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/*==========================================================================
SeqAn - The Library for Sequence Analysis
http://www.seqan.de
============================================================================
Copyright (C) 2007
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 3 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
============================================================================
$Id:
==========================================================================*/
#ifndef SEQAN_HEADER_PROFILE_H
#define SEQAN_HEADER_PROFILE_H
namespace SEQAN_NAMESPACE_MAIN
{
//////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////
// Functions
//////////////////////////////////////////////////////////////////////////////
/**
.Function.convertPatternToProfile:
..summary:Converts a pattern into a profile which consists of a set of frequency distributions.
..cat:Motif Search
..signature:convertPatternToProfile(profile,begin,end)
..param.profile:A StringSet of @Class.FrequencyDistribution|frequency distributions@.
...type:Class.StringSet
..param.begin:An iterator pointing to the beginning of a given sequence pattern which is either
a @Shortcut.DnaString@ or a @Shortcut.Peptide@.
...type:Concept.Iterator
...type:Shortcut.DnaIterator
...type:Shortcut.PeptideIterator
..param.end:An iterator pointing to the end of a given sequence pattern which is either
a @Shortcut.DnaString@ or a @Shortcut.Peptide@.
...type:Concept.Iterator
...type:Shortcut.DnaIterator
...type:Shortcut.PeptideIterator
..remarks:The number of @Class.FrequencyDistribution@ objects which together form the profile
equals the length of the given sequence.
..remarks:e.g.:$profile[0]$ represents the frequency distribution for the first residue of
the given sequence.
..see:Function.convertResidueToFrequencyDist
*/
template<typename TProfile, typename TIterStr>
void
convertPatternToProfile(TProfile & profile,
TIterStr str_begin,
TIterStr str_end)
{
typedef typename Position<TProfile>::Type TPos;
unsigned int str_size = str_end-str_begin;
resize(profile, str_size);
TPos pos = 0;
while(str_begin!=str_end)
{
convertResidueToFrequencyDist(profile[pos], *str_begin);
++str_begin;
++pos;
}
}
//////////////////////////////////////////////////////////////////////////////
/**
.Function.convertSetOfPatternsToProfile:
..summary:Converts a set of sequence patterns into a profile.
..cat:Motif Search
..signature:convertSetOfPatternsToProfile(profile,l_mers,pseudocount_mode)
..param.profile:A StringSet of @Class.FrequencyDistribution|frequency distributions@.
...type:Class.StringSet
..param.l_mers:The set of sequence patterns.
...type:Class.StringSet
..param.pseudocount_mode:The @Class.Pseudocount@ object for determining the pseudocount method.
...type:Class.Pseudocount
..remarks:This function is used, for example, in the refinement step of the PROJECTION algorithm to convert
the collection of l-mers inside the corresponding buckets into a profile.
*/
template<typename TProfile, typename TStrings, typename TPseudocountMode>
void
convertSetOfPatternsToProfile(TProfile & profile,
TStrings & l_mers,
TPseudocountMode & pseudocount)
{
typedef typename Value<TStrings>::Type TString;
typedef typename Value<TProfile>::Type TFrequencyDistribution;
typename Size<TString>::Type l = length(l_mers[0]);
resize(profile, l);
typename Iterator<TStrings>::Type l_mers_iter, l_mers_end;
typename Iterator<TString>::Type l_mer_iter, l_mer_end;
l_mers_iter = begin(l_mers);
l_mers_end = end(l_mers);
while(l_mers_iter!=l_mers_end)
{
l_mer_iter = begin(*l_mers_iter);
l_mer_end = end(*l_mers_iter);
while(l_mer_iter!=l_mer_end)
{
++profile[(int)(l_mer_iter-begin(*l_mers_iter))][(int)*l_mer_iter];
++l_mer_iter;
}
++l_mers_iter;
}
normalize(profile, pseudocount);
}
//////////////////////////////////////////////////////////////////////////////
/**
.Function.normalize:
..summary:Determines the normalized frequencies.
..cat:Motif Search
..signature:normalize(container)
..signature:normalize(profile,pseudocount_mode)
..param.container:The @Class.FrequencyDistribution@ or @Class.StringSet@ (of @Class.FrequencyDistribution|frequency distributions@) object.
...type:Class.FrequencyDistribution
...type:Class.StringSet
..param.profile:A StringSet of @Class.FrequencyDistribution|frequency distributions@.
...type:Class.StringSet
..param.pseudocount_mode:The @Class.Pseudocount@ object for determining the pseudocount method.
...type:Class.Pseudocount
..remarks:If necessary, pseudocounts are first added to the frequency values before normalizing them
when the parameter $container$ is a StringSet of @Class.FrequencyDistribution|frequency distributions@ (profile).
*/
template<typename TProfile>
void
normalize(TProfile & profile)
{
typename Iterator<TProfile>::Type iter = begin(profile);
typename Iterator<TProfile>::Type iter_end = end(profile);
while(iter!=iter_end)
{
normalize(*iter);
++iter;
}
}
//////////////////////////////////////////////////////////////////////////////
/**
.Function.completeProfile:
..summary:Concatenates the background frequency with the profile for the motif component.
..cat:Motif Search
..signature:completeProfile(profile,background_distribution)
..param.profile:A StringSet of @Class.FrequencyDistribution|frequency distributions@.
...type:Class.StringSet
..param.background_distribution:The @Class.FrequencyDistribution@ object which represents the backround distribution.
...type:Class.FrequencyDistribution
..remarks:The first row of the final profile (probability matrix) represents the @Class.FrequencyDistribution|background distribution@.
*/
template<typename TProfile>
void
completeProfile(TProfile & profile,
typename Value<TProfile>::Type & background_distribution)
{
TProfile copy(profile);
resize(profile, length(copy)+1);
profile[0] = background_distribution;
typename Iterator<TProfile>::Type iter = begin(copy);
int counter = 1;
for(; !atEnd(iter, copy); goNext(iter))
{
profile[counter] = *iter;
++counter;
}
}
//////////////////////////////////////////////////////////////////////////////
/**
.Function.display:
..summary:Displays a given set of strings.
..cat:Motif Search
..signature:display(strings)
..param.strings:A StringSet.
...type:Class.StringSet
..remarks:This function can also be used to display a profile (probability matrix)
which is a set of @Class.FrequencyDistribution|frequency distributions@.
*/
template<typename TStrings>
void
display(TStrings & strings)
{
if(length(strings)!=0)
{
typename Iterator<TStrings>::Type iter = begin(strings);
int counter = 0;
for(; !atEnd(iter, strings); goNext(iter))
{
std::cout << "[" << counter << "]: " << *iter << "\n";
++counter;
}
std::cout << "\n";
}
else
{
std::cout << "EMPTY STRINGS !!!\n";
}
}
//////////////////////////////////////////////////////////////////////////////////////////////
} // namespace SEQAN_NAMESPACE_MAIN
#endif //#ifndef SEQAN_HEADER_...
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