RNAlib-2.4.17
snofold.h
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/* function from fold.c */
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#ifndef VIENNA_RNA_PACKAGE_SNOFOLD_H
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#define VIENNA_RNA_PACKAGE_SNOFOLD_H
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#include <
ViennaRNA/datastructures/basic.h
>
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#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
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/* Normal fold */
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int
snofold(
const
char
*sequence,
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char
*structure,
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const
int
max_assym,
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const
int
threshold,
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const
int
min_s2,
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const
int
max_s2,
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const
int
half_stem,
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const
int
max_half_stem);
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void
snofree_arrays(
const
int
length);
/* free arrays for mfe folding */
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void
snoinitialize_fold(
int
length);
/* allocate arrays for folding */
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void
snoupdate_fold_params(
void
);
/* recalculate parameters */
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int
snoloop_energy(
short
*ptable,
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short
*s,
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short
*s1,
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int
i);
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void
snoexport_fold_arrays(
int
**indx_p,
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int
**mLoop_p,
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int
**cLoop,
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folden
***fold_p,
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folden
***fold_p_XS);
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char
*snobacktrack_fold_from_pair(
const
char
*sequence,
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int
i,
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int
j);
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/* alifold */
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float
alisnofold(
const
char
**strings,
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const
int
max_assym,
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const
int
threshloop,
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const
int
min_s2,
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const
int
max_s2,
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const
int
half_stem,
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const
int
max_half_stem);
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void
alisnofree_arrays(
const
int
length);
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char
*alisnobacktrack_fold_from_pair(
const
char
**sequence,
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int
i,
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int
j,
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int
*cov);
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extern
double
cv_fact
/* =1 */
;
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extern
double
nc_fact
/* =1 */
;
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/* max number of mismatch >>>>>..(( )).>>>> */
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#define MISMATCH 3
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#endif
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#endif
cv_fact
double cv_fact
This variable controls the weight of the covariance term in the energy function of alignment folding ...
node
Data structure for RNAsnoop (fold energy list)
Definition:
basic.h:239
basic.h
Various data structures and pre-processor macros.
nc_fact
double nc_fact
This variable controls the magnitude of the penalty for non-compatible sequences in the covariance te...
ViennaRNA
snofold.h
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