added shared file type to get.groups and remove.groups

[mothur.git] / preclustercommand.cpp

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index 9299a6c6fc26e222869d515eb3fc362d0671bced..3f6e0c975750d7e6bd69845a32e11e7e20b2b68a 100644 (file)
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -124,6 +124,7 @@ PreClusterCommand::PreClusterCommand(string option) {
                                else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }
                        else if (fastafile == "not open") { abort = true; }     
+                       else { m->setFastaFile(fastafile); }
                        
                        //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"){  
@@ -136,7 +137,7 @@ PreClusterCommand::PreClusterCommand(string option) {
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not found") { namefile =  "";  }
                        else if (namefile == "not open") { abort = true; }      
-                       else {  readNameFile();  }
+                       else {  readNameFile();  m->setNameFile(namefile); }
                        
                        string temp     = validParameter.validFile(parameters, "diffs", false);                         if(temp == "not found"){        temp = "1"; }
                        convert(temp, diffs); 
@@ -225,7 +226,7 @@ int PreClusterCommand::execute(){
                
                m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); 
                
-               if (m->control_pressed) { remove(newFastaFile.c_str()); remove(newNamesFile.c_str()); return 0; }
+               if (m->control_pressed) { m->mothurRemove(newFastaFile); m->mothurRemove(newNamesFile); return 0; }
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();