X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=database.cpp;h=f587f42f4440261934277d2adab1e8fe006f97ee;hp=f84c9e1bd8f3c3f2111cde09657966f5c787b1eb;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=1244c4907c07baea86b0f0676d098a29d2e95a39

diff --git a/database.cpp b/database.cpp
index f84c9e1..f587f42 100644
--- a/database.cpp
+++ b/database.cpp
@@ -13,73 +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);
-	}*/
-	
-	while (!fastaFile.eof()) {
-		Sequence temp(fastaFile);
-		
-		templateSequences.push_back(temp);
-		
-		//save longest base
-		if (temp.getUnaligned().length() > longest)  { longest = temp.getUnaligned().length(); }
-		
-		gobble(fastaFile);
-	}
-	
-	numSeqs = templateSequences.size();
-	
-	fastaFile.close();
-	//all of this is elsewhere already!
-	
-	mothurOut("DONE.");
-	mothurOutEndLine();	cout.flush();
-
+	numSeqs = 0;
+	m = MothurOut::getInstance();
 }
 /**************************************************************************************************/
 
-Database::~Database(){														
-
-		templateSequences.clear();
-}
+Database::~Database(){}
 
 /**************************************************************************************************/
 
@@ -91,5 +32,3 @@ float Database::getSearchScore()	{	return searchScore;		}	//	we're assuming that
 int Database::getLongestBase()	{	return longest+1;		}	
 
 /**************************************************************************************************/
-
-