From 7298954532521b9c7ec16c3f4f05c2318bdcb871 Mon Sep 17 00:00:00 2001
From: Valerio Mariani <valerio.mariani@unibas.ch>
Date: Thu, 27 Jan 2011 21:57:30 +0100
Subject: [PATCH] Added GetCoverage function
---
modules/seq/base/pymod/export_sequence.cc | 1 +
modules/seq/base/src/alignment_handle.cc | 8 ++++++++
modules/seq/base/src/alignment_handle.hh | 7 +++++++
.../seq/base/src/impl/sequence_list_impl.cc | 18 ++++++++++++++++++
.../seq/base/src/impl/sequence_list_impl.hh | 2 +-
5 files changed, 35 insertions(+), 1 deletion(-)
diff --git a/modules/seq/base/pymod/export_sequence.cc b/modules/seq/base/pymod/export_sequence.cc
index ab36fdaed..b3632fc50 100644
--- a/modules/seq/base/pymod/export_sequence.cc
+++ b/modules/seq/base/pymod/export_sequence.cc
@@ -301,6 +301,7 @@ void export_sequence()
.def("GetLength", &AlignmentHandle::GetLength)
.def("__len__", &AlignmentHandle::GetLength)
.def("GetSequences", &AlignmentHandle::GetSequences)
+ .def("GetCoverage", &AlignmentHandle::GetSequences)
.def("AttachView", attach_view_a)
.def("AttachView", attach_view_b)
.def("Cut", &AlignmentHandle::Cut)
diff --git a/modules/seq/base/src/alignment_handle.cc b/modules/seq/base/src/alignment_handle.cc
index d2a7ab85d..bf2c12fdf 100644
--- a/modules/seq/base/src/alignment_handle.cc
+++ b/modules/seq/base/src/alignment_handle.cc
@@ -263,4 +263,12 @@ int AlignmentHandle::GetSequenceOffset(int seq_index)
this->CheckValidity();
return impl_->GetSequence(seq_index)->GetOffset();
}
+
+Real AlignmentHandle::GetCoverage(int seq_index) const
+{
+ this->CheckValidity();
+ return impl_->GetCoverage(seq_index);
+}
+
+
}}
diff --git a/modules/seq/base/src/alignment_handle.hh b/modules/seq/base/src/alignment_handle.hh
index bcba027d9..823e78be1 100644
--- a/modules/seq/base/src/alignment_handle.hh
+++ b/modules/seq/base/src/alignment_handle.hh
@@ -158,6 +158,13 @@ public:
iterator end() const;
bool IsValid() const { return impl_.get()!=0; }
+
+ ///\brief get coverage of a specifi sequence
+ ///
+ /// returns a value representing how extensively the specified sequence
+ /// covers the first sequence (sequence 0). The function return a value
+ /// between 0 (no coverage) and 1 (full coverage)
+ Real GetCoverage(int seq_index) const;
private:
void CheckValidity() const;
diff --git a/modules/seq/base/src/impl/sequence_list_impl.cc b/modules/seq/base/src/impl/sequence_list_impl.cc
index b955d8b4c..16759dbcf 100644
--- a/modules/seq/base/src/impl/sequence_list_impl.cc
+++ b/modules/seq/base/src/impl/sequence_list_impl.cc
@@ -178,4 +178,22 @@ SequenceListImplPtr SequenceListImpl::Slice(int first, int n) const
}
}
+Real SequenceListImpl::GetCoverage(int seq_index) const
+{
+ int a=0, b=0;
+ String seq_string_0 = GetSequence(0)->GetString();
+ String seq_string_index = GetSequence(seq_index)->GetString();
+ for (int i=0; i<GetSequence(0)->GetLength(); ++i) {
+ if (seq_string_0[i]!='-') {
+ a+=1;
+ if (seq_string_index[i]!='-') {
+ b+=1;
+ }
+ }
+ }
+ Real coverage=Real(b)/Real(a);
+ return coverage;
+}
+
+
}}}
diff --git a/modules/seq/base/src/impl/sequence_list_impl.hh b/modules/seq/base/src/impl/sequence_list_impl.hh
index 66bedd61f..ab382b8c8 100644
--- a/modules/seq/base/src/impl/sequence_list_impl.hh
+++ b/modules/seq/base/src/impl/sequence_list_impl.hh
@@ -78,7 +78,7 @@ public:
return this->GetMaxLength()==this->GetMinLength();
}
-
+ Real GetCoverage(int seq_index) const;
SequenceListImplPtr Copy() const;
--
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