added count file to get.groups and remove.groups. added shortcut parameter to classif...

[mothur.git] / classify.cpp

diff --git a/classify.cpp b/classify.cpp
index 212e563f94c4ae7af3ba0916d1040afd9b0e11fa..f44e66c359873f6830dac72d99fb1727a73c27ad 100644 (file)
--- a/classify.cpp
+++ b/classify.cpp
@@ -200,7 +200,8 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                                }
                                fastaFile.close();
 
-                               database->generateDB();
+                if ((method == "kmer") && (!shortcuts)) {;} //don't print
+                else {database->generateDB(); }
                                
                        }else if ((method == "kmer") && (!needToGenerate)) {    
                                ifstream kmerFileTest(kmerDBName.c_str());
@@ -260,9 +261,6 @@ int Classify::readTaxonomy(string file) {
                MPI_File inMPI;
                MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
                MPI_Comm_size(MPI_COMM_WORLD, &processors);
-
-               //char* inFileName = new char[file.length()];
-               //memcpy(inFileName, file.c_str(), file.length());
                
                char inFileName[1024];
                strcpy(inFileName, file.c_str());