/usr/include/BALL/STRUCTURE/nucleotideMapping.h is in libball1.4-dev 1.4.3~beta1-3.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 | #ifndef BALL_STRUCTURE_NUCLEOTIDEMAPPING_H
#define BALL_STRUCTURE_NUCLEOTIDEMAPPING_H
#include <string>
#include <BALL/DATATYPE/hashMap.h>
namespace BALL
{
class Chain;
class Residue;
/**
* This class defines the mapping between complementary bases in to strands
* of DNA. Ideally this should be tightly coupled with NucleicAcid, however as
* this is currently broken this class has to do the job. This also explains
* why a Chain is required as an input.
*
* @todo: Fix these issues once Nucleotide works properly and is supported throughout BALL
*/
class BALL_EXPORT NucleotideMapping
{
public:
typedef std::pair<const std::string, const std::string> Alignment;
NucleotideMapping();
///@name Factory methods
///@{
/**
* This method constructs a Nucleotide mapping by simply assuming, that the first base on the 5' end
* of a is complementary to the first base on the 3' end of b.
*
* @param a The first nucleic acid, it is assumed that it is available in 5' -> 3' order.
* @param b The second nucleic acid, it is assumed that it is available in 5' -> 3' order.
* @param offset_a start matching at the base in strand a with index offset_a instead of 0
* @param offset_b start matching at the base in strand b with index offset_b instead of 0
*/
static NucleotideMapping assignNaively(Chain& a, Chain& b, unsigned int offset_a = 0, unsigned int offset_b = 0);
/**
* This method tries to reconstruct the base complementarity information by looking at the atom distances between
* the two nucleic acids. Äote that this can fail if the strands are strongly deformed.
*
* @param a The first nucleic acid, it is assumed that it is available in 5' -> 3' order.
* @param b The second nucleic acid, it is assumed that it is available in 5' -> 3' order.
*/
static NucleotideMapping assignFromDistances(Chain& a, Chain& b);
/**
* Construct a NucleotideMapping given a sequence alignment of the strands. Note that residue names
* are not actually checked, but rather any pair of characters different from '-' are considered
* as an instruction to align the next bases. E.g: for the sequences ATGC and TCCG this would be a valid input:
* <p>
* *-***
* **-**
* </p>
* Also the alignment does not need to cover the full length of the sequences. The assignment process simply
* stops when the end of the alignment is reached.
* @param a The first nucleic acid, it is assumed that it is available in 5' -> 3' order.
* @param b The second nucleic acid, it is assumed that it is available in 5' -> 3' order.
* @param alignment A pair of strings defining the mapping between the two strands.
* it may only consist of the characters forming the respective abbreviation of the bases
* and '-' for gaps.
*/
static NucleotideMapping assignFromAlignment(Chain& a, Chain& b, const Alignment& alignment);
///@}
///@name Accessors
///@{
/**
* Get a pointer to the first DNA strand
*/
Chain* getFirstStrand() const;
/**
* Get a pointer to the second DNA strand
*/
Chain* getSecondStrand() const;
/**
* Given a nucleotide a located in the first strand. This method returns the
* nucleotide complementary to a located in the second strand.
* First and second refers to the order the strands were passed in at creation time.
*
* @return If a is not mapped, either because it is not member of the first strand or
* because it has no complementary base 0 is returned
*/
Residue* firstToSecond(Residue* a) const;
/**
* Given a nucleotide b located in the second strand. This method returns the
* nucleotide complementary to b located in the first strand.
* First and second refers to the order the strands were passed in at creation time.
*
* @return If a is not mapped, either because it is not member of the first strand or
* because it has no complementary base NULL is returned
*/
Residue* secondToFirst(Residue* b) const;
///@}
private:
typedef HashMap<Residue*, Residue*> NucleotideMap;
NucleotideMapping(Chain& a, Chain& b, const NucleotideMap& a_to_b, const NucleotideMap& b_to_a);
Chain* a_;
Chain* b_;
NucleotideMap a_to_b_;
NucleotideMap b_to_a_;
};
}
#endif //BALL_STRUCTURE_NUCLEOTIDEMAPPING_H
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