#include "sequence.hpp"
/***********************************************************************/
-
Sequence::Sequence(){
m = MothurOut::getInstance();
initialize();
}
-
/***********************************************************************/
-
Sequence::Sequence(string newName, string sequence) {
try {
m = MothurOut::getInstance();
exit(1);
}
}
+/***********************************************************************/
+Sequence::Sequence(string newName, string sequence, string justUnAligned) {
+ try {
+ m = MothurOut::getInstance();
+ initialize();
+ name = newName;
+
+ //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(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 << pid << " after name " << name << endl;
- name = name.substr(1);
-
- string sequence;
-cout << pid << " name = " << name << endl;
- //read comments
- while ((name[0] == '#') && fastaString) {
- while (!fastaString.eof()) { char c = fastaString.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
- sequence = getCommentString(fastaString);
+
+ if (name.length() != 0) {
+
+ name = name.substr(1);
+ string sequence;
+
+ //read comments
+ while ((name[0] == '#') && fastaString) {
+ while (!fastaString.eof()) { 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;
+ }
+ }
- if (fastaString) {
- fastaString >> name;
- name = name.substr(1);
- }else {
- name = "";
- break;
+ while (!fastaString.eof()) { char c = fastaString.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
+
+ sequence = getSequenceString(fastaString);
+ setAligned(sequence);
+ //setUnaligned removes any gap characters for us
+ setUnaligned(sequence);
+ }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaString.tellg()) + ". Blank name."); m->mothurOutEndLine(); }
+
+ }
+ 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, string JustUnaligned){
+ try {
+ m = MothurOut::getInstance();
+
+ initialize();
+ fastaString >> name;
+
+ if (name.length() != 0) {
+
+ name = name.substr(1);
+ string sequence;
+
+ //read comments
+ while ((name[0] == '#') && fastaString) {
+ while (!fastaString.eof()) { 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 << pid << "in while comment" << endl;
- }
- cout << pid << "after mothur comment" << endl;
- while (!fastaString.eof()) { char c = fastaString.get(); cout << pid << " char = " << int(c) << endl; if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
- cout << pid << " after mothur name" << endl;
- sequence = getSequenceString(fastaString);
- cout << pid << " after mothur sequence" << endl;
- setAligned(sequence);
- //setUnaligned removes any gap characters for us
- setUnaligned(sequence);
+
+ while (!fastaString.eof()) { char c = fastaString.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
+
+ sequence = getSequenceString(fastaString);
+
+ //setUnaligned removes any gap characters for us
+ setUnaligned(sequence);
+ }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaString.tellg()) + ". Blank name."); m->mothurOutEndLine(); }
+
}
catch(exception& e) {
m->errorOut(e, "Sequence", "Sequence");
}
}
+
//********************************************************************************************************************
//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){
m = MothurOut::getInstance();
initialize();
fastaFile >> name;
- name = name.substr(1);
- string sequence;
+
+ if (name.length() != 0) {
- //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);
+ name = name.substr(1);
- if (fastaFile) {
- fastaFile >> name;
- name = name.substr(1);
- }else {
- name = "";
- break;
- }
- }
+ string sequence;
- //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
+ //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;
+ }
+ }
+
+ //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);
+ }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); }
+
+ }
+ 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, string JustUnaligned){
+ try {
+ m = MothurOut::getInstance();
+ initialize();
+ fastaFile >> name;
- sequence = getSequenceString(fastaFile);
+ if (name.length() != 0) {
+ 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;
+ }
+ }
+
+ //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);
+
+ //setUnaligned removes any gap characters for us
+ setUnaligned(sequence);
+ }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); }
- 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 {
while(fastaFile){
letter=fastaFile.get();
if((letter == '\r') || (letter == '\n')){
- gobble(fastaFile); //in case its a \r\n situation
+ m->gobble(fastaFile); //in case its a \r\n situation
break;
}
}
try {
char letter;
string sequence = "";
-int pid;
-MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+
while(!fastaFile.eof()){
letter= fastaFile.get();
- cout << pid << '\t' << letter << endl;
+
if(letter == '>'){
fastaFile.putback(letter);
break;
while(fastaFile){
letter=fastaFile.get();
if((letter == '\r') || (letter == '\n')){
- gobble(fastaFile); //in case its a \r\n situation
+ m->gobble(fastaFile); //in case its a \r\n situation
break;
}
}
//********************************************************************************************************************
string Sequence::getAligned(){
- return aligned;
+ if(isAligned == 0) { return unaligned; }
+ else { return aligned; }
}
//********************************************************************************************************************
//********************************************************************************************************************
+void Sequence::removeAmbigBases(){
+
+ for(int j=0;j<alignmentLength;j++){
+ if(aligned[j] != 'A' && aligned[j] != 'T' && aligned[j] != 'G' && aligned[j] != 'C'){
+ aligned[j] = '-';
+ }
+ }
+ setUnaligned(aligned);
+}
+
+//********************************************************************************************************************
+
int Sequence::getLongHomoPolymer(){
if(longHomoPolymer == -1){
longHomoPolymer = 1;
aligned = temp;
}
-
-//********************************************************************************************************************
+/**************************************************************************************************/
projects / mothur.git / blobdiff