paralellized the indicator command

[mothur.git] / matrixoutputcommand.cpp

diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index adb145aecfd388a9eee5941e30d7bc31a8404358..780091027a66340b5ac94ff9480c792cba18281b 100644 (file)
--- a/matrixoutputcommand.cpp
+++ b/matrixoutputcommand.cpp
@@ -157,6 +157,7 @@ MatrixOutputCommand::MatrixOutputCommand(string option)  {
                                if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }else if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+                       else { m->setSharedFile(sharedfile); }
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  
@@ -597,7 +598,7 @@ int MatrixOutputCommand::driver(vector<SharedRAbundVector*> thisLookup, int star
                                                
                                                if (m->control_pressed) { return 1; }
                                                
-                                               seqDist temp(l, k, (1.0 - tempdata[0]));
+                                               seqDist temp(l, k, tempdata[0]);
                                                calcDists[i].push_back(temp);
                                        }
                                }