added read.shared, broke up globaldata a bit

[mothur.git] / collectsharedcommand.cpp

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index a6479da20d4e5b52a09cdb06d76676f26ed583e4..217045a4a1fc5dc0c83986f3b3a0345b755e1f6c 100644 (file)
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -28,34 +28,41 @@ CollectSharedCommand::CollectSharedCommand(){
                globaldata = GlobalData::getInstance();
                string fileNameRoot;
                fileNameRoot = getRootName(globaldata->inputFileName);
-               //groupmap = globaldata->gGroupmap;
+               format = globaldata->getFormat();
+               validCalculator = new ValidCalculators();
                
                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+"shared.chao")));
-                       }else if (globaldata->sharedEstimators[i] == "sharedSobs") { 
-                               cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(fileNameRoot+"shared.sobs")));
-                       }else if (globaldata->sharedEstimators[i] == "sharedAce") { 
-                               cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace")));
-                       }else if (globaldata->sharedEstimators[i] == "sharedJabund") {  
-                               cDisplays.push_back(new CollectDisplay(new SharedJAbund(), new SharedOneColumnFile(fileNameRoot+"shared.jabund")));
-                       }else if (globaldata->sharedEstimators[i] == "sharedSorensonAbund") { 
-                               cDisplays.push_back(new CollectDisplay(new SharedSorAbund(), new SharedOneColumnFile(fileNameRoot+"shared.sorabund")));
-                       }else if (globaldata->sharedEstimators[i] == "sharedJclass") { 
-                               cDisplays.push_back(new CollectDisplay(new SharedJclass(), new SharedOneColumnFile(fileNameRoot+"shared.jclass")));
-                       }else if (globaldata->sharedEstimators[i] == "sharedSorClass") { 
-                               cDisplays.push_back(new CollectDisplay(new SharedSorClass(), new SharedOneColumnFile(fileNameRoot+"shared.sorclass")));
-                       }else if (globaldata->sharedEstimators[i] == "sharedJest") { 
-                               cDisplays.push_back(new CollectDisplay(new SharedJest(), new SharedOneColumnFile(fileNameRoot+"shared.jest")));
-                       }else if (globaldata->sharedEstimators[i] == "sharedSorEst") { 
-                               cDisplays.push_back(new CollectDisplay(new SharedSorEst(), new SharedOneColumnFile(fileNameRoot+"shared.sorest")));
-                       }else if (globaldata->sharedEstimators[i] == "SharedThetaYC") { 
-                               cDisplays.push_back(new CollectDisplay(new SharedThetaYC(), new SharedOneColumnFile(fileNameRoot+"shared.thetayc")));
-                       }else if (globaldata->sharedEstimators[i] == "SharedThetaN") { 
-                               cDisplays.push_back(new CollectDisplay(new SharedThetaN(), new SharedOneColumnFile(fileNameRoot+"shared.thetan")));
+               for (i=0; i<globaldata->Estimators.size(); i++) {
+                       if (validCalculator->isValidCalculator("shared", globaldata->Estimators[i]) == true) { 
+                               if (globaldata->Estimators[i] == "sharedchao") { 
+                                       cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(fileNameRoot+"shared.chao")));
+                               }else if (globaldata->Estimators[i] == "sharedsobs") { 
+                                       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")));
+                               }
                        }
                }
+               
+               //reset calc for next command
+               globaldata->setCalc("");
+
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function CollectSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -82,12 +89,25 @@ CollectSharedCommand::~CollectSharedCommand(){
 int CollectSharedCommand::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 (cDisplays.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){
                
@@ -102,14 +122,20 @@ int CollectSharedCommand::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<cDisplays.size();i++){    delete cDisplays[i];    }