added dist.shared command

[mothur.git] / matrixoutputcommand.cpp

diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index 7b9ea960f3c6b979463cacc9e363ba5a6006ae44..a5e7a4ede8b0fbb77724bba444516251f353c12c 100644 (file)
--- a/matrixoutputcommand.cpp
+++ b/matrixoutputcommand.cpp
@@ -125,8 +125,8 @@ int MatrixOutputCommand::execute(){
                                                                
                                                                data = matrixCalculators[i]->getValues(subset); //saves the calculator outputs
                                                                //save values in similarity matrix
-                                                               simMatrix[k][l] = data[0];
-                                                               simMatrix[l][k] = data[0];
+                                                               simMatrix[k][l] = 1.0 - data[0];  //convert similiarity to distance
+                                                               simMatrix[l][k] = 1.0 - data[0];  //convert similiarity to distance
                                                        }
                                                }
                                        }