changed random forest output filename

[mothur.git] / database.cpp

diff --git a/database.cpp b/database.cpp
index 534747ac9208df062efc2bf2149430ff417d4a72..f587f42f4440261934277d2adab1e8fe006f97ee 100644 (file)
--- a/database.cpp
+++ b/database.cpp
@@ -13,60 +13,14 @@
 
 /**************************************************************************************************/
 
-Database::Database(string fastaFileName){              //      This assumes that the template database is in fasta format, may 
-                                                                                               //      need to alter this in the future?
+Database::Database(){          
        longest = 0;
-       
-       ifstream fastaFile;
-       openInputFile(fastaFileName, fastaFile);
-       
-       mothurOutEndLine();
-       mothurOut("Reading in the " + fastaFileName + " template sequences...\t");      cout.flush();
-
-       //all of this is elsewhere already!
-       numSeqs=count(istreambuf_iterator<char>(fastaFile),istreambuf_iterator<char>(), '>');   //      count the number of
-       fastaFile.seekg(0);                                                                                                                                             //      sequences
-       
-       templateSequences.resize(numSeqs);
-       
-       string seqName, sequence;
-       for(int i=0;i<numSeqs;i++){
-               fastaFile >> seqName;
-               seqName = seqName.substr(1);
-               char letter;
-               string aligned;
-               
-               while(fastaFile && (letter=fastaFile.get()) != '>'){
-                       if(isprint(letter)){
-                               letter = toupper(letter);
-                               if(letter == 'U'){letter = 'T';}
-                               aligned += letter;
-                       }
-               }
-               templateSequences[i] = Sequence(seqName, aligned);
-               
-               //necessary because Sequence constructor by default sets whatever it reads to unaligned
-               //the setUnaligned function remove gap char.
-               templateSequences[i].setUnaligned(templateSequences[i].getUnaligned());
-               
-               if (templateSequences[i].getUnaligned().length() > longest)  { longest = templateSequences[i].getUnaligned().length(); }
-               
-               fastaFile.putback(letter);
-       }
-       
-       fastaFile.close();
-       //all of this is elsewhere already!
-       
-       mothurOut("DONE.");
-       mothurOutEndLine();     cout.flush();
-
+       numSeqs = 0;
+       m = MothurOut::getInstance();
 }
 /**************************************************************************************************/
 
-Database::~Database(){                                                                                                         
-
-               templateSequences.clear();
-}
+Database::~Database(){}
 
 /**************************************************************************************************/
 
@@ -78,4 +32,3 @@ float Database::getSearchScore()      {       return searchScore;             }       //      we're assuming that
 int Database::getLongestBase() {       return longest+1;               }       
 
 /**************************************************************************************************/
-