From 91f4cdd89d822365c9fddf8ea31a2a48a5fa006b Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 21 Aug 2015 13:57:47 +0200
Subject: [PATCH] allow to extract sequence from HMM
---
modules/seq/base/doc/seq.rst | 4 ++++
modules/seq/base/pymod/export_hmm.cc | 1 +
modules/seq/base/src/hmm.cc | 10 ++++++++++
modules/seq/base/src/hmm.hh | 17 +++++++++++++++++
4 files changed, 32 insertions(+)
diff --git a/modules/seq/base/doc/seq.rst b/modules/seq/base/doc/seq.rst
index cecd2fd1b..da94a428b 100644
--- a/modules/seq/base/doc/seq.rst
+++ b/modules/seq/base/doc/seq.rst
@@ -503,6 +503,10 @@ single columns containing amino acid frequencies and transition probabilities.
:param col: Column to add
:type col: :class:`HMMColumn`
+ .. attribute:: sequence
+
+ Sequence of the columns
+
.. attribute:: columns
Iterable columns of the HMM
diff --git a/modules/seq/base/pymod/export_hmm.cc b/modules/seq/base/pymod/export_hmm.cc
index 944892f80..fea380dca 100644
--- a/modules/seq/base/pymod/export_hmm.cc
+++ b/modules/seq/base/pymod/export_hmm.cc
@@ -44,5 +44,6 @@ void export_hmm()
make_function(&HMM::GetColumns,
return_value_policy<copy_const_reference>()))
.add_property("avg_entropy", &HMM::GetAverageEntropy)
+ .add_property("sequence",&HMM::GetSequence)
;
}
diff --git a/modules/seq/base/src/hmm.cc b/modules/seq/base/src/hmm.cc
index 07555a3c5..e53b06273 100644
--- a/modules/seq/base/src/hmm.cc
+++ b/modules/seq/base/src/hmm.cc
@@ -149,6 +149,16 @@ HMMPtr HMM::Load(const std::string& filename) {
return hmm;
}
+String HMM::GetSequence() const{
+
+ std::stringstream ss;
+ for(HMMColumnList::const_iterator i = this->columns_begin();
+ i != this->columns_end(); ++i){
+ ss << i->GetOneLetterCode();
+ }
+ return ss.str();
+}
+
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 9f1871827..0dcaf3686 100644
--- a/modules/seq/base/src/hmm.hh
+++ b/modules/seq/base/src/hmm.hh
@@ -17,26 +17,36 @@ typedef enum {
class HMMColumn {
public:
+
HMMColumn() : n_eff_(0.0), n_eff_ins_(0.0), n_eff_del_(0.0) {
memset(freq_, 0, sizeof(Real)*20);
memset(trans_, 0, sizeof(Real)*9);
}
+
HMMColumn(const HMMColumn& rhs): olc_(rhs.olc_), n_eff_(rhs.n_eff_),
n_eff_ins_(rhs.n_eff_ins_), n_eff_del_(rhs.n_eff_del_) {
memcpy(freq_, rhs.freq_, sizeof(Real)*20);
memcpy(trans_, rhs.trans_, sizeof(Real)*9);
}
+
Real GetTransitionFreq(HMMState from, HMMState to) const {
return trans_[from][to];
}
+
void SetTransitionFreq(HMMState from, HMMState to, Real freq){
trans_[from][to] = freq;
}
+
void SetNEff(Real val) { n_eff_ = val; }
+
void SetNEffIns(Real val) { n_eff_ins_ = val; }
+
void SetNEffDel(Real val) { n_eff_del_ = val; }
+
Real GetNEff() const { return n_eff_; }
+
Real GetNEffIns() const { return n_eff_ins_; }
+
Real GetNEffDel() const { return n_eff_del_; }
Real GetFreq(char ch) const {
@@ -169,11 +179,17 @@ typedef std::vector<HMMColumn> HMMColumnList;
class HMM {
public:
HMM() {}
+
static HMMPtr Load(const std::string& filename);
+
const std::vector<HMMColumn>& GetColumns() const { return columns_; }
+
const HMMColumn& GetNullModel() const { return null_model_; }
+
void SetNullModel(const HMMColumn& null_model) { null_model_ = null_model; }
+ String GetSequence() const;
+
//some functions to make it behave like a vector
size_t size() const { return columns_.size(); }
@@ -200,6 +216,7 @@ class HMM {
HMMColumnList::iterator columns_end() { return columns_.end(); }
HMMColumnList::const_iterator columns_begin() const { return columns_.begin(); }
HMMColumnList::iterator columns_begin() { return columns_.begin(); }
+
Real GetAverageEntropy() const;
friend std::ofstream& operator<<(std::ofstream& os, HMM& hmm){
--
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