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LocARNA-1.8.11
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Parameters for scoring. More...
#include <scoring.hh>
Public Member Functions | |
| ScoringParams (score_t basematch_, score_t basemismatch_, score_t indel_, score_t indel_loop_, score_t indel_opening_, score_t indel_opening_loop_, RibosumFreq *ribosum_, Ribofit *ribofit_, score_t unpaired_penalty_, score_t struct_weight_, score_t tau_factor_, score_t exclusion_, double exp_probA_, double exp_probB_, double temp_, bool stacking_, bool new_stacking_, bool mea_scoring_, score_t alpha_factor_, score_t beta_factor_, score_t gamma_factor_, score_t probability_scale_) | |
Public Attributes | |
| const score_t | basematch |
| const score_t | basemismatch |
| constant cost of a base mismatch | |
| const score_t | indel |
| cost per indel (for linear or affine gap cost). | |
| const score_t | indel_loop |
| cost per indel for loops (for linear or affine gap cost). | |
| const score_t | indel_opening |
| cost per gap (for affine gap-cost). Use affine gap cost if non-zero. | |
| const score_t | indel_opening_loop |
| cost per gap for loops(for affine gap-cost). Use affine gap cost if non-zero. | |
| const RibosumFreq * | ribosum |
| const Ribofit * | ribofit |
| const score_t | unpaired_penalty |
| penalty/cost for unpaired bases matched/mismatched/gapped | |
| const score_t | struct_weight |
| const score_t | tau_factor |
| const score_t | exclusion |
| cost of one exclusion. | |
| const double | exp_probA |
| const double | exp_probB |
| const double | temperature |
| const bool | stacking |
| turn on/off stacking terms | |
| const bool | new_stacking |
| turn on/off new stacking terms | |
| const bool | mea_scoring |
| turn on/off mea scoring | |
| const score_t | alpha_factor |
| weight for mea contribution "unstructured" | |
| const score_t | beta_factor |
| weight for mea contribution "structure" | |
| const score_t | gamma_factor |
| weight for mea contribution "consensus" | |
| const score_t | probability_scale |
Parameters for scoring.
Contains all parameters for doing the scoring of alignments in class Scoring. The class encapsulates the configuration of the score.
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inline |
Construct with all scoring parameters
| basematch_ | |
| basemismatch_ | |
| indel_ | |
| indel_loop_ | |
| indel_opening_ | |
| indel_opening_loop_ | |
| ribosum_ | |
| ribofit_ | |
| unpaired_penalty_ | |
| struct_weight_ | |
| tau_factor_ | |
| exclusion_ | |
| exp_probA_ | |
| exp_probB_ | |
| temp_ | |
| stacking_ | |
| new_stacking_ | |
| mea_scoring_ | |
| alpha_factor_ | |
| beta_factor_ | |
| gamma_factor_ | |
| probability_scale_ |
| const score_t LocARNA::ScoringParams::basematch |
constant bonus for a base match. together with basemismatch yields the simplest form of base match/mismatch scoring. Can be replaced by RIBOSUM scores.
| const score_t LocARNA::ScoringParams::probability_scale |
resolution of the mea score. Since the mea score is composed from probabilities and scores are integral there must be some factor to scale the probabilities in order to get scores.
| const Ribofit* LocARNA::ScoringParams::ribofit |
the ribofit matrix, if non-null it is used for base match/mismatch instead of constant values and as contribution for arc-matchs (tau_factor). Overrides ribosum
| const RibosumFreq* LocARNA::ScoringParams::ribosum |
the ribosum matrix, if non-null (and ribofit==null) it is used for base match/mismatch instead of constant values and as contribution for arc-matchs (tau_factor)
| const score_t LocARNA::ScoringParams::struct_weight |
Factor for structure contribution in the classic score. Maximal contribution of 1/2 arc match
| const score_t LocARNA::ScoringParams::tau_factor |
Factor for the contribution of sequence score or ribosum score to arc matchs
1.8.11
