X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequence.cpp;h=aa1f1c7eae3c0b1cb08105a070a172169ecf320e;hb=49b8297d25caae7ad4cf1e5208a4a66fdfe071fe;hp=98aa7b01862c494018c710ec607f5132d8ce2db1;hpb=544469443afe44920bdf279aefd26d29534cabaf;p=mothur.git

diff --git a/sequence.cpp b/sequence.cpp
index 98aa7b0..aa1f1c7 100644
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -7,8 +7,6 @@
  *
  */
 
-using namespace std;
-
 #include "sequence.hpp"
 
 /***********************************************************************/
@@ -32,11 +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
@@ -91,7 +89,7 @@ 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++) {
 			if(isalpha(sequence[j]))	{	temp += sequence[j];	}