LibShuffCommand::LibShuffCommand(string option){
try {
-
globaldata = GlobalData::getInstance();
abort = false;
Groups.clear();
userform = validParameter.validFile(parameters, "form", false); if (userform == "not found") { userform = "integral"; }
if (abort == false) {
-
+
matrix = globaldata->gMatrix; //get the distance matrix
setGroups(); //set the groups to be analyzed and sorts them
-
+
/********************************************************************************************/
//this is needed because when we read the matrix we sort it into groups in alphabetical order
//the rest of the command and the classes used in this command assume specific order
/********************************************************************************************/
matrix->setGroups(globaldata->gGroupmap->namesOfGroups);
vector<int> sizes;
- for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) { sizes.push_back(globaldata->gGroupmap->getNumSeqs(globaldata->gGroupmap->namesOfGroups[i])); }
+ for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) { sizes.push_back(globaldata->gGroupmap->getNumSeqs(globaldata->gGroupmap->namesOfGroups[i])); }
matrix->setSizes(sizes);
-
+
if(userform == "discrete"){
form = new DLibshuff(matrix, iters, step, cutOff);
try {
if (abort == true) { return 0; }
-
+
savedDXYValues = form->evaluateAll();
savedMinValues = form->getSavedMins();
-
+
pValueCounts.resize(numGroups);
for(int i=0;i<numGroups;i++){
pValueCounts[i].assign(numGroups, 0);