fixed bug in sequencedb read for windows users and substr error in trim.seqs

[mothur.git] / sequencedb.cpp

diff --git a/sequencedb.cpp b/sequencedb.cpp
index ca201d5a211695138540fe585314773fe4020f90..32fc14644698ddedb4248aba10ea3ed3415bf7be 100644 (file)
--- a/sequencedb.cpp
+++ b/sequencedb.cpp
@@ -30,23 +30,11 @@ SequenceDB::SequenceDB(int newSize) {
 
 SequenceDB::SequenceDB(ifstream& filehandle) {
        try{
-               string name, sequence, line;
-               sequence = "";
-               int c;
-               string temp;
-               
-               
+                               
                //read through file
-               while ((c = filehandle.get()) != EOF) {
-                       name = ""; sequence = ""; 
-                       //is this a name
-                       if (c == '>') { 
-                               name = readName(filehandle); 
-                               sequence = readSequence(filehandle); 
-                       }else {  mothurOut("Error fasta in your file. Please correct."); mothurOutEndLine(); }
-
+               while (!filehandle.eof()) {
                        //input sequence info into sequencedb
-                       Sequence newSequence(name, sequence);
+                       Sequence newSequence(filehandle);
                        data.push_back(newSequence);
                        
                        //takes care of white space