fixed multiple bugs for 1.4 release

[mothur.git] / collectsharedcommand.cpp

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 96e495a58f9dd1bdc58256baf1ae47c51a9c87b2..582628d8f6a98151efb9a525bf9cdc26383be379 100644 (file)
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -30,7 +30,7 @@
 #include "sharedmorisitahorn.h"
 #include "sharedbraycurtis.h"
 #include "sharedjackknife.h"
-#include "sharedwhittaker.h"
+#include "whittaker.h"
 
 
 
@@ -129,21 +129,12 @@ int CollectSharedCommand::execute(){
                //if the users entered no valid calculators don't execute command
                if (cDisplays.size() == 0) { return 0; }
                
-               if (format == "sharedfile") {
-                       read = new ReadOTUFile(globaldata->inputFileName);      
-                       read->read(&*globaldata); 
+               read = new ReadOTUFile(globaldata->inputFileName);      
+               read->read(&*globaldata); 
                        
-                       input = globaldata->ginput;
-                       order = input->getSharedOrderVector();
-               }else {
-                       //you are using a list and a groupfile
-                       read = new ReadOTUFile(globaldata->inputFileName);      
-                       read->read(&*globaldata); 
+               input = globaldata->ginput;
+               order = input->getSharedOrderVector();
                
-                       input = globaldata->ginput;
-                       SharedList = globaldata->gSharedList;
-                       order = SharedList->getSharedOrderVector();
-               }
                set<string> orderList;
                
                //set users groups
@@ -151,8 +142,11 @@ int CollectSharedCommand::execute(){
                util->updateGroupIndex(globaldata->Groups, globaldata->gGroupmap->groupIndex);
 
                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);
                                convert(globaldata->getFreq(), freq);
@@ -164,24 +158,15 @@ int CollectSharedCommand::execute(){
                        }
                        
                        //get next line to process
-                       if (format == "sharedfile") {
-                               order = input->getSharedOrderVector();
-                       }else {
-                               //you are using a list and a groupfile
-                               SharedList = input->getSharedListVector(); //get new list vector to process
-                               if (SharedList != NULL) {
-                                       order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
-                               }else {
-                                       break;
-                               }
-                       }
-                       
+                       delete order;
+                       order = input->getSharedOrderVector();
                        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