diff --git a/modules/seq/alg/doc/seqalg.rst b/modules/seq/alg/doc/seqalg.rst
index c0f9b885b87534ca78f74ee31635b7b1257757b2..31274af12bbbbe32bfb0ca17083f0acf9738b458 100644
--- a/modules/seq/alg/doc/seqalg.rst
+++ b/modules/seq/alg/doc/seqalg.rst
@@ -261,24 +261,59 @@ Algorithms for Alignments
Substitution Weight Matrices and BLOSUM Matrices
--------------------------------------------------------------------------------
-.. autoclass:: SubstWeightMatrix
- :members:
+.. class:: SubstWeightMatrix
+
+ Substitution weights for alignment algorithms
+
+ .. method:: GetWeight(olc_one, olc_two)
+
+ Get :class:`int` weight for pair of characters
+
+ :param olc_one: first character
+ :type olc_one: :class:`string`
+ :param olc_two: second character
+ :type olc_two: :class:`string`
+
+ .. method:: SetWeight(olc_one, olc_two, weight)
+
+ Set :class:`int` weight for pair of characters
+
+ :param olc_one: first character
+ :type olc_one: :class:`string`
+ :param olc_two: second character
+ :type olc_two: :class:`string`
+ :param weight: the weight
+ :type weight: :class:`int`
+
+ .. method:: GetMinWeight()
+
+ Returns the minimal weight of the matrix
+
+ .. method:: GetMaxWeight()
+
+ Returns the maximum weight of the matrix
+
+ .. method:: GetName()
+
+ Getter for name (empty string if not set)
+
+ .. method:: SetName(name)
+
+ Setter for name
+
+ :param name: Name to be set
+ :type name: :class:`str`
.. _blosum:
-Four preset BLOSUM (BLOcks SUbstitution Matrix) matrices are available at
-different levels of sequence identity:
+Four already preset BLOSUM (BLOcks SUbstitution Matrix) matrices are available
+at different levels of sequence identity:
- BLOSUM45
- BLOSUM62
- BLOSUM80
- BLOSUM100
-Two naive substitution matrices:
-
-- IDENTITY: Matches have score of 1, all other are 0
-- MATCH: Matches have score of 1, all other are -1
-
Nucleotide substitution matrices:
- NUC44: Nucleotide substitution matrix used in blastn that can deal with IUPAC
@@ -286,6 +321,14 @@ Nucleotide substitution matrices:
equivalence, i.e. you can just do `m.GetWeight('G', 'U')` instead of first
translating 'U' to 'T'.
+They can be directly accessed upon importing the sequence module:
+
+.. code-block:: python
+
+ from ost import seq
+ mat = seq.alg.BLOSUM62
+ print(mat.GetWeight('A', 'A'))
+
.. _contact-prediction:
diff --git a/modules/seq/alg/pymod/mat.py b/modules/seq/alg/pymod/mat.py
index f00ec2237076edc72287478f6057309a0dfcbe60..873d2b42ac58aa6ec2ab14b7e0b3fb38fef5facc 100644
--- a/modules/seq/alg/pymod/mat.py
+++ b/modules/seq/alg/pymod/mat.py
@@ -9,9 +9,6 @@ BLOSUM45 = _InitMatrix(SubstWeightMatrix.Preset.BLOSUM45)
BLOSUM62 = _InitMatrix(SubstWeightMatrix.Preset.BLOSUM62)
BLOSUM80 = _InitMatrix(SubstWeightMatrix.Preset.BLOSUM80)
BLOSUM100 = _InitMatrix(SubstWeightMatrix.Preset.BLOSUM100)
-IDENTITY = _InitMatrix(SubstWeightMatrix.Preset.IDENTITY)
-MATCH = _InitMatrix(SubstWeightMatrix.Preset.MATCH)
NUC44 = _InitMatrix(SubstWeightMatrix.Preset.NUC44)
-__all__=['BLOSUM45','BLOSUM62','BLOSUM80','BLOSUM100', 'IDENTITY', 'MATCH',
- 'NUC44']
+__all__=['BLOSUM45','BLOSUM62','BLOSUM80','BLOSUM100','NUC44']
diff --git a/modules/seq/alg/pymod/wrap_seq_alg.cc b/modules/seq/alg/pymod/wrap_seq_alg.cc
index 508a8cc5a72064a8498ce0665286ab9d4ddc11e4..cc57693e8899ce11547a0cec8366133408670b29 100644
--- a/modules/seq/alg/pymod/wrap_seq_alg.cc
+++ b/modules/seq/alg/pymod/wrap_seq_alg.cc
@@ -215,6 +215,9 @@ void export_contact_prediction()
.def("GetMinWeight", &SubstWeightMatrix::GetMinWeight)
