changed random forest output filename

[mothur.git] / database.cpp

diff --git a/database.cpp b/database.cpp
index 5b93321a4c8b0f25915d479407f5152918d12f6a..f587f42f4440261934277d2adab1e8fe006f97ee 100644 (file)
--- a/database.cpp
+++ b/database.cpp
@@ -7,57 +7,28 @@
  *
  */
 
-using namespace std;
-
-
+#include "mothur.h"
 #include "sequence.hpp"
 #include "database.hpp"
 
 /**************************************************************************************************/
 
-Database::Database(string fastaFileName){              //      This assumes that the template database is in fasta format, may 
-                                                                                               //      need to alter this in the future?
-
-       ifstream fastaFile;
-       openInputFile(fastaFileName, fastaFile);
-
-       cout << endl << "Reading in the " << fastaFileName << " template sequences...\t";       cout.flush();
-
-       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++){
-//             templateSequences[i] = new Sequence();          //      We're storing the aligned template sequences as a vector of
-                                                                                                       //      pointers to Sequence objects
-               fastaFile >> seqName;
-//             templateSequences[i]->setName(seqName);
-               
-               char letter;
-               string aligned;
-               
-               while(fastaFile && (letter=fastaFile.get()) != '>'){
-                       if(isprint(letter)){
-                               letter = toupper(letter);
-                               if(letter == 'U'){letter = 'T';}
-                               aligned += letter;
-                       }
-               }
-               templateSequences[i] = new Sequence(seqName, aligned);
-//             templateSequences[i]->setAligned(aligned);      //      Obviously, we need the fully aligned template sequence
-//             templateSequences[i]->setUnaligned(aligned);//  We will also need the unaligned sequence for pairwise alignments
-               fastaFile.putback(letter);                                      //      and database searches
-       }
-       
-       fastaFile.close();
-       cout << "DONE." << endl;        cout.flush();
-
+Database::Database(){          
+       longest = 0;
+       numSeqs = 0;
+       m = MothurOut::getInstance();
 }
+/**************************************************************************************************/
+
+Database::~Database(){}
 
 /**************************************************************************************************/
 
 float Database::getSearchScore()       {       return searchScore;             }       //      we're assuming that the search is already done
 
+
+/**************************************************************************************************/
+
+int Database::getLongestBase() {       return longest+1;               }       
+
 /**************************************************************************************************/