From cf6c07d3f6bc8053e5f0be76689ed8255e06346d Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Tue, 5 Oct 2010 09:23:13 +0200
Subject: [PATCH] changed second arg of MergePairwiseAlignments to
ConstSequenceHandle
---
modules/seq/alg/src/merge_pairwise_alignments.cc | 12 ++++++------
modules/seq/alg/src/merge_pairwise_alignments.hh | 2 +-
2 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/modules/seq/alg/src/merge_pairwise_alignments.cc b/modules/seq/alg/src/merge_pairwise_alignments.cc
index 35126c2bd..f91cc3439 100644
--- a/modules/seq/alg/src/merge_pairwise_alignments.cc
+++ b/modules/seq/alg/src/merge_pairwise_alignments.cc
@@ -34,7 +34,7 @@ typedef std::map<int, int> ShiftMap;
namespace {
void update_shifts(const AlignmentHandle& aln,
- const SequenceHandle& ref_seq,
+ const ConstSequenceHandle& ref_seq,
ShiftMap& shifts)
{
ConstSequenceHandle s1=aln.GetSequence(0);
@@ -68,8 +68,8 @@ void update_shifts(const AlignmentHandle& aln,
}
}
-SequenceHandle shift_reference(const SequenceHandle& ref_seq,
- const ShiftMap& shifts)
+SequenceHandle shift_reference(const ConstSequenceHandle& ref_seq,
+ const ShiftMap& shifts)
{
std::ostringstream new_sequence;
String ref_str=ref_seq.GetString();
@@ -86,7 +86,7 @@ SequenceHandle shift_reference(const SequenceHandle& ref_seq,
}
new_sequence << ref_str.substr(last);
SequenceHandle s=CreateSequence(ref_seq.GetName(),
- new_sequence.str());
+ new_sequence.str());
if (ref_seq.HasAttachedView())
s.AttachView(ref_seq.GetAttachedView());
s.SetOffset(s.GetOffset());
@@ -94,7 +94,7 @@ SequenceHandle shift_reference(const SequenceHandle& ref_seq,
}
SequenceHandle realign_sequence(const AlignmentHandle& aln,
- const ShiftMap& shifts)
+ const ShiftMap& shifts)
{
std::ostringstream new_sequence;
ConstSequenceHandle s1=aln.GetSequence(0);
@@ -130,7 +130,7 @@ SequenceHandle realign_sequence(const AlignmentHandle& aln,
}
AlignmentHandle MergePairwiseAlignments(const AlignmentList& pairwise_alns,
- const SequenceHandle& ref_seq)
+ const ConstSequenceHandle& ref_seq)
{
ShiftMap shifts;
diff --git a/modules/seq/alg/src/merge_pairwise_alignments.hh b/modules/seq/alg/src/merge_pairwise_alignments.hh
index e021dbe09..565b31441 100644
--- a/modules/seq/alg/src/merge_pairwise_alignments.hh
+++ b/modules/seq/alg/src/merge_pairwise_alignments.hh
@@ -43,7 +43,7 @@ namespace ost { namespace seq { namespace alg {
/// contain any gaps.
AlignmentHandle DLLEXPORT_OST_SEQ_ALG
MergePairwiseAlignments(const AlignmentList& pairwise_alns,
- const SequenceHandle& ref_seq);
+ const ConstSequenceHandle& ref_seq);
}}}
#endif
--
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