modified sequence class to read fasta files with comments. this required modification...

[mothur.git] / secondarystructurecommand.cpp

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index 7156082f8b1b43228a62c6cf93abec9f2d900109..c2c104e71b1f535cd2a818afe268e5d7e1ed4c24 100644 (file)
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -91,11 +91,13 @@ int AlignCheckCommand::execute(){
                
                while(!in.eof()){
                        
-                       Sequence seq(in);
-                       statData data = getStats(seq.getAligned());
-                       
-                       out << seq.getName() << '\t' << data.pound << '\t' << data.dash << '\t' << data.plus << '\t' << data.equal << '\t';
-                       out << data.loop << '\t' << data.tilde << '\t' << data.total << endl;
+                       Sequence seq(in);  gobble(in);
+                       if (seq.getName() != "") {
+                               statData data = getStats(seq.getAligned());
+                               
+                               out << seq.getName() << '\t' << data.pound << '\t' << data.dash << '\t' << data.plus << '\t' << data.equal << '\t';
+                               out << data.loop << '\t' << data.tilde << '\t' << data.total << endl;
+                       }
                }
 
                in.close();