X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequence.cpp;h=090ee14c1c838098aaaeb1a831ec01e3272ed512;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=872a0f091d49fddac359d528c53c799a50ef3c66;hpb=de67504f85e091a3049ef4c5df8e77f7dcb1d814;p=mothur.git

diff --git a/sequence.cpp b/sequence.cpp
index 872a0f0..090ee14 100644
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -76,10 +76,15 @@ Sequence::Sequence(istringstream& 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 = getSequenceString(fastaString);		
+			int numAmbig = 0;
+			sequence = getSequenceString(fastaString, numAmbig);
+			
 			setAligned(sequence);	
 			//setUnaligned removes any gap characters for us						
-			setUnaligned(sequence);		
+			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(); }
 		
 	}
@@ -118,10 +123,14 @@ Sequence::Sequence(istringstream& fastaString, string JustUnaligned){
 			
 			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);		
+			int numAmbig = 0;
+			sequence = getSequenceString(fastaString, numAmbig);
 			
 			//setUnaligned removes any gap characters for us						
-			setUnaligned(sequence);		
+			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(); }
 		
 	}
@@ -163,11 +172,15 @@ Sequence::Sequence(ifstream& fastaFile){
 			//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);		
-	
+			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(); }
 
 	}
@@ -205,10 +218,14 @@ Sequence::Sequence(ifstream& fastaFile, string JustUnaligned){
 			//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);		
+			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(); }
 		
 	}
@@ -219,10 +236,11 @@ Sequence::Sequence(ifstream& fastaFile, string JustUnaligned){
 }
 
 //********************************************************************************************************************
-string Sequence::getSequenceString(ifstream& fastaFile) {
+string Sequence::getSequenceString(ifstream& fastaFile, int& numAmbig) {
 	try {
 		char letter;
 		string sequence = "";	
+		numAmbig = 0;
 		
 		while(fastaFile){
 			letter= fastaFile.get();
@@ -233,6 +251,10 @@ string Sequence::getSequenceString(ifstream& fastaFile) {
 			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;
 			}
 		}
@@ -267,10 +289,11 @@ string Sequence::getCommentString(ifstream& fastaFile) {
 	}
 }
 //********************************************************************************************************************
-string Sequence::getSequenceString(istringstream& fastaFile) {
+string Sequence::getSequenceString(istringstream& fastaFile, int& numAmbig) {
 	try {
 		char letter;
-		string sequence = "";	
+		string sequence = "";
+		numAmbig = 0;
 		
 		while(!fastaFile.eof()){
 			letter= fastaFile.get();
@@ -282,6 +305,10 @@ string Sequence::getSequenceString(istringstream& fastaFile) {
 			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;
 			}
 		}
@@ -427,6 +454,13 @@ string Sequence::getAligned(){
 	else				{  return aligned;  }
 }
 
+//********************************************************************************************************************
+
+string Sequence::getInlineSeq(){
+	return name + '\t' + aligned;	
+}
+
+
 //********************************************************************************************************************
 
 string Sequence::getPairwise(){
@@ -514,7 +548,7 @@ int Sequence::getLongHomoPolymer(){
 //********************************************************************************************************************
 
 int Sequence::getStartPos(){
-	if(endPos == -1){
+	if(startPos == -1){
 		for(int j = 0; j < alignmentLength; j++) {
 			if(aligned[j] != '.'){
 				startPos = j + 1;
@@ -529,6 +563,17 @@ int Sequence::getStartPos(){
 
 //********************************************************************************************************************
 
+void Sequence::padToPos(int start){
+
+	for(int j = startPos-1; j < start-1; j++) {
+		aligned[j] = '.';
+	}
+	startPos = start;
+
+}
+
+//********************************************************************************************************************
+
 int Sequence::getEndPos(){
 	if(endPos == -1){
 		for(int j=alignmentLength-1;j>=0;j--){
@@ -545,10 +590,20 @@ int Sequence::getEndPos(){
 
 //********************************************************************************************************************
 
+void Sequence::padFromPos(int end){
+	
+	for(int j = end; j < endPos; j++) {
+		aligned[j] = '.';
+	}
+	endPos = end;
+	
+}
+
+//********************************************************************************************************************
+
 bool Sequence::getIsAligned(){
 	return isAligned;
 }
-
 //********************************************************************************************************************
 
 void Sequence::reverseComplement(){