#include "sharedsobscollectsummary.h"
#include "sharedchao1.h"
#include "sharedace.h"
+#include "sharednseqs.h"
#include "sharedjabund.h"
#include "sharedsorabund.h"
#include "sharedjclass.h"
#include "sharedsorest.h"
#include "sharedthetayc.h"
#include "sharedthetan.h"
+#include "sharedkstest.h"
+#include "sharedbdiversity.h"
+#include "sharedochiai.h"
+//#include "sharedanderberg.h"
+#include "sharedkulczynski.h"
+#include "sharedkulczynskicody.h"
+#include "sharedlennon.h"
+#include "sharedmorisitahorn.h"
+#include "sharedbraycurtis.h"
//**********************************************************************************************************************
format = globaldata->getFormat();
validCalculator = new ValidCalculators();
- //set users groups
- setGroups();
-
int i;
for (i=0; i<globaldata->Estimators.size(); i++) {
if (validCalculator->isValidCalculator("sharedsummary", globaldata->Estimators[i]) == true) {
sumCalculators.push_back(new SharedThetaYC());
}else if (globaldata->Estimators[i] == "sharedthetan") {
sumCalculators.push_back(new SharedThetaN());
+ }else if (globaldata->Estimators[i] == "sharedkstest") {
+ sumCalculators.push_back(new SharedKSTest());
+ }else if (globaldata->Estimators[i] == "sharednseqs") {
+ sumCalculators.push_back(new SharedNSeqs());
+ }else if (globaldata->Estimators[i] == "sharedochiai") {
+ sumCalculators.push_back(new SharedOchiai());
+ //}else if (globaldata->Estimators[i] == "sharedanderberg") {
+ //sumCalculators.push_back(new SharedAnderberg());
+ }else if (globaldata->Estimators[i] == "sharedkulczynski") {
+ sumCalculators.push_back(new SharedKulczynski());
+ }else if (globaldata->Estimators[i] == "sharedkulczynskicody") {
+ sumCalculators.push_back(new SharedKulczynskiCody());
+ }else if (globaldata->Estimators[i] == "sharedlennon") {
+ sumCalculators.push_back(new SharedLennon());
+ }else if (globaldata->Estimators[i] == "sharedmorisitahorn") {
+ sumCalculators.push_back(new SharedMorHorn());
+ }else if (globaldata->Estimators[i] == "sharedbraycurtis") {
+ sumCalculators.push_back(new SharedBrayCurtis());
+ }
+ else if (globaldata->Estimators[i] == "sharedbdiversity") {
+ sumCalculators.push_back(new SharedBDiversity());
}
+
}
}
-
//reset calc for next command
globaldata->setCalc("");
order = SharedList->getSharedOrderVector();
}
+ //set users groups
+ setGroups();
+
//output estimator names as column headers
outputFileHandle << "label" <<'\t' << "comparison" << '\t';
for(int i=0;i<sumCalculators.size();i++){
outputFileHandle << '\t' << sumCalculators[i]->getName();
}
outputFileHandle << endl;
-
+
while(order != NULL){
if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
for (int l = n; l < lookup.size(); l++) {
outputFileHandle << order->getLabel() << '\t' << (lookup[k]->getGroup() + lookup[l]->getGroup()) << '\t' << '\t'; //print out label and group
+ outputFileHandle << order->getLabel() << '\t';
+
+ //sort groups to be alphanumeric
+ if (lookup[k]->getGroup() > lookup[l]->getGroup()) {
+ outputFileHandle << (lookup[l]->getGroup() +'\t' + lookup[k]->getGroup()) << '\t'; //print out groups
+ }else{
+ outputFileHandle << (lookup[k]->getGroup() +'\t' + lookup[l]->getGroup()) << '\t'; //print out groups
+ }
+
for(int i=0;i<sumCalculators.size();i++){
sumCalculators[i]->getValues(lookup[k], lookup[l]); //saves the calculator outputs
outputFileHandle << '\t';
try {
lookup.clear();
//create and initialize vector of sharedvectors, one for each group
- for (int i = 0; i < globaldata->gGroupmap->getNumGroups(); i++) {
+ for (int i = 0; i < globaldata->Groups.size(); i++) {
SharedRAbundVector* temp = new SharedRAbundVector(order->getNumBins());
temp->setLabel(order->getLabel());
- temp->setGroup(globaldata->gGroupmap->namesOfGroups[i]);
+ temp->setGroup(globaldata->Groups[i]);
lookup.push_back(temp);
}
}
}
}
-
- //get rid of vectors from groups you don't want to analyze
- for (int r = 0; r < lookup.size(); r++) {
- if (inUsersGroups(lookup[r]->getGroup(), globaldata->Groups) != true) {
- lookup.erase(lookup.begin()+r);
- }
- }
-
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";