[med-svn] [Git][med-team/vienna-rna][upstream] New upstream version 2.4.14+dfsg
Steffen Möller
gitlab at salsa.debian.org
Mon Jun 22 17:29:57 BST 2020
Steffen Möller pushed to branch upstream at Debian Med / vienna-rna
Commits:
bbc579f5 by Steffen Moeller at 2020-06-22T17:52:11+02:00
New upstream version 2.4.14+dfsg
- - - - -
18 changed files:
- − doc/refman-html
- − install-sh
- − interfaces/Perl/RNA.pm
- − interfaces/Perl/RNA_wrap.cpp
- − interfaces/Perl/version.i
- − interfaces/Python3/RNA.py
- − interfaces/Python3/RNA_wrap.cpp
- − interfaces/Python3/version.i
- − packaging/macosx/resources/welcome.txt
- − src/Kinfold/INSTALL
- − src/Kinfold/configure
- − src/Kinwalker/configure
- − src/RNAforester/INSTALL
- − src/RNAforester/configure
- − src/RNAforester/g2-0.72/configure
- − src/RNAlocmin/configure
- − src/ViennaRNA/static/energy_parameter_sets.h
- − src/ViennaRNA/static/templates_postscript.h
Changes:
=====================================
doc/refman-html deleted
=====================================
=====================================
install-sh deleted
=====================================
@@ -1,501 +0,0 @@
-#!/bin/sh
-# install - install a program, script, or datafile
-
-scriptversion=2016-01-11.22; # UTC
-
-# This originates from X11R5 (mit/util/scripts/install.sh), which was
-# later released in X11R6 (xc/config/util/install.sh) with the
-# following copyright and license.
-#
-# Copyright (C) 1994 X Consortium
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to
-# deal in the Software without restriction, including without limitation the
-# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
-# sell copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN
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=====================================
interfaces/Perl/RNA.pm deleted
=====================================
@@ -1,2974 +0,0 @@
-# This file was automatically generated by SWIG (http://www.swig.org).
-# Version 3.0.12
-#
-# Do not make changes to this file unless you know what you are doing--modify
-# the SWIG interface file instead.
-
-package RNA;
-use base qw(Exporter);
-use base qw(DynaLoader);
-package RNAc;
-bootstrap RNA;
-package RNA;
- at EXPORT = qw();
-=head1 NAME
-
-RNA - interface to the ViennaRNA C-library (libRNA.a)
-
-=head1 SYNOPSIS
-
- use RNA;
- $seq = "CGCAGGGAUACCCGCG";
- ($struct, $mfe) = RNA::fold($seq); #predict mfe structure of $seq
- RNA::PS_rna_plot($seq, $struct, "rna.ps"); # write PS plot to rna.ps
- $F = RNA::pf_fold($seq); # compute partition function and pair pobabilities
- RNA::PS_dot_plot($seq, "dot.ps"); # write dot plot to dot.ps
- ...
-
-=head1 DESCRIPTION
-
-The RNA.pm package gives access to almost all functions in the libRNA.a
-library of the Vienna RNA PACKAGE. The Perl wrapper is generated using
-SWIG http://www.swig.org/ with relatively little manual intervention.
-For each C function in the library the perl package provides a function
-of the same name and calling convention (with few exceptions). For
-detailed information you should therefore also consult the documentation
-of the library (info RNAlib).
-
-Note that in general C arrays are wrapped into opaque objects that can
-only be accessed via helper functions. SWIG provides a couple of general
-purpose helper functions, see the section at the end of this file. C
-structures are wrapped into Perl objects using SWIG's shadow class
-mechanism, resulting in a tied hash with keys named after the structure
-members.
-
-For the interrested reader we list for each scalar type of the
-corepsonding C variable in brackets, and point out the header files
-containing the C declaration.
-
-=head2 Folding Routines
-
-Minimum free Energy Folding (from fold.h)
-
-=over 4
-
-=item fold SEQUENCE
-
-=item fold SEQUENCE, CONSTRAINTS
-
-computes the minimum free energy structure of the string SEQUENCE and returns
-the predicted structure and energy, e.g.
-
- ($structure, $mfe) = RNA::fold("UGUGUCGAUGUGCUAU");
-
-If a second argument is supplied and
-L<$fold_constrained|/$fold_constrained>==1 the CONSTRAINTS string is
-used to specify constraints on the predicted structure. The
-characters '|', 'x', '<', '>' mark bases that are paired, unpaired,
-paired upstream, or downstream, respectively; matching brackets "( )"
-denote base pairs, dots '.' are used for unconstrained bases.
-
-In the two argument version the CONSTRAINTS string is modified and holds the
-predicted structure upon return. This is done for backwards compatibility only,
-and might change in future versions.
-
-=item energy_of_struct SEQUENCE, STRUCTURE
-
-returns the energy of SEQUENCE on STRUCTURE (in kcal/mol). The string structure
-must hold a valid secondary structure in bracket notation.
-
-=item update_fold_params
-
-recalculate the pair matrix and energy parameters after a change in folding
-parameters. In many cases (such as changes to
-L<$temperature|/$temperature>) the fold() routine will call
-update_fold_params automatically when necessary.
-
-=item free_arrays
-
-frees memory allocated internally when calling L<fold|/fold>.
-
-
-=item cofold SEQUENCE
-
-=item cofold SEQUENCE, CONSTRAINTS
-
-works as fold, but SEQUENCE may be the concatenation of two RNAs in order
-compute their hybridization structure. E.g.:
-
- $seq1 ="CGCAGGGAUACCCGCG";
- $seq2 ="GCGCCCAUAGGGACGC";
- $RNA::cut_point = length($seq1)+1;
- ($costruct, $comfe) = RNA::cofold($seq1 . $seq2);
-
-=item duplexfold SEQ1 SEQ2
-
-compute the structure upon hybridization of SEQ1 and SEQ2. In contrast to
-cofold only intra-molecular pairs are allowed. Thus, the algorithm runs in
-O(n1*n2) time where n1 and n2 are the lengths of the sequences. The result
-is returned in a C struct containing the innermost base pair (i,j) the
-structure and energy. E.g:
-
- $seq1 ="CGCAGGGAUACCCGCG";
- $seq2 ="GCGCCCAUAGGGACGC";
- $dup = RNA::duplexfold($seq1, $seq2);
- print "Region ", $dup->{i}+1-length($seq1), " to ",
- $dup->{i}, " of seq1 ",
- "pairs up with ", $dup->{j}, " to ",
- $dup->{j}+length($dup->{structure})-length($seq1)-2,
- " of seq2\n";
-
-=back
-
-Partition function Folding (from part_func.h)
-
-=over 4
-
-=item pf_fold SEQUENCE
-
-=item pf_fold SEQUENCE, CONSTRAINTS
-
-calculates the partition function over all possible secondary
-structures and the matrix of pair probabilities for SEQUENCE and
-returns a two element list consisting of a string summarizing possible
-structures. See below on how to access the pair probability matrix. As
-with L<fold|/fold> the second argument can be used to specify folding
-constraints. Constraints are implemented by excluding base pairings
-that contradict the constraint, but without bonus
-energies. Constraints of type '|' (paired base) are ignored. In the
-two argument version CONSTRAINTS is modified to contain the structure
-string on return (obsolete feature, for backwards compatibility only)
-
-=item get_pr I, J
-
-After calling C<pf_fold> the global C variable C<pr> points to the
-computed pair probabilities. Perl access to the C is facilitated by
-the C<get_pr> helper function that looks up and returns the
-probability of the pair (I,J).
-
-=item free_pf_arrays
-
-frees memory allocated for pf_fold
-
-=item update_pf_params LENGTH
-
-recalculate energy parameters for pf_fold. In most cases (such as
-simple changes to L<$temperature|/$temperature>) C<pf_fold>
-will take appropriate action automatically.
-
-=item pbacktrack SEQUENCE
-
-return a random structure chosen according to it's Boltzmann probability..
-Use to produce samples representing the thermodynamic ensemble of
-structures.
-
- RNA::pf_fold($sequence);
- for (1..1000) {
- push @sample, RNA::pbacktrack($sequence);
- }
-
-=item co_pf_fold SEQUENCE
-
-=item co_pf_fold SEQUENCE, CONSTRAINTS
-
-calculates the partition function over all possible secondary
-structures and the matrix of pair probabilities for SEQUENCE.
-SEQUENCE is a concatenation of two sequences (see cofold).
-Returns a five element list consisting of a string summarizing possible
-structures as first element. The second element is the Gibbs free energy of Sequence 1 (as computed also with pf_fold), the third element the Gibbs free energy of Sequence 2. The fourth element is the Gibbs free energy of all structures that have INTERmolecular base pairs, and finally the fifth element is the Gibbs free energy of the whole ensemble (dimers as well as monomers).
-See above on how to access the pair probability matrix. As
-with L<fold|/fold> the second argument can be used to specify folding
-constraints. Constraints are implemented by excluding base pairings
-that contradict the constraint, but without bonus
-energies. Constraints of type '|' (paired base) are ignored. In the
-two argument version CONSTRAINTS is modified to contain the structure
-string on return (obsolete feature, for backwards compatibility only)
-
-=item free_co_pf_arrays
-
-frees memory allocated for co_pf_fold
-
-=item update_pf_co_params LENGTH
-
-recalculate energy parameters for co_pf_fold. In most cases (such as
-simple changes to L<$temperature|/$temperature>) C<co_pf_fold>
-will take appropriate action automatically.
-
-=item get_concentrations FdAB, FdAA, FdBB, FA, FB, CONCA, CONCB
-
-calculates equilibrium concentrations of the three dimers AB, AA, and BB, as well as the two monomers A and B out of the free energies of the duplexes (FdAB, FdAA, FdBB, these are the fourth elements returned by co_pf_fold), the monomers (FA, FB (e.g. the second and third elements returned by co_pf_fold with sequences AB) and the start concentrations of A and B. It returns as first element the concentration of AB dimer, than AA and BB dimer, as fourth element the A monomer concentration, and as fifth and last element the B monomer concentration.
-So, to compute concentrations, you first have to run 3 co_pf_folds (with sequences AB, AA and BB).
-
-=back
-
-Suboptimal Folding (from subopt.h)
-
-=over 4
-
-=item subopt SEQUENCE, CONSTRAINTS, DELTA
-
-=item subopt SEQUENCE, CONSTRAINTS, DELTA, FILEHANDLE
-
-compute all structures of SEQUENCE within DELTA*0.01 kcal/mol of the
-optimum. If specified, results are written to FILEHANDLE and nothing
-is returned. Else, the C function returnes a list of C structs of type
-SOLUTION. The list is wrapped by SWIG as a perl object that can be
-accesses as follows:
-
- $solution = subopt($seq, undef, 500);
- for (0..$solution->size()-1) {
- printf "%s %6.2f\n", $solution->get($_)->{structure},
- $solution->get($_)->{energy};
- }
-
-=back
-
-Alignment Folding (from alifold.h)
-
-=over 4
-
-=item alifold REF
-
-=item fold REF, CONSTRAINTS
-
-similar to fold() but compute the consensus structure for a set of aligned
-sequences. E.g.:
-
- @align = ("GCCAUCCGAGGGAAAGGUU",
- "GAUCGACAGCGUCU-AUCG",
- "CCGUCUUUAUGAGUCCGGC");
- ($consens_struct, $consens_en) = RNA::alifold(\@align);
-
-=item consensus REF
-=item consens_mis REF
-
-compute a simple consensus sequence or "most informative sequence" form an
-alignment. The simple consensus returns the most frequent character for
-each column, the MIS uses the IUPAC symbol that contains all characters
-that are overrepresented in the column.
-
- $mis = consensus_mis(\@align);
-
-
-=back
-
-Inverse Folding (from inverse.h)
-
-=over 4
-
-=item inverse_fold START, TARGET
-
-find a sequence that folds into structure TARGET, by optimizing the
-sequence until its mfe structure (as returned by L<fold|/fold>) is
-TARGET. Startpoint of the optimization is the sequence START. Returns
-a list containing the sequence found and the final value of the cost
-function, i.e. 0 if the search was successful. A random start sequence
-can be generated using L<random_string|/random_string>.
-
-=item inverse_pf_fold START, TARGET
-
-optimizes a sequence (beginning with START) by maximising the
-frequency of the structure TARGET in the thermodynamic ensemble
-of structures. Returns a list containing the optimized sequence and
-the final value of the cost function. The cost function is given by
-C<energy_of_struct(seq, TARGET) - pf_fold(seq)>, i.e.C<-RT*log(p(TARGET))>
-
-=item $final_cost [float]
-
-holds the value of the cost function where the optimization in
-C<inverse_pf_fold> should stop. For values <=0 the optimization will
-only terminate at a local optimimum (which might take very long to reach).
