* Mothur
*
* Created by Thomas Ryabin on 4/13/09.
- * Copyright 2009 __MyCompanyName__. All rights reserved.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
/***********************************************************************/
SequenceDB::SequenceDB() {}
+/***********************************************************************/
+//the clear function free's the memory
+SequenceDB::~SequenceDB() { clear(); }
/***********************************************************************/
SequenceDB::SequenceDB(int newSize) {
- data.resize(newSize);
+ data.resize(newSize, Sequence());
}
/***********************************************************************/
-SequenceDB::SequenceDB(ifstream&) {}
+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);
+ }
+}
/***********************************************************************/
/***********************************************************************/
void SequenceDB::set(int index, string newUnaligned) {
- Sequence newSeq(data[index].getName(), newUnaligned);
- data[index] = newSeq;
+ try {
+ data[index] = Sequence(data[index].getName(), newUnaligned);
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SequenceDB class Function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SequenceDB class function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
}
/***********************************************************************/
void SequenceDB::set(int index, Sequence newSeq) {
- data[index] = newSeq;
+ try {
+ data[index] = newSeq;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SequenceDB class Function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SequenceDB class function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
}
/***********************************************************************/
/***********************************************************************/
-void SequenceDB::changeSize(int newSize) {
- data.resize(newSize);
+void SequenceDB::resize(int newSize) {
+ try {
+ data.resize(newSize);
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SequenceDB class Function resize. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SequenceDB class function resize. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
}
/***********************************************************************/
void SequenceDB::clear() {
- data.clear();
+ try {
+ data.clear();
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SequenceDB class Function clear. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SequenceDB class function clear. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
}
/***********************************************************************/
/***********************************************************************/
void SequenceDB::print(ostream& out) {
- for(int i = 0; i < data.size(); i++)
- data[i].printSequence(out);
+ try {
+ for(int i = 0; i < data.size(); i++) {
+ data[i].printSequence(out);
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SequenceDB class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SequenceDB class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
}
/***********************************************************************/
-void SequenceDB::add(Sequence newSequence) {
+void SequenceDB::push_back(Sequence newSequence) {
try {
data.push_back(newSequence);
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the RAbundVector class Function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "Standard Error: " << e.what() << " has occurred in the SequenceDB class Function add. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
catch(...) {
- cout << "An unknown error has occurred in the RAbundVector class function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "An unknown error has occurred in the SequenceDB class function add. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
-}
\ No newline at end of file
+}
+
+/***********************************************************************/
+
projects / mothur.git / blobdiff