*
*/
-using namespace std;
-
-
+#include "mothur.h"
#include "sequence.hpp"
#include "database.hpp"
ifstream fastaFile;
openInputFile(fastaFileName, fastaFile);
+
+ mothurOutEndLine();
+ mothurOut("Reading in the " + fastaFileName + " template sequences...\t"); cout.flush();
- 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
string seqName, sequence;
for(int i=0;i<numSeqs;i++){
-// templateSequences[i] = new Sequence(); // We're storing the aligned template sequences as a vector of
- // pointers to Sequence objects
fastaFile >> seqName;
-// templateSequences[i]->setName(seqName);
-
+ seqName = seqName.substr(1);
char letter;
string aligned;
aligned += letter;
}
}
- templateSequences[i] = new Sequence(seqName, aligned);
-// templateSequences[i]->setAligned(aligned); // Obviously, we need the fully aligned template sequence
-// templateSequences[i]->setUnaligned(aligned);// We will also need the unaligned sequence for pairwise alignments
- fastaFile.putback(letter); // and database searches
+ templateSequences[i] = Sequence(seqName, aligned);
+ fastaFile.putback(letter);
}
fastaFile.close();
- cout << "DONE." << endl; cout.flush();
+ //all of this is elsewhere already!
+
+ mothurOut("DONE.");
+ mothurOutEndLine(); cout.flush();
+
+}
+/**************************************************************************************************/
+
+Database::~Database(){
+ templateSequences.clear();
}
/**************************************************************************************************/