-
-=item $symbolset [char *]
-
-the string symbolset holds the allowed characters to be used by
-C<inverse_fold> and C<inverse_pf_fold>, the default alphabet is "AUGC"
-
-
-=item $give_up [int]
-
-If non-zero stop optimization when its clear that no exact solution
-can be found. Else continue and eventually return an approximate
-solution. Default 0.
-
-=back
-
-Cofolding of two RNA molecules (from cofold.h)
-
-=over 4
-
-
-=back
-
-Global Variables to Modify Folding (from fold_vars.h)
-
-=over 4
-
-=item $noGU [int]
-
-Do not allow GU pairs to form, default 0.
-
-=item $no_closingGU [int]
-
-allow GU only inside stacks, default 0.
-
-=item $tetra_loop [int]
-
-Fold with specially stable 4-loops, default 1.
-
-=item $energy_set [int]
-
-0 = BP; 1=any mit GC; 2=any mit AU-parameter, default 0.
-
-=item $dangles [int]
-
-How to compute dangling ends. 0: no dangling end energies, 1: "normal"
-dangling ends (default), 2: simplified dangling ends, 3: "normal" +
-co-axial stacking. Note that L<pf_fold|/pf_fold> treats cases 1 and 3
-as 2. The same holds for the main computation in L<subopt|/subopt>,
-however subopt will re-evalute energies using
-L<energy_of_struct|energy_of_struct> for cases 1 and 3. See the more
-detailed discussion in RNAlib.texinfo.
-
-=item $nonstandards [char *]
-
-contains allowed non standard bases, default empty string ""
-
-=item $temperature [double]
-
-temperature in degrees Celsius for rescaling parameters, default 37C.
-
-=item $logML [int]
-
-use logarithmic multiloop energy function in
-L<energy_of_struct|/energy_of_struct>, default 0.
-
-=item $noLonelyPairs [int]
-
-consider only structures without isolated base pairs (helices of length 1).
-For L<pf_fold|/pf_fold> only eliminates pairs
-that can B<only> occur as isolated pairs. Default 0.
-
-=item $base_pair [struct bond *]
-
-list of base pairs from last call to L<fold|/fold>. Better use
-the structure string returned by L<fold|/fold>.
-
-=item $pf_scale [double]
-
-scaling factor used by L<pf_fold|/pf_fold> to avoid overflows. Should
-be set to exp(-F/(RT*length)) where F is a guess for the ensmble free
-energy (e.g. use the mfe).
-
-
-=item $fold_constrained [int]
-
-apply constraints in the folding algorithms, default 0.
-
-=item $do_backtrack [int]
-
-If 0 do not compute the pair probabilities in L<pf_fold|/pf_fold>
-(only the partition function). Default 1.
-
-=item $backtrack_type [char]
-
-usually 'F'; 'C' require (1,N) to be bonded; 'M' backtrack as if the
-sequence was part of a multi loop. Used by L<inverse_fold|/inverse_fold>
-
-=item $pr [double *]
-
-the base pairing prob. matrix computed by L<pf_fold|/pf_fold>.
-
-=item $iindx [int *]
-
-Array of indices for moving withing the C<pr> array. Better use
-L<get_pr|/get_pr>.
-
-=back
-
-from move_set.h
-
-=over 4
-
-=item move_standard SEQUENCE, STRUCTURE, MOVE_TYPE, VERBOSITY, SHIFTS, noLP
-
-Walking method to find local minima. There are three different kinds available
-which can be cosen using the MOVE_TYPE enum:
-0 - GRADIENT: take the neighbouring structure with the lowest energy
-1 - FIRST: take the first neighbour with a lower energy
-2 - ADAPTIVE: randomly choose a neighbour
-STRUCTURE is the start structure and will also be used to return the target structure.
-Others are options set as integers.
-
-=back
-
-=head2 Parsing and Comparing Structures
-
-from RNAstruct.h: these functions convert between strings
-representating secondary structures with various levels of coarse
-graining. See the documentation of the C library for details
-
-=over 4
-
-=item b2HIT STRUCTURE
-
-Full -> HIT [incl. root]
-
-=item b2C STRUCTURE
-
-Full -> Coarse [incl. root]
-
-=item b2Shapiro STRUCTURE
-
-Full -> weighted Shapiro [i.r.]
-
-=item add_root STRUCTURE
-
-{Tree} -> ({Tree}R)
-
-=item expand_Shapiro COARSE
-
-add S for stacks to coarse struct
-
-=item expand_Full STRUCTURE
-
-Full -> FFull
-
-=item unexpand_Full FSTRUCTURE
-
-FFull -> Full
-
-=item unweight WCOARSE
-
-remove weights from coarse struct
-
-=item unexpand_aligned_F ALIGN
-
-
-
-=item parse_structure STRUCTURE
-
-computes structure statistics, and fills the following global variables:
-
-$loops [int] number of loops (and stacks)
-$unpaired [int] number of unpaired positions
-$pairs [int] number of paired positions
-$loop_size[int *] holds all loop sizes
-$loop_degree[int *] holds all loop degrees
-$helix_size[int *] holds all helix lengths
-
-=back
-
-from treedist.h: routines for computing tree-edit distances between structures
-
-=over 4
-
-=item make_tree XSTRUCT
-
-convert a structure string as produced by the expand_... functions to a
-Tree, useable as input to tree_edit_distance.
-
-=item tree_edit_distance T1, T2
-
-compare to structures using tree editing. C<T1>, C<T2> must have been
-created using C<tree_edit_distance>
-
-=item print_tree T
-
-mainly for debugging
-
-=item free_tree T
-
-free space allocated by make_tree
-
-=back
-
-from stringdist.h routines to compute structure distances via string-editing
-
-=over 4
-
-=item Make_swString STRUCTURE
-
-[ returns swString * ]
-make input for string_edit_distance
-
-=item string_edit_distance S1, S2
-
-[ returns float ]
-compare to structures using string alignment. C<S1>, C<S2> should be
-created using C<Make_swString>
-
-=back
-
-from profiledist
-
-=over
-
-=item Make_bp_profile LENGTH
-
-[ returns (float *) ]
-condense pair probability matrix C<pr> into a vector containing
-probabilities for unpaired, upstream paired and downstream paired.
-This resulting probability profile is used as input for
-profile_edit_distance
-
-=item profile_edit_distance T1, T2
-
-[ returns float ]
-align two probability profiles produced by C<Make_bp_profile>
-
-=item print_bppm T
-
-[ returns void ]
-print string representation of probability profile
-
-=item free_profile T
-
-[ returns void ]
-free space allocated in Make_bp_profile
-
-=back
-
-Global variables for computing structure distances
-
-=over 4
-
-=item $edit_backtrack [int]
-
-set to 1 if you want backtracking
-
-=item $aligned_line [(char *)[2]]
-
-containes alignmed structures after computing structure distance with
-C<edit_backtrack==1>
-
-=item $cost_matrix [int]
-
-0 usual costs (default), 1 Shapiro's costs
-
-=back
-
-=head2 Utilities (from utils.h)
-
-=over 4
-
-=item space SIZE
-
-allocate memory from C. Usually not needed in Perl
-
-=item nrerror MESSGAE
-
-die with error message. Better use Perl's C<die>
-
-=item $xsubi [unsigned short[3]]
-
-libRNA uses the rand48 48bit random number generator if available, the
-current random number is always stored in $xsubi.
-
-=item init_rand
-
-initialize the $xsubi random number from current time
-
-=item urn
-
-returns a random number between 0 and 1 using the random number
-generator from the RNA library.
-
-=item int_urn FROM, TO
-
-returns random integer in the range [FROM..TO]
-
-=item time_stamp
-
-current date in a string. In perl you might as well use C<locatime>
-
-=item random_string LENGTH, SYMBOLS
-
-returns a string of length LENGTH using characters from the string
-SYMBOLS
-
-=item hamming S1, S2
-
-calculate hamming distance of the strings C<S1> and C<S2>.
-
-
-=item pack_structure STRUCTURE
-
-pack secondary structure, using a 5:1 compression via 3
-encoding. Returns the packed string.
-
-=item unpack_structure PACKED
-
-unpacks a secondary structure packed with pack_structure
-
-=item make_pair_table STRUCTURE
-
-returns a pair table as a newly allocated (short *) C array, such
-that: table[i]=j if (i.j) pair or 0 if i is unpaired, table[0]
-contains the length of the structure.
-
-=item bp_distance STRUCTURE1, STRUCTURE2
-
-returns the base pair distance of the two STRUCTURES. dist = {number
-of base pairs in one structure but not in the other} same as edit
-distance with open-pair close-pair as move-set
-
-=back
-
-from PS_plot.h
-
-=over 4
-
-=item PS_rna_plot SEQUENCE, STRUCTURE, FILENAME
-
-write PostScript drawing of structure to FILENAME. Returns 1 on
-sucess, 0 else.
-
-=item PS_rna_plot_a SEQUENCE, STRUCTURE, FILENAME, PRE, POST
-
-write PostScript drawing of structure to FILENAME. The strings PRE and
-POST contain PostScript code that is included verbatim in the plot just
-before (after) the data. Returns 1 on sucess, 0 else.
-
-=item gmlRNA SEQUENCE, STRUCTURE, FILENAME, OPTION
-
-write structure drawing in gml (Graph Meta Language) to
-FILENAME. OPTION should be a single character. If uppercase the gml
-output will include the SEQUENCE as node labels. IF OPTION equal 'x'
-or 'X' write graph with coordinates (else only connectivity
-information). Returns 1 on sucess, 0 else.
-
-=item ssv_rna_plot SEQUENCE, STRUCTURE, SSFILE
-
-write structure drfawing as coord file for SStructView Returns 1 on
-sucess, 0 else.
-
-=item xrna_plot SEQUENCE, STRUCTURE, SSFILE
-
-write structure drawing as ".ss" file for further editing in XRNA.
-Returns 1 on sucess, 0 else.
-
-=item PS_dot_plot SEQUENCE, FILENAME
-
-write a PostScript dot plot of the pair probability matix to
-FILENAME. Returns 1 on sucess, 0 else.
-
-=item $rna_plot_type [int]
-
-Select layout algorithm for structure drawings. Currently available
-0= simple coordinates, 1= naview, default 1.
-
-=back
-
-from read_epars.c
-
-=over 4
-
-=item read_parameter_file FILENAME
-
-read energy parameters from FILENAME
-
-=item write_parameter_file FILENAME
-
-write energy parameters to FILENAME
-
-=back
-
-=head2 SWIG helper functions
-
-The package includes generic helper functions to access C arrays
-of type C<int>, C<float> and C<double>, such as:
-
-=over 4
-
-=item intP_getitem POINTER, INDEX
-
-return the element INDEX from the array
-
-=item intP_setitem POINTER, INDEX, VALUE
-
-set element INDEX to VALUE
-
-=item new_intP NELEM
-
-allocate a new C array of integers with NELEM elements and return the pointer
-
-=item delete_intP POINTER
-
-deletes the C array by calling free()
-
-=back
-
-substituting C<intP> with C<floatP>, C<doubleP>, C<ushortP>,
-C<shortP>, gives the corresponding functions for arrays of float or
-double, unsigned short, and short. You need to know the correct C
-type however, and the functions work only for arrays of simple types.
-Note, that the shortP... functions were used for unsigned short in previous
-versions, while starting with v1.8.3 it can only access signed short arrays.
-
-On the lowest level the C<cdata> function gives direct access to any data
-in the form of a Perl string.
-
-=over
-
-=item cdata POINTER, SIZE
-
-copies SIZE bytes at POINTER to a Perl string (with binary data)
-
-=item memmove POINTER, STRING
-
-copies the (binary) string STRING to the memory location pointed to by
-POINTER.
-Note: memmove is broken in current swig versions (e.g. 1.3.31)
-
-=back
-
-In combination with Perl's C<unpack> this provides a generic way to convert
-C data structures to Perl. E.g.
-
- RNA::parse_structure($structure); # fills the $RNA::loop_degree array
- @ldegrees = unpack "I*", RNA::cdata($RNA::loop_degree, ($RNA::loops+1)*4);
-
-Warning: using these functions with wrong arguments will corrupt your
-memory and lead to a segmentation fault.
