changed all shared commands so that they read the shared file generated by the read...

[mothur.git] / collectsharedcommand.cpp

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 6c47f2d5a6b2e4ac178d61128e4e0739a7c41666..86b35a5191d268452d86a2994dd1bcafd06a3001 100644 (file)
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -20,7 +20,7 @@
 #include "sharedthetayc.h"
 #include "sharedthetan.h"
 #include "sharedkstest.h"
-#include "sharedbdiversity.h"
+#include "whittaker.h"
 #include "sharednseqs.h"
 #include "sharedochiai.h"
 #include "sharedanderbergs.h"
@@ -29,6 +29,8 @@
 #include "sharedlennon.h"
 #include "sharedmorisitahorn.h"
 #include "sharedbraycurtis.h"
+#include "sharedjackknife.h"
+#include "sharedwhittaker.h"
 
 
 
@@ -52,42 +54,43 @@ CollectSharedCommand::CollectSharedCommand(){
                                        cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(fileNameRoot+"shared.sobs")));
                                }else if (globaldata->Estimators[i] == "sharedace") { 
                                        cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace")));
-                               }else if (globaldata->Estimators[i] == "sharedjabund") {        
-                                       cDisplays.push_back(new CollectDisplay(new SharedJAbund(), new SharedOneColumnFile(fileNameRoot+"shared.jabund")));
-                               }else if (globaldata->Estimators[i] == "sharedsorensonabund") { 
-                                       cDisplays.push_back(new CollectDisplay(new SharedSorAbund(), new SharedOneColumnFile(fileNameRoot+"shared.sorabund")));
-                               }else if (globaldata->Estimators[i] == "sharedjclass") { 
-                                       cDisplays.push_back(new CollectDisplay(new SharedJclass(), new SharedOneColumnFile(fileNameRoot+"shared.jclass")));
-                               }else if (globaldata->Estimators[i] == "sharedsorclass") { 
-                                       cDisplays.push_back(new CollectDisplay(new SharedSorClass(), new SharedOneColumnFile(fileNameRoot+"shared.sorclass")));
-                               }else if (globaldata->Estimators[i] == "sharedjest") { 
-                                       cDisplays.push_back(new CollectDisplay(new SharedJest(), new SharedOneColumnFile(fileNameRoot+"shared.jest")));
-                               }else if (globaldata->Estimators[i] == "sharedsorest") { 
-                                       cDisplays.push_back(new CollectDisplay(new SharedSorEst(), new SharedOneColumnFile(fileNameRoot+"shared.sorest")));
-                               }else if (globaldata->Estimators[i] == "sharedthetayc") { 
-                                       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] == "jabund") {      
+                                       cDisplays.push_back(new CollectDisplay(new JAbund(), new SharedOneColumnFile(fileNameRoot+"jabund")));
+                               }else if (globaldata->Estimators[i] == "sorabund") { 
+                                       cDisplays.push_back(new CollectDisplay(new SorAbund(), new SharedOneColumnFile(fileNameRoot+"sorabund")));
+                               }else if (globaldata->Estimators[i] == "jclass") { 
+                                       cDisplays.push_back(new CollectDisplay(new Jclass(), new SharedOneColumnFile(fileNameRoot+"jclass")));
+                               }else if (globaldata->Estimators[i] == "sorclass") { 
+                                       cDisplays.push_back(new CollectDisplay(new SorClass(), new SharedOneColumnFile(fileNameRoot+"sorclass")));
+                               }else if (globaldata->Estimators[i] == "jest") { 
+                                       cDisplays.push_back(new CollectDisplay(new Jest(), new SharedOneColumnFile(fileNameRoot+"jest")));
+                               }else if (globaldata->Estimators[i] == "sorest") { 
+                                       cDisplays.push_back(new CollectDisplay(new SorEst(), new SharedOneColumnFile(fileNameRoot+"sorest")));
+                               }else if (globaldata->Estimators[i] == "thetayc") { 
+                                       cDisplays.push_back(new CollectDisplay(new ThetaYC(), new SharedOneColumnFile(fileNameRoot+"thetayc")));
+                               }else if (globaldata->Estimators[i] == "thetan") { 
+                                       cDisplays.push_back(new CollectDisplay(new ThetaN(), new SharedOneColumnFile(fileNameRoot+"thetan")));
+                               }else if (globaldata->Estimators[i] == "kstest") { 
+                                       cDisplays.push_back(new CollectDisplay(new KSTest(), new SharedOneColumnFile(fileNameRoot+"kstest")));
+                               }else if (globaldata->Estimators[i] == "whittaker") { 
+                                       cDisplays.push_back(new CollectDisplay(new Whittaker(), new SharedOneColumnFile(fileNameRoot+"whittaker")));
                                }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")));
+
+                               }else if (globaldata->Estimators[i] == "ochiai") { 
+                                       cDisplays.push_back(new CollectDisplay(new Ochiai(), new SharedOneColumnFile(fileNameRoot+"ochiai")));
+                               }else if (globaldata->Estimators[i] == "anderberg") { 
+                                       cDisplays.push_back(new CollectDisplay(new Anderberg(), new SharedOneColumnFile(fileNameRoot+"anderberg")));
+                               }else if (globaldata->Estimators[i] == "skulczynski") { 
+                                       cDisplays.push_back(new CollectDisplay(new Kulczynski(), new SharedOneColumnFile(fileNameRoot+"kulczynski")));
+                               }else if (globaldata->Estimators[i] == "kulczynskicody") { 
+                                       cDisplays.push_back(new CollectDisplay(new KulczynskiCody(), new SharedOneColumnFile(fileNameRoot+"kulczynskicody")));
+                               }else if (globaldata->Estimators[i] == "lennon") { 
+                                       cDisplays.push_back(new CollectDisplay(new Lennon(), new SharedOneColumnFile(fileNameRoot+"lennon")));
+                               }else if (globaldata->Estimators[i] == "morisitahorn") { 
+                                       cDisplays.push_back(new CollectDisplay(new MorHorn(), new SharedOneColumnFile(fileNameRoot+"morisitahorn")));
+                               }else if (globaldata->Estimators[i] == "braycurtis") { 
+                                       cDisplays.push_back(new CollectDisplay(new BrayCurtis(), new SharedOneColumnFile(fileNameRoot+"braycurtis")));
                                }
                        }
                }
@@ -126,21 +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 ReadPhilFile(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 ReadPhilFile(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
@@ -161,18 +155,7 @@ 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;
-                               }
-                       }
-                       
+                       order = input->getSharedOrderVector();
                        count++;
                }
                set<string>::iterator i;