X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectsharedcommand.cpp;h=6ee2943777f4053bb89f6d86e400269f3af30789;hb=25cde7ff05bbe741da1712f2c740e0bc8706e523;hp=b3f798145bc4de3abe460aa0e8dbccd8825178c6;hpb=addc715b6d7ea52440751cec10edad03e1a19b37;p=mothur.git

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index b3f7981..6ee2943 100644
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -19,6 +19,14 @@
 #include "sharedsorest.h"
 #include "sharedthetayc.h"
 #include "sharedthetan.h"
+#include "sharednseqs.h"
+#include "sharedochiai.h"
+#include "sharedanderberg.h"
+#include "sharedkulczynski.h"
+#include "sharedkulczynskicody.h"
+#include "sharedlennon.h"
+#include "sharedmorisitahorn.h"
+#include "sharedbraycurtis.h"
 
 
 //**********************************************************************************************************************
@@ -56,6 +64,22 @@ CollectSharedCommand::CollectSharedCommand(){
 					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] == "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")));
 				}
 			}
 		}
@@ -109,6 +133,9 @@ int CollectSharedCommand::execute(){
 			order = SharedList->getSharedOrderVector();
 		}
 		set<string> orderList;
+		
+		//set users groups
+		setGroups();
 
 		while(order != NULL){
 			orderList.insert(order->getLabel());
@@ -142,8 +169,11 @@ int CollectSharedCommand::execute(){
 		for(i = globaldata->labels.begin(); i != globaldata->labels.end(); ++i)
 			if(orderList.count(*i) == 0)
 				cout << "'" << *i << "'" << " is not a valid label.\n";
-		globaldata->clearLabels();
 		for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}	
+		
+		//reset groups parameter
+		globaldata->Groups.clear();  globaldata->setGroups("");
+		
 		return 0;
 	}
 	catch(exception& e) {
@@ -158,3 +188,50 @@ int CollectSharedCommand::execute(){
 
 
 //**********************************************************************************************************************
+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);
+	}		
+
+}
+/***********************************************************/
+