added count file to trim.seqs, get.groups, get.lineage, get.seqs, heatmap.sim, list...

[mothur.git] / classify.cpp

diff --git a/classify.cpp b/classify.cpp
index 212e563f94c4ae7af3ba0916d1040afd9b0e11fa..459c90f9ddd769628b0fc9061e7bd504a88b2900 100644 (file)
--- a/classify.cpp
+++ b/classify.cpp
@@ -61,7 +61,8 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                                        names.push_back(temp.getName());
                                        database->addSequence(temp);    
                                }
-                               database->generateDB();
+                               if ((method == "kmer") && (!shortcuts)) {;} //don't print
+                else {database->generateDB(); }
                        }else if ((method == "kmer") && (!needToGenerate)) {    
                                ifstream kmerFileTest(kmerDBName.c_str());
                                database->readKmerDB(kmerFileTest);     
@@ -200,7 +201,8 @@ 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 +262,6 @@ 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());