try {
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
-
-
+
+ //get shared file
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+ else if (sharedfile == "not found") {
+ //if there is a current shared file, use it
+ sharedfile = m->getSharedFile();
+ if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setSharedFile(sharedfile); }
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(sharedfile); }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ m->splitAtDash(groups, Groups);
+ }
+ m->setGroups(Groups);
+
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
InputData* input = new InputData(sharedfile, "sharedfile");
vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
string lastLabel = lookup[0]->getLabel();
-
+
+
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
set<string> userLabels = labels;
//math goes here
- int N = lookUp.size();
+ int N = m->getNumGroups();
double H;
double tmp = 0.0;
vector<groupRank> vec;
+ vector<string> groups = m->getGroups();
string group;
int count;
double sum;
//merge all groups into a vector
+
+
+
//rank function here
assignRank(vec);
for (int i=0;i<N;i++) {
count = 0;
sum = 0;
- //group = next group
+ group = groups[i];
for(int j;j<vec.size();j++) {
if (vec[j].group == group) {
count++;
}
//**********************************************************************************************************************
-
+void KruskalWallisCommand::assignValue(vector<groupRank> &vec) {
+
+}
//**********************************************************************************************************************
//**********************************************************************************************************************
//**********************************************************************************************************************
\ No newline at end of file