paralellized the indicator command

[mothur.git] / summarysharedcommand.cpp

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index 30761e10d4a3048d1af36071471865bd793e28b7..b3b4b1869f4368c3c7555d5a711e95acb54c9283 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -161,7 +161,7 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
                                sharedfile = m->getSharedFile(); 
                                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 { m->setSharedFile(sharedfile); }
                        
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
@@ -580,7 +580,7 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
                                                        ifstream intemp;
                                                        m->openInputFile(tempdistFileName, intemp);
                                                        
-                                                       for (int i = 0; i < calcDists.size(); i++) {
+                                                       for (int k = 0; k < calcDists.size(); k++) {
                                                                int size = 0;
                                                                intemp >> size; m->gobble(intemp);
                                                                        
@@ -592,7 +592,7 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
                                                                        intemp >> seq1 >> seq2 >> dist;   m->gobble(intemp);
                                                                        
                                                                        seqDist tempDist(seq1, seq2, dist);
-                                                                       calcDists[i].push_back(tempDist);
+                                                                       calcDists[k].push_back(tempDist);
                                                                }
                                                        }
                                                        intemp.close();
@@ -733,7 +733,7 @@ int SummarySharedCommand::driver(vector<SharedRAbundVector*> thisLookup, int sta
                                        outputFileHandle << '\t';
                                        sumCalculators[i]->print(outputFileHandle);
                                        
-                                       seqDist temp(l, k, (1.0 - tempdata[0]));
+                                       seqDist temp(l, k, tempdata[0]);
                                        calcDists[i].push_back(temp);
                                }
                                outputFileHandle << endl;