-
-=head1 AUTHOR
-
-Ivo L. Hofacker <ivo at tbi.univie.ac.at>
-
-=cut
-
-# ---------- BASE METHODS -------------
-
-package RNA;
-
-sub TIEHASH {
- my ($classname,$obj) = @_;
- return bless $obj, $classname;
-}
-
-sub CLEAR { }
-
-sub FIRSTKEY { }
-
-sub NEXTKEY { }
-
-sub FETCH {
- my ($self,$field) = @_;
- my $member_func = "swig_${field}_get";
- $self->$member_func();
-}
-
-sub STORE {
- my ($self,$field,$newval) = @_;
- my $member_func = "swig_${field}_set";
- $self->$member_func($newval);
-}
-
-sub this {
- my $ptr = shift;
- return tied(%$ptr);
-}
-
-
-# ------- FUNCTION WRAPPERS --------
-
-package RNA;
-
-*new_intP = *RNAc::new_intP;
-*delete_intP = *RNAc::delete_intP;
-*intP_getitem = *RNAc::intP_getitem;
-*intP_setitem = *RNAc::intP_setitem;
-*new_floatP = *RNAc::new_floatP;
-*delete_floatP = *RNAc::delete_floatP;
-*floatP_getitem = *RNAc::floatP_getitem;
-*floatP_setitem = *RNAc::floatP_setitem;
-*new_doubleP = *RNAc::new_doubleP;
-*delete_doubleP = *RNAc::delete_doubleP;
-*doubleP_getitem = *RNAc::doubleP_getitem;
-*doubleP_setitem = *RNAc::doubleP_setitem;
-*new_ushortP = *RNAc::new_ushortP;
-*delete_ushortP = *RNAc::delete_ushortP;
-*ushortP_getitem = *RNAc::ushortP_getitem;
-*ushortP_setitem = *RNAc::ushortP_setitem;
-*new_shortP = *RNAc::new_shortP;
-*delete_shortP = *RNAc::delete_shortP;
-*shortP_getitem = *RNAc::shortP_getitem;
-*shortP_setitem = *RNAc::shortP_setitem;
-*cdata = *RNAc::cdata;
-*memmove = *RNAc::memmove;
-*params_load = *RNAc::params_load;
-*params_save = *RNAc::params_save;
-*params_load_from_string = *RNAc::params_load_from_string;
-*params_load_RNA_Turner2004 = *RNAc::params_load_RNA_Turner2004;
-*params_load_RNA_Turner1999 = *RNAc::params_load_RNA_Turner1999;
-*params_load_RNA_Langdon2018 = *RNAc::params_load_RNA_Langdon2018;
-*params_load_RNA_misc_special_hairpins = *RNAc::params_load_RNA_misc_special_hairpins;
-*last_parameter_file = *RNAc::last_parameter_file;
-*read_parameter_file = *RNAc::read_parameter_file;
-*write_parameter_file = *RNAc::write_parameter_file;
-*gettype = *RNAc::gettype;
-*settype = *RNAc::settype;
-*init_rand = *RNAc::init_rand;
-*urn = *RNAc::urn;
-*int_urn = *RNAc::int_urn;
-*hamming = *RNAc::hamming;
-*hamming_bound = *RNAc::hamming_bound;
-*encode_seq = *RNAc::encode_seq;
-*random_string = *RNAc::random_string;
-*hamming_distance = *RNAc::hamming_distance;
-*hamming_distance_bound = *RNAc::hamming_distance_bound;
-*pack_structure = *RNAc::pack_structure;
-*unpack_structure = *RNAc::unpack_structure;
-*db_from_ptable = *RNAc::db_from_ptable;
-*db_flatten = *RNAc::db_flatten;
-*db_from_WUSS = *RNAc::db_from_WUSS;
-*ptable = *RNAc::ptable;
-*ptable_from_string = *RNAc::ptable_from_string;
-*ptable_pk = *RNAc::ptable_pk;
-*pt_pk_remove = *RNAc::pt_pk_remove;
-*plist = *RNAc::plist;
-*db_from_plist = *RNAc::db_from_plist;
-*db_pk_remove = *RNAc::db_pk_remove;
-*db_to_tree_string = *RNAc::db_to_tree_string;
-*tree_string_unweight = *RNAc::tree_string_unweight;
-*tree_string_to_db = *RNAc::tree_string_to_db;
-*make_loop_index = *RNAc::make_loop_index;
-*loopidx_from_ptable = *RNAc::loopidx_from_ptable;
-*bp_distance = *RNAc::bp_distance;
-*dist_mountain = *RNAc::dist_mountain;
-*db_pack = *RNAc::db_pack;
-*db_unpack = *RNAc::db_unpack;
-*db_to_element_string = *RNAc::db_to_element_string;
-*consensus = *RNAc::consensus;
-*consens_mis = *RNAc::consens_mis;
-*aln_mpi = *RNAc::aln_mpi;
-*aln_pscore = *RNAc::aln_pscore;
-*aln_conservation_struct = *RNAc::aln_conservation_struct;
-*aln_conservation_col = *RNAc::aln_conservation_col;
-*move_standard = *RNAc::move_standard;
-*filename_sanitize = *RNAc::filename_sanitize;
-*get_xy_coordinates = *RNAc::get_xy_coordinates;
-*simple_circplot_coordinates = *RNAc::simple_circplot_coordinates;
-*naview_xy_coordinates = *RNAc::naview_xy_coordinates;
-*simple_xy_coordinates = *RNAc::simple_xy_coordinates;
-*my_PS_rna_plot_snoop_a = *RNAc::my_PS_rna_plot_snoop_a;
-*file_PS_rnaplot = *RNAc::file_PS_rnaplot;
-*file_PS_rnaplot_a = *RNAc::file_PS_rnaplot_a;
-*gmlRNA = *RNAc::gmlRNA;
-*ssv_rna_plot = *RNAc::ssv_rna_plot;
-*svg_rna_plot = *RNAc::svg_rna_plot;
-*xrna_plot = *RNAc::xrna_plot;
-*PS_rna_plot = *RNAc::PS_rna_plot;
-*PS_rna_plot_a = *RNAc::PS_rna_plot_a;
-*PS_rna_plot_a_gquad = *RNAc::PS_rna_plot_a_gquad;
-*file_PS_aln = *RNAc::file_PS_aln;
-*PS_color_dot_plot = *RNAc::PS_color_dot_plot;
-*PS_color_dot_plot_turn = *RNAc::PS_color_dot_plot_turn;
-*PS_dot_plot_turn = *RNAc::PS_dot_plot_turn;
-*PS_dot_plot_list = *RNAc::PS_dot_plot_list;
-*PS_dot_plot = *RNAc::PS_dot_plot;
-*eval_structure_simple = *RNAc::eval_structure_simple;
-*eval_circ_structure = *RNAc::eval_circ_structure;
-*eval_gquad_structure = *RNAc::eval_gquad_structure;
-*eval_circ_gquad_structure = *RNAc::eval_circ_gquad_structure;
-*eval_structure_pt_simple = *RNAc::eval_structure_pt_simple;
-*energy_of_structure = *RNAc::energy_of_structure;
-*energy_of_circ_structure = *RNAc::energy_of_circ_structure;
-*energy_of_gquad_structure = *RNAc::energy_of_gquad_structure;
-*energy_of_structure_pt = *RNAc::energy_of_structure_pt;
-*energy_of_move = *RNAc::energy_of_move;
-*energy_of_move_pt = *RNAc::energy_of_move_pt;
-*loop_energy = *RNAc::loop_energy;
-*energy_of_struct = *RNAc::energy_of_struct;
-*energy_of_struct_pt = *RNAc::energy_of_struct_pt;
-*energy_of_circ_struct = *RNAc::energy_of_circ_struct;
-*E_ext_stem = *RNAc::E_ext_stem;
-*exp_E_ext_stem = *RNAc::exp_E_ext_stem;
-*E_Stem = *RNAc::E_Stem;
-*E_ExtLoop = *RNAc::E_ExtLoop;
-*exp_E_ExtLoop = *RNAc::exp_E_ExtLoop;
-*exp_E_Stem = *RNAc::exp_E_Stem;
-*E_Hairpin = *RNAc::E_Hairpin;
-*exp_E_Hairpin = *RNAc::exp_E_Hairpin;
-*E_IntLoop = *RNAc::E_IntLoop;
-*exp_E_IntLoop = *RNAc::exp_E_IntLoop;
-*E_IntLoop_Co = *RNAc::E_IntLoop_Co;
-*ubf_eval_int_loop = *RNAc::ubf_eval_int_loop;
-*ubf_eval_int_loop2 = *RNAc::ubf_eval_int_loop2;
-*ubf_eval_ext_int_loop = *RNAc::ubf_eval_ext_int_loop;
-*E_ml_rightmost_stem = *RNAc::E_ml_rightmost_stem;
-*E_MLstem = *RNAc::E_MLstem;
-*exp_E_MLstem = *RNAc::exp_E_MLstem;
-*maximum_matching = *RNAc::maximum_matching;
-*fold = *RNAc::fold;
-*alifold = *RNAc::alifold;
-*cofold = *RNAc::cofold;
-*circfold = *RNAc::circfold;
-*free_arrays = *RNAc::free_arrays;
-*update_fold_params = *RNAc::update_fold_params;
-*circalifold = *RNAc::circalifold;
-*free_alifold_arrays = *RNAc::free_alifold_arrays;
-*free_co_arrays = *RNAc::free_co_arrays;
-*update_cofold_params = *RNAc::update_cofold_params;
-*initialize_cofold = *RNAc::initialize_cofold;
-*Lfoldz = *RNAc::Lfoldz;
-*Lfold = *RNAc::Lfold;
-*aliLfold = *RNAc::aliLfold;
-*pf_fold = *RNAc::pf_fold;
-*pf_circ_fold = *RNAc::pf_circ_fold;
-*pf_float_precision = *RNAc::pf_float_precision;
-*pbacktrack = *RNAc::pbacktrack;
-*pbacktrack5 = *RNAc::pbacktrack5;
-*pbacktrack_circ = *RNAc::pbacktrack_circ;
-*free_pf_arrays = *RNAc::free_pf_arrays;
-*update_pf_params = *RNAc::update_pf_params;
-*mean_bp_distance = *RNAc::mean_bp_distance;
-*init_pf_fold = *RNAc::init_pf_fold;
-*centroid = *RNAc::centroid;
-*co_pf_fold = *RNAc::co_pf_fold;
-*get_concentrations = *RNAc::get_concentrations;
-*free_co_pf_arrays = *RNAc::free_co_pf_arrays;
-*update_co_pf_params = *RNAc::update_co_pf_params;
-*get_pr = *RNAc::get_pr;
-*get_centroid_struct_pl = *RNAc::get_centroid_struct_pl;
-*get_centroid_struct_pr = *RNAc::get_centroid_struct_pr;
-*MEA_from_plist = *RNAc::MEA_from_plist;
-*pfl_fold = *RNAc::pfl_fold;
-*pfl_fold_up = *RNAc::pfl_fold_up;
-*subopt = *RNAc::subopt;
-*zukersubopt = *RNAc::zukersubopt;
-*inverse_fold = *RNAc::inverse_fold;
-*inverse_pf_fold = *RNAc::inverse_pf_fold;
-*b2HIT = *RNAc::b2HIT;
-*b2C = *RNAc::b2C;
-*b2Shapiro = *RNAc::b2Shapiro;
-*add_root = *RNAc::add_root;
-*expand_Shapiro = *RNAc::expand_Shapiro;
-*expand_Full = *RNAc::expand_Full;
-*unexpand_Full = *RNAc::unexpand_Full;
-*unweight = *RNAc::unweight;
-*unexpand_aligned_F = *RNAc::unexpand_aligned_F;
-*parse_structure = *RNAc::parse_structure;
-*make_tree = *RNAc::make_tree;
-*tree_edit_distance = *RNAc::tree_edit_distance;
-*print_tree = *RNAc::print_tree;
-*free_tree = *RNAc::free_tree;
-*Make_swString = *RNAc::Make_swString;
-*string_edit_distance = *RNAc::string_edit_distance;
-*profile_edit_distance = *RNAc::profile_edit_distance;
-*Make_bp_profile_bppm = *RNAc::Make_bp_profile_bppm;
-*print_bppm = *RNAc::print_bppm;
-*free_profile = *RNAc::free_profile;
-*Make_bp_profile = *RNAc::Make_bp_profile;
-*deref_any = *RNAc::deref_any;
-*get_aligned_line = *RNAc::get_aligned_line;
-*file_SHAPE_read = *RNAc::file_SHAPE_read;
-*extract_record_rest_structure = *RNAc::extract_record_rest_structure;
-*read_record = *RNAc::read_record;
-*get_multi_input_line = *RNAc::get_multi_input_line;
-*file_msa_detect_format = *RNAc::file_msa_detect_format;
-*file_msa_write = *RNAc::file_msa_write;
-*file_msa_read = *RNAc::file_msa_read;
-*file_msa_read_record = *RNAc::file_msa_read_record;
-*file_commands_read = *RNAc::file_commands_read;
-*enumerate_necklaces = *RNAc::enumerate_necklaces;
-*rotational_symmetry = *RNAc::rotational_symmetry;
-*duplexfold = *RNAc::duplexfold;
-*duplex_subopt = *RNAc::duplex_subopt;
-*aliduplexfold = *RNAc::aliduplexfold;
-*aliduplex_subopt = *RNAc::aliduplex_subopt;
-*path_options_findpath = *RNAc::path_options_findpath;
-*get_path = *RNAc::get_path;
-*find_saddle = *RNAc::find_saddle;
-*free_path = *RNAc::free_path;
-*fc_add_perl_callback = *RNAc::fc_add_perl_callback;
-*fc_add_perl_data = *RNAc::fc_add_perl_data;
-*sc_add_f_perl_callback = *RNAc::sc_add_f_perl_callback;
-*sc_add_bt_perl_callback = *RNAc::sc_add_bt_perl_callback;
-*sc_add_exp_f_perl_callback = *RNAc::sc_add_exp_f_perl_callback;
-*sc_add_perl_data = *RNAc::sc_add_perl_data;
-*ud_set_data = *RNAc::ud_set_data;
