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 6a15eb5f7d23f93272811a975beedc649a0d9ce9..685f0726e6ec5042d32379874e54b83e8a6eff26 100644 (file)
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -34,10 +34,9 @@ Sequence::Sequence(ifstream& fastaFile){
        initialize();
        fastaFile >> name;
        name = name.substr(1);
-       char c;
-       
-       while ((c = fastaFile.get()) != EOF)    {       if (c == 10){   break;  }       } // get rest of line if there's any crap there
        
+       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;
        
@@ -54,7 +53,7 @@ Sequence::Sequence(ifstream& fastaFile){
                }
        }
 
-       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
@@ -90,7 +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];    }