X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequence.cpp;h=38e9b6230838424dd136562111f25967f6822099;hb=c27e902ede71ea4d20af65752ef04459c101611b;hp=752e081e367fc6d572b5622e0b4eb6003a28f9bb;hpb=648ec37228eb16075ace911dd5a5773cdfe683da;p=mothur.git

diff --git a/sequence.cpp b/sequence.cpp
index 752e081..38e9b62 100644
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -10,55 +10,213 @@
 #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);
+	}			
+}
 
-	initialize();	
-	name = newName;
+//********************************************************************************************************************
+//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();
 	
-	//setUnaligned removes any gap characters for us
-	setUnaligned(sequence);
-	setAligned(sequence);
+		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
+			
+			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;
+				}
+			}
+			
+			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");
+		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;
 
-	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 (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);		
+		
+			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(); }
 		
-		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
+	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);		
-   	
-	setAligned(sequence);	
-	//setUnaligned removes any gap characters for us						
-	setUnaligned(sequence);								
+		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(); }
+
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Sequence", "Sequence");
+		exit(1);
+	}							
 }
+
 //********************************************************************************************************************
 string Sequence::getSequenceString(ifstream& fastaFile) {
 	try {
@@ -81,7 +239,7 @@ string Sequence::getSequenceString(ifstream& fastaFile) {
 		return sequence;
 	}
 	catch(exception& e) {
-		errorOut(e, "Sequence", "getSequenceString");
+		m->errorOut(e, "Sequence", "getSequenceString");
 		exit(1);
 	}
 }
@@ -103,11 +261,59 @@ string Sequence::getCommentString(ifstream& fastaFile) {
 		return sequence;
 	}
 	catch(exception& e) {
-		errorOut(e, "Sequence", "getCommentString");
+		m->errorOut(e, "Sequence", "getCommentString");
+		exit(1);
+	}
+}
+//********************************************************************************************************************
+string Sequence::getSequenceString(istringstream& fastaFile) {
+	try {
+		char letter;
+		string sequence = "";	
+		
+		while(!fastaFile.eof()){
+			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);
 	}
 }
-
 //********************************************************************************************************************
 
 void Sequence::initialize(){
@@ -216,7 +422,8 @@ string Sequence::getName(){
 //********************************************************************************************************************
 
 string Sequence::getAligned(){
-	return aligned;
+	if(isAligned == 0)	{ return unaligned; }
+	else				{  return aligned;  }
 }
 
 //********************************************************************************************************************
@@ -273,6 +480,18 @@ int Sequence::getAmbigBases(){
 
 //********************************************************************************************************************
 
+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;
@@ -345,5 +564,4 @@ void Sequence::reverseComplement(){
 	aligned = temp;
 	
 }
-
-//********************************************************************************************************************
+/**************************************************************************************************/