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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()
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)) {
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;
// can do fast comparison
if (a.seq_start == b.seq_start and a.seq_count == b.seq_count) {
return true;