created mothurOut class to handle logfiles

[mothur.git] / alignmentdb.cpp

diff --git a/alignmentdb.cpp b/alignmentdb.cpp
index 5c758ecebb249710be141813a734eb571b88da32..59405efe05963c8d153828d7f8f56976c440f197 100644 (file)
--- a/alignmentdb.cpp
+++ b/alignmentdb.cpp
@@ -16,13 +16,14 @@
 /**************************************************************************************************/
 AlignmentDB::AlignmentDB(string fastaFileName, string method, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch){              //      This assumes that the template database is in fasta format, may 
        try {                                                                                   //      need to alter this in the future?
+               m = MothurOut::getInstance();
                longest = 0;
 
                ifstream fastaFile;
                openInputFile(fastaFileName, fastaFile);
                
-               mothurOutEndLine();
-               mothurOut("Reading in the " + fastaFileName + " template sequences...\t");      cout.flush();
+               m->mothurOutEndLine();
+               m->mothurOut("Reading in the " + fastaFileName + " template sequences...\t");   cout.flush();
                
                while (!fastaFile.eof()) {
                        Sequence temp(fastaFile);  gobble(fastaFile);
@@ -39,8 +40,8 @@ AlignmentDB::AlignmentDB(string fastaFileName, string method, int kmerSize, floa
                fastaFile.close();
                //all of this is elsewhere already!
                
-               mothurOut("DONE.");
-               mothurOutEndLine();     cout.flush();
+               m->mothurOut("DONE.");
+               m->mothurOutEndLine();  cout.flush();
                
                //in case you delete the seqs and then ask for them
                emptySequence = Sequence();
@@ -61,8 +62,8 @@ AlignmentDB::AlignmentDB(string fastaFileName, string method, int kmerSize, floa
                else if(method == "suffix")             {       search = new SuffixDB(numSeqs);                                                         }
                else if(method == "blast")              {       search = new BlastDB(gapOpen, gapExtend, match, misMatch);      }
                else {
-                       mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8.");
-                       mothurOutEndLine();
+                       m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8.");
+                       m->mothurOutEndLine();
                        search = new KmerDB(fastaFileName, 8);
                }
                
@@ -82,7 +83,7 @@ AlignmentDB::AlignmentDB(string fastaFileName, string method, int kmerSize, floa
                search->setNumSeqs(numSeqs);
        }
        catch(exception& e) {
-               errorOut(e, "AlignmentDB", "AlignmentDB");
+               m->errorOut(e, "AlignmentDB", "AlignmentDB");
                exit(1);
        }
 }
@@ -99,7 +100,7 @@ Sequence AlignmentDB::findClosestSequence(Sequence* seq) {
                
        }
        catch(exception& e) {
-               errorOut(e, "AlignmentDB", "findClosestSequence");
+               m->errorOut(e, "AlignmentDB", "findClosestSequence");
                exit(1);
        }
 }