added read.shared, broke up globaldata a bit

[mothur.git] / rarefactsharedcommand.cpp

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index 5e36299505246ecbdbae8c64822a59e916f54dcc..45c2e2ebbdfc0004a8e1d6acb551649fe82b1239 100644 (file)
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -17,13 +17,21 @@ RareFactSharedCommand::RareFactSharedCommand(){
                globaldata = GlobalData::getInstance();
                string fileNameRoot;
                fileNameRoot = getRootName(globaldata->inputFileName);
+               format = globaldata->getFormat();
+               validCalculator = new ValidCalculators();
                                
                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+"shared.rarefaction", "")));
+               for (i=0; i<globaldata->Estimators.size(); i++) {
+                       if (validCalculator->isValidCalculator("sharedrarefaction", globaldata->Estimators[i]) == true) { 
+                               if (globaldata->Estimators[i] == "sharedobserved") { 
+                                       rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));
+                               }
                        }
                }
+               
+               //reset calc for next command
+               globaldata->setCalc("");
+
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function RareFactSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -50,12 +58,25 @@ RareFactSharedCommand::~RareFactSharedCommand(){
 int RareFactSharedCommand::execute(){
        try {
                int count = 1;
-               read = new ReadPhilFile(globaldata->inputFileName);     
-               read->read(&*globaldata); 
                
-               input = globaldata->ginput;
-               SharedList = globaldata->gSharedList;
-               order = SharedList->getSharedOrderVector();
+               //if the users entered no valid calculators don't execute command
+               if (rDisplays.size() == 0) { return 0; }
+
+               if (format == "sharedfile") {
+                       read = new ReadPhilFile(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;
+                       SharedList = globaldata->gSharedList;
+                       order = SharedList->getSharedOrderVector();
+               }
                
                while(order != NULL){
                
@@ -71,14 +92,20 @@ int RareFactSharedCommand::execute(){
                                cout << order->getLabel() << '\t' << count << endl;
                        }
                        
-                       SharedList = input->getSharedListVector(); //get new list vector to process
-                       if (SharedList != NULL) {
-                               order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
-                               count++;
+                       //get next line to process
+                       if (format == "sharedfile") {
+                               order = input->getSharedOrderVector();
                        }else {
-                               break;
+                               //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;
+                               }
                        }
-               
+                       
+                       count++;
                }
        
                for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }