputFileName = "dist"; }
+ else if (type == "column") { outputFileName = "dist"; }
+ 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, "DistanceCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+DistanceCommand::DistanceCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["phylip"] = tempOutNames;
+ outputTypes["column"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DistanceCommand", "DistanceCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+DistanceCommand::DistanceCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+ Estimators.clear();
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+
+ else {
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string, string> parameters = parser.getParameters();
+
+ ValidParameters validParameter("dist.seqs");
+ map<string, string>::iterator it2;
+
+ //check to make sure all parameters are valid for command
+ for (it2 = parameters.begin(); it2 != parameters.end(); it2++) {
+ if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) { abort = true; }