Move alphabet type into SeqString

[mussa.git] / alg / seq_span.cpp

diff --git a/alg/seq_span.cpp b/alg/seq_span.cpp
index 3382bd8fd4288133207a2e4af1afeb96a922a689..2870f0f077f112f57cc2c60857926e2974af1f4b 100644 (file)
--- a/alg/seq_span.cpp
+++ b/alg/seq_span.cpp
@@ -21,8 +21,9 @@ SeqSpan::SeqSpan(const SeqSpan *p)
 {
 }
 
-SeqSpan::SeqSpan(const std::string &seq_)
-  : seq(new SeqString(seq_)),
+SeqSpan::SeqSpan(const std::string &seq_,
+                 AlphabetRef a)
+  : seq(new SeqString(seq_, a)),
     seq_start(0),
     seq_count(seq_.length()),
     parent()
@@ -79,10 +80,6 @@ bool operator<(const SeqSpan& a, const SeqSpan& b)
 bool operator==(const SeqSpan& a, const SeqSpan& b)
 {
   if (SeqSpan::isFamily(a, b)) {
-    std::cout << "  " << a.seq_start 
-              <<  " " << b.seq_start
-              <<  " " << a.seq_count
-              <<  " " << b.seq_count << std::endl;
     // can do fast comparison
     if (a.seq_start == b.seq_start and a.seq_count == b.seq_count) {
       return true;