added set.dir command and modified commands to redirect input and output, removed...

[mothur.git] / sequencedb.cpp

diff --git a/sequencedb.cpp b/sequencedb.cpp
index ca201d5a211695138540fe585314773fe4020f90..b3da429fc57c9da7081640876ee9fbedda808e25 100644 (file)
--- a/sequencedb.cpp
+++ b/sequencedb.cpp
@@ -30,24 +30,13 @@ 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);
-                       data.push_back(newSequence);
+                       Sequence newSequence(filehandle);
+                       
+                       if (newSequence.getName() != "") {   data.push_back(newSequence);  }
                        
                        //takes care of white space
                        gobble(filehandle);