/***********************************************************************/
-Sequence::Sequence() {}
+Sequence::Sequence(){
+ initialize();
+}
/***********************************************************************/
Sequence::Sequence(string newName, string sequence) {
+
+ initialize();
name = newName;
if(sequence.find_first_of('-') != string::npos) {
setAligned(sequence);
}
setUnaligned(sequence);
+
}
-
//********************************************************************************************************************
-string Sequence::convert2ints() {
-
- if(unaligned == "") { /* need to throw an error */ }
+Sequence::Sequence(ifstream& fastaFile){
+ initialize();
- string processed;
+ string accession; // provided a file handle to a fasta-formatted sequence file, read in the next
+ fastaFile >> accession; // accession number and sequence we find...
+ setName(accession);
+
+ char letter;
+ string sequence;
- for(int i=0;i<unaligned.length();i++) {
- if(toupper(unaligned[i]) == 'A') { processed += '0'; }
- else if(toupper(unaligned[i]) == 'C') { processed += '1'; }
- else if(toupper(unaligned[i]) == 'G') { processed += '2'; }
- else if(toupper(unaligned[i]) == 'T') { processed += '3'; }
- else if(toupper(unaligned[i]) == 'U') { processed += '3'; }
- else { processed += '4'; }
+ while(fastaFile){
+ letter= fastaFile.get();
+ if(letter == '>'){
+ fastaFile.putback(letter);
+ break;
+ }
+ else if(isprint(letter)){
+ letter = toupper(letter);
+ if(letter == 'U'){letter = 'T';}
+ sequence += letter;
+ }
+
}
- return processed;
+
+ if(sequence.find_first_of('-') != string::npos){ // if there are any gaps in the sequence, assume that it is
+ setAligned(sequence); // an alignment file
+ }
+ setUnaligned(sequence); // also set the unaligned sequence file
}
//********************************************************************************************************************
+void Sequence::initialize(){
+
+ name = "";
+ unaligned = "";
+ aligned = "";
+ pairwise = "";
+
+ numBases = 0;
+ alignmentLength = 0;
+ isAligned = 0;
+ startPos = -1;
+ endPos = -1;
+ longHomoPolymer = -1;
+ ambigBases = -1;
+
+}
+
+//********************************************************************************************************************
+
void Sequence::setName(string seqName) {
if(seqName[0] == '>') { name = seqName.substr(1); }
else { name = seqName; }
else {
unaligned = sequence;
}
+ numBases = unaligned.length();
}
//********************************************************************************************************************
void Sequence::setAligned(string sequence){
+
+ //if the alignment starts or ends with a gap, replace it with a period to indicate missing data
aligned = sequence;
+ alignmentLength = aligned.length();
+
+ if(aligned[0] == '-'){
+ for(int i=0;i<alignmentLength;i++){
+ if(aligned[i] == '-'){
+ aligned[i] = '.';
+ }
+ else{
+ break;
+ }
+ }
+ for(int i=alignmentLength-1;i>=0;i--){
+ if(aligned[i] == '-'){
+ aligned[i] = '.';
+ }
+ else{
+ break;
+ }
+ }
+ }
+ isAligned = 1;
}
//********************************************************************************************************************
//********************************************************************************************************************
+string Sequence::convert2ints() {
+
+ if(unaligned == "") { /* need to throw an error */ }
+
+ string processed;
+
+ for(int i=0;i<unaligned.length();i++) {
+ if(toupper(unaligned[i]) == 'A') { processed += '0'; }
+ else if(toupper(unaligned[i]) == 'C') { processed += '1'; }
+ else if(toupper(unaligned[i]) == 'G') { processed += '2'; }
+ else if(toupper(unaligned[i]) == 'T') { processed += '3'; }
+ else if(toupper(unaligned[i]) == 'U') { processed += '3'; }
+ else { processed += '4'; }
+ }
+ return processed;
+}
+
+//********************************************************************************************************************
+
string Sequence::getName(){
return name;
}
//********************************************************************************************************************
-int Sequence::getLength(){
- if(unaligned.length() > aligned.length())
- return unaligned.length();
- return aligned.length();
+int Sequence::getNumBases(){
+ return numBases;
}
//********************************************************************************************************************
void Sequence::printSequence(ostream& out){
- string toPrint = unaligned;
- if(aligned.length() > unaligned.length())
- toPrint = aligned;
- out << ">" << name << "\n" << toPrint << "\n";
+
+ out << ">" << name << endl;
+ if(isAligned){
+ out << aligned << endl;
+ }
+ else{
+ out << unaligned << endl;
+ }
+}
+
+//********************************************************************************************************************
+
+int Sequence::getAlignLength(){
+ return alignmentLength;
+}
+
+//********************************************************************************************************************
+
+int Sequence::getAmbigBases(){
+ if(ambigBases == -1){
+ ambigBases = 0;
+ for(int j=0;j<numBases;j++){
+ if(unaligned[j] != 'A' && unaligned[j] != 'T' && unaligned[j] != 'G' && unaligned[j] != 'C'){
+ ambigBases++;
+ }
+ }
+ }
+
+ return ambigBases;
+}
+
+//********************************************************************************************************************
+
+int Sequence::getLongHomoPolymer(){
+ if(longHomoPolymer == -1){
+ longHomoPolymer = 1;
+ int homoPolymer = 1;
+ for(int j=1;j<numBases;j++){
+ if(unaligned[j] == unaligned[j-1]){
+ homoPolymer++;
+ }
+ else{
+ if(homoPolymer > longHomoPolymer){ longHomoPolymer = homoPolymer; }
+ homoPolymer = 1;
+ }
+ }
+ if(homoPolymer > longHomoPolymer){ longHomoPolymer = homoPolymer; }
+ }
+ return longHomoPolymer;
+}
+
+//********************************************************************************************************************
+
+int Sequence::getStartPos(){
+ if(endPos == -1){
+ for(int j = 0; j < alignmentLength; j++) {
+ if(aligned[j] != '.'){
+ startPos = j + 1;
+ break;
+ }
+ }
+ }
+ if(isAligned == 0){ startPos = 1; }
+
+ return startPos;
+}
+
+//********************************************************************************************************************
+
+int Sequence::getEndPos(){
+ if(endPos == -1){
+ for(int j=alignmentLength-1;j>=0;j--){
+ if(aligned[j] != '.'){
+ endPos = j + 1;
+ break;
+ }
+ }
+ }
+ if(isAligned == 0){ endPos = numBases; }
+
+ return endPos;
+}
+
+//********************************************************************************************************************
+
+bool Sequence::getIsAligned(){
+ return isAligned;
+}
+
+//********************************************************************************************************************
+
+void Sequence::reverseComplement(){
+
+ string temp;
+ for(int i=numBases-1;i>=0;i--){
+ if(unaligned[i] == 'A') { temp += 'T'; }
+ else if(unaligned[i] == 'T'){ temp += 'A'; }
+ else if(unaligned[i] == 'G'){ temp += 'C'; }
+ else if(unaligned[i] == 'C'){ temp += 'G'; }
+ else { temp += 'N'; }
+ }
+ unaligned = temp;
+
}
//********************************************************************************************************************
projects / mothur.git / blobdiff