try {
string name, sequence, line;
sequence = "";
-
- getline(in, line);
- name = line.substr(1, line.length()); //rips off '>'
-
+ int c;
+ string temp;
+
+
//read through file
- while (getline(in, line)) {
- if (isalnum(line.at(0))){ //if it's a sequence line
- sequence += line;
- }
- else{
- //input sequence info into map
- it = data.find(sequence);
- if (it == data.end()) { //it's unique.
- data[sequence].groupname = name; //group name will be the name of the first duplicate sequence found.
- data[sequence].groupnumber = 1;
- data[sequence].names = name;
- }else { // its a duplicate.
- data[sequence].names += "," + name;
- data[sequence].groupnumber++;
- }
- name = (line.substr(1, (line.npos))); //The line you just read is a new name so rip off '>'
- sequence = "";
- }
+ while ((c = in.get()) != EOF) {
+ name = ""; sequence = "";
+ //is this a name
+ if (c == '>') {
+ name = readName(in);
+ sequence = readSequence(in);
+ }else { cout << "Error fasta in your file. Please correct." << endl; }
+
+ //store info in map
+ //input sequence info into map
+ seqmap[name] = sequence;
+ it = data.find(sequence);
+ if (it == data.end()) { //it's unique.
+ data[sequence].groupname = name; //group name will be the name of the first duplicate sequence found.
+ data[sequence].groupnumber = 1;
+ data[sequence].names = name;
+ }else { // its a duplicate.
+ data[sequence].names += "," + name;
+ data[sequence].groupnumber++;
+ }
+
+ gobble(in);
}
-
- //store last sequence and name info.
- it = data.find(sequence);
- if (it == data.end()) { //it's unique.
- data[sequence].groupname = name; //group name will be the name of the first duplicate sequence found.
- data[sequence].groupnumber = 1;
- data[sequence].names = name;
- }else { // its a duplicate.
- data[sequence].names += "," + name;
- data[sequence].groupnumber++;
- }
+
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the FastaMap class Function readFastaFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
}
}
/*******************************************************************************/
+string FastaMap::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 FastaMap class Function readName. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the FastaMap class function readName. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/*******************************************************************************/
+string FastaMap::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 FastaMap class Function readSequence. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the FastaMap class function readSequence. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/*******************************************************************************/
string FastaMap::getGroupName(string seq) { //pass a sequence name get its group
return data[seq].groupname;
}
return data[seq].groupnumber;
}
/*******************************************************************************/
-void FastaMap::push_back(string seq, string Name) {//sequencename, name
- data[seq].groupname = Name;
- data[seq].names = Name;
-}
-/*******************************************************************************/
-void FastaMap::set(string seq, string groupName, string Names) {
- data[seq].groupname = groupName;
- data[seq].names = Names;
-}
+string FastaMap::getSequence(string name) {
+ it2 = seqmap.find(name);
+ if (it2 == seqmap.end()) { //it's not found
+ return "not found";
+ }else { // found it
+ return it2->second;
+ }
+}
/*******************************************************************************/
-void FastaMap::clear() { //clears out data
- data.clear();
+void FastaMap::push_back(string name, string seq) {
+ it = data.find(seq);
+ if (it == data.end()) { //it's unique.
+ data[seq].groupname = name; //group name will be the name of the first duplicate sequence found.
+ data[seq].groupnumber = 1;
+ data[seq].names = name;
+ }else { // its a duplicate.
+ data[seq].names += "," + name;
+ data[seq].groupnumber++;
+ }
+
+ seqmap[name] = seq;
}
/*******************************************************************************/
-int FastaMap::size(){ //returns datas size which is the number of unique sequences
+int FastaMap::sizeUnique(){ //returns datas size which is the number of unique sequences
return data.size();
}
/*******************************************************************************/
-void FastaMap::print(ostream& out){ //prints data
+void FastaMap::printNamesFile(ostream& out){ //prints data
try {
// two column file created with groupname and them list of identical sequence names
for (it = data.begin(); it != data.end(); it++) {
}
}
/*******************************************************************************/
+void FastaMap::printCondensedFasta(ostream& out){ //prints data
+ try {
+ //creates a fasta file
+ for (it = data.begin(); it != data.end(); it++) {
+ out << ">" << it->second.groupname << endl;
+ out << it->first << endl;
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the FastaMap class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the FastaMap class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/*******************************************************************************/
+
projects / mothur.git / blobdiff