X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequence.cpp;h=71dd3a925fab8eb7771803c6db557dfb9d10200b;hb=b447f829850ae054e42560c7c3ed71b14f3f40bb;hp=b73bfab7caefdb0a97e5f7cc8f3271ec3e51cb57;hpb=17a6a53298a907c005fa93fb82af9e533adcda09;p=mothur.git

diff --git a/sequence.cpp b/sequence.cpp
index b73bfab..71dd3a9 100644
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -10,14 +10,11 @@
 #include "sequence.hpp"
 
 /***********************************************************************/
-
 Sequence::Sequence(){
 	m = MothurOut::getInstance();
 	initialize();
 }
-
 /***********************************************************************/
-
 Sequence::Sequence(string newName, string sequence) {
 	try {
 		m = MothurOut::getInstance();
@@ -33,24 +30,36 @@ Sequence::Sequence(string newName, string 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();
-	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 << "after name "  << endl;
 		name = name.substr(1);
 		string sequence;
-		
+	
 		//read comments
 		while ((name[0] == '#') && fastaString) { 
-			while (fastaString)	{	char c = fastaString.get(); if (c == 10 || c == 13){	break;	}	} // get rest of line if there's any crap there
+			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) {  
@@ -61,12 +70,10 @@ Sequence::Sequence(istringstream& fastaString){
 				break;
 			}
 		}
-	cout << "after mothur comment" << endl;	
-		//read real sequence
-		while (fastaString)	{	char c = fastaString.get(); if (c == 10 || c == 13){	break;	}	} // get rest of line if there's any crap there
-	cout << "after mothur name" << endl;	
+		
+		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);		
-	cout << "after mothur sequence" << endl;	
 		setAligned(sequence);	
 		//setUnaligned removes any gap characters for us						
 		setUnaligned(sequence);		
@@ -76,6 +83,44 @@ Sequence::Sequence(istringstream& fastaString){
 		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;
+		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);		
+	}
+	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
@@ -115,6 +160,44 @@ Sequence::Sequence(ifstream& fastaFile){
 		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;
+		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);	
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Sequence", "Sequence");
+		exit(1);
+	}							
+}
+
 //********************************************************************************************************************
 string Sequence::getSequenceString(ifstream& fastaFile) {
 	try {
@@ -169,8 +252,9 @@ string Sequence::getSequenceString(istringstream& fastaFile) {
 		char letter;
 		string sequence = "";	
 		
-		while(fastaFile){
+		while(!fastaFile.eof()){
 			letter= fastaFile.get();
+	
 			if(letter == '>'){
 				fastaFile.putback(letter);
 				break;
@@ -319,7 +403,8 @@ string Sequence::getName(){
 //********************************************************************************************************************
 
 string Sequence::getAligned(){
-	return aligned;
+	if(isAligned == 0)	{ return unaligned; }
+	else				{  return aligned;  }
 }
 
 //********************************************************************************************************************
@@ -448,5 +533,4 @@ void Sequence::reverseComplement(){
 	aligned = temp;
 	
 }
-
-//********************************************************************************************************************
+/**************************************************************************************************/