#include "sequence.hpp"
/***********************************************************************/
-
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;
+
+ m->checkName(name);
+
+ //setUnaligned removes any gap characters for us
+ setUnaligned(sequence);
setAligned(sequence);
}
- setUnaligned(sequence);
+ catch(exception& e) {
+ m->errorOut(e, "Sequence", "Sequence");
+ exit(1);
+ }
+}
+/***********************************************************************/
+Sequence::Sequence(string newName, string sequence, string justUnAligned) {
+ try {
+ m = MothurOut::getInstance();
+ initialize();
+ name = newName;
+
+ m->checkName(name);
+
+ //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();
+ initialize();
+ name = getSequenceName(fastaString);
+
+ if (!m->control_pressed) {
+ 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;
+ }
+ }
+
+ while (!fastaString.eof()) { char c = fastaString.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
+
+ int numAmbig = 0;
+ sequence = getSequenceString(fastaString, numAmbig);
+
+ setAligned(sequence);
+ //setUnaligned removes any gap characters for us
+ setUnaligned(sequence);
+
+ if ((numAmbig / (float) numBases) > 0.25) { m->mothurOut("[WARNING]: We found more than 25% of the bases in sequence " + name + " to be ambiguous. Mothur is not setup to process protein sequences."); 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();
+ name = getSequenceName(fastaString);
+
+ if (!m->control_pressed) {
+ 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;
+ }
+ }
+
+ while (!fastaString.eof()) { char c = fastaString.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
+
+ int numAmbig = 0;
+ sequence = getSequenceString(fastaString, numAmbig);
+
+ //setUnaligned removes any gap characters for us
+ setUnaligned(sequence);
+
+ if ((numAmbig / (float) numBases) > 0.25) { m->mothurOut("[WARNING]: We found more than 25% of the bases in sequence " + name + " to be ambiguous. Mothur is not setup to process protein sequences."); m->mothurOutEndLine(); }
+
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Sequence", "Sequence");
+ exit(1);
+ }
+}
-Sequence::Sequence(ifstream& fastaFile){
- initialize();
- fastaFile >> name;
- name = name.substr(1);
-
- while (!fastaFile.eof()) { char c = fastaFile.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
+//********************************************************************************************************************
+//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){
+ try {
+ m = MothurOut::getInstance();
+ initialize();
+ name = getSequenceName(fastaFile);
+
+ if (!m->control_pressed) {
+
+ 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
+
+ int numAmbig = 0;
+ sequence = getSequenceString(fastaFile, numAmbig);
+
+ setAligned(sequence);
+ //setUnaligned removes any gap characters for us
+ setUnaligned(sequence);
+
+ if ((numAmbig / (float) numBases) > 0.25) { m->mothurOut("[WARNING]: We found more than 25% of the bases in sequence " + name + " to be ambiguous. Mothur is not setup to process protein sequences."); m->mothurOutEndLine(); }
+
+ }
- char letter;
- string 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, string& extraInfo, bool getInfo){
+ try {
+ m = MothurOut::getInstance();
+ initialize();
+ extraInfo = "";
+
+ name = getSequenceName(fastaFile);
+
+ if (!m->control_pressed) {
+ 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 info after sequence name
+ while (!fastaFile.eof()) {
+ char c = fastaFile.get();
+ if (c == 10 || c == 13 || c == -1){ break; }
+ extraInfo += c;
+ }
+
+ int numAmbig = 0;
+ sequence = getSequenceString(fastaFile, numAmbig);
+
+ setAligned(sequence);
+ //setUnaligned removes any gap characters for us
+ setUnaligned(sequence);
+
+ if ((numAmbig / (float) numBases) > 0.25) { m->mothurOut("[WARNING]: We found more than 25% of the bases in sequence " + name + " to be ambiguous. Mothur is not setup to process protein sequences."); 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();
+ name = getSequenceName(fastaFile);
+
+ if (!m->control_pressed) {
+ 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
+
+ int numAmbig = 0;
+ sequence = getSequenceString(fastaFile, numAmbig);
+
+ //setUnaligned removes any gap characters for us
+ setUnaligned(sequence);
+
+ if ((numAmbig / (float) numBases) > 0.25) { m->mothurOut("[WARNING]: We found more than 25% of the bases in sequence " + name + " to be ambiguous. Mothur is not setup to process protein sequences."); m->mothurOutEndLine(); }
+
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Sequence", "Sequence");
+ exit(1);
+ }
+}
+//********************************************************************************************************************
+string Sequence::getSequenceName(ifstream& fastaFile) {
+ try {
+ string name = "";
+
+ fastaFile >> name;
+
+ if (name.length() != 0) {
+
+ name = name.substr(1);
+
+ m->checkName(name);
+
+ }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ return name;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Sequence", "getSequenceName");
+ exit(1);
+ }
+}
+//********************************************************************************************************************
+string Sequence::getSequenceName(istringstream& fastaFile) {
+ try {
+ string name = "";
+
+ fastaFile >> name;
+
+ if (name.length() != 0) {
+
+ name = name.substr(1);
+
+ m->checkName(name);
+
+ }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ return name;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Sequence", "getSequenceName");
+ exit(1);
+ }
+}
+//********************************************************************************************************************
+string Sequence::getSequenceString(ifstream& fastaFile, int& numAmbig) {
+ try {
+ char letter;
+ string sequence = "";
+ numAmbig = 0;
+
+ while(fastaFile){
+ letter= fastaFile.get();
+ if(letter == '>'){
+ fastaFile.putback(letter);
+ break;
+ }else if (letter == ' ') {;}