-*ud_set_prod_rule_cb = *RNAc::ud_set_prod_rule_cb;
-*ud_set_exp_prod_rule_cb = *RNAc::ud_set_exp_prod_rule_cb;
-*ud_set_prob_cb = *RNAc::ud_set_prob_cb;
-*Lfold_cb = *RNAc::Lfold_cb;
-*Lfoldz_cb = *RNAc::Lfoldz_cb;
-*aliLfold_cb = *RNAc::aliLfold_cb;
-*pfl_fold_cb = *RNAc::pfl_fold_cb;
-*pfl_fold_up_cb = *RNAc::pfl_fold_up_cb;
-
-############# Class : RNA::intArray ##############
-
-package RNA::intArray;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_intArray(@_);
- bless $self, $pkg if defined($self);
-}
-
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_intArray($self);
- delete $OWNER{$self};
- }
-}
-
-*getitem = *RNAc::intArray_getitem;
-*setitem = *RNAc::intArray_setitem;
-*cast = *RNAc::intArray_cast;
-*frompointer = *RNAc::intArray_frompointer;
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::floatArray ##############
-
-package RNA::floatArray;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_floatArray(@_);
- bless $self, $pkg if defined($self);
-}
-
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_floatArray($self);
- delete $OWNER{$self};
- }
-}
-
-*getitem = *RNAc::floatArray_getitem;
-*setitem = *RNAc::floatArray_setitem;
-*cast = *RNAc::floatArray_cast;
-*frompointer = *RNAc::floatArray_frompointer;
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::doubleArray ##############
-
-package RNA::doubleArray;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_doubleArray(@_);
- bless $self, $pkg if defined($self);
-}
-
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_doubleArray($self);
- delete $OWNER{$self};
- }
-}
-
-*getitem = *RNAc::doubleArray_getitem;
-*setitem = *RNAc::doubleArray_setitem;
-*cast = *RNAc::doubleArray_cast;
-*frompointer = *RNAc::doubleArray_frompointer;
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::DoublePair ##############
-
-package RNA::DoublePair;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_DoublePair(@_);
- bless $self, $pkg if defined($self);
-}
-
-*swig_first_get = *RNAc::DoublePair_first_get;
-*swig_first_set = *RNAc::DoublePair_first_set;
-*swig_second_get = *RNAc::DoublePair_second_get;
-*swig_second_set = *RNAc::DoublePair_second_set;
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_DoublePair($self);
- delete $OWNER{$self};
- }
-}
-
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::IntVector ##############
-
-package RNA::IntVector;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_IntVector(@_);
- bless $self, $pkg if defined($self);
-}
-
-*size = *RNAc::IntVector_size;
-*empty = *RNAc::IntVector_empty;
-*clear = *RNAc::IntVector_clear;
-*push = *RNAc::IntVector_push;
-*pop = *RNAc::IntVector_pop;
-*get = *RNAc::IntVector_get;
-*set = *RNAc::IntVector_set;
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_IntVector($self);
- delete $OWNER{$self};
- }
-}
-
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::UIntVector ##############
-
-package RNA::UIntVector;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_UIntVector(@_);
- bless $self, $pkg if defined($self);
-}
-
-*size = *RNAc::UIntVector_size;
-*empty = *RNAc::UIntVector_empty;
-*clear = *RNAc::UIntVector_clear;
-*push = *RNAc::UIntVector_push;
-*pop = *RNAc::UIntVector_pop;
-*get = *RNAc::UIntVector_get;
-*set = *RNAc::UIntVector_set;
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_UIntVector($self);
- delete $OWNER{$self};
- }
-}
-
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::DoubleVector ##############
-
-package RNA::DoubleVector;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_DoubleVector(@_);
- bless $self, $pkg if defined($self);
-}
-
-*size = *RNAc::DoubleVector_size;
-*empty = *RNAc::DoubleVector_empty;
-*clear = *RNAc::DoubleVector_clear;
-*push = *RNAc::DoubleVector_push;
-*pop = *RNAc::DoubleVector_pop;
-*get = *RNAc::DoubleVector_get;
-*set = *RNAc::DoubleVector_set;
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_DoubleVector($self);
- delete $OWNER{$self};
- }
-}
-
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::StringVector ##############
-
-package RNA::StringVector;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_StringVector(@_);
- bless $self, $pkg if defined($self);
-}
-
-*size = *RNAc::StringVector_size;
-*empty = *RNAc::StringVector_empty;
-*clear = *RNAc::StringVector_clear;
-*push = *RNAc::StringVector_push;
-*pop = *RNAc::StringVector_pop;
-*get = *RNAc::StringVector_get;
-*set = *RNAc::StringVector_set;
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_StringVector($self);
- delete $OWNER{$self};
- }
-}
-
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::ConstCharVector ##############
-
-package RNA::ConstCharVector;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_ConstCharVector(@_);
- bless $self, $pkg if defined($self);
-}
-
-*size = *RNAc::ConstCharVector_size;
-*empty = *RNAc::ConstCharVector_empty;
-*clear = *RNAc::ConstCharVector_clear;
-*push = *RNAc::ConstCharVector_push;
-*pop = *RNAc::ConstCharVector_pop;
-*get = *RNAc::ConstCharVector_get;
-*set = *RNAc::ConstCharVector_set;
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_ConstCharVector($self);
- delete $OWNER{$self};
- }
-}
-
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::SOLUTIONVector ##############
-
-package RNA::SOLUTIONVector;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_SOLUTIONVector(@_);
- bless $self, $pkg if defined($self);
-}
-
-*size = *RNAc::SOLUTIONVector_size;
-*empty = *RNAc::SOLUTIONVector_empty;
-*clear = *RNAc::SOLUTIONVector_clear;
-*push = *RNAc::SOLUTIONVector_push;
-*pop = *RNAc::SOLUTIONVector_pop;
-*get = *RNAc::SOLUTIONVector_get;
-*set = *RNAc::SOLUTIONVector_set;
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_SOLUTIONVector($self);
- delete $OWNER{$self};
- }
-}
-
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::CoordinateVector ##############
-
-package RNA::CoordinateVector;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_CoordinateVector(@_);
- bless $self, $pkg if defined($self);
-}
-
-*size = *RNAc::CoordinateVector_size;
-*empty = *RNAc::CoordinateVector_empty;
-*clear = *RNAc::CoordinateVector_clear;
-*push = *RNAc::CoordinateVector_push;
-*pop = *RNAc::CoordinateVector_pop;
-*get = *RNAc::CoordinateVector_get;
-*set = *RNAc::CoordinateVector_set;
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_CoordinateVector($self);
- delete $OWNER{$self};
- }
-}
-
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::DoubleDoubleVector ##############
-
-package RNA::DoubleDoubleVector;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_DoubleDoubleVector(@_);
- bless $self, $pkg if defined($self);
-}
-
-*size = *RNAc::DoubleDoubleVector_size;
-*empty = *RNAc::DoubleDoubleVector_empty;
-*clear = *RNAc::DoubleDoubleVector_clear;
-*push = *RNAc::DoubleDoubleVector_push;
-*pop = *RNAc::DoubleDoubleVector_pop;
-*get = *RNAc::DoubleDoubleVector_get;
-*set = *RNAc::DoubleDoubleVector_set;
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_DoubleDoubleVector($self);
- delete $OWNER{$self};
- }
-}
-
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::IntIntVector ##############
-
-package RNA::IntIntVector;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_IntIntVector(@_);
- bless $self, $pkg if defined($self);
-}
-
-*size = *RNAc::IntIntVector_size;
-*empty = *RNAc::IntIntVector_empty;
-*clear = *RNAc::IntIntVector_clear;
-*push = *RNAc::IntIntVector_push;
-*pop = *RNAc::IntIntVector_pop;
-*get = *RNAc::IntIntVector_get;
-*set = *RNAc::IntIntVector_set;
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_IntIntVector($self);
- delete $OWNER{$self};
- }
-}
-
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::ElemProbVector ##############
-
-package RNA::ElemProbVector;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_ElemProbVector(@_);
- bless $self, $pkg if defined($self);
-}
-
-*size = *RNAc::ElemProbVector_size;
-*empty = *RNAc::ElemProbVector_empty;
-*clear = *RNAc::ElemProbVector_clear;
-*push = *RNAc::ElemProbVector_push;
-*pop = *RNAc::ElemProbVector_pop;
-*get = *RNAc::ElemProbVector_get;
-*set = *RNAc::ElemProbVector_set;
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_ElemProbVector($self);
- delete $OWNER{$self};
- }
-}
-
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::PathVector ##############
-
-package RNA::PathVector;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_PathVector(@_);
- bless $self, $pkg if defined($self);
-}
-
-*size = *RNAc::PathVector_size;
-*empty = *RNAc::PathVector_empty;
-*clear = *RNAc::PathVector_clear;
-*push = *RNAc::PathVector_push;
-*pop = *RNAc::PathVector_pop;
-*get = *RNAc::PathVector_get;
-*set = *RNAc::PathVector_set;
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_PathVector($self);
- delete $OWNER{$self};
- }
-}
-
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::MoveVector ##############
-
-package RNA::MoveVector;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_MoveVector(@_);
- bless $self, $pkg if defined($self);
-}
-
-*size = *RNAc::MoveVector_size;
-*empty = *RNAc::MoveVector_empty;
-*clear = *RNAc::MoveVector_clear;
-*push = *RNAc::MoveVector_push;
-*pop = *RNAc::MoveVector_pop;
-*get = *RNAc::MoveVector_get;
-*set = *RNAc::MoveVector_set;
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_MoveVector($self);
- delete $OWNER{$self};
- }
-}
-
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::param ##############
-
-package RNA::param;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-*swig_hairpin_get = *RNAc::param_hairpin_get;
-*swig_hairpin_set = *RNAc::param_hairpin_set;
-*swig_bulge_get = *RNAc::param_bulge_get;
-*swig_bulge_set = *RNAc::param_bulge_set;
-*swig_internal_loop_get = *RNAc::param_internal_loop_get;
