changed random forest output filename

[mothur.git] / database.cpp

diff --git a/database.cpp b/database.cpp
index 153876f9e147e038a72074b490c8028033a308ce..f587f42f4440261934277d2adab1e8fe006f97ee 100644 (file)
--- a/database.cpp
+++ b/database.cpp
@@ -7,56 +7,28 @@
  *
  */
 
-using namespace std;
-
-#include <string>
-#include <vector>
-#include <fstream>
-#include <iostream>
-
+#include "mothur.h"
 #include "sequence.hpp"
 #include "database.hpp"
 
 /**************************************************************************************************/
 
-Database::Database(string fastaFileName){
-       
-       ifstream fastaFile(fastaFileName.c_str());
-       if(!fastaFile) {
-               cerr << "Error: Could not open " << fastaFileName << endl;
-               exit(1);
-       }
-       cout << endl << "Reading in the " << fastaFileName << " template sequences...\t";       cout.flush();
-
-       numSeqs=count(istreambuf_iterator<char>(fastaFile),istreambuf_iterator<char>(), '>');
-       fastaFile.seekg(0);
-       
-       templateSequences.resize(numSeqs);
-       
-       string seqName, sequence;
-       for(int i=0;i<numSeqs;i++){
-               templateSequences[i] = new Sequence();
-               
-               fastaFile >> seqName;
-               templateSequences[i]->setName(seqName);
-               
-               char letter;
-               string aligned;
-               
-               while(fastaFile && (letter=fastaFile.get()) != '>'){
-                       if(isprint(letter)){
-                               letter = toupper(letter);
-                               aligned += letter;
-                       }
-               }
-               templateSequences[i]->setAligned(aligned);
-               templateSequences[i]->setUnaligned(aligned);
-               fastaFile.putback(letter);
-       }
-       
-       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;               }       
 
 /**************************************************************************************************/