diff --git a/modules/seq/alg/src/merge_pairwise_alignments.cc b/modules/seq/alg/src/merge_pairwise_alignments.cc
index 9d60859a07b99b7dda1724f54306f91a7605690b..c522869cfa50c64a6609d59fb856b733aa6288cf 100644
--- a/modules/seq/alg/src/merge_pairwise_alignments.cc
+++ b/modules/seq/alg/src/merge_pairwise_alignments.cc
@@ -87,7 +87,8 @@ SequenceHandle shift_reference(const ConstSequenceHandle& ref_seq,
}
new_sequence << ref_str.substr(last);
SequenceHandle s=CreateSequence(ref_seq.GetName(),
- new_sequence.str());
+ new_sequence.str(),
+ ref_seq.GetRole());
if (ref_seq.HasAttachedView())
s.AttachView(ref_seq.GetAttachedView());
s.SetOffset(ref_seq.GetOffset());
@@ -122,7 +123,8 @@ SequenceHandle realign_sequence(const AlignmentHandle& aln,
}
new_sequence << s2.GetOneLetterCode(i);
}
- SequenceHandle s=CreateSequence(s2.GetName(), new_sequence.str());
+ SequenceHandle s=CreateSequence(s2.GetName(), new_sequence.str(),
+ s2.GetRole());
if (s2.HasAttachedView())
s.AttachView(s2.GetAttachedView());
s.SetOffset(s2.GetOffset());
diff --git a/modules/seq/alg/tests/test_merge_pairwise_alignments.cc b/modules/seq/alg/tests/test_merge_pairwise_alignments.cc
index 851f5c9f163911f1166492a25fd94ebcf4c5ea5a..25f9b836bd361560531922e2215bd3001cc909f0 100644
--- a/modules/seq/alg/tests/test_merge_pairwise_alignments.cc
+++ b/modules/seq/alg/tests/test_merge_pairwise_alignments.cc
@@ -34,15 +34,15 @@ BOOST_AUTO_TEST_SUITE(ost_seq_alg)
BOOST_AUTO_TEST_CASE(merge_pairwise_alignments_one)
{
- SequenceHandle ref=CreateSequence("REF", "abcdefghijklmn");
+ SequenceHandle ref=CreateSequence("REF", "abcdefghijklmn", "R");
SequenceHandle s1=CreateSequence("S1", "abcd---efghijklmn");
- SequenceHandle s2=CreateSequence("S2", "abcdxyzefghijklmn");
+ SequenceHandle s2=CreateSequence("S2", "abcdxyzefghijklmn", "X");
AlignmentHandle aln1=CreateAlignment();
aln1.AddSequence(s1);
aln1.AddSequence(s2);
SequenceHandle s3=CreateSequence("S1", "abcdefghij---klmn");
- SequenceHandle s4=CreateSequence("S2", "abcdefghijxyzklmn");
+ SequenceHandle s4=CreateSequence("S2", "abcdefghijxyzklmn", "Y");
AlignmentHandle aln2=CreateAlignment();
aln2.AddSequence(s3);
@@ -55,6 +55,9 @@ BOOST_AUTO_TEST_CASE(merge_pairwise_alignments_one)
BOOST_CHECK_EQUAL(seqs[0].GetString(), "abcd---efghij---klmn");
BOOST_CHECK_EQUAL(seqs[1].GetString(), "abcdxyzefghij---klmn");
BOOST_CHECK_EQUAL(seqs[2].GetString(), "abcd---efghijxyzklmn");
+ BOOST_CHECK_EQUAL(seqs[0].GetRole(), "R");
+ BOOST_CHECK_EQUAL(seqs[1].GetRole(), "X");
+ BOOST_CHECK_EQUAL(seqs[2].GetRole(), "Y");
}
BOOST_AUTO_TEST_CASE(merge_pairwise_alignments_two)
diff --git a/modules/seq/base/pymod/export_sequence.cc b/modules/seq/base/pymod/export_sequence.cc
index b278676fd5f537527d04f13e18780a25ee1fc670..269ce3a7cb584704d5074505180d653ffe93539c 100644
--- a/modules/seq/base/pymod/export_sequence.cc
+++ b/modules/seq/base/pymod/export_sequence.cc
@@ -257,6 +257,8 @@ void const_seq_handle_def(O& bp_class)
.add_property("last_non_gap", &C::GetLastNonGap)
.def("GetAttachedView", &C::GetAttachedView)
.def("GetGaplessString", &C::GetGaplessString)
+ .add_property("role", make_function(&C::GetRole,
+ return_value_policy<copy_const_reference>()))
.def("GetString", &C::GetString,
return_value_policy<copy_const_reference>())
.def("GetName", &C::GetName,
@@ -299,6 +301,9 @@ void export_sequence()
make_function(&SequenceHandle::GetString,
return_value_policy<copy_const_reference>()),
&SequenceHandle::SetString)
+ .add_property("role", make_function(&SequenceHandle::GetRole,
+ return_value_policy<copy_const_reference>()),
+ &SequenceHandle::SetRole)
.def("SetName", &SequenceHandle::SetName)
.add_property("name",
make_function(&SequenceHandle::GetName,
@@ -312,7 +317,8 @@ void export_sequence()
implicitly_convertible<SequenceHandle, ConstSequenceHandle>();
- def("CreateSequence", &CreateSequence);
