//**********************************************************************************************************************
vector<string> AmovaCommand::setParameters(){
try {
- CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pdesign);
- CommandParameter psets("sets", "String", "", "", "", "", "",false,false); parameters.push_back(psets);
- CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip);
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter palpha("alpha", "Number", "", "0.05", "", "", "",false,false); parameters.push_back(palpha);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","amova",false,true,true); parameters.push_back(pdesign);
+ CommandParameter psets("sets", "String", "", "", "", "", "","",false,false); parameters.push_back(psets);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","amova",false,true,true); parameters.push_back(pphylip);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter palpha("alpha", "Number", "", "0.05", "", "", "","",false,false); parameters.push_back(palpha);
+ 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 AmovaCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string tag = "";
- map<string, vector<string> >::iterator it;
+string AmovaCommand::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 == "amova") { tag = "amova"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file.\n"); }
- }
- return tag;
- }
- catch(exception& e) {
- m->errorOut(e, "AmovaCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "amova") { pattern = "[filename],amova"; } //makes file like: amazon.align
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AmovaCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
AmovaCommand::AmovaCommand(){
//create a new filename
ofstream AMOVAFile;
- string AMOVAFileName = outputDir + m->getRootName(m->getSimpleName(phylipFileName)) + getOutputFileNameTag("amova");
+ map<string, string> variables; variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(phylipFileName));
+ string AMOVAFileName = getOutputFileName("amova", variables);
+
m->openOutputFile(AMOVAFileName, AMOVAFile);
outputNames.push_back(AMOVAFileName); outputTypes["amova"].push_back(AMOVAFileName);
for(int i=0;i<iters;i++){
map<string, vector<int> > randomizedGroup = getRandomizedGroups(groupSampleMap);
double ssWithinRand = calcSSWithin(randomizedGroup);
- if(ssWithinRand < ssWithinOrig){ counter++; }
+ if(ssWithinRand <= ssWithinOrig){ counter++; }
}
double pValue = (double)counter / (double) iters;