fixed trim.seqs bug with qtrim parameter and added num=1 special case to database...

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 64bcd36764e044a911295870025095016be7fcc3..626659501a531db80f5193bef33e88793414a874 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -669,6 +669,21 @@ int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
                                                }
                                        }
                                        
+                                       //createdistance file from simMatrix
+                                       /*string o = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".dist";
+                                       ofstream outDist;
+                                       m->openOutputFile(o, outDist);
+                                       outDist << simMatrix.size() << endl;
+                                       for (int k = 0; k < simMatrix.size(); k++) {
+                                               outDist << thisLookup[k]->getGroup() << '\t';
+                                               for (int l = 0; l < k; l++) {
+                                                       outDist << (1.0-simMatrix[k][l]) << '\t';
+                                               }
+                                               outDist << endl;
+                                       }
+                                       outDist.close();*/
+
+                                       
                                        if (m->control_pressed) { return 1; }
                                        //creates tree from similarity matrix and write out file
                                        createTree();