//**********************************************************************************************************************
vector<string> ParsimonyCommand::setParameters(){
try {
- CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptree);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter prandom("random", "String", "", "", "", "", "",false,false); parameters.push_back(prandom);
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- 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);
+ CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none","parsimony-psummary",false,true,true); parameters.push_back(ptree);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter prandom("random", "String", "", "", "", "", "","",false,false); parameters.push_back(prandom);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); 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); }
}
}
//**********************************************************************************************************************
-string ParsimonyCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ParsimonyCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //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 == "parsimony") { outputFileName = "parsimony"; }
- else if (type == "psummary") { outputFileName = "psummary"; }
- 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, "ParsimonyCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "parsimony") { pattern = "[filename],parsimony"; }
+ else if (type == "psummary") { pattern = "[filename],psummary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParsimonyCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
ParsimonyCommand::ParsimonyCommand(){
try {
delete reader;
if(outputDir == "") { outputDir += m->hasPath(treefile); }
- output = new ColumnFile(outputDir + m->getSimpleName(treefile) + "." + getOutputFileNameTag("parsimony"), itersString);
- outputNames.push_back(outputDir + m->getSimpleName(treefile) + "." + getOutputFileNameTag("parsimony"));
- outputTypes["parsimony"].push_back(outputDir + m->getSimpleName(treefile) + "." + getOutputFileNameTag("parsimony"));
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getSimpleName(treefile) + ".";
+
+ output = new ColumnFile(getOutputFileName("parsimony",variables), itersString);
+ outputNames.push_back(getOutputFileName("parsimony",variables));
+ outputTypes["parsimony"].push_back(getOutputFileName("parsimony",variables));
- sumFile = outputDir + m->getSimpleName(treefile) + "." + getOutputFileNameTag("psummary");
+ sumFile = getOutputFileName("psummary",variables);
m->openOutputFile(sumFile, outSum);
outputNames.push_back(sumFile);
outputTypes["psummary"].push_back(sumFile);
//set tmaps namesOfSeqs
for (int j = 0; j < num; j++) {
- groupMap[toString(count)] = i;
+ groupMap[toString(count)] = toString(i);
nameMap.insert(toString(count));
count++;
}
getline(cin, s);
m->Treenames = ct->getNamesOfSeqs();
+ m->runParse = false;
}
catch(exception& e) {
m->errorOut(e, "ParsimonyCommand", "getUserInput");