-*swig_internal_loop_set = *RNAc::param_internal_loop_set;
-*swig_ninio_get = *RNAc::param_ninio_get;
-*swig_ninio_set = *RNAc::param_ninio_set;
-*swig_lxc_get = *RNAc::param_lxc_get;
-*swig_lxc_set = *RNAc::param_lxc_set;
-*swig_MLbase_get = *RNAc::param_MLbase_get;
-*swig_MLbase_set = *RNAc::param_MLbase_set;
-*swig_MLintern_get = *RNAc::param_MLintern_get;
-*swig_MLintern_set = *RNAc::param_MLintern_set;
-*swig_MLclosing_get = *RNAc::param_MLclosing_get;
-*swig_MLclosing_set = *RNAc::param_MLclosing_set;
-*swig_TerminalAU_get = *RNAc::param_TerminalAU_get;
-*swig_TerminalAU_set = *RNAc::param_TerminalAU_set;
-*swig_DuplexInit_get = *RNAc::param_DuplexInit_get;
-*swig_DuplexInit_set = *RNAc::param_DuplexInit_set;
-*swig_Tetraloop_E_get = *RNAc::param_Tetraloop_E_get;
-*swig_Tetraloop_E_set = *RNAc::param_Tetraloop_E_set;
-*swig_Tetraloops_get = *RNAc::param_Tetraloops_get;
-*swig_Tetraloops_set = *RNAc::param_Tetraloops_set;
-*swig_Triloop_E_get = *RNAc::param_Triloop_E_get;
-*swig_Triloop_E_set = *RNAc::param_Triloop_E_set;
-*swig_Triloops_get = *RNAc::param_Triloops_get;
-*swig_Triloops_set = *RNAc::param_Triloops_set;
-*swig_Hexaloop_E_get = *RNAc::param_Hexaloop_E_get;
-*swig_Hexaloop_E_set = *RNAc::param_Hexaloop_E_set;
-*swig_Hexaloops_get = *RNAc::param_Hexaloops_get;
-*swig_Hexaloops_set = *RNAc::param_Hexaloops_set;
-*swig_TripleC_get = *RNAc::param_TripleC_get;
-*swig_TripleC_set = *RNAc::param_TripleC_set;
-*swig_MultipleCA_get = *RNAc::param_MultipleCA_get;
-*swig_MultipleCA_set = *RNAc::param_MultipleCA_set;
-*swig_MultipleCB_get = *RNAc::param_MultipleCB_get;
-*swig_MultipleCB_set = *RNAc::param_MultipleCB_set;
-*swig_temperature_get = *RNAc::param_temperature_get;
-*swig_temperature_set = *RNAc::param_temperature_set;
-*swig_model_details_get = *RNAc::param_model_details_get;
-*swig_model_details_set = *RNAc::param_model_details_set;
-*swig_param_file_get = *RNAc::param_param_file_get;
-*swig_param_file_set = *RNAc::param_param_file_set;
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_param(@_);
- bless $self, $pkg if defined($self);
-}
-
-*get_temperature = *RNAc::param_get_temperature;
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_param($self);
- delete $OWNER{$self};
- }
-}
-
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::exp_param ##############
-
-package RNA::exp_param;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-*swig_exphairpin_get = *RNAc::exp_param_exphairpin_get;
-*swig_exphairpin_set = *RNAc::exp_param_exphairpin_set;
-*swig_expbulge_get = *RNAc::exp_param_expbulge_get;
-*swig_expbulge_set = *RNAc::exp_param_expbulge_set;
-*swig_expinternal_get = *RNAc::exp_param_expinternal_get;
-*swig_expinternal_set = *RNAc::exp_param_expinternal_set;
-*swig_lxc_get = *RNAc::exp_param_lxc_get;
-*swig_lxc_set = *RNAc::exp_param_lxc_set;
-*swig_expMLbase_get = *RNAc::exp_param_expMLbase_get;
-*swig_expMLbase_set = *RNAc::exp_param_expMLbase_set;
-*swig_expMLintern_get = *RNAc::exp_param_expMLintern_get;
-*swig_expMLintern_set = *RNAc::exp_param_expMLintern_set;
-*swig_expMLclosing_get = *RNAc::exp_param_expMLclosing_get;
-*swig_expMLclosing_set = *RNAc::exp_param_expMLclosing_set;
-*swig_expTermAU_get = *RNAc::exp_param_expTermAU_get;
-*swig_expTermAU_set = *RNAc::exp_param_expTermAU_set;
-*swig_expDuplexInit_get = *RNAc::exp_param_expDuplexInit_get;
-*swig_expDuplexInit_set = *RNAc::exp_param_expDuplexInit_set;
-*swig_exptetra_get = *RNAc::exp_param_exptetra_get;
-*swig_exptetra_set = *RNAc::exp_param_exptetra_set;
-*swig_exptri_get = *RNAc::exp_param_exptri_get;
-*swig_exptri_set = *RNAc::exp_param_exptri_set;
-*swig_exphex_get = *RNAc::exp_param_exphex_get;
-*swig_exphex_set = *RNAc::exp_param_exphex_set;
-*swig_Tetraloops_get = *RNAc::exp_param_Tetraloops_get;
-*swig_Tetraloops_set = *RNAc::exp_param_Tetraloops_set;
-*swig_expTriloop_get = *RNAc::exp_param_expTriloop_get;
-*swig_expTriloop_set = *RNAc::exp_param_expTriloop_set;
-*swig_Triloops_get = *RNAc::exp_param_Triloops_get;
-*swig_Triloops_set = *RNAc::exp_param_Triloops_set;
-*swig_Hexaloops_get = *RNAc::exp_param_Hexaloops_get;
-*swig_Hexaloops_set = *RNAc::exp_param_Hexaloops_set;
-*swig_expTripleC_get = *RNAc::exp_param_expTripleC_get;
-*swig_expTripleC_set = *RNAc::exp_param_expTripleC_set;
-*swig_expMultipleCA_get = *RNAc::exp_param_expMultipleCA_get;
-*swig_expMultipleCA_set = *RNAc::exp_param_expMultipleCA_set;
-*swig_expMultipleCB_get = *RNAc::exp_param_expMultipleCB_get;
-*swig_expMultipleCB_set = *RNAc::exp_param_expMultipleCB_set;
-*swig_kT_get = *RNAc::exp_param_kT_get;
-*swig_kT_set = *RNAc::exp_param_kT_set;
-*swig_pf_scale_get = *RNAc::exp_param_pf_scale_get;
-*swig_pf_scale_set = *RNAc::exp_param_pf_scale_set;
-*swig_temperature_get = *RNAc::exp_param_temperature_get;
-*swig_temperature_set = *RNAc::exp_param_temperature_set;
-*swig_alpha_get = *RNAc::exp_param_alpha_get;
-*swig_alpha_set = *RNAc::exp_param_alpha_set;
-*swig_model_details_get = *RNAc::exp_param_model_details_get;
-*swig_model_details_set = *RNAc::exp_param_model_details_set;
-*swig_param_file_get = *RNAc::exp_param_param_file_get;
-*swig_param_file_set = *RNAc::exp_param_param_file_set;
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_exp_param(@_);
- bless $self, $pkg if defined($self);
-}
-
-*get_temperature = *RNAc::exp_param_get_temperature;
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_exp_param($self);
- delete $OWNER{$self};
- }
-}
-
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::md ##############
-
-package RNA::md;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-*swig_temperature_get = *RNAc::md_temperature_get;
-*swig_temperature_set = *RNAc::md_temperature_set;
-*swig_betaScale_get = *RNAc::md_betaScale_get;
-*swig_betaScale_set = *RNAc::md_betaScale_set;
-*swig_pf_smooth_get = *RNAc::md_pf_smooth_get;
-*swig_pf_smooth_set = *RNAc::md_pf_smooth_set;
-*swig_dangles_get = *RNAc::md_dangles_get;
-*swig_dangles_set = *RNAc::md_dangles_set;
-*swig_special_hp_get = *RNAc::md_special_hp_get;
-*swig_special_hp_set = *RNAc::md_special_hp_set;
-*swig_noLP_get = *RNAc::md_noLP_get;
-*swig_noLP_set = *RNAc::md_noLP_set;
-*swig_noGU_get = *RNAc::md_noGU_get;
-*swig_noGU_set = *RNAc::md_noGU_set;
-*swig_noGUclosure_get = *RNAc::md_noGUclosure_get;
-*swig_noGUclosure_set = *RNAc::md_noGUclosure_set;
-*swig_logML_get = *RNAc::md_logML_get;
-*swig_logML_set = *RNAc::md_logML_set;
-*swig_circ_get = *RNAc::md_circ_get;
-*swig_circ_set = *RNAc::md_circ_set;
-*swig_gquad_get = *RNAc::md_gquad_get;
-*swig_gquad_set = *RNAc::md_gquad_set;
-*swig_uniq_ML_get = *RNAc::md_uniq_ML_get;
-*swig_uniq_ML_set = *RNAc::md_uniq_ML_set;
-*swig_energy_set_get = *RNAc::md_energy_set_get;
-*swig_energy_set_set = *RNAc::md_energy_set_set;
-*swig_backtrack_get = *RNAc::md_backtrack_get;
-*swig_backtrack_set = *RNAc::md_backtrack_set;
-*swig_backtrack_type_get = *RNAc::md_backtrack_type_get;
-*swig_backtrack_type_set = *RNAc::md_backtrack_type_set;
-*swig_compute_bpp_get = *RNAc::md_compute_bpp_get;
-*swig_compute_bpp_set = *RNAc::md_compute_bpp_set;
-*swig_nonstandards_get = *RNAc::md_nonstandards_get;
-*swig_nonstandards_set = *RNAc::md_nonstandards_set;
-*swig_max_bp_span_get = *RNAc::md_max_bp_span_get;
-*swig_max_bp_span_set = *RNAc::md_max_bp_span_set;
-*swig_min_loop_size_get = *RNAc::md_min_loop_size_get;
-*swig_min_loop_size_set = *RNAc::md_min_loop_size_set;
-*swig_window_size_get = *RNAc::md_window_size_get;
-*swig_window_size_set = *RNAc::md_window_size_set;
-*swig_oldAliEn_get = *RNAc::md_oldAliEn_get;
-*swig_oldAliEn_set = *RNAc::md_oldAliEn_set;
-*swig_ribo_get = *RNAc::md_ribo_get;
-*swig_ribo_set = *RNAc::md_ribo_set;
-*swig_cv_fact_get = *RNAc::md_cv_fact_get;
-*swig_cv_fact_set = *RNAc::md_cv_fact_set;
-*swig_nc_fact_get = *RNAc::md_nc_fact_get;
-*swig_nc_fact_set = *RNAc::md_nc_fact_set;
-*swig_sfact_get = *RNAc::md_sfact_get;
-*swig_sfact_set = *RNAc::md_sfact_set;
-*swig_rtype_get = *RNAc::md_rtype_get;
-*swig_rtype_set = *RNAc::md_rtype_set;
-*swig_alias_get = *RNAc::md_alias_get;
-*swig_alias_set = *RNAc::md_alias_set;
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_md(@_);
- bless $self, $pkg if defined($self);
-}
-
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_md($self);
- delete $OWNER{$self};
- }
-}
-
-*reset = *RNAc::md_reset;
-*set_from_globals = *RNAc::md_set_from_globals;
-*option_string = *RNAc::md_option_string;
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::ep ##############
-
-package RNA::ep;
-use overload
- '""' => sub { $_[0]->__str__()},
- "=" => sub { my $class = ref($_[0]); $class->new($_[0]) },
- "fallback" => 1;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-*swig_i_get = *RNAc::ep_i_get;
-*swig_i_set = *RNAc::ep_i_set;
-*swig_j_get = *RNAc::ep_j_get;
-*swig_j_set = *RNAc::ep_j_set;
-*swig_p_get = *RNAc::ep_p_get;
-*swig_p_set = *RNAc::ep_p_set;
-*swig_type_get = *RNAc::ep_type_get;
-*swig_type_set = *RNAc::ep_type_set;
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_ep(@_);
- bless $self, $pkg if defined($self);
-}
-
-*__str__ = *RNAc::ep___str__;
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_ep($self);
- delete $OWNER{$self};
- }
-}
-
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::struct_en ##############
-
-package RNA::struct_en;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-*swig_energy_get = *RNAc::struct_en_energy_get;
-*swig_energy_set = *RNAc::struct_en_energy_set;
-*swig_structure_get = *RNAc::struct_en_structure_get;
-*swig_structure_set = *RNAc::struct_en_structure_set;
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_struct_en(@_);
- bless $self, $pkg if defined($self);
-}
-