+ else if(isprint(letter)){
+ letter = toupper(letter);
+ if(letter == 'U'){letter = 'T';}
+ if(letter != '.' && letter != '-' && letter != 'A' && letter != 'T' && letter != 'G' && letter != 'C' && letter != 'N'){
+ letter = 'N';
+ numAmbig++;
+ }
+ 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(ifstream& fastaFile) {
+ try {
+ char letter;
+ string sequence = "";
+
+ while(fastaFile){
+ letter=fastaFile.get();
+ if((letter == '\r') || (letter == '\n')){
+ m->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, int& numAmbig) {
+ try {
+ char letter;
+ string sequence = "";
+ numAmbig = 0;
+
+ while(!fastaFile.eof()){
+ letter= fastaFile.get();
- while(fastaFile){
- letter= fastaFile.get();
- if(letter == '>'){
- fastaFile.putback(letter);
- break;
+ if(letter == '>'){
+ fastaFile.putback(letter);
+ break;
+ }else if (letter == ' ') {;}
+ else if(isprint(letter)){
+ letter = toupper(letter);
+ if(letter == 'U'){letter = 'T';}
+ if(letter != '.' && letter != '-' && letter != 'A' && letter != 'T' && letter != 'G' && letter != 'C' && letter != 'N'){
+ letter = 'N';
+ numAmbig++;
+ }
+ sequence += letter;
+ }
}
- 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')){
+ m->gobble(fastaFile); //in case its a \r\n situation
+ break;
+ }
}
+
+ return sequence;
}
-
- if((sequence.find_first_of('-') != string::npos) || (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", "getCommentString");
+ exit(1);
}
- setUnaligned(sequence); // also set the unaligned sequence file
}
-
//********************************************************************************************************************
void Sequence::initialize(){
//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++){
//********************************************************************************************************************
string Sequence::getAligned(){
- return aligned;
+ if(isAligned == 0) { return unaligned; }
+ else { return aligned; }
}
+//********************************************************************************************************************
+
+string Sequence::getInlineSeq(){
+ return name + '\t' + aligned;
+}
+
+
//********************************************************************************************************************
string Sequence::getPairwise(){
int Sequence::getNumBases(){
return numBases;
}
+//********************************************************************************************************************
+
+int Sequence::getNumNs(){
+ int numNs = 0;
+ for (int i = 0; i < unaligned.length(); i++) {
+ if(toupper(unaligned[i]) == 'N') { numNs++; }
+ }
+ return numNs;
+}
//********************************************************************************************************************
//********************************************************************************************************************
+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;
//********************************************************************************************************************
int Sequence::getStartPos(){
- if(endPos == -1){
+ if(startPos == -1){
for(int j = 0; j < alignmentLength; j++) {
- if(aligned[j] != '.'){
+ if((aligned[j] != '.')&&(aligned[j] != '-')){
startPos = j + 1;
break;
}
//********************************************************************************************************************
+void Sequence::padToPos(int start){
+
+ for(int j = startPos-1; j < start-1; j++) {
+ aligned[j] = '.';
+ }
+ startPos = start;
+
+}
+//********************************************************************************************************************
+
+int Sequence::filterToPos(int start){
+
+ if (start > aligned.length()) { start = aligned.length(); m->mothurOut("[ERROR]: start to large.\n"); }
+
+ for(int j = 0; j < start; j++) {
+ aligned[j] = '.';
+ }
+
+ //things like ......----------AT become ................AT
+ for(int j = start; j < aligned.length(); j++) {
+ if (isalpha(aligned[j])) { break; }
+ else { aligned[j] = '.'; }
+ }
+ setUnaligned(aligned);
+
+ return 0;
+
+}
+//********************************************************************************************************************
+
+int Sequence::filterFromPos(int end){
+
+ if (end > aligned.length()) { end = aligned.length(); m->mothurOut("[ERROR]: end to large.\n"); }
+
+ for(int j = end; j < aligned.length(); j++) {
+ aligned[j] = '.';
+ }
+
+ for(int j = aligned.length()-1; j < 0; j--) {
+ if (isalpha(aligned[j])) { break; }
+ else { aligned[j] = '.'; }
+ }
+
+ setUnaligned(aligned);
+
+ return 0;
+}
+//********************************************************************************************************************
+
int Sequence::getEndPos(){
if(endPos == -1){
for(int j=alignmentLength-1;j>=0;j--){
- if(aligned[j] != '.'){
+ if((aligned[j] != '.')&&(aligned[j] != '-')){
endPos = j + 1;
break;
}
//********************************************************************************************************************
+void Sequence::padFromPos(int end){
+ //cout << end << '\t' << endPos << endl;
+ for(int j = end; j < endPos; j++) {
+ aligned[j] = '.';
+ }
+ endPos = end;
+
+}
+
+//********************************************************************************************************************
+
bool Sequence::getIsAligned(){
return isAligned;
}
-
//********************************************************************************************************************
void Sequence::reverseComplement(){
else { temp += 'N'; }
}
unaligned = temp;
+ aligned = temp;
}
//********************************************************************************************************************
+
+void Sequence::trim(int length){
+
+ if(numBases > length){
+ unaligned = unaligned.substr(0,length);
+ numBases = length;
+ aligned = "";
+ isAligned = 0;
+ }
+
+}
+
+///**************************************************************************************************/
projects / mothur.git / blobdiff