+SequenceDB::SequenceDB(ifstream& filehandle) {
+ try{
+ string name, sequence, line;
+ sequence = "";
+ int c;
+ string temp;
+
+
+ //read through file
+ while ((c = filehandle.get()) != EOF) {
+ name = ""; sequence = "";
+ //is this a name
+ if (c == '>') {
+ name = readName(filehandle);
+ sequence = readSequence(filehandle);
+ }else { cout << "Error fasta in your file. Please correct." << endl; }
+
+ //input sequence info into sequencedb
+ Sequence newSequence(name, sequence);
+ data.push_back(newSequence);
+
+ //takes care of white space
+ gobble(filehandle);
+ }
+
+ filehandle.close();
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SequenceDB class Function SequenceDB. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SequenceDB class function SequenceDB. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/*******************************************************************************/
+string SequenceDB::readName(ifstream& in) {
+ try{
+ string name = "";
+ int c;
+ string temp;
+
+ while ((c = in.get()) != EOF) {
+ //if c is not a line return
+ if (c != 10) {
+ name += c;
+ }else { break; }
+ }
+
+ return name;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SequenceDB class Function readName. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SequenceDB class function readName. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/*******************************************************************************/
+string SequenceDB::readSequence(ifstream& in) {
+ try{
+ string sequence = "";
+ string line;
+ int pos, c;
+
+ while (!in.eof()) {
+ //save position in file in case next line is a new name.
+ pos = in.tellg();
+ line = "";
+ in >> line;
+ //if you are at a new name
+ if (line[0] == '>') {
+ //put file pointer back since you are now at a new name
+ in.seekg(pos, ios::beg);
+ c = in.get(); //because you put it back to a newline char
+ break;
+ }else { sequence += line; }
+ }
+
+ return sequence;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SequenceDB class Function readSequence. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SequenceDB class function readSequence. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}