From 73291a940f65e9db8cf6cfdb996a79e43498ab84 Mon Sep 17 00:00:00 2001
From: Niklaus Johner <nij2003@med.cornell.edu>
Date: Thu, 10 Nov 2011 10:13:51 -0500
Subject: [PATCH] Added a function to find the index of a sequence in an
alignment from its name AlignmentHandle::FindSequenceIndex()
---
modules/seq/base/pymod/export_sequence.cc | 1 +
modules/seq/base/src/alignment_handle.cc | 5 +++++
modules/seq/base/src/alignment_handle.hh | 4 +++-
modules/seq/base/src/impl/sequence_list_impl.cc | 12 ++++++++++++
modules/seq/base/src/impl/sequence_list_impl.hh | 2 ++
5 files changed, 23 insertions(+), 1 deletion(-)
diff --git a/modules/seq/base/pymod/export_sequence.cc b/modules/seq/base/pymod/export_sequence.cc
index 407633775..7b7631041 100644
--- a/modules/seq/base/pymod/export_sequence.cc
+++ b/modules/seq/base/pymod/export_sequence.cc
@@ -337,6 +337,7 @@ void export_sequence()
.def("GetResidue", &AlignmentHandle::GetResidue)
.def("AddSequence", &AlignmentHandle::AddSequence)
.def("FindSequence", &AlignmentHandle::FindSequence)
+ .def("FindSequenceIndex", &AlignmentHandle::FindSequenceIndex)
.def("Copy", &AlignmentHandle::Copy)
.def("ToString", &AlignmentHandle::ToString)
.def("GetLength", &AlignmentHandle::GetLength)
diff --git a/modules/seq/base/src/alignment_handle.cc b/modules/seq/base/src/alignment_handle.cc
index 3e4ed4256..8432d3c90 100644
--- a/modules/seq/base/src/alignment_handle.cc
+++ b/modules/seq/base/src/alignment_handle.cc
@@ -166,6 +166,11 @@ ConstSequenceHandle AlignmentHandle::FindSequence(const String& name) const
return ConstSequenceHandle(impl_->FindSequence(name));
}
+int AlignmentHandle::FindSequenceIndex(const String& name) const
+{
+ this->CheckValidity();
+ return impl_->FindSequenceIndex(name);
+}
void AlignmentHandle::Cut(int start, int end)
{
diff --git a/modules/seq/base/src/alignment_handle.hh b/modules/seq/base/src/alignment_handle.hh
index 9a109215b..5a59cef72 100644
--- a/modules/seq/base/src/alignment_handle.hh
+++ b/modules/seq/base/src/alignment_handle.hh
@@ -97,7 +97,9 @@ public:
/// If several sequences have the same name, the first matching sequence will
/// be returned.
ConstSequenceHandle FindSequence(const String& name) const;
-
+
+ int FindSequenceIndex(const String& name) const;
+
/// \brief attach view to given sequence
/// \sa SequenceHandle::AttachView(const mol::EntityView&)
void AttachView(int seq_index, const mol::EntityView& view);
diff --git a/modules/seq/base/src/impl/sequence_list_impl.cc b/modules/seq/base/src/impl/sequence_list_impl.cc
index f0ef01531..bd332872b 100644
--- a/modules/seq/base/src/impl/sequence_list_impl.cc
+++ b/modules/seq/base/src/impl/sequence_list_impl.cc
@@ -58,6 +58,18 @@ SequenceImplPtr SequenceListImpl::FindSequence(const String& name) const
return SequenceImplPtr();
}
+
+int SequenceListImpl::FindSequenceIndex(const String& name) const
+{
+ for (size_t i=0; i<list_.size(); ++i) {
+ if (list_[i]->GetName()==name) {
+ return int(i);
+ }
+ }
+ return -1;
+}
+
+
String SequenceListImpl::ToString(int width) const
{
std::stringstream buffer;
diff --git a/modules/seq/base/src/impl/sequence_list_impl.hh b/modules/seq/base/src/impl/sequence_list_impl.hh
index 7be941f73..52443dcd6 100644
--- a/modules/seq/base/src/impl/sequence_list_impl.hh
+++ b/modules/seq/base/src/impl/sequence_list_impl.hh
@@ -65,6 +65,8 @@ public:
SequenceImplPtr FindSequence(const String& name) const;
+ int FindSequenceIndex(const String& name) const;
+
String ToString(int width=80) const;
SequenceListImplPtr Slice(int first, int n) const;
--
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