#include "sharedsorest.h"
#include "sharedthetayc.h"
#include "sharedthetan.h"
+#include "sharedkstest.h"
+#include "sharedbdiversity.h"
+#include "sharednseqs.h"
+#include "sharedochiai.h"
+#include "sharedanderbergs.h"
+#include "sharedkulczynski.h"
+#include "sharedkulczynskicody.h"
+#include "sharedlennon.h"
+#include "sharedmorisitahorn.h"
+#include "sharedbraycurtis.h"
+
//**********************************************************************************************************************
cDisplays.push_back(new CollectDisplay(new SharedThetaYC(), new SharedOneColumnFile(fileNameRoot+"shared.thetayc")));
}else if (globaldata->Estimators[i] == "sharedthetan") {
cDisplays.push_back(new CollectDisplay(new SharedThetaN(), new SharedOneColumnFile(fileNameRoot+"shared.thetan")));
+ }else if (globaldata->Estimators[i] == "sharedkstest") {
+ cDisplays.push_back(new CollectDisplay(new SharedKSTest(), new SharedOneColumnFile(fileNameRoot+"shared.kstest")));
+ }else if (globaldata->Estimators[i] == "sharedbdiversity") {
+ cDisplays.push_back(new CollectDisplay(new SharedBDiversity(), new SharedOneColumnFile(fileNameRoot+"shared.bdiversity")));
+ }else if (globaldata->Estimators[i] == "sharednseqs") {
+ cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(fileNameRoot+"shared.nseqs")));
+ }else if (globaldata->Estimators[i] == "sharedochiai") {
+ cDisplays.push_back(new CollectDisplay(new SharedOchiai(), new SharedOneColumnFile(fileNameRoot+"shared.ochiai")));
+ }else if (globaldata->Estimators[i] == "sharedanderberg") {
+ cDisplays.push_back(new CollectDisplay(new SharedAnderberg(), new SharedOneColumnFile(fileNameRoot+"shared.anderberg")));
+ }else if (globaldata->Estimators[i] == "sharedkulczynski") {
+ cDisplays.push_back(new CollectDisplay(new SharedKulczynski(), new SharedOneColumnFile(fileNameRoot+"shared.kulczynski")));
+ }else if (globaldata->Estimators[i] == "sharedkulczynskicody") {
+ cDisplays.push_back(new CollectDisplay(new SharedKulczynskiCody(), new SharedOneColumnFile(fileNameRoot+"shared.kulczynskicody")));
+ }else if (globaldata->Estimators[i] == "sharedlennon") {
+ cDisplays.push_back(new CollectDisplay(new SharedLennon(), new SharedOneColumnFile(fileNameRoot+"shared.lennon")));
+ }else if (globaldata->Estimators[i] == "sharedmorisitahorn") {
+ cDisplays.push_back(new CollectDisplay(new SharedMorHorn(), new SharedOneColumnFile(fileNameRoot+"shared.morisitahorn")));
+ }else if (globaldata->Estimators[i] == "sharedbraycurtis") {
+ cDisplays.push_back(new CollectDisplay(new SharedBrayCurtis(), new SharedOneColumnFile(fileNameRoot+"shared.braycurtis")));
}
}
}
SharedList = globaldata->gSharedList;
order = SharedList->getSharedOrderVector();
}
+ set<string> orderList;
+ //set users groups
+ setGroups();
+
while(order != NULL){
-
+ orderList.insert(order->getLabel());
if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
//create collectors curve
cCurve = new Collect(order, cDisplays);
count++;
}
-
+ set<string>::iterator i;
+ for(i = globaldata->labels.begin(); i != globaldata->labels.end(); ++i)
+ if(orderList.count(*i) == 0)
+ cout << "'" << *i << "'" << " is not a valid label.\n";
for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
+
+ //reset groups parameter
+ globaldata->Groups.clear(); globaldata->setGroups("");
+
return 0;
}
catch(exception& e) {
//**********************************************************************************************************************
+void CollectSharedCommand::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) || (globaldata->Groups.size() == 1)) {
+ cout << "When using the groups parameter you must have at least 2 valid groups. 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]);
+ }
+ }
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the CollectSharedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+
+}
+/***********************************************************/
+