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

[mothur.git] / collectsharedcommand.cpp

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 63a267d043d143d85435ba5c3259389df6f387af..76f7abb5682661620f958b66c84637f0add5c54d 100644 (file)
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -8,6 +8,7 @@
  */
 
 #include "collectsharedcommand.h"
+#include "sharedsobs.h"
 #include "sharedchao1.h"
 #include "sharedace.h"
 #include "sharedjabund.h"
@@ -32,25 +33,27 @@ CollectSharedCommand::CollectSharedCommand(){
                int i;
                for (i=0; i<globaldata->sharedEstimators.size(); i++) {
                        if (globaldata->sharedEstimators[i] == "sharedChao") { 
-                               cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(fileNameRoot+"sharedChao", groupmap->namesOfGroups)));
+                               cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(fileNameRoot+"shared.chao", groupmap->namesOfGroups)));
+                       }else if (globaldata->sharedEstimators[i] == "sharedSobs") { 
+                               cDisplays.push_back(new CollectDisplay(new SharedSobs(), new SharedOneColumnFile(fileNameRoot+"shared.sobs", groupmap->namesOfGroups)));
                        }else if (globaldata->sharedEstimators[i] == "sharedAce") { 
-                               cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"sharedAce", groupmap->namesOfGroups)));
+                               cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace", groupmap->namesOfGroups)));
                        }else if (globaldata->sharedEstimators[i] == "sharedJabund") {  
-                               cDisplays.push_back(new CollectDisplay(new SharedJAbund(), new SharedOneColumnFile(fileNameRoot+"SharedJabund", groupmap->namesOfGroups)));
+                               cDisplays.push_back(new CollectDisplay(new SharedJAbund(), new SharedOneColumnFile(fileNameRoot+"shared.jabund", groupmap->namesOfGroups)));
                        }else if (globaldata->sharedEstimators[i] == "sharedSorensonAbund") { 
-                               cDisplays.push_back(new CollectDisplay(new SharedSorAbund(), new SharedOneColumnFile(fileNameRoot+"SharedSorensonAbund", groupmap->namesOfGroups)));
+                               cDisplays.push_back(new CollectDisplay(new SharedSorAbund(), new SharedOneColumnFile(fileNameRoot+"shared.sorensonabund", groupmap->namesOfGroups)));
                        }else if (globaldata->sharedEstimators[i] == "sharedJclass") { 
-                               cDisplays.push_back(new CollectDisplay(new SharedJclass(), new SharedOneColumnFile(fileNameRoot+"SharedJclass", groupmap->namesOfGroups)));
+                               cDisplays.push_back(new CollectDisplay(new SharedJclass(), new SharedOneColumnFile(fileNameRoot+"shared.jclass", groupmap->namesOfGroups)));
                        }else if (globaldata->sharedEstimators[i] == "sharedSorClass") { 
-                               cDisplays.push_back(new CollectDisplay(new SharedSorClass(), new SharedOneColumnFile(fileNameRoot+"SharedSorClass", groupmap->namesOfGroups)));
+                               cDisplays.push_back(new CollectDisplay(new SharedSorClass(), new SharedOneColumnFile(fileNameRoot+"shared.sorclass", groupmap->namesOfGroups)));
                        }else if (globaldata->sharedEstimators[i] == "sharedJest") { 
-                               cDisplays.push_back(new CollectDisplay(new SharedJest(), new SharedOneColumnFile(fileNameRoot+"SharedJest", groupmap->namesOfGroups)));
+                               cDisplays.push_back(new CollectDisplay(new SharedJest(), new SharedOneColumnFile(fileNameRoot+"shared.jest", groupmap->namesOfGroups)));
                        }else if (globaldata->sharedEstimators[i] == "sharedSorEst") { 
-                               cDisplays.push_back(new CollectDisplay(new SharedSorEst(), new SharedOneColumnFile(fileNameRoot+"SharedSorEst", groupmap->namesOfGroups)));
+                               cDisplays.push_back(new CollectDisplay(new SharedSorEst(), new SharedOneColumnFile(fileNameRoot+"shared.sorest", groupmap->namesOfGroups)));
                        }else if (globaldata->sharedEstimators[i] == "SharedThetaYC") { 
-                               cDisplays.push_back(new CollectDisplay(new SharedThetaYC(), new SharedOneColumnFile(fileNameRoot+"SharedThetaYC", groupmap->namesOfGroups)));
+                               cDisplays.push_back(new CollectDisplay(new SharedThetaYC(), new SharedOneColumnFile(fileNameRoot+"shared.thetayc", groupmap->namesOfGroups)));
                        }else if (globaldata->sharedEstimators[i] == "SharedThetaN") { 
-                               cDisplays.push_back(new CollectDisplay(new SharedThetaN(), new SharedOneColumnFile(fileNameRoot+"SharedThetaN", groupmap->namesOfGroups)));
+                               cDisplays.push_back(new CollectDisplay(new SharedThetaN(), new SharedOneColumnFile(fileNameRoot+"shared.thetan", groupmap->namesOfGroups)));
                        }
                }
        }
@@ -83,8 +86,8 @@ int CollectSharedCommand::execute(){
                read->read(&*globaldata); 
                
                input = globaldata->ginput;
-               list = globaldata->glist;
-               order = list->getSharedOrderVector();
+               SharedList = globaldata->gSharedList;
+               order = SharedList->getSharedOrderVector();
                
                while(order != NULL){
                
@@ -99,9 +102,9 @@ int CollectSharedCommand::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;