+++ /dev/null
-/*
- * sequence.cpp
- *
- *
- * Created by Pat Schloss on 12/15/08.
- * Copyright 2008 Patrick D. Schloss. All rights reserved.
- *
- */
-
-#include "sequence.hpp"
-
-/***********************************************************************/
-Sequence::Sequence(){
- m = MothurOut::getInstance();
- initialize();
-}
-/***********************************************************************/
-Sequence::Sequence(string newName, string sequence) {
- try {
- m = MothurOut::getInstance();
- initialize();
- name = newName;
-
- //setUnaligned removes any gap characters for us
- setUnaligned(sequence);
- setAligned(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;
-
- //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();
- 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;
- }
- }
-
- 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(); }
-
- }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;
- }
- }
-
- 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(); }
-
- }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(ifstream& fastaFile){
- try {
- m = MothurOut::getInstance();
- initialize();
- fastaFile >> name;
-
- 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
-
- 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(); }
-
- }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& extraInfo, bool getInfo){
- try {
- m = MothurOut::getInstance();
- initialize();
- fastaFile >> name;
- extraInfo = "";
-
- 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 info after sequence name
- while (!fastaFile.eof()) {
- char c = fastaFile.get();
- if (c == 10 || c == 13){ 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(); }
-
- }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;
-
- 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
-
- 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(); }
-
- }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);
- }
-}
-
-//********************************************************************************************************************
-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(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();
-
- if(letter == '>'){
- fastaFile.putback(letter);
- break;
- }
- 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(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;
- }
- catch(exception& e) {
- m->errorOut(e, "Sequence", "getCommentString");
- exit(1);
- }
-}
-//********************************************************************************************************************
-
-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; }
-}
-
-//********************************************************************************************************************
-
-void Sequence::setUnaligned(string sequence){
-
- 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]; }
- }
- unaligned = temp;
- }
- 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();
- setUnaligned(sequence);
-
- 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;
-}
-
-//********************************************************************************************************************
-
-void Sequence::setPairwise(string sequence){
- pairwise = sequence;
-}
-
-//********************************************************************************************************************
-
-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;
-}
-
-//********************************************************************************************************************
-
-string Sequence::getAligned(){
- if(isAligned == 0) { return unaligned; }
- else { return aligned; }
-}
-
-//********************************************************************************************************************
-
-string Sequence::getInlineSeq(){
- return name + '\t' + aligned;
-}
-
-
-//********************************************************************************************************************
-
-string Sequence::getPairwise(){
- return pairwise;
-}
-
-//********************************************************************************************************************
-
-string Sequence::getUnaligned(){
- return unaligned;
-}
-
-//********************************************************************************************************************
-
-int Sequence::getNumBases(){
- return numBases;
-}
-
-//********************************************************************************************************************
-
-void Sequence::printSequence(ostream& out){
-
- 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;
-}
-
-//********************************************************************************************************************
-
-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 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(startPos == -1){
- for(int j = 0; j < alignmentLength; j++) {
- if(aligned[j] != '.'){
- startPos = j + 1;
- break;
- }
- }
- }
- if(isAligned == 0){ startPos = 1; }
-
- return startPos;
-}
-
-//********************************************************************************************************************
-
-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-1; j++) {
- aligned[j] = '.';
- }
-
- //things like ......----------AT become ................AT
- for(int j = start-1; 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] != '.'){
- endPos = j + 1;
- break;
- }
- }
- }
- if(isAligned == 0){ endPos = numBases; }
-
- return endPos;
-}
-
-//********************************************************************************************************************
-
-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(){
-
- 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;
- aligned = temp;
-
-}
-
-//********************************************************************************************************************
-
-void Sequence::trim(int length){
-
- if(numBases > length){
- unaligned = unaligned.substr(0,length);
- numBases = length;
- }
-
-}
-
-///**************************************************************************************************/
projects / mothur.git / blobdiff