+//**********************************************************************************************************************
+vector<string> ClearcutCommand::setParameters(){
+ try {
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "FastaPhylip", "FastaPhylip", "none","tree",false,false,true); parameters.push_back(pphylip);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "FastaPhylip", "FastaPhylip", "none","tree",false,false,true); parameters.push_back(pfasta);
+ CommandParameter pverbose("verbose", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pverbose);
+ CommandParameter pquiet("quiet", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pquiet);
+ CommandParameter pversion("version", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pversion);
+ CommandParameter pseed("seed", "String", "", "", "*", "", "","",false,false); parameters.push_back(pseed);
+ CommandParameter pnorandom("norandom", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pnorandom);
+ CommandParameter pshuffle("shuffle", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pshuffle);
+ CommandParameter pneighbor("neighbor", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pneighbor);
+ CommandParameter pexpblen("expblen", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pexpblen);
+ CommandParameter pexpdist("expdist", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pexpdist);
+ CommandParameter pDNA("DNA", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pDNA);
+ CommandParameter pprotein("protein", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pprotein);
+ CommandParameter pjukes("jukes", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pjukes);
+ CommandParameter pkimura("kimura", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pkimura);
+ CommandParameter pstdout("stdout", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pstdout);
+ CommandParameter pntrees("ntrees", "Number", "", "1", "", "", "","",false,false); parameters.push_back(pntrees);
+ CommandParameter pmatrixout("matrixout", "String", "", "", "", "", "","",false,false); parameters.push_back(pmatrixout);
+ 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, "ClearcutCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ClearcutCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The clearcut command interfaces mothur with the clearcut program written by Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho.\n";
+ helpString += "For more information about clearcut refer to http://bioinformatics.hungry.com/clearcut/ \n";
+ helpString += "The clearcut command parameters are phylip, fasta, version, verbose, quiet, seed, norandom, shuffle, neighbor, expblen, expdist, ntrees, matrixout, stdout, kimura, jukes, protein, DNA. \n";
+ helpString += "The phylip parameter allows you to enter your phylip formatted distance matrix. \n";
+ helpString += "The fasta parameter allows you to enter your aligned fasta file, if you enter a fastafile you specify if the sequences are DNA or protein using the DNA or protein parameters. \n";
+
+ helpString += "The version parameter prints out the version of clearcut you are using, default=F. \n";
+ helpString += "The verbose parameter prints out more output from clearcut, default=F. \n";
+ helpString += "The quiet parameter turns on silent operation mode, default=F. \n";
+ helpString += "The seed parameter allows you to explicitly set the PRNG seed to a specific value. \n";
+ helpString += "The norandom parameter allows you to attempt joins deterministically, default=F. \n";
+ helpString += "The shuffle parameter allows you to randomly shuffle the distance matrix, default=F. \n";
+ helpString += "The neighbor parameter allows you to use traditional Neighbor-Joining algorithm, default=T. \n";
+
+ helpString += "The DNA parameter allows you to indicate your fasta file contains DNA sequences, default=F. \n";
+ helpString += "The protein parameter allows you to indicate your fasta file contains protein sequences, default=F. \n";
+
+ helpString += "The stdout parameter outputs your tree to STDOUT, default=F. \n";
+ helpString += "The matrixout parameter allows you to specify a filename to output a distance matrix to. \n";
+ helpString += "The ntrees parameter allows you to specify the number of output trees, default=1. \n";
+ helpString += "The expblen parameter allows you to use exponential notation for branch lengths, default=F. \n";
+ helpString += "The expdist parameter allows you to use exponential notation for distance outputs, default=F. \n";
+
+ helpString += "The clearcut command should be in the following format: \n";
+ helpString += "clearcut(phylip=yourDistanceFile) \n";
+ helpString += "Example: clearcut(phylip=abrecovery.phylip.dist) \n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClearcutCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ClearcutCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "matrixout") { pattern = "[filename],"; }
+ else if (type == "tree") { pattern = "[filename],tre"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClearcutCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ClearcutCommand::ClearcutCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["tree"] = tempOutNames;
+ outputTypes["matrixout"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClearcutCommand", "ClearcutCommand");
+ exit(1);
+ }
+}