X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=database.cpp;h=f587f42f4440261934277d2adab1e8fe006f97ee;hp=44e663bde3c9a9d9bd40895ef1a600779594ce21;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=544469443afe44920bdf279aefd26d29534cabaf

diff --git a/database.cpp b/database.cpp
index 44e663b..f587f42 100644
--- a/database.cpp
+++ b/database.cpp
@@ -7,55 +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();
-
-	//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] = new Sequence(seqName, aligned);
-		fastaFile.putback(letter);
-	}
-	
-	fastaFile.close();
-	//all of this is elsewhere already!
-	
-	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;		}	
+
 /**************************************************************************************************/