finishing the container classes, combining read.otu and read.list commands. some...

[mothur.git] / rarefactsharedcommand.cpp

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index 4ed479555ab7ac66a75e789e71f9be5053ec3ae2..189be88de11e4160b4e185727e324a581063727f 100644 (file)
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -28,7 +28,7 @@ RareFactSharedCommand::RareFactSharedCommand(){
                int i;
                for (i=0; i<globaldata->sharedRareEstimators.size(); i++) {
                        if (globaldata->sharedRareEstimators[i] == "sharedobserved") { 
-                               rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"sharedObserved", groups)));
+                               rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"r_shared.observed", groups)));
                        }
                }
        }
@@ -61,8 +61,8 @@ int RareFactSharedCommand::execute(){
                read->read(&*globaldata); 
                
                input = globaldata->ginput;
-               list = globaldata->glist;
-               order = list->getSharedOrderVector();
+               SharedList = globaldata->gSharedList;
+               order = SharedList->getSharedOrderVector();
                
                while(order != NULL){
                
@@ -78,9 +78,9 @@ int RareFactSharedCommand::execute(){
                                cout << order->getLabel() << '\t' << count << endl;
                        }
                        
-                       list = input->getListVector(); //get new list vector to process
-                       if (list != NULL) {
-                               order = list->getSharedOrderVector(); //gets new order vector with group info.
+                       SharedList = input->getSharedListVector(); //get new list vector to process
+                       if (SharedList != NULL) {
+                               order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
                                count++;
                        }else {
                                break;