*/
#include "fastamap.h"
+#include "sequence.hpp"
/*******************************************************************************/
- FastaMap::FastaMap(ifstream& in) {
- //int numberOfSequences = 0;
-
- string name, sequence, line;
- sequence = "";
-
- getline(in, line);
- name = line.substr(1, line.length()); //rips off '>'
-
- //read through file
- while (getline(in, line)) {
- if (isalnum(line.at(0))){ //if it's a sequence line
- sequence += line;
- }
- else{
+
+void FastaMap::readFastaFile(ifstream& in) {
+ try {
+ string name, sequence, line;
+ sequence = "";
+// int c;
+ string temp;
+
+
+ //read through file
+// 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
+ while(!in.eof()){
+ Sequence currSeq(in);
+ name = currSeq.getName();
+ sequence = currSeq.getUnaligned();
+ 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].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 '>'
+ data[sequence].groupnumber++;
+ }
+
+ gobble(in);
}
+
+ }
+ 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";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the FastaMap class function readFastaFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
}
-
- //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++;
- }
}
+
/*******************************************************************************/
+
string FastaMap::getGroupName(string seq) { //pass a sequence name get its group
return data[seq].groupname;
}
+
/*******************************************************************************/
-int FastaMap::getGroupNumber(string seq) { //pass a sequence name get number of sequence in its group
- return data[seq].groupnumber;
-}
-/*******************************************************************************/
+
string FastaMap::getNames(string seq) { //pass a sequence get the string of names in the group separated by ','s.
return data[seq].names;
}
+
/*******************************************************************************/
-void FastaMap::push_back(string seq, string Name) {//sequencename, name
- data[seq].groupname = Name;
- data[seq].groupnumber = 1;
- data[seq].names = Name;
+
+int FastaMap::getGroupNumber(string seq) { //pass a sequence get the number of identical sequences.
+ return data[seq].groupnumber;
}
+
+/*******************************************************************************/
+
+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::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++) {
+ out << it->second.groupname << '\t' << it->second.names << 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);
+ }
+}
+
/*******************************************************************************/
-void FastaMap::print(ostream&){ //prints data
+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