added sort to heatmap to put shared otus at the top and updated some error checking

[mothur.git] / collectsharedcommand.cpp

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index c473c2d77e819164d62799095ea6bf849d27c42a..ec35dd601e75abd3ea7b65e32aabcaa1c13b1c90 100644 (file)
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -19,6 +19,17 @@
 #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"
+
 
 
 //**********************************************************************************************************************
@@ -31,9 +42,6 @@ CollectSharedCommand::CollectSharedCommand(){
                format = globaldata->getFormat();
                validCalculator = new ValidCalculators();
                
-               //set users groups
-               setGroups();
-               
                int i;
                for (i=0; i<globaldata->Estimators.size(); i++) {
                        if (validCalculator->isValidCalculator("shared", globaldata->Estimators[i]) == true) { 
@@ -59,6 +67,26 @@ 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] == "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")));
                                }
                        }
                }
@@ -112,6 +140,9 @@ int CollectSharedCommand::execute(){
                        order = SharedList->getSharedOrderVector();
                }
                set<string> orderList;
+               
+               //set users groups
+               setGroups();
 
                while(order != NULL){
                        orderList.insert(order->getLabel());