#include <HelixConstraint.h>
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| size_t | minBP |
| | the minimal number of base pairs allowed in the helix (>=2)
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| |
| size_t | maxBP |
| | the maximal number of base pairs allowed in the helix (>=maxBP)
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| |
| size_t | maxIL |
| | the maximally allowed size of internal loops in the helix
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| |
| E_type | maxED |
| | the maximal ED value (per sequence) allowed for a helix
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| |
| E_type | maxE |
| | the maximal energie allowed for a helix
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| |
| bool | checkFullE |
| |
Encodes helix constraints to be used for interaction prediction.
- Author
- Rick Gelhausen
◆ HelixConstraint()
| IntaRNA::HelixConstraint::HelixConstraint |
( |
const size_t |
minBP, |
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const size_t |
maxBP, |
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const size_t |
maxIL, |
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const E_type |
maxED, |
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const E_type |
maxE, |
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const bool |
noED |
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) |
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inline |
Constructor
- Parameters
-
| minBP | minimal number of base pairs a helix is allowed to have (>= 2) |
| maxBP | maximal number of base pairs a helix is allowed to have (>= bpMin) |
| maxIL | maximal size for each internal loop during helix computation |
| maxED | maximal allowed energy for ED-values |
| maxE | maximal allowed energy during helix computation @parem noED whether or not ED values are added in the computation of helices |
◆ ~HelixConstraint()
| IntaRNA::HelixConstraint::~HelixConstraint |
( |
| ) |
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inlinevirtual |
◆ evalFullE()
| bool IntaRNA::HelixConstraint::evalFullE |
( |
| ) |
const |
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inline |
Whether or not only the full interaction energy (including E_init, ED, dangling end contributions, etc) are to be used for energy check (getMaxE()) or the loop-terms only.
- Returns
- true if the full helix energy is to be considered
◆ getMaxBasePairs()
| size_t IntaRNA::HelixConstraint::getMaxBasePairs |
( |
| ) |
const |
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inline |
Provides the maximum number of base pairs allowed within an helix (>=minBP)
- Returns
- the maximum number of base pairs an helix is allowed to have (>=maxBP)
◆ getMaxE()
| E_type IntaRNA::HelixConstraint::getMaxE |
( |
| ) |
const |
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inline |
Provides the maximally allowed energy for a helix to be considered
- Returns
- the maximally allowed energy for a helix
◆ getMaxED()
| E_type IntaRNA::HelixConstraint::getMaxED |
( |
| ) |
const |
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inline |
Provides the maximally allowed ED value (per sequence) for a helix to be considered
- Returns
- the maximally allowed ED value (per sequence) for a helix
◆ getMaxIL()
| size_t IntaRNA::HelixConstraint::getMaxIL |
( |
| ) |
const |
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inline |
Provides the maximally allowed size of each internal loop considered in an helix
- Returns
- the maximally allowed size of each internal loop considered in an helix
◆ getMaxLength1()
| size_t IntaRNA::HelixConstraint::getMaxLength1 |
( |
| ) |
const |
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inline |
Provides the maximal length of the helix in seq1
- Returns
- the maximal length of the helix in seq1
◆ getMaxLength2()
| size_t IntaRNA::HelixConstraint::getMaxLength2 |
( |
| ) |
const |
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inline |
Provides the maximal length of the helix in seq2
- Returns
- the maximal length of the helix in seq2
◆ getMinBasePairs()
| size_t IntaRNA::HelixConstraint::getMinBasePairs |
( |
| ) |
const |
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inline |
Provides the minimum number of base pairs allowed within an helix (>=2)
- Returns
- the minimum number of base pairs an helix is allowed to have (>=2)
◆ getMinInternalLoopSize()
| size_t IntaRNA::HelixConstraint::getMinInternalLoopSize |
( |
| ) |
const |
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inline |
Provides the minimum interior loop length depending on the maximum allowed number of unpaired bases
- Returns
- minimum interior loop length
◆ operator<<
| std::ostream & operator<< |
( |
std::ostream & |
out, |
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const HelixConstraint & |
c |
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) |
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friend |
Prints the helix constraint details to stream
- Parameters
-
| out | the ostream to write to |
| c | the object to add |
- Returns
- the altered stream out
◆ checkFullE
| bool IntaRNA::HelixConstraint::checkFullE |
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protected |
decision variable, whether the full helix energy is to be used for energy checks (true) or the loop-terms only (false)
◆ maxBP
| size_t IntaRNA::HelixConstraint::maxBP |
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protected |
the maximal number of base pairs allowed in the helix (>=maxBP)
◆ maxE
| E_type IntaRNA::HelixConstraint::maxE |
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protected |
the maximal energie allowed for a helix
◆ maxED
| E_type IntaRNA::HelixConstraint::maxED |
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protected |
the maximal ED value (per sequence) allowed for a helix
◆ maxIL
| size_t IntaRNA::HelixConstraint::maxIL |
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protected |
the maximally allowed size of internal loops in the helix
◆ minBP
| size_t IntaRNA::HelixConstraint::minBP |
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protected |
the minimal number of base pairs allowed in the helix (>=2)
The documentation for this class was generated from the following file:
