rarefaction.shared() fixed bug

[mothur.git] / collectsharedcommand.cpp

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 434d4a44311f57300c42623c0b052cff012d9e10..1f5ed558985d4361a4145b9811d19f508b79a630 100644 (file)
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -28,32 +28,32 @@ CollectSharedCommand::CollectSharedCommand(){
                globaldata = GlobalData::getInstance();
                string fileNameRoot;
                fileNameRoot = getRootName(globaldata->inputFileName);
-               groupmap = globaldata->gGroupmap;
+               //groupmap = globaldata->gGroupmap;
                
                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", groupmap->namesOfGroups)));
+                               cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(fileNameRoot+"shared.chao")));
                        }else if (globaldata->sharedEstimators[i] == "sharedSobs") { 
-                               cDisplays.push_back(new CollectDisplay(new SharedSobs(), new SharedOneColumnFile(fileNameRoot+"shared.sobs", groupmap->namesOfGroups)));
+                               cDisplays.push_back(new CollectDisplay(new SharedSobs(), new SharedOneColumnFile(fileNameRoot+"shared.sobs")));
                        }else if (globaldata->sharedEstimators[i] == "sharedAce") { 
-                               cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace", groupmap->namesOfGroups)));
+                               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", groupmap->namesOfGroups)));
+                               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", groupmap->namesOfGroups)));
+                               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", groupmap->namesOfGroups)));
+                               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", groupmap->namesOfGroups)));
+                               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", groupmap->namesOfGroups)));
+                               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", groupmap->namesOfGroups)));
+                               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", groupmap->namesOfGroups)));
+                               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", groupmap->namesOfGroups)));
+                               cDisplays.push_back(new CollectDisplay(new SharedThetaN(), new SharedOneColumnFile(fileNameRoot+"shared.thetan")));
                        }
                }
        }