fixed bug in summary.shared for groups

[mothur.git] / summarycommand.cpp

diff --git a/summarycommand.cpp b/summarycommand.cpp
index c6170d10263a0b1e35fa4c03e39e61fc016e0087..36a4e0efb5fc9fdbbe8587eca17886c8b5c55ea4 100644 (file)
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -22,26 +22,37 @@
 SummaryCommand::SummaryCommand(){
        try {
                globaldata = GlobalData::getInstance();
+               validCalculator = new ValidCalculators();
                int i;
-               for (i=0; i<globaldata->summaryEstimators.size(); i++) {
-                       if(globaldata->summaryEstimators[i] == "sobs"){
-                               sumCalculators.push_back(new Sobs());
-                       }else if(globaldata->summaryEstimators[i] == "chao"){
-                               sumCalculators.push_back(new Chao1());
-                       }else if(globaldata->summaryEstimators[i] == "ace"){
-                               sumCalculators.push_back(new Ace());
-                       }else if(globaldata->summaryEstimators[i] == "jack"){
-                               sumCalculators.push_back(new Jackknife());
-                       }else if(globaldata->summaryEstimators[i] == "shannon"){
-                               sumCalculators.push_back(new Shannon());
-                       }else if(globaldata->summaryEstimators[i] == "npshannon"){
-                               sumCalculators.push_back(new NPShannon());
-                       }else if(globaldata->summaryEstimators[i] == "simpson"){
-                               sumCalculators.push_back(new Simpson());
-                       }else if(globaldata->summaryEstimators[i] == "bootstrap"){
-                               sumCalculators.push_back(new Bootstrap());
+               
+               for (i=0; i<globaldata->Estimators.size(); i++) {
+                       if (validCalculator->isValidCalculator("summary", globaldata->Estimators[i]) == true) { 
+                               if(globaldata->Estimators[i] == "sobs"){
+                                       sumCalculators.push_back(new Sobs());
+                               }else if(globaldata->Estimators[i] == "chao"){
+                                       sumCalculators.push_back(new Chao1());
+                               }else if(globaldata->Estimators[i] == "ace"){
+                                       convert(globaldata->getAbund(), abund);
+                                       if(abund < 5)
+                                               abund = 10;
+                                       sumCalculators.push_back(new Ace(abund));
+                               }else if(globaldata->Estimators[i] == "jack"){
+                                       sumCalculators.push_back(new Jackknife());
+                               }else if(globaldata->Estimators[i] == "shannon"){
+                                       sumCalculators.push_back(new Shannon());
+                               }else if(globaldata->Estimators[i] == "npshannon"){
+                                       sumCalculators.push_back(new NPShannon());
+                               }else if(globaldata->Estimators[i] == "simpson"){
+                                       sumCalculators.push_back(new Simpson());
+                               }else if(globaldata->Estimators[i] == "bootstrap"){
+                                       sumCalculators.push_back(new Bootstrap());
+                               }
                        }
                }
+               
+               //reset calc for next command
+               globaldata->setCalc("");
+
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the SummaryCommand class Function SummaryCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -64,6 +75,10 @@ SummaryCommand::~SummaryCommand(){
 
 int SummaryCommand::execute(){
        try {
+       
+               //if the users entered no valid calculators don't execute command
+               if (sumCalculators.size() == 0) { return 0; }
+
                outputFileName = ((getRootName(globaldata->inputFileName)) + "summary");
                openOutputFile(outputFileName, outputFileHandle);
                outputFileHandle << "label";