From 71e280b4ec6faba353988637dafc2ebdfc514ff1 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Sun, 30 Aug 2015 15:26:37 +0200
Subject: [PATCH] Function to extract subpart of HMM
---
modules/seq/base/pymod/export_hmm.cc | 1 +
modules/seq/base/src/hmm.cc | 21 +++++++++++++++++++++
modules/seq/base/src/hmm.hh | 2 ++
3 files changed, 24 insertions(+)
diff --git a/modules/seq/base/pymod/export_hmm.cc b/modules/seq/base/pymod/export_hmm.cc
index 8ca851939..72a072215 100644
--- a/modules/seq/base/pymod/export_hmm.cc
+++ b/modules/seq/base/pymod/export_hmm.cc
@@ -52,6 +52,7 @@ void export_hmm()
class_<HMM, HMMPtr>("HMM", init<>())
.def("Load", &HMM::Load).staticmethod("Load")
.def("AddColumn", &HMM::push_back)
+ .def("Extract", &HMM::Extract)
.add_property("null_model", make_function(&HMM::GetNullModel,
return_value_policy<copy_const_reference>()))
.add_property("columns",
diff --git a/modules/seq/base/src/hmm.cc b/modules/seq/base/src/hmm.cc
index 390a55b82..fd953d5f5 100644
--- a/modules/seq/base/src/hmm.cc
+++ b/modules/seq/base/src/hmm.cc
@@ -159,6 +159,27 @@ String HMM::GetSequence() const{
return ss.str();
}
+HMMPtr HMM::Extract(uint from, uint to){
+
+ if(to <= from){
+ throw std::runtime_error("Second index must be bigger than first one!");
+ }
+
+ if(to >= this->size()){
+ throw std::runtime_error("Invalid index!");
+ }
+
+ HMMPtr return_hmm(new HMM);
+ return_hmm->SetNullModel(null_model_);
+ for(uint i = from; i < to; ++i){
+ return_hmm->push_back(columns_[i]);
+ }
+
+ return return_hmm;
+}
+
+
+
Real HMM::GetAverageEntropy() const {
Real n_eff=0.0;
diff --git a/modules/seq/base/src/hmm.hh b/modules/seq/base/src/hmm.hh
index 82826948e..68b83db1e 100644
--- a/modules/seq/base/src/hmm.hh
+++ b/modules/seq/base/src/hmm.hh
@@ -194,6 +194,8 @@ class HMM {
String GetSequence() const;
+ HMMPtr Extract(uint from, uint to);
+
//some functions to make it behave like a vector
size_t size() const { return columns_.size(); }
--
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