added logfile feature

[mothur.git] / blastdb.cpp

diff --git a/blastdb.cpp b/blastdb.cpp
index e442fa229b49e08d5c7b80495d3c8a10d75d9430..0cba83323db70f0748e4e6a5ec0d902ee8294945 100644 (file)
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -19,7 +19,7 @@ gapOpen(gO), gapExtend(gE), match(m), misMatch(mM) {
        
        globaldata = GlobalData::getInstance();
        
-       cout << "Generating the temporary BLAST database...\t"; cout.flush();
+       mothurOut("Generating the temporary BLAST database...\t");      cout.flush();
 
        int randNumber = rand();
        dbFileName = toString(randNumber) + ".template.unaligned.fasta";
@@ -42,7 +42,7 @@ gapOpen(gO), gapExtend(gE), match(m), misMatch(mM) {
        string formatdbCommand = path + "blast/bin/formatdb -p F -o T -i " + dbFileName;        //      format the database, -o option gives us the ability
        system(formatdbCommand.c_str());                                                                //      to get the right sequence names, i think. -p F
                                                                                                                                        //      option tells formatdb that seqs are DNA, not prot
-       cout << "DONE." << endl << endl;        cout.flush();
+       mothurOut("DONE."); mothurOutEndLine(); mothurOutEndLine(); cout.flush();
        emptySequence = Sequence();
        emptySequence.setName("no_match");
        emptySequence.setUnaligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");