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_struct_en($self);
- delete $OWNER{$self};
- }
-}
-
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::COORDINATE ##############
-
-package RNA::COORDINATE;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-*get = *RNAc::COORDINATE_get;
-*swig_X_get = *RNAc::COORDINATE_X_get;
-*swig_X_set = *RNAc::COORDINATE_X_set;
-*swig_Y_get = *RNAc::COORDINATE_Y_get;
-*swig_Y_set = *RNAc::COORDINATE_Y_set;
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_COORDINATE(@_);
- bless $self, $pkg if defined($self);
-}
-
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_COORDINATE($self);
- delete $OWNER{$self};
- }
-}
-
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::pbacktrack_mem ##############
-
-package RNA::pbacktrack_mem;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_pbacktrack_mem(@_);
- bless $self, $pkg if defined($self);
-}
-
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_pbacktrack_mem($self);
- delete $OWNER{$self};
- }
-}
-
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::SOLUTION ##############
-
-package RNA::SOLUTION;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-*swig_energy_get = *RNAc::SOLUTION_energy_get;
-*swig_energy_set = *RNAc::SOLUTION_energy_set;
-*swig_structure_get = *RNAc::SOLUTION_structure_get;
-*swig_structure_set = *RNAc::SOLUTION_structure_set;
-*get = *RNAc::SOLUTION_get;
-*size = *RNAc::SOLUTION_size;
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_SOLUTION($self);
- delete $OWNER{$self};
- }
-}
-
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_SOLUTION(@_);
- bless $self, $pkg if defined($self);
-}
-
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::subopt_solution ##############
-
-package RNA::subopt_solution;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-*swig_energy_get = *RNAc::subopt_solution_energy_get;
-*swig_energy_set = *RNAc::subopt_solution_energy_set;
-*swig_structure_get = *RNAc::subopt_solution_structure_get;
-*swig_structure_set = *RNAc::subopt_solution_structure_set;
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_subopt_solution($self);
- delete $OWNER{$self};
- }
-}
-
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_subopt_solution(@_);
- bless $self, $pkg if defined($self);
-}
-
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::SuboptVector ##############
-
-package RNA::SuboptVector;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_SuboptVector(@_);
- bless $self, $pkg if defined($self);
-}
-
-*size = *RNAc::SuboptVector_size;
-*empty = *RNAc::SuboptVector_empty;
-*clear = *RNAc::SuboptVector_clear;
-*push = *RNAc::SuboptVector_push;
-*pop = *RNAc::SuboptVector_pop;
-*get = *RNAc::SuboptVector_get;
-*set = *RNAc::SuboptVector_set;
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_SuboptVector($self);
- delete $OWNER{$self};
- }
-}
-
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::cmd ##############
-
-package RNA::cmd;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_cmd(@_);
- bless $self, $pkg if defined($self);
-}
-
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_cmd($self);
- delete $OWNER{$self};
- }
-}
-
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::duplexT ##############
-
-package RNA::duplexT;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-*swig_i_get = *RNAc::duplexT_i_get;
-*swig_i_set = *RNAc::duplexT_i_set;
-*swig_j_get = *RNAc::duplexT_j_get;
-*swig_j_set = *RNAc::duplexT_j_set;
-*swig_structure_get = *RNAc::duplexT_structure_get;
-*swig_structure_set = *RNAc::duplexT_structure_set;
-*swig_energy_get = *RNAc::duplexT_energy_get;
-*swig_energy_set = *RNAc::duplexT_energy_set;
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_duplexT($self);
- delete $OWNER{$self};
- }
-}
-
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::duplex_list_t ##############
-
-package RNA::duplex_list_t;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-*swig_i_get = *RNAc::duplex_list_t_i_get;
-*swig_i_set = *RNAc::duplex_list_t_i_set;
-*swig_j_get = *RNAc::duplex_list_t_j_get;
-*swig_j_set = *RNAc::duplex_list_t_j_set;
-*swig_energy_get = *RNAc::duplex_list_t_energy_get;
-*swig_energy_set = *RNAc::duplex_list_t_energy_set;
-*swig_structure_get = *RNAc::duplex_list_t_structure_get;
-*swig_structure_set = *RNAc::duplex_list_t_structure_set;
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_duplex_list_t($self);
- delete $OWNER{$self};
- }
-}
-
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_duplex_list_t(@_);
- bless $self, $pkg if defined($self);
-}
-
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::DuplexVector ##############
-
-package RNA::DuplexVector;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_DuplexVector(@_);
- bless $self, $pkg if defined($self);
-}
-
-*size = *RNAc::DuplexVector_size;
-*empty = *RNAc::DuplexVector_empty;
-*clear = *RNAc::DuplexVector_clear;
-*push = *RNAc::DuplexVector_push;
-*pop = *RNAc::DuplexVector_pop;
-*get = *RNAc::DuplexVector_get;
-*set = *RNAc::DuplexVector_set;
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_DuplexVector($self);
- delete $OWNER{$self};
- }
-}
-
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::move ##############
-
-package RNA::move;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-*swig_pos_5_get = *RNAc::move_pos_5_get;
-*swig_pos_5_set = *RNAc::move_pos_5_set;
-*swig_pos_3_get = *RNAc::move_pos_3_get;
-*swig_pos_3_set = *RNAc::move_pos_3_set;
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_move(@_);
- bless $self, $pkg if defined($self);
-}
-
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_move($self);
- delete $OWNER{$self};
- }
-}
-
-*is_removal = *RNAc::move_is_removal;
-*is_insertion = *RNAc::move_is_insertion;
-*is_shift = *RNAc::move_is_shift;
-*compare = *RNAc::move_compare;
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::path ##############
-
-package RNA::path;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-*swig_type_get = *RNAc::path_type_get;
-*swig_type_set = *RNAc::path_type_set;
-*swig_en_get = *RNAc::path_en_get;
-*swig_en_set = *RNAc::path_en_set;
-*swig_s_get = *RNAc::path_s_get;
-*swig_s_set = *RNAc::path_s_set;
-*swig_move_get = *RNAc::path_move_get;
-*swig_move_set = *RNAc::path_move_set;
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_path($self);
- delete $OWNER{$self};
- }
-}
-
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_path(@_);
- bless $self, $pkg if defined($self);
-}
-
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::path_options ##############
-
-package RNA::path_options;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_path_options(@_);
- bless $self, $pkg if defined($self);
-}
-
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_path_options($self);
- delete $OWNER{$self};
- }
-}
-
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::basepair ##############
-
-package RNA::basepair;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-*swig_i_get = *RNAc::basepair_i_get;
-*swig_i_set = *RNAc::basepair_i_set;
-*swig_j_get = *RNAc::basepair_j_get;
-*swig_j_set = *RNAc::basepair_j_set;
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_basepair(@_);
- bless $self, $pkg if defined($self);
-}
-
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_basepair($self);
- delete $OWNER{$self};
- }
-}
-
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-############# Class : RNA::fold_compound ##############
-
-package RNA::fold_compound;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
- at ISA = qw( RNA );
-%OWNER = ();
-%ITERATORS = ();
-*exp_params_rescale = *RNAc::fold_compound_exp_params_rescale;
-*plist_from_probs = *RNAc::fold_compound_plist_from_probs;
-*constraints_add = *RNAc::fold_compound_constraints_add;
-*hc_init = *RNAc::fold_compound_hc_init;
-*hc_add_up = *RNAc::fold_compound_hc_add_up;
-*hc_add_bp_nonspecific = *RNAc::fold_compound_hc_add_bp_nonspecific;
-*hc_add_bp = *RNAc::fold_compound_hc_add_bp;
-*hc_add_from_db = *RNAc::fold_compound_hc_add_from_db;
-*sc_remove = *RNAc::fold_compound_sc_remove;
-*sc_init = *RNAc::fold_compound_sc_init;
-*sc_add_up = *RNAc::fold_compound_sc_add_up;
-*sc_add_bp = *RNAc::fold_compound_sc_add_bp;
-*sc_set_bp = *RNAc::fold_compound_sc_set_bp;
-*sc_set_up = *RNAc::fold_compound_sc_set_up;
-*sc_set_stack = *RNAc::fold_compound_sc_set_stack;
-*sc_add_stack = *RNAc::fold_compound_sc_add_stack;
-*sc_add_SHAPE_deigan = *RNAc::fold_compound_sc_add_SHAPE_deigan;
-*sc_add_SHAPE_deigan_ali = *RNAc::fold_compound_sc_add_SHAPE_deigan_ali;
-*sc_add_SHAPE_zarringhalam = *RNAc::fold_compound_sc_add_SHAPE_zarringhalam;
-*sc_add_hi_motif = *RNAc::fold_compound_sc_add_hi_motif;
-*eval_structure = *RNAc::fold_compound_eval_structure;
-*eval_structure_pt = *RNAc::fold_compound_eval_structure_pt;
-*eval_structure_verbose = *RNAc::fold_compound_eval_structure_verbose;
-*eval_structure_pt_verbose = *RNAc::fold_compound_eval_structure_pt_verbose;
-*eval_covar_structure = *RNAc::fold_compound_eval_covar_structure;
-*eval_loop_pt = *RNAc::fold_compound_eval_loop_pt;
-*eval_move = *RNAc::fold_compound_eval_move;
-*eval_move_pt = *RNAc::fold_compound_eval_move_pt;
-*E_ext_loop = *RNAc::fold_compound_E_ext_loop;
-*E_hp_loop = *RNAc::fold_compound_E_hp_loop;
-*E_ext_hp_loop = *RNAc::fold_compound_E_ext_hp_loop;
-*eval_ext_hp_loop = *RNAc::fold_compound_eval_ext_hp_loop;
-*eval_hp_loop = *RNAc::fold_compound_eval_hp_loop;
-*exp_E_hp_loop = *RNAc::fold_compound_exp_E_hp_loop;
-*E_int_loop = *RNAc::fold_compound_E_int_loop;
-*eval_int_loop = *RNAc::fold_compound_eval_int_loop;
-*E_ext_int_loop = *RNAc::fold_compound_E_ext_int_loop;
-*E_stack = *RNAc::fold_compound_E_stack;
-*exp_E_int_loop = *RNAc::fold_compound_exp_E_int_loop;
