continued work on chimeras and fixed bug in trim.seqs and reverse.seqs that was due...

[mothur.git] / sequence.cpp

diff --git a/sequence.cpp b/sequence.cpp
index e997cc2872cba1e4deeeffc3d3c1c32009568fcf..b2c2b53d0b4078e6e296312662dcdfe0ffe5fbec 100644 (file)
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -21,20 +21,21 @@ Sequence::Sequence(string newName, string sequence) {
 
        initialize();   
        name = newName;
-       if(sequence.find_first_of('-') != string::npos) {
-               setAligned(sequence);
-       }
+       
+       //setUnaligned removes any gap characters for us
        setUnaligned(sequence);
+       setAligned(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;
@@ -50,13 +51,11 @@ 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
-               setAligned(sequence);                                                   //      an alignment file
-       }
-       setUnaligned(sequence);                                                         //      also set the unaligned sequence file
+       setAligned(sequence);   
+       //setUnaligned removes any gap characters for us                                                
+       setUnaligned(sequence);                                                         
 }
 
 //********************************************************************************************************************
@@ -89,7 +88,7 @@ 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];    }
@@ -292,6 +291,7 @@ void Sequence::reverseComplement(){
                else                                            {       temp += 'N';    }
        }
        unaligned = temp;
+       aligned = temp;
        
 }