5 * Created by Pat Schloss on 12/15/08.
6 * Copyright 2008 Patrick D. Schloss. All rights reserved.
10 #include "sequence.hpp"
12 /***********************************************************************/
18 /***********************************************************************/
20 Sequence::Sequence(string newName, string sequence) {
25 //setUnaligned removes any gap characters for us
26 setUnaligned(sequence);
30 //********************************************************************************************************************
32 Sequence::Sequence(ifstream& fastaFile){
36 name = name.substr(1);
38 while (!fastaFile.eof()) { char c = fastaFile.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
44 letter= fastaFile.get();
46 fastaFile.putback(letter);
49 else if(isprint(letter)){
50 letter = toupper(letter);
51 if(letter == 'U'){letter = 'T';}
57 //setUnaligned removes any gap characters for us
58 setUnaligned(sequence);
61 //********************************************************************************************************************
63 void Sequence::initialize(){
80 //********************************************************************************************************************
82 void Sequence::setName(string seqName) {
83 if(seqName[0] == '>') { name = seqName.substr(1); }
84 else { name = seqName; }
87 //********************************************************************************************************************
89 void Sequence::setUnaligned(string sequence){
91 if(sequence.find_first_of('.') != string::npos || sequence.find_first_of('-') != string::npos) {
93 for(int j=0;j<sequence.length();j++) {
94 if(isalpha(sequence[j])) { temp += sequence[j]; }
101 numBases = unaligned.length();
105 //********************************************************************************************************************
107 void Sequence::setAligned(string sequence){
109 //if the alignment starts or ends with a gap, replace it with a period to indicate missing data
111 alignmentLength = aligned.length();
113 if(aligned[0] == '-'){
114 for(int i=0;i<alignmentLength;i++){
115 if(aligned[i] == '-'){
122 for(int i=alignmentLength-1;i>=0;i--){
123 if(aligned[i] == '-'){
134 //********************************************************************************************************************
136 void Sequence::setPairwise(string sequence){
140 //********************************************************************************************************************
142 string Sequence::convert2ints() {
144 if(unaligned == "") { /* need to throw an error */ }
148 for(int i=0;i<unaligned.length();i++) {
149 if(toupper(unaligned[i]) == 'A') { processed += '0'; }
150 else if(toupper(unaligned[i]) == 'C') { processed += '1'; }
151 else if(toupper(unaligned[i]) == 'G') { processed += '2'; }
152 else if(toupper(unaligned[i]) == 'T') { processed += '3'; }
153 else if(toupper(unaligned[i]) == 'U') { processed += '3'; }
154 else { processed += '4'; }
159 //********************************************************************************************************************
161 string Sequence::getName(){
165 //********************************************************************************************************************
167 string Sequence::getAligned(){
171 //********************************************************************************************************************
173 string Sequence::getPairwise(){
177 //********************************************************************************************************************
179 string Sequence::getUnaligned(){
183 //********************************************************************************************************************
185 int Sequence::getNumBases(){
189 //********************************************************************************************************************
191 void Sequence::printSequence(ostream& out){
193 out << ">" << name << endl;
195 out << aligned << endl;
198 out << unaligned << endl;
202 //********************************************************************************************************************
204 int Sequence::getAlignLength(){
205 return alignmentLength;
208 //********************************************************************************************************************
210 int Sequence::getAmbigBases(){
211 if(ambigBases == -1){
213 for(int j=0;j<numBases;j++){
214 if(unaligned[j] != 'A' && unaligned[j] != 'T' && unaligned[j] != 'G' && unaligned[j] != 'C'){
223 //********************************************************************************************************************
225 int Sequence::getLongHomoPolymer(){
226 if(longHomoPolymer == -1){
229 for(int j=1;j<numBases;j++){
230 if(unaligned[j] == unaligned[j-1]){
234 if(homoPolymer > longHomoPolymer){ longHomoPolymer = homoPolymer; }
238 if(homoPolymer > longHomoPolymer){ longHomoPolymer = homoPolymer; }
240 return longHomoPolymer;
243 //********************************************************************************************************************
245 int Sequence::getStartPos(){
247 for(int j = 0; j < alignmentLength; j++) {
248 if(aligned[j] != '.'){
254 if(isAligned == 0){ startPos = 1; }
259 //********************************************************************************************************************
261 int Sequence::getEndPos(){
263 for(int j=alignmentLength-1;j>=0;j--){
264 if(aligned[j] != '.'){
270 if(isAligned == 0){ endPos = numBases; }
275 //********************************************************************************************************************
277 bool Sequence::getIsAligned(){
281 //********************************************************************************************************************
283 void Sequence::reverseComplement(){
286 for(int i=numBases-1;i>=0;i--){
287 if(unaligned[i] == 'A') { temp += 'T'; }
288 else if(unaligned[i] == 'T'){ temp += 'A'; }
289 else if(unaligned[i] == 'G'){ temp += 'C'; }
290 else if(unaligned[i] == 'C'){ temp += 'G'; }
291 else { temp += 'N'; }
297 //********************************************************************************************************************