-*exp_E_interior_loop = *RNAc::fold_compound_exp_E_interior_loop;
-*maxmimum_matching = *RNAc::fold_compound_maxmimum_matching;
-*mfe = *RNAc::fold_compound_mfe;
-*mfe_dimer = *RNAc::fold_compound_mfe_dimer;
-*backtrack = *RNAc::fold_compound_backtrack;
-*mfe_window = *RNAc::fold_compound_mfe_window;
-*mfe_window_zscore = *RNAc::fold_compound_mfe_window_zscore;
-*pf = *RNAc::fold_compound_pf;
-*mean_bp_distance = *RNAc::fold_compound_mean_bp_distance;
-*ensemble_defect = *RNAc::fold_compound_ensemble_defect;
-*positional_entropy = *RNAc::fold_compound_positional_entropy;
-*pr_structure = *RNAc::fold_compound_pr_structure;
-*pr_energy = *RNAc::fold_compound_pr_energy;
-*pf_dimer = *RNAc::fold_compound_pf_dimer;
-*bpp = *RNAc::fold_compound_bpp;
-*centroid = *RNAc::fold_compound_centroid;
-*MEA = *RNAc::fold_compound_MEA;
-*subopt = *RNAc::fold_compound_subopt;
-*subopt_zuker = *RNAc::fold_compound_subopt_zuker;
-*sequence_add = *RNAc::fold_compound_sequence_add;
-*sequence_remove = *RNAc::fold_compound_sequence_remove;
-*sequence_remove_all = *RNAc::fold_compound_sequence_remove_all;
-*sequence_prepare = *RNAc::fold_compound_sequence_prepare;
-*ud_add_motif = *RNAc::fold_compound_ud_add_motif;
-*ud_remove = *RNAc::fold_compound_ud_remove;
-*commands_apply = *RNAc::fold_compound_commands_apply;
-*file_commands_apply = *RNAc::fold_compound_file_commands_apply;
-*rotational_symmetry_db = *RNAc::fold_compound_rotational_symmetry_db;
-*neighbors = *RNAc::fold_compound_neighbors;
-*path = *RNAc::fold_compound_path;
-*path_gradient = *RNAc::fold_compound_path_gradient;
-*path_random = *RNAc::fold_compound_path_random;
-*path_findpath_saddle = *RNAc::fold_compound_path_findpath_saddle;
-*path_findpath = *RNAc::fold_compound_path_findpath;
-*path_direct = *RNAc::fold_compound_path_direct;
-*add_auxdata = *RNAc::fold_compound_add_auxdata;
-*add_callback = *RNAc::fold_compound_add_callback;
-*sc_add_data = *RNAc::fold_compound_sc_add_data;
-*sc_add_f = *RNAc::fold_compound_sc_add_f;
-*sc_add_bt = *RNAc::fold_compound_sc_add_bt;
-*sc_add_exp_f = *RNAc::fold_compound_sc_add_exp_f;
-*ud_set_data = *RNAc::fold_compound_ud_set_data;
-*ud_set_prod_rule_cb = *RNAc::fold_compound_ud_set_prod_rule_cb;
-*ud_set_exp_prod_rule_cb = *RNAc::fold_compound_ud_set_exp_prod_rule_cb;
-*ud_set_prob_cb = *RNAc::fold_compound_ud_set_prob_cb;
-*subopt_cb = *RNAc::fold_compound_subopt_cb;
-*pbacktrack = *RNAc::fold_compound_pbacktrack;
-*pbacktrack5 = *RNAc::fold_compound_pbacktrack5;
-*mfe_window_cb = *RNAc::fold_compound_mfe_window_cb;
-*mfe_window_zscore_cb = *RNAc::fold_compound_mfe_window_zscore_cb;
-*probs_window = *RNAc::fold_compound_probs_window;
-sub new {
- my $pkg = shift;
- my $self = RNAc::new_fold_compound(@_);
- bless $self, $pkg if defined($self);
-}
-
-sub DESTROY {
- return unless $_[0]->isa('HASH');
- my $self = tied(%{$_[0]});
- return unless defined $self;
- delete $ITERATORS{$self};
- if (exists $OWNER{$self}) {
- RNAc::delete_fold_compound($self);
- delete $OWNER{$self};
- }
-}
-
-*type = *RNAc::fold_compound_type;
-*length = *RNAc::fold_compound_length;
-sub DISOWN {
- my $self = shift;
- my $ptr = tied(%$self);
- delete $OWNER{$ptr};
-}
-
-sub ACQUIRE {
- my $self = shift;
- my $ptr = tied(%$self);
- $OWNER{$ptr} = 1;
-}
-
-
-# ------- CONSTANT STUBS -------
-
-package RNA;
-
-sub PARAMETER_FORMAT_DEFAULT () { $RNAc::PARAMETER_FORMAT_DEFAULT }
-sub UNKNOWN () { $RNAc::UNKNOWN }
-sub QUIT () { $RNAc::QUIT }
-sub S () { $RNAc::S }
-sub S_H () { $RNAc::S_H }
-sub HP () { $RNAc::HP }
-sub HP_H () { $RNAc::HP_H }
-sub B () { $RNAc::B }
-sub B_H () { $RNAc::B_H }
-sub IL () { $RNAc::IL }
-sub IL_H () { $RNAc::IL_H }
-sub MMH () { $RNAc::MMH }
-sub MMH_H () { $RNAc::MMH_H }
-sub MMI () { $RNAc::MMI }
-sub MMI_H () { $RNAc::MMI_H }
-sub MMI1N () { $RNAc::MMI1N }
-sub MMI1N_H () { $RNAc::MMI1N_H }
-sub MMI23 () { $RNAc::MMI23 }
-sub MMI23_H () { $RNAc::MMI23_H }
-sub MMM () { $RNAc::MMM }
-sub MMM_H () { $RNAc::MMM_H }
-sub MME () { $RNAc::MME }
-sub MME_H () { $RNAc::MME_H }
-sub D5 () { $RNAc::D5 }
-sub D5_H () { $RNAc::D5_H }
-sub D3 () { $RNAc::D3 }
-sub D3_H () { $RNAc::D3_H }
-sub INT11 () { $RNAc::INT11 }
-sub INT11_H () { $RNAc::INT11_H }
-sub INT21 () { $RNAc::INT21 }
-sub INT21_H () { $RNAc::INT21_H }
-sub INT22 () { $RNAc::INT22 }
-sub INT22_H () { $RNAc::INT22_H }
-sub ML () { $RNAc::ML }
-sub TL () { $RNAc::TL }
-sub TRI () { $RNAc::TRI }
-sub HEX () { $RNAc::HEX }
-sub NIN () { $RNAc::NIN }
-sub MISC () { $RNAc::MISC }
-sub GASCONST () { $RNAc::GASCONST }
-sub K0 () { $RNAc::K0 }
-sub INF () { $RNAc::INF }
-sub EMAX () { $RNAc::EMAX }
-sub FORBIDDEN () { $RNAc::FORBIDDEN }
-sub BONUS () { $RNAc::BONUS }
-sub NBPAIRS () { $RNAc::NBPAIRS }
-sub TURN () { $RNAc::TURN }
-sub MAXLOOP () { $RNAc::MAXLOOP }
-sub UNIT () { $RNAc::UNIT }
-sub MINPSCORE () { $RNAc::MINPSCORE }
-sub NBASES () { $RNAc::NBASES }
-sub MAXALPHA () { $RNAc::MAXALPHA }
-sub FILENAME_MAX_LENGTH () { $RNAc::FILENAME_MAX_LENGTH }
-sub FILENAME_ID_LENGTH () { $RNAc::FILENAME_ID_LENGTH }
-sub PLIST_TYPE_BASEPAIR () { $RNAc::PLIST_TYPE_BASEPAIR }
-sub PLIST_TYPE_GQUAD () { $RNAc::PLIST_TYPE_GQUAD }
-sub PLIST_TYPE_H_MOTIF () { $RNAc::PLIST_TYPE_H_MOTIF }
-sub PLIST_TYPE_I_MOTIF () { $RNAc::PLIST_TYPE_I_MOTIF }
-sub PLIST_TYPE_UD_MOTIF () { $RNAc::PLIST_TYPE_UD_MOTIF }
-sub PLIST_TYPE_STACK () { $RNAc::PLIST_TYPE_STACK }
-sub STRUCTURE_TREE_HIT () { $RNAc::STRUCTURE_TREE_HIT }
-sub STRUCTURE_TREE_SHAPIRO_SHORT () { $RNAc::STRUCTURE_TREE_SHAPIRO_SHORT }
-sub STRUCTURE_TREE_SHAPIRO () { $RNAc::STRUCTURE_TREE_SHAPIRO }
-sub STRUCTURE_TREE_SHAPIRO_EXT () { $RNAc::STRUCTURE_TREE_SHAPIRO_EXT }
-sub STRUCTURE_TREE_SHAPIRO_WEIGHT () { $RNAc::STRUCTURE_TREE_SHAPIRO_WEIGHT }
-sub STRUCTURE_TREE_EXPANDED () { $RNAc::STRUCTURE_TREE_EXPANDED }
-sub BRACKETS_RND () { $RNAc::BRACKETS_RND }
-sub BRACKETS_ANG () { $RNAc::BRACKETS_ANG }
-sub BRACKETS_SQR () { $RNAc::BRACKETS_SQR }
-sub BRACKETS_CLY () { $RNAc::BRACKETS_CLY }
-sub BRACKETS_ALPHA () { $RNAc::BRACKETS_ALPHA }
-sub BRACKETS_DEFAULT () { $RNAc::BRACKETS_DEFAULT }
-sub BRACKETS_ANY () { $RNAc::BRACKETS_ANY }
-sub ALN_DEFAULT () { $RNAc::ALN_DEFAULT }
-sub ALN_RNA () { $RNAc::ALN_RNA }
-sub ALN_DNA () { $RNAc::ALN_DNA }
-sub ALN_UPPERCASE () { $RNAc::ALN_UPPERCASE }
-sub ALN_LOWERCASE () { $RNAc::ALN_LOWERCASE }
-sub MEASURE_SHANNON_ENTROPY () { $RNAc::MEASURE_SHANNON_ENTROPY }
-sub GRADIENT () { $RNAc::GRADIENT }
-sub FIRST () { $RNAc::FIRST }
-sub ADAPTIVE () { $RNAc::ADAPTIVE }
-sub DECOMP_PAIR_HP () { $RNAc::DECOMP_PAIR_HP }
-sub DECOMP_PAIR_IL () { $RNAc::DECOMP_PAIR_IL }
-sub DECOMP_PAIR_ML () { $RNAc::DECOMP_PAIR_ML }
-sub DECOMP_ML_ML_ML () { $RNAc::DECOMP_ML_ML_ML }
-sub DECOMP_ML_STEM () { $RNAc::DECOMP_ML_STEM }
-sub DECOMP_ML_ML () { $RNAc::DECOMP_ML_ML }
-sub DECOMP_ML_UP () { $RNAc::DECOMP_ML_UP }
-sub DECOMP_ML_ML_STEM () { $RNAc::DECOMP_ML_ML_STEM }
-sub DECOMP_ML_COAXIAL () { $RNAc::DECOMP_ML_COAXIAL }
-sub DECOMP_EXT_EXT () { $RNAc::DECOMP_EXT_EXT }
-sub DECOMP_EXT_UP () { $RNAc::DECOMP_EXT_UP }
-sub DECOMP_EXT_STEM () { $RNAc::DECOMP_EXT_STEM }
-sub DECOMP_EXT_EXT_EXT () { $RNAc::DECOMP_EXT_EXT_EXT }
-sub DECOMP_EXT_STEM_EXT () { $RNAc::DECOMP_EXT_STEM_EXT }
-sub DECOMP_EXT_STEM_OUTSIDE () { $RNAc::DECOMP_EXT_STEM_OUTSIDE }
-sub DECOMP_EXT_EXT_STEM () { $RNAc::DECOMP_EXT_EXT_STEM }
-sub DECOMP_EXT_EXT_STEM1 () { $RNAc::DECOMP_EXT_EXT_STEM1 }
-sub CONSTRAINT_DB () { $RNAc::CONSTRAINT_DB }
-sub CONSTRAINT_DB_ENFORCE_BP () { $RNAc::CONSTRAINT_DB_ENFORCE_BP }
-sub CONSTRAINT_DB_PIPE () { $RNAc::CONSTRAINT_DB_PIPE }
-sub CONSTRAINT_DB_DOT () { $RNAc::CONSTRAINT_DB_DOT }
-sub CONSTRAINT_DB_X () { $RNAc::CONSTRAINT_DB_X }
-sub CONSTRAINT_DB_ANG_BRACK () { $RNAc::CONSTRAINT_DB_ANG_BRACK }
-sub CONSTRAINT_DB_RND_BRACK () { $RNAc::CONSTRAINT_DB_RND_BRACK }
-sub CONSTRAINT_DB_INTRAMOL () { $RNAc::CONSTRAINT_DB_INTRAMOL }
-sub CONSTRAINT_DB_INTERMOL () { $RNAc::CONSTRAINT_DB_INTERMOL }
-sub CONSTRAINT_DB_GQUAD () { $RNAc::CONSTRAINT_DB_GQUAD }
-sub CONSTRAINT_DB_DEFAULT () { $RNAc::CONSTRAINT_DB_DEFAULT }
-sub CONSTRAINT_CONTEXT_EXT_LOOP () { $RNAc::CONSTRAINT_CONTEXT_EXT_LOOP }
-sub CONSTRAINT_CONTEXT_HP_LOOP () { $RNAc::CONSTRAINT_CONTEXT_HP_LOOP }
-sub CONSTRAINT_CONTEXT_INT_LOOP () { $RNAc::CONSTRAINT_CONTEXT_INT_LOOP }
-sub CONSTRAINT_CONTEXT_INT_LOOP_ENC () { $RNAc::CONSTRAINT_CONTEXT_INT_LOOP_ENC }
-sub CONSTRAINT_CONTEXT_MB_LOOP () { $RNAc::CONSTRAINT_CONTEXT_MB_LOOP }
-sub CONSTRAINT_CONTEXT_MB_LOOP_ENC () { $RNAc::CONSTRAINT_CONTEXT_MB_LOOP_ENC }
-sub CONSTRAINT_CONTEXT_ENFORCE () { $RNAc::CONSTRAINT_CONTEXT_ENFORCE }
-sub CONSTRAINT_CONTEXT_NO_REMOVE () { $RNAc::CONSTRAINT_CONTEXT_NO_REMOVE }
-sub CONSTRAINT_CONTEXT_ALL_LOOPS () { $RNAc::CONSTRAINT_CONTEXT_ALL_LOOPS }
-sub CONSTRAINT_CONTEXT_NONE () { $RNAc::CONSTRAINT_CONTEXT_NONE }
-sub CONSTRAINT_CONTEXT_CLOSING_LOOPS () { $RNAc::CONSTRAINT_CONTEXT_CLOSING_LOOPS }
-sub CONSTRAINT_CONTEXT_ENCLOSED_LOOPS () { $RNAc::CONSTRAINT_CONTEXT_ENCLOSED_LOOPS }
-sub PBACKTRACK_DEFAULT () { $RNAc::PBACKTRACK_DEFAULT }
-sub PBACKTRACK_NON_REDUNDANT () { $RNAc::PBACKTRACK_NON_REDUNDANT }
-sub EXT_LOOP () { $RNAc::EXT_LOOP }
-sub HP_LOOP () { $RNAc::HP_LOOP }
-sub INT_LOOP () { $RNAc::INT_LOOP }
-sub MB_LOOP () { $RNAc::MB_LOOP }
-sub ANY_LOOP () { $RNAc::ANY_LOOP }
-sub PROBS_WINDOW_BPP () { $RNAc::PROBS_WINDOW_BPP }
-sub PROBS_WINDOW_UP () { $RNAc::PROBS_WINDOW_UP }
-sub PROBS_WINDOW_STACKP () { $RNAc::PROBS_WINDOW_STACKP }
-sub PROBS_WINDOW_UP_SPLIT () { $RNAc::PROBS_WINDOW_UP_SPLIT }
-sub PROBS_WINDOW_PF () { $RNAc::PROBS_WINDOW_PF }
-sub MAXDOS () { $RNAc::MAXDOS }
-sub FILE_FORMAT_MSA_CLUSTAL () { $RNAc::FILE_FORMAT_MSA_CLUSTAL }
