Initial revision

[mothur.git] / database.cpp

diff --git a/database.cpp b/database.cpp
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+/*
+ *  database.cpp
+ *  
+ *
+ *  Created by Pat Schloss on 12/16/08.
+ *  Copyright 2008 Patrick D. Schloss. All rights reserved.
+ *
+ */
+
+using namespace std;
+
+#include <string>
+#include <vector>
+#include <fstream>
+#include <iostream>
+
+#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();
+
+}
+
+/**************************************************************************************************/