+ def("CreateSequence", &CreateSequence,
+ (arg("name"), arg("seq"), arg("role")="UNKNOWN"));
/*class_<SequenceHandleList>("SequenceHandleList", init<>())
.def(vector_indexing_suite<SequenceHandleList>())
;*/
@@ -348,6 +354,9 @@ void export_sequence()
.def("GetSequences", &AlignmentHandle::GetSequences)
.def("GetCoverage", &AlignmentHandle::GetCoverage)
.def("AttachView", attach_view_a)
+ .def("SetSequenceRole", &AlignmentHandle::SetSequenceRole)
+ .def("GetSequenceRole", &AlignmentHandle::GetSequenceRole,
+ return_value_policy<copy_const_reference>())
.def("AttachView", attach_view_b)
.def("Cut", &AlignmentHandle::Cut)
.def("MakeRegion", &AlignmentHandle::MakeRegion)
diff --git a/modules/seq/base/src/alignment_handle.cc b/modules/seq/base/src/alignment_handle.cc
index 8432d3c9035e7bfacce6d77f2244df05c4d37358..47a4fd0dd371747b35761519f15c696751fa3a4a 100644
--- a/modules/seq/base/src/alignment_handle.cc
+++ b/modules/seq/base/src/alignment_handle.cc
@@ -313,4 +313,20 @@ mol::EntityViewPair AlignmentHandle::GetMatchingBackboneViews(int idx0, int idx1
return mol::EntityViewPair(v1, v2);
}
+
+const String& AlignmentHandle::GetSequenceRole(int seq_index)
+{
+ this->CheckValidity();
+ return impl_->GetSequence(seq_index)->GetRole();
+
+}
+
+void AlignmentHandle::SetSequenceRole(int seq_index, const String& role)
+{
+ this->CheckValidity();
+ impl_->GetSequence(seq_index)->SetRole(role);
+
+}
+
+
}}
diff --git a/modules/seq/base/src/alignment_handle.hh b/modules/seq/base/src/alignment_handle.hh
index 5a59cef72240dcce57f6ba5f28b24e3663dc33dc..9990e170570d4c19f4c0f4a9eaf5129ea1b2f60f 100644
--- a/modules/seq/base/src/alignment_handle.hh
+++ b/modules/seq/base/src/alignment_handle.hh
@@ -170,6 +170,10 @@ public:
/// between 0 (no coverage) and 1 (full coverage)
Real GetCoverage(int seq_index) const;
+
+ const String& GetSequenceRole(int seq_index);
+
+ void SetSequenceRole(int seq_index, const String& role);
private:
void CheckValidity() const;
impl::SequenceListImplPtr impl_;
diff --git a/modules/seq/base/src/impl/sequence_impl.cc b/modules/seq/base/src/impl/sequence_impl.cc
index 05da39c29b5f167ea6f8e4452da516b69c0610bb..733eaf1b8e17f765581a4cb1e527beb2bf3483ef 100644
--- a/modules/seq/base/src/impl/sequence_impl.cc
+++ b/modules/seq/base/src/impl/sequence_impl.cc
@@ -55,11 +55,12 @@ bool SequenceImpl::IsSequenceStringSane(const String& seq_string)
}
SequenceImplPtr SequenceImpl::FromString(const String& seq_name,
- const String& seq_string)
+ const String& seq_string,
+ const String& role)
{
if (SequenceImpl::IsSequenceStringSane(seq_string)) {
- return SequenceImplPtr(new SequenceImpl(seq_name, seq_string));
+ return SequenceImplPtr(new SequenceImpl(seq_name, seq_string, role));
}
throw InvalidSequence();
}
@@ -102,15 +103,15 @@ void SequenceImpl::SetString(const String& seq)
}
SequenceImpl::SequenceImpl(const String& seq_name,
- const String& seq_string)
- : seq_name_(seq_name), seq_string_(seq_string), offset_(0)
+ const String& seq_string, const String& role)
+ : seq_name_(seq_name), seq_string_(seq_string), seq_role_(role), offset_(0)
{
this->ShiftsFromSequence();
}
SequenceImplPtr SequenceImpl::Copy() const
{
- SequenceImplPtr new_seq(new SequenceImpl(seq_name_, seq_string_));
+ SequenceImplPtr new_seq(new SequenceImpl(seq_name_, seq_string_, seq_role_));
new_seq->offset_=offset_;
new_seq->shifts_=shifts_;
new_seq->attached_view_=attached_view_;
diff --git a/modules/seq/base/src/impl/sequence_impl.hh b/modules/seq/base/src/impl/sequence_impl.hh
index 50f722eaeaa2483ce1eb0bbbdc33403352e9bd4f..fecad2ca921599ecd85c58ee33e6c184bdbd5a52 100644
--- a/modules/seq/base/src/impl/sequence_impl.hh
+++ b/modules/seq/base/src/impl/sequence_impl.hh
@@ -50,7 +50,8 @@ class DLLEXPORT_OST_SEQ SequenceImpl : public GenericPropContainerImpl {
public:
/// \brief Construct new sequence object from sequence_string.
