amendment to previous commit

modules/seq/base/src/alignment_handle.cc

@@ -69,8 +69,8 @@ void AlignmentHandle::AddSequence(const ConstSequenceHandle& sequence)
   if (!sequence.IsValid()) {
     throw InvalidSequence();
   }
-  if (!(impl_->GetCount()>0 &&
-      impl_->GetSequence(0)->GetLength()!=sequence.GetLength())) {
+  if (impl_->GetCount()>0 &&
+      impl_->GetSequence(0)->GetLength()!=sequence.GetLength()) {
     throw std::runtime_error("sequence doesn't have the same length as the "
                              "alignment");
   }
@@ -141,7 +141,7 @@ AlignmentHandle AlignmentFromSequenceList(const SequenceList& seq_list)
   if (seq_list.IsValid() && seq_list.SequencesHaveEqualLength()) {
     return AlignmentHandle(seq_list.Impl());
   }
-  throw InvalidAlignment();
+  throw std::runtime_error("sequences have different lengths");
 }
 
 ConstSequenceList AlignmentHandle::GetSequences() const

modules/seq/base/tests/test_alignment.cc

@@ -64,11 +64,12 @@ BOOST_AUTO_TEST_CASE(alignment_triv)
   a = CreateAlignment();
   BOOST_CHECK_NO_THROW(a.AddSequence(CreateSequence("S1","-asdf-")));
   BOOST_CHECK_THROW(a.AddSequence(SequenceHandle()),InvalidSequence);
-  BOOST_CHECK_THROW(a.AddSequence(CreateSequence("S2","-asdf-f")),InvalidSequence);
+  BOOST_CHECK_THROW(a.AddSequence(CreateSequence("S2","-asdf-f")),
+                    std::runtime_error);
   SequenceList list = CreateSequenceList();
   list.AddSequence(CreateSequence("S1", "-asdf-"));
   list.AddSequence(CreateSequence("S2", "fasdfas"));
-  BOOST_CHECK_THROW(AlignmentFromSequenceList(list),InvalidAlignment);
+  BOOST_CHECK_THROW(AlignmentFromSequenceList(list), std::runtime_error);
   list = CreateSequenceList();
   list.AddSequence(CreateSequence("S1", "-asdf-"));
   list.AddSequence(CreateSequence("S2", "fasdfa"));