added binary file operations to mothurout class. added comment to sequence class...

[mothur.git] / getmetacommunitycommand.h

diff --git a/getmetacommunitycommand.h b/getmetacommunitycommand.h
index 2264c87b9af87c5f3363f5774116ff95bb691b8f..7697430cca6164b695ed92526dd190926ec1eb5e 100644 (file)
--- a/getmetacommunitycommand.h
+++ b/getmetacommunitycommand.h
@@ -22,14 +22,14 @@ public:
     ~GetMetaCommunityCommand(){}
     
     vector<string> setParameters();
-    string getCommandName()                    { return "get.metacommunity";           }
+    string getCommandName()                    { return "get.communitytype";           }
     string getCommandCategory()                { return "OTU-Based Approaches";         }
     
     string getOutputPattern(string);
     
        string getHelpString();
-    string getCitation() { return "http://www.mothur.org/wiki/Get.metacommunity"; }
-    string getDescription()            { return "brief description"; }
+    string getCitation() { return "Holmes I, Harris K, Quince C (2012) Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics. PLoS ONE 7(2): e30126. doi:10.1371/journal.pone.0030126 http://www.mothur.org/wiki/get.communitytype"; }
+    string getDescription()            { return "Assigns samples to bins using a Dirichlet multinomial mixture model"; }
     
     int execute();
     void help() { m->mothurOut(getHelpString()); }
@@ -146,7 +146,7 @@ static DWORD WINAPI MyMetaCommunityThreadFunction(LPVOID lpParam){
             pDataArray->outputNames.push_back(pDataArray->matrix[i]);
             
             findQ->printZMatrix(pDataArray->matrix[i], pDataArray->m->getGroups());
-            findQ->printRelAbund(pDataArray->relabunds[i], pDataArray->m->currentBinLabels);
+            findQ->printRelAbund(pDataArray->relabunds[i], pDataArray->m->currentSharedBinLabels);
             
             if(pDataArray->optimizegap != -1 && (numPartitions - pDataArray->minPartition) >= pDataArray->optimizegap && numPartitions >= pDataArray->minpartitions){ break; }