added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / otuhierarchycommand.cpp

diff --git a/otuhierarchycommand.cpp b/otuhierarchycommand.cpp
index cc5703223c7db32f31a2bf6db21d256145100f06..2f99aa6091452933f6796f21aa043449bfce1dd4 100644 (file)
--- a/otuhierarchycommand.cpp
+++ b/otuhierarchycommand.cpp
@@ -110,6 +110,7 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option) {
                                        abort = true;
                                }
                        }else if (listFile == "not open") { abort = true; }     
+                       else { m->setListFile(listFile); }
                        
                        //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"){  
@@ -185,7 +186,7 @@ int OtuHierarchyCommand::execute(){
                //go through each bin in "big" otu and output the bins in "little" otu which created it
                for (int i = 0; i < lists[1].getNumBins(); i++) {
                
-                       if (m->control_pressed) { outputTypes.clear(); out.close(); remove(outputFileName.c_str()); return 0; }
+                       if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(outputFileName); return 0; }
                        
                        string names = lists[1].get(i);
                        
@@ -218,7 +219,7 @@ int OtuHierarchyCommand::execute(){
                
                out.close();
                
-               if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0; }
+               if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); return 0; }
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Name: "); m->mothurOutEndLine();