venn command with up to 4 groups using sharedsobs, sharedchao and sharedace estimator...

[mothur.git] / venncommand.cpp

diff --git a/venncommand.cpp b/venncommand.cpp
index 85dcd93c33d9b1df4baf8dcbef8bf16e2677154b..56284811af853a6504cac1adf026d6b6e67f3214 100644 (file)
--- a/venncommand.cpp
+++ b/venncommand.cpp
@@ -8,14 +8,61 @@
  */
 
 #include "venncommand.h"
+#include "ace.h"
+#include "sobs.h"
+#include "chao1.h"
+#include "jackknife.h"
+#include "sharedsobscollectsummary.h"
+#include "sharedchao1.h"
+#include "sharedace.h"
+
 
 //**********************************************************************************************************************
 
 VennCommand::VennCommand(){
        try {
                globaldata = GlobalData::getInstance();
-               venn = new Venn();
                format = globaldata->getFormat();
+               validCalculator = new ValidCalculators();
+               
+               int i;
+               
+               if (format == "list") {
+                       for (i=0; i<globaldata->Estimators.size(); i++) {
+                               if (validCalculator->isValidCalculator("vennsingle", globaldata->Estimators[i]) == true) { 
+                                       if (globaldata->Estimators[i] == "sobs") { 
+                                               vennCalculators.push_back(new Sobs());
+                                       }else if (globaldata->Estimators[i] == "chao") { 
+                                               vennCalculators.push_back(new Chao1());
+                                       }else if (globaldata->Estimators[i] == "ace") {
+                                               convert(globaldata->getAbund(), abund);
+                                               if(abund < 5)
+                                                       abund = 10;
+                                               vennCalculators.push_back(new Ace(abund));
+                                       }else if (globaldata->Estimators[i] == "jack") {        
+                                               vennCalculators.push_back(new Jackknife());
+                                       }
+                               }
+                       }
+               }else {
+                       for (i=0; i<globaldata->Estimators.size(); i++) {
+                               if (validCalculator->isValidCalculator("vennshared", globaldata->Estimators[i]) == true) { 
+                                       if (globaldata->Estimators[i] == "sharedsobs") { 
+                                               vennCalculators.push_back(new SharedSobsCS());
+                                       }else if (globaldata->Estimators[i] == "sharedchao") { 
+                                               vennCalculators.push_back(new SharedChao1());
+                                       }else if (globaldata->Estimators[i] == "sharedace") { 
+                                               vennCalculators.push_back(new SharedAce());
+                                       }
+                               }
+                       }
+               }
+               
+               venn = new Venn();
+               
+               //reset calc for next command
+               globaldata->setCalc("");
+
                
        }
        catch(exception& e) {
@@ -41,6 +88,9 @@ int VennCommand::execute(){
        try {
                int count = 1;  
                
+               //if the users entered no valid calculators don't execute command
+               if (vennCalculators.size() == 0) { return 0; }
+               
                if (format == "sharedfile") {
                        //you have groups
                        read = new ReadPhilFile(globaldata->inputFileName);     
@@ -75,7 +125,7 @@ int VennCommand::execute(){
                                if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){                       
        
                                        cout << order->getLabel() << '\t' << count << endl;
-                                       venn->getPic(order);
+                                       venn->getPic(order, vennCalculators);
 
                                }
                                                
@@ -103,7 +153,7 @@ int VennCommand::execute(){
                                if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(ordersingle->getLabel()) == 1){                 
        
                                        cout << ordersingle->getLabel() << '\t' << count << endl;
-                                       venn->getPic(ordersingle);
+                                       venn->getPic(ordersingle, vennCalculators);
                                        
                                }