static SequenceImplPtr FromString(const String& seq_name,
- const String& sequence_string);
+ const String& sequence_string,
+ const String& role="UNKNOWN");
/// \brief Get residue index corresponding to given sequence position
/// \param pos zero-based index
@@ -105,7 +106,8 @@ public:
///
/// If you want to check whether the sequence String does only contain
/// valid characters use \c CreateSequence instead.
- SequenceImpl(const String& seq_name, const String& sequence_string);
+ SequenceImpl(const String& seq_name, const String& sequence_string,
+ const String& role);
/// \brief get one letter code of residue at position
char GetOneLetterCode(int position) const;
@@ -148,7 +150,15 @@ public:
{
return seq_string_[index];
}
+ const String& GetRole() const
+ {
+ return seq_role_;
+ }
+ void SetRole(const String& role)
+ {
+ seq_role_=role;
+ }
private:
/// \brief Recalculates gap shifts from sequence.
@@ -169,6 +179,7 @@ private:
} Shift;
String seq_name_;
String seq_string_;
+ String seq_role_;
std::list<Shift> shifts_;
bool editing_;
int offset_;
diff --git a/modules/seq/base/src/sequence_handle.cc b/modules/seq/base/src/sequence_handle.cc
index f14758d803963bcbaba26cbf9507f78d031517af..54cc19589bfb045f045d4f414f26a573cd2e4136 100644
--- a/modules/seq/base/src/sequence_handle.cc
+++ b/modules/seq/base/src/sequence_handle.cc
@@ -59,6 +59,25 @@ char ConstSequenceHandle::operator[](int index) const
+const String& ConstSequenceHandle::GetRole() const
+{
+ this->CheckValidity();
+ return Impl()->GetRole();
+}
+
+
+const String& SequenceHandle::GetRole() const
+{
+ this->CheckValidity();
+ return Impl()->GetRole();
+}
+
+void SequenceHandle::SetRole(const String& role) const
+{
+ this->CheckValidity();
+ Impl()->SetRole(role);
+}
+
void ConstSequenceHandle::CheckValidity() const
{
@@ -78,9 +97,10 @@ impl::SequenceImplPtr& ConstSequenceHandle::Impl() const
}
-SequenceHandle CreateSequence(const String& name, const String& seq)
+SequenceHandle CreateSequence(const String& name, const String& seq,
+ const String& role)
{
- return SequenceHandle(impl::SequenceImpl::FromString(name, seq));
+ return SequenceHandle(impl::SequenceImpl::FromString(name, seq, role));
}
@@ -222,6 +242,7 @@ SequenceHandle SequenceFromInfo(info::InfoGroup& group)
}
#endif
+
std::ostream& operator<<(std::ostream& os, const ConstSequenceHandle& sequence)
{
if (sequence.IsValid()) {
diff --git a/modules/seq/base/src/sequence_handle.hh b/modules/seq/base/src/sequence_handle.hh
index e08c005e40eea176521a8290a5e3a0e88216d316..8117d7117b1da68d377e94ed418b5310846ad41b 100644
--- a/modules/seq/base/src/sequence_handle.hh
+++ b/modules/seq/base/src/sequence_handle.hh
@@ -122,6 +122,8 @@ public:
/// \sa SequenceHandle::AttachView(const mol::EntityView&, const String&)
bool HasAttachedView() const;
+ const String& GetRole() const;
+
bool operator==(const ConstSequenceHandle& rhs) const;
bool operator!=(const ConstSequenceHandle& rhs) const;
@@ -286,6 +288,10 @@ public:
/// \internal
SequenceHandle(const impl::SequenceImplPtr& impl);
+ const String& GetRole() const;
+
+ void SetRole(const String& role) const;
+
impl::SequenceImplPtr& Impl() const;
GenericPropContainerImpl* GpImpl();
@@ -297,9 +303,9 @@ private:
};
SequenceHandle DLLEXPORT_OST_SEQ CreateSequence(const String& name,
- const String& seq);
-
-#if(OST_INFO_ENABLED)
+ const String& seq,
+ const String& role="UNKNOWN");
+
/// \brief export sequence to info
void DLLEXPORT_OST_SEQ SequenceToInfo(const ConstSequenceHandle& sequence,
info::InfoGroup& group);