#include "ace.h"
#include "sobs.h"
#include "chao1.h"
-#include "jackknife.h"
+//#include "jackknife.h"
#include "sharedsobscollectsummary.h"
#include "sharedchao1.h"
#include "sharedace.h"
globaldata = GlobalData::getInstance();
format = globaldata->getFormat();
validCalculator = new ValidCalculators();
+ util = new SharedUtil();
int i;
if(abund < 5)
abund = 10;
vennCalculators.push_back(new Ace(abund));
- }else if (globaldata->Estimators[i] == "jack") {
- vennCalculators.push_back(new Jackknife());
+ //}else if (globaldata->Estimators[i] == "jack") {
+ //vennCalculators.push_back(new Jackknife());
}
}
}
delete input;
delete read;
delete venn;
+ delete util;
}
//**********************************************************************************************************************
if (format != "list") {
- setGroups();
+ util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "venn");
+ globaldata->setGroups("");
while(order != NULL){
}
//reset groups parameter
- globaldata->Groups.clear(); globaldata->setGroups("");
+ globaldata->Groups.clear();
}else{
while(ordersingle != NULL){
}
//**********************************************************************************************************************
-void VennCommand::setGroups() {
- try {
- //if the user has not entered specific groups to analyze then do them all
- if (globaldata->Groups.size() != 0) {
- if (globaldata->Groups[0] != "all") {
- //check that groups are valid
- for (int i = 0; i < globaldata->Groups.size(); i++) {
- if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
- cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
- // erase the invalid group from globaldata->Groups
- globaldata->Groups.erase(globaldata->Groups.begin()+i);
- }
- }
-
- //if the user only entered invalid groups
- if (globaldata->Groups.size() == 0) {
- if (globaldata->gGroupmap->namesOfGroups.size() > 4) {
- cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using the first four groups in your groupfile." << endl;
- for (int i = 0; i < 4; i++) {
- globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
- }
- }else {
- cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using all the groups in your groupfile." << endl;
- for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
- }
- }
-
- }
- }else{//user has enter "all" and wants the default groups
- globaldata->Groups.clear();
- for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
- }
- globaldata->setGroups("");
- }
- }else {
- for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
- }
- }
-
-
- //check to make sure their are only 3 groups
- if (globaldata->Groups.size() > 4) {
- cout << "You may only use up to 4 groups at a time with this command. I will choose the first four and disregard the rest." << endl;
- for (int i = 4; i < globaldata->Groups.size(); i++) {
- globaldata->Groups.erase(globaldata->Groups.begin()+i);
- }
- }
-
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the VennCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the VennCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
-}
-/***********************************************************/