.def("GetMaxWeight", &SubstWeightMatrix::GetMaxWeight)
.def("AssignPreset", &SubstWeightMatrix::AssignPreset)
+ .def("SetName", &SubstWeightMatrix::SetName)
+ .def("GetName", &SubstWeightMatrix::GetName,
+ return_value_policy<copy_const_reference>())
;
enum_<SubstWeightMatrix::Preset>("Preset")
@@ -222,8 +225,6 @@ void export_contact_prediction()
.value("BLOSUM62", SubstWeightMatrix::BLOSUM62)
.value("BLOSUM80", SubstWeightMatrix::BLOSUM80)
.value("BLOSUM100", SubstWeightMatrix::BLOSUM100)
- .value("IDENTITY", SubstWeightMatrix::IDENTITY)
- .value("MATCH", SubstWeightMatrix::MATCH)
.value("NUC44", SubstWeightMatrix::NUC44)
;
}
diff --git a/modules/seq/alg/src/subst_weight_matrix.cc b/modules/seq/alg/src/subst_weight_matrix.cc
index 6d22a0b9cbd65b8fd104055fefa6a81567511936..3c7ee7225b33c99d54925ce94fa3685ed082c89d 100644
--- a/modules/seq/alg/src/subst_weight_matrix.cc
+++ b/modules/seq/alg/src/subst_weight_matrix.cc
@@ -170,28 +170,6 @@ void FillNucData(ost::seq::alg::SubstWeightMatrix* subst,
}
}
-void FillIdentity(ost::seq::alg::SubstWeightMatrix* subst) {
- char chars[26] = {'A','B','C','D','E','F','G','H','I','J','K','L','M','N','O',
- 'P','Q','R','S','T','U','V','W','X','Y','Z'};
- for(uint i = 0; i < 26; ++i) {
- subst->SetWeight(chars[i], chars[i], 1.0);
- }
-}
-
-void FillMatch(ost::seq::alg::SubstWeightMatrix* subst) {
- char chars[26] = {'A','B','C','D','E','F','G','H','I','J','K','L','M','N','O',
- 'P','Q','R','S','T','U','V','W','X','Y','Z'};
- for(uint i = 0; i < 26; ++i) {
- for(uint j = 0; j < 26; ++j) {
- if(i == j){
- subst->SetWeight(chars[i], chars[j], 1.0);
- } else {
- subst->SetWeight(chars[i], chars[j], -1.0);
- }
- }
- }
-}
-
}
namespace ost { namespace seq { namespace alg {
@@ -205,34 +183,30 @@ void SubstWeightMatrix::AssignPreset(SubstWeightMatrix::Preset p)
switch(p){
case BLOSUM45:{
FillData(this,RAW_BLOSUM45_DATA);
+ this->SetName("blosum45");
break;
}
case BLOSUM62:{
FillData(this,RAW_BLOSUM62_DATA);
+ this->SetName("blosum62");
break;
}
case BLOSUM80:{
FillData(this,RAW_BLOSUM80_DATA);
+ this->SetName("blosum80");
break;
}
case BLOSUM100:{
FillData(this,RAW_BLOSUM100_DATA);
- break;
- }
- case IDENTITY:{
- FillIdentity(this);
- break;
- }
- case MATCH:{
- FillMatch(this);
+ this->SetName("blosum100");
break;
}
case NUC44:{
FillNucData(this,RAW_NUC44_DATA);
+ this->SetName("nuc44");
break;
}
}
}
-
}}}
diff --git a/modules/seq/alg/src/subst_weight_matrix.hh b/modules/seq/alg/src/subst_weight_matrix.hh
index 50636399e659fd037971f2a48d89f8c09453652f..a0e1e5862f4bd5cb748e935e647a5468424aa098 100644
--- a/modules/seq/alg/src/subst_weight_matrix.hh
+++ b/modules/seq/alg/src/subst_weight_matrix.hh
@@ -22,6 +22,7 @@
#include <ctype.h>
#include <string.h>
#include <boost/shared_ptr.hpp>
+#include <ost/base.hh>
#include <ost/config.hh>
#include <ost/seq/alg/module_config.hh>
@@ -44,9 +45,7 @@ public:
BLOSUM62 = 1,
BLOSUM80 = 2,
BLOSUM100 = 3,
- IDENTITY = 4,
- MATCH = 5,
- NUC44 = 6};
+ NUC44 = 4};
/// \brief Initialize substitution matrix with zero.
///
/// In order to get a useful substitution weight matrix, use SetWeight().
@@ -92,6 +91,10 @@ public:
}
}
+ void SetName(const String& name) { name_ = name; }
+
+ const String& GetName() { return name_; }
+
private:
int Index(char aa_one, char aa_two) const {
return (toupper(aa_one)-'A')*ALPHABET_SIZE+(toupper(aa_two)-'A');
@@ -104,6 +107,7 @@ private:
WeightType weights_[ALPHABET_SIZE*ALPHABET_SIZE];
WeightType max_weight_;
WeightType min_weight_;
+ String name_;
};
}}}