X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=database.cpp;h=f587f42f4440261934277d2adab1e8fe006f97ee;hp=153876f9e147e038a72074b490c8028033a308ce;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05

diff --git a/database.cpp b/database.cpp
index 153876f..f587f42 100644
--- 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;		}	
 
 /**************************************************************************************************/