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

@@ -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)

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)
 {

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);

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;

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;