X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sequence.cpp;h=d6073d75da3ed630b27b626bbba8615d79b58858;hp=3f64db5fe5e7ec7b01bd4d8b413585580d766cc8;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05

diff --git a/sequence.cpp b/sequence.cpp
index 3f64db5..d6073d7 100644
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -7,70 +7,452 @@
  *
  */
 
-using namespace std;
-
-#include <string>
-#include <fstream>
-
 #include "sequence.hpp"
 
+/***********************************************************************/
+Sequence::Sequence(){
+	m = MothurOut::getInstance();
+	initialize();
+}
+/***********************************************************************/
+Sequence::Sequence(string newName, string sequence) {
+	try {
+		m = MothurOut::getInstance();
+		initialize();	
+		name = newName;
+        
+        m->checkName(name);
+		
+		//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;
+        
+        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(){}
 
 //********************************************************************************************************************
-
+//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 accession;
-	fastaFile >> accession;
-	setName(accession);
+	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;
-	
-	while(fastaFile && letter != '>'){
-	
-		letter = fastaFile.get();
+	}
+	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(isalpha(letter)){
+		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);
 		
-			sequence += letter;
+		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(); }
 			
 		}
 		
 	}
-	fastaFile.putback(letter);
-
-	if(sequence.find_first_of('-') != string::npos){
-		setAligned(sequence);
+	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();
+	
+			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(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);
 	}
-	setUnaligned(sequence);
 }
-
-
 //********************************************************************************************************************
 
-string Sequence::convert2ints(){
+void Sequence::initialize(){
 	
-	if(unaligned == "")	{	/* need to throw an error */	}
+	name = "";
+	unaligned = "";
+	aligned = "";
+	pairwise = "";
 	
-	string processed;
+	numBases = 0;
+	alignmentLength = 0;
+	isAligned = 0;
+	startPos = -1;
+	endPos = -1;
+	longHomoPolymer = -1;
+	ambigBases = -1;
 	
-	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;
-}
+}	
 
 //********************************************************************************************************************
 
-void Sequence::setName(string seqName){
+void Sequence::setName(string seqName) {
 	if(seqName[0] == '>')	{	name = seqName.substr(1);	}
 	else					{	name = seqName;				}
 }
@@ -79,23 +461,48 @@ void Sequence::setName(string seqName){
 
 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++){
+		for(int j=0;j<sequence.length();j++) {
 			if(isalpha(sequence[j]))	{	temp += sequence[j];	}
 		}
 		unaligned = temp;
 	}
-	else{
+	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;	
 }
 
 //********************************************************************************************************************
@@ -106,16 +513,43 @@ void Sequence::setPairwise(string sequence){
 
 //********************************************************************************************************************
 
-string Sequence::getSeqName(){
+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(){
-	return aligned;
+	if(isAligned == 0)	{ return unaligned; }
+	else				{  return aligned;  }
 }
 
+//********************************************************************************************************************
+
+string Sequence::getInlineSeq(){
+	return name + '\t' + aligned;	
+}
+
+
 //********************************************************************************************************************
 
 string Sequence::getPairwise(){
@@ -129,3 +563,211 @@ string Sequence::getUnaligned(){
 }
 
 //********************************************************************************************************************
+
+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::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] != '.')&&(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; 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] != '.')&&(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;
+        aligned = "";
+        isAligned = 0;
+	}
+	
+}
+
+///**************************************************************************************************/