/**************************************************************************************************/
-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(){}
/**************************************************************************************************/
int Database::getLongestBase() { return longest+1; }
/**************************************************************************************************/
-