/***********************************************************************/
Sequence::Sequence(){
+ m = MothurOut::getInstance();
initialize();
}
/***********************************************************************/
Sequence::Sequence(string newName, string sequence) {
-
- initialize();
- name = newName;
- if(sequence.find_first_of('-') != string::npos) {
+ try {
+ m = MothurOut::getInstance();
+ initialize();
+ name = newName;
+
+ //setUnaligned removes any gap characters for us
+ setUnaligned(sequence);
setAligned(sequence);
}
- setUnaligned(sequence);
-
+ catch(exception& e) {
+ m->errorOut(e, "Sequence", "Sequence");
+ exit(1);
+ }
}
//********************************************************************************************************************
+//this function will jump over commented out sequences, but if the last sequence in a file is commented out it makes a blank seq
+Sequence::Sequence(istringstream& fastaString){
+ try {
+ m = MothurOut::getInstance();
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+ cout << pid << " after mothur instance " << &name << endl;
+ initialize();
+ cout << "after mothur initialize" << endl;
+ fastaString >> name;
+ cout << "after name " << endl;
+ name = name.substr(1);
+ string sequence;
+
+ //read comments
+ while ((name[0] == '#') && fastaString) {
+ while (fastaString) { char c = fastaString.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
+ sequence = getCommentString(fastaString);
+
+ if (fastaString) {
+ fastaString >> name;
+ name = name.substr(1);
+ }else {
+ name = "";
+ break;
+ }
+ }
+ cout << "after mothur comment" << endl;
+ //read real sequence
+ while (fastaString) { char c = fastaString.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
+ cout << "after mothur name" << endl;
+ sequence = getSequenceString(fastaString);
+ cout << "after mothur sequence" << endl;
+ setAligned(sequence);
+ //setUnaligned removes any gap characters for us
+ setUnaligned(sequence);
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Sequence", "Sequence");
+ exit(1);
+ }
+}
+//********************************************************************************************************************
+//this function will jump over commented out sequences, but if the last sequence in a file is commented out it makes a blank seq
Sequence::Sequence(ifstream& fastaFile){
- initialize();
-
- 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;
-
- while(fastaFile){
- letter= fastaFile.get();
- if(letter == '>'){
- fastaFile.putback(letter);
- break;
+ try {
+ m = MothurOut::getInstance();
+ initialize();
+ fastaFile >> name;
+ name = name.substr(1);
+ string sequence;
+
+ //read comments
+ while ((name[0] == '#') && fastaFile) {
+ while (!fastaFile.eof()) { char c = fastaFile.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
+ sequence = getCommentString(fastaFile);
+
+ if (fastaFile) {
+ fastaFile >> name;
+ name = name.substr(1);
+ }else {
+ name = "";
+ break;
+ }
}
- else if(isprint(letter)){
- letter = toupper(letter);
- if(letter == 'U'){letter = 'T';}
- sequence += letter;
+
+ //read real sequence
+ while (!fastaFile.eof()) { char c = fastaFile.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
+
+ sequence = getSequenceString(fastaFile);
+
+ setAligned(sequence);
+ //setUnaligned removes any gap characters for us
+ setUnaligned(sequence);
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Sequence", "Sequence");
+ exit(1);
+ }
+}
+//********************************************************************************************************************
+string Sequence::getSequenceString(ifstream& fastaFile) {
+ try {
+ char letter;
+ string sequence = "";
+
+ 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 sequence;
}
-
- if(sequence.find_first_of('-') != string::npos){ // if there are any gaps in the sequence, assume that it is
- setAligned(sequence); // an alignment file
+ catch(exception& e) {
+ m->errorOut(e, "Sequence", "getSequenceString");
+ exit(1);
+ }
+}
+//********************************************************************************************************************
+//comment can contain '>' so we need to account for that
+string Sequence::getCommentString(ifstream& fastaFile) {
+ try {
+ char letter;
+ string sequence = "";
+
+ while(fastaFile){
+ letter=fastaFile.get();
+ if((letter == '\r') || (letter == '\n')){
+ gobble(fastaFile); //in case its a \r\n situation
+ break;
+ }
+ }
+
+ return sequence;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Sequence", "getCommentString");
+ exit(1);
+ }
+}
+//********************************************************************************************************************
+string Sequence::getSequenceString(istringstream& fastaFile) {
+ try {
+ char letter;
+ string sequence = "";
+
+ 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 sequence;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Sequence", "getSequenceString");
+ exit(1);
+ }
+}
+//********************************************************************************************************************
+//comment can contain '>' so we need to account for that
+string Sequence::getCommentString(istringstream& fastaFile) {
+ try {
+ char letter;
+ string sequence = "";
+
+ while(fastaFile){
+ letter=fastaFile.get();
+ if((letter == '\r') || (letter == '\n')){
+ gobble(fastaFile); //in case its a \r\n situation
+ break;
+ }
+ }
+
+ return sequence;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Sequence", "getCommentString");
+ exit(1);
}
- setUnaligned(sequence); // also set the unaligned sequence file
}
-
//********************************************************************************************************************
void Sequence::initialize(){
void Sequence::setUnaligned(string sequence){
- if(sequence.find_first_of('-') != string::npos) {
+ if(sequence.find_first_of('.') != string::npos || sequence.find_first_of('-') != string::npos) {
string temp = "";
for(int j=0;j<sequence.length();j++) {
if(isalpha(sequence[j])) { temp += sequence[j]; }
//if the alignment starts or ends with a gap, replace it with a period to indicate missing data
aligned = sequence;
alignmentLength = aligned.length();
+ setUnaligned(sequence);
if(aligned[0] == '-'){
for(int i=0;i<alignmentLength;i++){
else { temp += 'N'; }
}
unaligned = temp;
+ aligned = temp;
}
projects / mothur.git / blobdiff