X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequence.cpp;h=580f68ae7706ed15a11f9f460e29a56bd441767b;hb=786d5631d9cd5baa6ed6ef16f8b4b384cbc7470f;hp=e9487c519e0d3e0378266eb537d15e28979546dc;hpb=a6c698b20eda3671d22466ab6b98b36331a30804;p=mothur.git

diff --git a/sequence.cpp b/sequence.cpp
index e9487c5..580f68a 100644
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -7,8 +7,6 @@
  *
  */
 
-using namespace std;
-
 #include "sequence.hpp"
 
 /***********************************************************************/
@@ -25,7 +23,6 @@ Sequence::Sequence(string newName, string sequence) {
 	name = newName;
 	if(sequence.find_first_of('-') != string::npos) {
 		setAligned(sequence);
-		isAligned = 1;
 	}
 	setUnaligned(sequence);
 	
@@ -33,10 +30,12 @@ Sequence::Sequence(string newName, string sequence) {
 //********************************************************************************************************************
 
 Sequence::Sequence(ifstream& fastaFile){
+
+	initialize();
+	fastaFile >> name;
+	name = name.substr(1);
 	
-	string accession;				//	provided a file handle to a fasta-formatted sequence file, read in the next
-	fastaFile >> accession;			//	accession number and sequence we find...
-	setName(accession);
+	while (!fastaFile.eof())	{	char c = fastaFile.get(); if (c == 10 || c == 13){	break;	}	} // get rest of line if there's any crap there
 
 	char letter;
 	string sequence;
@@ -52,7 +51,6 @@ Sequence::Sequence(ifstream& fastaFile){
 			if(letter == 'U'){letter = 'T';}
 			sequence += letter;
 		}
-		
 	}
 
 	if(sequence.find_first_of('-') != string::npos){	//	if there are any gaps in the sequence, assume that it is
@@ -131,7 +129,7 @@ void Sequence::setAligned(string sequence){
 			}
 		}
 	}
-	
+	isAligned = 1;	
 }
 
 //********************************************************************************************************************
@@ -249,11 +247,13 @@ int Sequence::getStartPos(){
 	if(endPos == -1){
 		for(int j = 0; j < alignmentLength; j++) {
 			if(aligned[j] != '.'){
-				startPos = j;
+				startPos = j + 1;
 				break;
 			}
 		}
-	}	
+	}
+	if(isAligned == 0){	startPos = 1;	}
+
 	return startPos;
 }
 
@@ -263,11 +263,13 @@ int Sequence::getEndPos(){
 	if(endPos == -1){
 		for(int j=alignmentLength-1;j>=0;j--){
 			if(aligned[j] != '.'){
-				endPos = j;
+				endPos = j + 1;
 				break;
 			}
 		}
 	}
+	if(isAligned == 0){	endPos = numBases;	}
+	
 	return endPos;
 }
 
@@ -278,3 +280,19 @@ bool Sequence::getIsAligned(){
 }
 
 //********************************************************************************************************************
+
+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;
+	
+}
+
+//********************************************************************************************************************