5 * Created by Pat Schloss on 12/15/08.
6 * Copyright 2008 Patrick D. Schloss. All rights reserved.
12 #include "sequence.hpp"
14 /***********************************************************************/
20 /***********************************************************************/
22 Sequence::Sequence(string newName, string sequence) {
26 if(sequence.find_first_of('-') != string::npos) {
30 setUnaligned(sequence);
33 //********************************************************************************************************************
35 Sequence::Sequence(ifstream& fastaFile){
37 string accession; // provided a file handle to a fasta-formatted sequence file, read in the next
38 fastaFile >> accession; // accession number and sequence we find...
45 letter= fastaFile.get();
47 fastaFile.putback(letter);
50 else if(isprint(letter)){
51 letter = toupper(letter);
52 if(letter == 'U'){letter = 'T';}
58 if(sequence.find_first_of('-') != string::npos){ // if there are any gaps in the sequence, assume that it is
59 setAligned(sequence); // an alignment file
61 setUnaligned(sequence); // also set the unaligned sequence file
64 //********************************************************************************************************************
66 void Sequence::initialize(){
83 //********************************************************************************************************************
85 void Sequence::setName(string seqName) {
86 if(seqName[0] == '>') { name = seqName.substr(1); }
87 else { name = seqName; }
90 //********************************************************************************************************************
92 void Sequence::setUnaligned(string sequence){
94 if(sequence.find_first_of('-') != string::npos) {
96 for(int j=0;j<sequence.length();j++) {
97 if(isalpha(sequence[j])) { temp += sequence[j]; }
102 unaligned = sequence;
104 numBases = unaligned.length();
108 //********************************************************************************************************************
110 void Sequence::setAligned(string sequence){
112 //if the alignment starts or ends with a gap, replace it with a period to indicate missing data
114 alignmentLength = aligned.length();
116 if(aligned[0] == '-'){
117 for(int i=0;i<alignmentLength;i++){
118 if(aligned[i] == '-'){
125 for(int i=alignmentLength-1;i>=0;i--){
126 if(aligned[i] == '-'){
137 //********************************************************************************************************************
139 void Sequence::setPairwise(string sequence){
143 //********************************************************************************************************************
145 string Sequence::convert2ints() {
147 if(unaligned == "") { /* need to throw an error */ }
151 for(int i=0;i<unaligned.length();i++) {
152 if(toupper(unaligned[i]) == 'A') { processed += '0'; }
153 else if(toupper(unaligned[i]) == 'C') { processed += '1'; }
154 else if(toupper(unaligned[i]) == 'G') { processed += '2'; }
155 else if(toupper(unaligned[i]) == 'T') { processed += '3'; }
156 else if(toupper(unaligned[i]) == 'U') { processed += '3'; }
157 else { processed += '4'; }
162 //********************************************************************************************************************
164 string Sequence::getName(){
168 //********************************************************************************************************************
170 string Sequence::getAligned(){
174 //********************************************************************************************************************
176 string Sequence::getPairwise(){
180 //********************************************************************************************************************
182 string Sequence::getUnaligned(){
186 //********************************************************************************************************************
188 int Sequence::getNumBases(){
192 //********************************************************************************************************************
194 void Sequence::printSequence(ostream& out){
196 out << ">" << name << endl;
198 out << aligned << endl;
201 out << unaligned << endl;
205 //********************************************************************************************************************
207 int Sequence::getAlignLength(){
208 return alignmentLength;
211 //********************************************************************************************************************
213 int Sequence::getAmbigBases(){
214 if(ambigBases == -1){
216 for(int j=0;j<numBases;j++){
217 if(unaligned[j] != 'A' && unaligned[j] != 'T' && unaligned[j] != 'G' && unaligned[j] != 'C'){
226 //********************************************************************************************************************
228 int Sequence::getLongHomoPolymer(){
229 if(longHomoPolymer == -1){
232 for(int j=1;j<numBases;j++){
233 if(unaligned[j] == unaligned[j-1]){
237 if(homoPolymer > longHomoPolymer){ longHomoPolymer = homoPolymer; }
241 if(homoPolymer > longHomoPolymer){ longHomoPolymer = homoPolymer; }
243 return longHomoPolymer;
246 //********************************************************************************************************************
248 int Sequence::getStartPos(){
250 for(int j = 0; j < alignmentLength; j++) {
251 if(aligned[j] != '.'){
260 //********************************************************************************************************************
262 int Sequence::getEndPos(){
264 for(int j=alignmentLength-1;j>=0;j--){
265 if(aligned[j] != '.'){
274 //********************************************************************************************************************
276 bool Sequence::getIsAligned(){
280 //********************************************************************************************************************