added getline function to mothur and modified places where we use getline to use...

[mothur.git] / sequence.cpp

diff --git a/sequence.cpp b/sequence.cpp
index e997cc2872cba1e4deeeffc3d3c1c32009568fcf..685f0726e6ec5042d32379874e54b83e8a6eff26 100644 (file)
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -30,11 +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;
@@ -50,10 +51,9 @@ 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
+       if((sequence.find_first_of('-') != string::npos) || (sequence.find_first_of('.') != string::npos)) {    //      if there are any gaps in the sequence, assume that it is
                setAligned(sequence);                                                   //      an alignment file
        }
        setUnaligned(sequence);                                                         //      also set the unaligned sequence file
@@ -89,7 +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];    }