added read.shared, broke up globaldata a bit

[mothur.git] / summarysharedcommand.cpp

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index c451ef7aeb6ead4065f55a18bea99cb1840b530f..f31f7e10e1f19e47781d2d47dd9db09ebafa05cf 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -25,33 +25,43 @@
 SummarySharedCommand::SummarySharedCommand(){
        try {
                globaldata = GlobalData::getInstance();
+               outputFileName = ((getRootName(globaldata->inputFileName)) + "shared.summary");
+               openOutputFile(outputFileName, outputFileHandle);
+               format = globaldata->getFormat();
+               validCalculator = new ValidCalculators();
                
                int i;
-               for (i=0; i<globaldata->sharedSummaryEstimators.size(); i++) {
-                       if (globaldata->sharedSummaryEstimators[i] == "sharedSobs") { 
-                               sumCalculators.push_back(new SharedSobsCS());
-                       }else if (globaldata->sharedSummaryEstimators[i] == "sharedChao") { 
-                               sumCalculators.push_back(new SharedChao1());
-                       }else if (globaldata->sharedSummaryEstimators[i] == "sharedAce") { 
-                               sumCalculators.push_back(new SharedAce());
-                       }else if (globaldata->sharedSummaryEstimators[i] == "sharedJabund") {   
-                               sumCalculators.push_back(new SharedJAbund());
-                       }else if (globaldata->sharedSummaryEstimators[i] == "sharedSorensonAbund") { 
-                               sumCalculators.push_back(new SharedSorAbund());
-                       }else if (globaldata->sharedSummaryEstimators[i] == "sharedJclass") { 
-                               sumCalculators.push_back(new SharedJclass());
-                       }else if (globaldata->sharedSummaryEstimators[i] == "sharedSorClass") { 
-                               sumCalculators.push_back(new SharedSorClass());
-                       }else if (globaldata->sharedSummaryEstimators[i] == "sharedJest") { 
-                               sumCalculators.push_back(new SharedJest());
-                       }else if (globaldata->sharedSummaryEstimators[i] == "sharedSorEst") { 
-                               sumCalculators.push_back(new SharedSorEst());
-                       }else if (globaldata->sharedSummaryEstimators[i] == "SharedThetaYC") { 
-                               sumCalculators.push_back(new SharedThetaYC());
-                       }else if (globaldata->sharedSummaryEstimators[i] == "SharedThetaN") { 
-                               sumCalculators.push_back(new SharedThetaN());
+               for (i=0; i<globaldata->Estimators.size(); i++) {
+                       if (validCalculator->isValidCalculator("sharedsummary", globaldata->Estimators[i]) == true) { 
+                               if (globaldata->Estimators[i] == "sharedsobs") { 
+                                       sumCalculators.push_back(new SharedSobsCS());
+                               }else if (globaldata->Estimators[i] == "sharedchao") { 
+                                       sumCalculators.push_back(new SharedChao1());
+                               }else if (globaldata->Estimators[i] == "sharedace") { 
+                                       sumCalculators.push_back(new SharedAce());
+                               }else if (globaldata->Estimators[i] == "sharedjabund") {        
+                                       sumCalculators.push_back(new SharedJAbund());
+                               }else if (globaldata->Estimators[i] == "sharedsorensonabund") { 
+                                       sumCalculators.push_back(new SharedSorAbund());
+                               }else if (globaldata->Estimators[i] == "sharedjclass") { 
+                                       sumCalculators.push_back(new SharedJclass());
+                               }else if (globaldata->Estimators[i] == "sharedsorclass") { 
+                                       sumCalculators.push_back(new SharedSorClass());
+                               }else if (globaldata->Estimators[i] == "sharedjest") { 
+                                       sumCalculators.push_back(new SharedJest());
+                               }else if (globaldata->Estimators[i] == "sharedsorest") { 
+                                       sumCalculators.push_back(new SharedSorEst());
+                               }else if (globaldata->Estimators[i] == "sharedthetayc") { 
+                                       sumCalculators.push_back(new SharedThetaYC());
+                               }else if (globaldata->Estimators[i] == "sharedthetan") { 
+                                       sumCalculators.push_back(new SharedThetaN());
+                               }
                        }
                }
+               
+               //reset calc for next command
+               globaldata->setCalc("");
+
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function SummarySharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -73,23 +83,34 @@ SummarySharedCommand::~SummarySharedCommand(){
 
 int SummarySharedCommand::execute(){
        try {
-               outputFileName = ((getRootName(globaldata->inputFileName)) + "shared.summary");
-               openOutputFile(outputFileName, outputFileHandle);
-       
-               read = new ReadPhilFile(globaldata->inputFileName);     
-               read->read(&*globaldata); 
+               int count = 1;  
                
+               //if the users entered no valid calculators don't execute command
+               if (sumCalculators.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();
+               }
+               
+               //output estimator names as column headers
                outputFileHandle << "label" <<'\t' << "comparison" << '\t'; 
                for(int i=0;i<sumCalculators.size();i++){
                        outputFileHandle << '\t' << sumCalculators[i]->getName();
                }
                outputFileHandle << endl;
-               
-               SharedList = globaldata->gSharedList;
-               input = globaldata->ginput;
-               order = SharedList->getSharedOrderVector();
-               
-               int count = 1;
+
                while(order != NULL){
                
                        if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){                       
@@ -115,13 +136,19 @@ int SummarySharedCommand::execute(){
                                }
                        }
                
-                       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++;
                }
        
                return 0;