added read.shared, broke up globaldata a bit

[mothur.git] / rarefactcommand.cpp

diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index c2204e7a573969a2f4d1d80f41eb9defb3c53070..7e4ced55244665b4c3540f71491ce6dd4f003517 100644 (file)
--- a/rarefactcommand.cpp
+++ b/rarefactcommand.cpp
@@ -25,28 +25,34 @@ RareFactCommand::RareFactCommand(){
                globaldata = GlobalData::getInstance();
                string fileNameRoot;
                fileNameRoot = getRootName(globaldata->inputFileName);
+               validCalculator = new ValidCalculators();
+               
                int i;
-               for (i=0; i<globaldata->rareEstimators.size(); i++) {
-                       if (globaldata->rareEstimators[i] == "sobs") { 
-                               rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(fileNameRoot+"rarefaction")));
-                       }else if (globaldata->rareEstimators[i] == "chao") { 
-                               rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"r_chao")));
-                       }else if (globaldata->rareEstimators[i] == "ace") { 
-                               rDisplays.push_back(new RareDisplay(new Ace(), new ThreeColumnFile(fileNameRoot+"r_ace")));
-                       }else if (globaldata->rareEstimators[i] == "jack") { 
-                               rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"r_jack")));
-                       }else if (globaldata->rareEstimators[i] == "shannon") { 
-                               rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"r_shannon")));
-                       }else if (globaldata->rareEstimators[i] == "npshannon") { 
-                               rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+"r_npshannon")));
-                       }else if (globaldata->rareEstimators[i] == "simpson") { 
-                               rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"r_simpson")));
-                       }else if (globaldata->rareEstimators[i] == "bootstrap") { 
-                               rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+"r_bootstrap")));
+               for (i=0; i<globaldata->Estimators.size(); i++) {
+                       if (validCalculator->isValidCalculator("rarefaction", globaldata->Estimators[i]) == true) { 
+                               if (globaldata->Estimators[i] == "sobs") { 
+                                       rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(fileNameRoot+"rarefaction")));
+                               }else if (globaldata->Estimators[i] == "chao") { 
+                                       rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"r_chao")));
+                               }else if (globaldata->Estimators[i] == "ace") { 
+                                       rDisplays.push_back(new RareDisplay(new Ace(), new ThreeColumnFile(fileNameRoot+"r_ace")));
+                               }else if (globaldata->Estimators[i] == "jack") { 
+                                       rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"r_jack")));
+                               }else if (globaldata->Estimators[i] == "shannon") { 
+                                       rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"r_shannon")));
+                               }else if (globaldata->Estimators[i] == "npshannon") { 
+                                       rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+"r_npshannon")));
+                               }else if (globaldata->Estimators[i] == "simpson") { 
+                                       rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"r_simpson")));
+                               }else if (globaldata->Estimators[i] == "bootstrap") { 
+                                       rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+"r_bootstrap")));
+                               }
                        }
                }
-       
-       
+               
+               //reset calc for next command
+               globaldata->setCalc("");
+
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the RareFactCommand class Function RareFactCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -73,6 +79,10 @@ RareFactCommand::~RareFactCommand(){
 int RareFactCommand::execute(){
        try {
                int count = 1;
+               
+               //if the users entered no valid calculators don't execute command
+               if (rDisplays.size() == 0) { return 0; }
+
                read = new ReadPhilFile(globaldata->inputFileName);     
                read->read(&*globaldata);