-sub FILE_FORMAT_MSA_DEFAULT () { $RNAc::FILE_FORMAT_MSA_DEFAULT }
-sub FILE_FORMAT_MSA_FASTA () { $RNAc::FILE_FORMAT_MSA_FASTA }
-sub FILE_FORMAT_MSA_MAF () { $RNAc::FILE_FORMAT_MSA_MAF }
-sub FILE_FORMAT_MSA_NOCHECK () { $RNAc::FILE_FORMAT_MSA_NOCHECK }
-sub FILE_FORMAT_MSA_STOCKHOLM () { $RNAc::FILE_FORMAT_MSA_STOCKHOLM }
-sub FILE_FORMAT_MSA_MIS () { $RNAc::FILE_FORMAT_MSA_MIS }
-sub FILE_FORMAT_MSA_UNKNOWN () { $RNAc::FILE_FORMAT_MSA_UNKNOWN }
-sub FILE_FORMAT_MSA_QUIET () { $RNAc::FILE_FORMAT_MSA_QUIET }
-sub FILE_FORMAT_MSA_SILENT () { $RNAc::FILE_FORMAT_MSA_SILENT }
-sub FILE_FORMAT_MSA_APPEND () { $RNAc::FILE_FORMAT_MSA_APPEND }
-sub SEQUENCE_RNA () { $RNAc::SEQUENCE_RNA }
-sub SEQUENCE_DNA () { $RNAc::SEQUENCE_DNA }
-sub UNSTRUCTURED_DOMAIN_EXT_LOOP () { $RNAc::UNSTRUCTURED_DOMAIN_EXT_LOOP }
-sub UNSTRUCTURED_DOMAIN_HP_LOOP () { $RNAc::UNSTRUCTURED_DOMAIN_HP_LOOP }
-sub UNSTRUCTURED_DOMAIN_INT_LOOP () { $RNAc::UNSTRUCTURED_DOMAIN_INT_LOOP }
-sub UNSTRUCTURED_DOMAIN_MB_LOOP () { $RNAc::UNSTRUCTURED_DOMAIN_MB_LOOP }
-sub UNSTRUCTURED_DOMAIN_ALL_LOOPS () { $RNAc::UNSTRUCTURED_DOMAIN_ALL_LOOPS }
-sub UNSTRUCTURED_DOMAIN_MOTIF () { $RNAc::UNSTRUCTURED_DOMAIN_MOTIF }
-sub CMD_PARSE_DEFAULTS () { $RNAc::CMD_PARSE_DEFAULTS }
-sub CMD_PARSE_HC () { $RNAc::CMD_PARSE_HC }
-sub CMD_PARSE_SC () { $RNAc::CMD_PARSE_SC }
-sub CMD_PARSE_SD () { $RNAc::CMD_PARSE_SD }
-sub CMD_PARSE_UD () { $RNAc::CMD_PARSE_UD }
-sub MOVESET_INSERTION () { $RNAc::MOVESET_INSERTION }
-sub MOVESET_DELETION () { $RNAc::MOVESET_DELETION }
-sub MOVESET_SHIFT () { $RNAc::MOVESET_SHIFT }
-sub MOVESET_NO_LP () { $RNAc::MOVESET_NO_LP }
-sub MOVESET_DEFAULT () { $RNAc::MOVESET_DEFAULT }
-sub NEIGHBOR_CHANGE () { $RNAc::NEIGHBOR_CHANGE }
-sub NEIGHBOR_INVALID () { $RNAc::NEIGHBOR_INVALID }
-sub NEIGHBOR_NEW () { $RNAc::NEIGHBOR_NEW }
-sub PATH_STEEPEST_DESCENT () { $RNAc::PATH_STEEPEST_DESCENT }
-sub PATH_RANDOM () { $RNAc::PATH_RANDOM }
-sub PATH_NO_TRANSITION_OUTPUT () { $RNAc::PATH_NO_TRANSITION_OUTPUT }
-sub PATH_DEFAULT () { $RNAc::PATH_DEFAULT }
-sub PATH_TYPE_DOT_BRACKET () { $RNAc::PATH_TYPE_DOT_BRACKET }
-sub PATH_TYPE_MOVES () { $RNAc::PATH_TYPE_MOVES }
-sub FC_TYPE_SINGLE () { $RNAc::FC_TYPE_SINGLE }
-sub FC_TYPE_COMPARATIVE () { $RNAc::FC_TYPE_COMPARATIVE }
-sub STATUS_MFE_PRE () { $RNAc::STATUS_MFE_PRE }
-sub STATUS_MFE_POST () { $RNAc::STATUS_MFE_POST }
-sub STATUS_PF_PRE () { $RNAc::STATUS_PF_PRE }
-sub STATUS_PF_POST () { $RNAc::STATUS_PF_POST }
-sub OPTION_DEFAULT () { $RNAc::OPTION_DEFAULT }
-sub OPTION_MFE () { $RNAc::OPTION_MFE }
-sub OPTION_PF () { $RNAc::OPTION_PF }
-sub OPTION_HYBRID () { $RNAc::OPTION_HYBRID }
-sub OPTION_EVAL_ONLY () { $RNAc::OPTION_EVAL_ONLY }
-sub OPTION_WINDOW () { $RNAc::OPTION_WINDOW }
-
-# ------- VARIABLE STUBS --------
-
-package RNA;
-
-*temperature = *RNAc::temperature;
-*dangles = *RNAc::dangles;
-*betaScale = *RNAc::betaScale;
-*pf_smooth = *RNAc::pf_smooth;
-*tetra_loop = *RNAc::tetra_loop;
-*special_hp = *RNAc::special_hp;
-*noLonelyPairs = *RNAc::noLonelyPairs;
-*noLP = *RNAc::noLP;
-*noGU = *RNAc::noGU;
-*no_closingGU = *RNAc::no_closingGU;
-*noGUclosure = *RNAc::noGUclosure;
-*logML = *RNAc::logML;
-*circ = *RNAc::circ;
-*gquad = *RNAc::gquad;
-*uniq_ML = *RNAc::uniq_ML;
-*energy_set = *RNAc::energy_set;
-*backtrack = *RNAc::backtrack;
-*backtrack_type = *RNAc::backtrack_type;
-*do_backtrack = *RNAc::do_backtrack;
-*compute_bpp = *RNAc::compute_bpp;
-*max_bp_span = *RNAc::max_bp_span;
-*min_loop_size = *RNAc::min_loop_size;
-*window_size = *RNAc::window_size;
-*oldAliEn = *RNAc::oldAliEn;
-*ribo = *RNAc::ribo;
-*cv_fact = *RNAc::cv_fact;
-*nc_fact = *RNAc::nc_fact;
-*sfact = *RNAc::sfact;
-*pf_scale = *RNAc::pf_scale;
-*nonstandards = *RNAc::nonstandards;
-*xsubi = *RNAc::xsubi;
-*rna_plot_type = *RNAc::rna_plot_type;
-*cut_point = *RNAc::cut_point;
-*eos_debug = *RNAc::eos_debug;
-*st_back = *RNAc::st_back;
-*mirnatog = *RNAc::mirnatog;
-*F_monomer = *RNAc::F_monomer;
-*subopt_sorted = *RNAc::subopt_sorted;
-*print_energy = *RNAc::print_energy;
-*density_of_states = *RNAc::density_of_states;
-*symbolset = *RNAc::symbolset;
-*final_cost = *RNAc::final_cost;
-*give_up = *RNAc::give_up;
-*inv_verbose = *RNAc::inv_verbose;
-*loop_size = *RNAc::loop_size;
-*helix_size = *RNAc::helix_size;
-*loop_degree = *RNAc::loop_degree;
-*loops = *RNAc::loops;
-*unpaired = *RNAc::unpaired;
-*pairs = *RNAc::pairs;
-*edit_backtrack = *RNAc::edit_backtrack;
-*aligned_line = *RNAc::aligned_line;
-*cost_matrix = *RNAc::cost_matrix;
-*base_pair = *RNAc::base_pair;
-*pr = *RNAc::pr;
-*iindx = *RNAc::iindx;
-*fold_constrained = *RNAc::fold_constrained;
-*csv = *RNAc::csv;
-*RibosumFile = *RNAc::RibosumFile;
-*james_rule = *RNAc::james_rule;
-
-our $VERSION = '2.4.14';
-sub VERSION () { $VERSION };
-1;
=====================================
interfaces/Perl/RNA_wrap.cpp deleted
=====================================
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=====================================
interfaces/Perl/version.i deleted
=====================================
@@ -1,11 +0,0 @@
-%{
-/** @file version.i.in
- * @brief Set $RNA::VERSION to the bindings version
- */
-%}
-
-%perlcode %{
-our $VERSION = '2.4.14';
-sub VERSION () { $VERSION };
-%}
-
=====================================
interfaces/Python3/RNA.py deleted
=====================================
The diff for this file was not included because it is too large.
=====================================
interfaces/Python3/RNA_wrap.cpp deleted
=====================================
The diff for this file was not included because it is too large.
=====================================
interfaces/Python3/version.i deleted
=====================================
@@ -1,10 +0,0 @@
-%{
-/** @file version.i.in
- * @brief Set RNA.__version__ to the bindings version
- */
-%}
-
-%pythoncode %{
-__version__ = '2.4.14'
-%}
-
=====================================
packaging/macosx/resources/welcome.txt deleted
=====================================
@@ -1,10 +0,0 @@
-This is Version 2.4.14 of the ViennaRNA Package.
-------------------------------------------------
-
-The ViennaRNA Package consists of a few stand alone programs and a
-library that you can link your own programs with. The library can
-also be accessed through our scripting interfaces for Perl and Python
-
-Together with this version we distribute the Kinfold, RNAforester,
-and Kinwalker programs.
-
=====================================
src/Kinfold/INSTALL deleted
=====================================
@@ -1,182 +0,0 @@
-Basic Installation
-==================
-
- These are generic installation instructions.
-
- The `configure' shell script attempts to guess correct values for
-various system-dependent variables used during compilation. It uses
-those values to create a `Makefile' in each directory of the package.
-It may also create one or more `.h' files containing system-dependent
-definitions. Finally, it creates a shell script `config.status' that
-you can run in the future to recreate the current configuration, a file
-`config.cache' that saves the results of its tests to speed up
-reconfiguring, and a file `config.log' containing compiler output
-(useful mainly for debugging `configure').
-
- If you need to do unusual things to compile the package, please try
-to figure out how `configure' could check whether to do them, and mail
-diffs or instructions to the address given in the `README' so they can
-be considered for the next release. If at some point `config.cache'
-contains results you don't want to keep, you may remove or edit it.
-
- The file `configure.in' is used to create `configure' by a program
-called `autoconf'. You only need `configure.in' if you want to change
-it or regenerate `configure' using a newer version of `autoconf'.
-
-The simplest way to compile this package is:
-
- 1. `cd' to the directory containing the package's source code and type
- `./configure' to configure the package for your system. If you're
- using `csh' on an old version of System V, you might need to type
- `sh ./configure' instead to prevent `csh' from trying to execute
- `configure' itself.
-
- Running `configure' takes awhile. While running, it prints some
- messages telling which features it is checking for.
-
- 2. Type `make' to compile the package.
-
- 3. Optionally, type `make check' to run any self-tests that come with
- the package.
-
- 4. Type `make install' to install the programs and any data files and
- documentation.
-
- 5. You can remove the program binaries and object files from the
- source code directory by typing `make clean'. To also remove the
- files that `configure' created (so you can compile the package for
- a different kind of computer), type `make distclean'. There is
- also a `make maintainer-clean' target, but that is intended mainly
- for the package's developers. If you use it, you may have to get
- all sorts of other programs in order to regenerate files that came
- with the distribution.
-
-Compilers and Options
-=====================
-
- Some systems require unusual options for compilation or linking that
-the `configure' script does not know about. You can give `configure'
-initial values for variables by setting them in the environment. Using
-a Bourne-compatible shell, you can do that on the command line like
-this:
- CC=c89 CFLAGS=-O2 LIBS=-lposix ./configure
-
-Or on systems that have the `env' program, you can do it like this:
- env CPPFLAGS=-I/usr/local/include LDFLAGS=-s ./configure
-
-Compiling For Multiple Architectures
-====================================
-
- You can compile the package for more than one kind of computer at the
-same time, by placing the object files for each architecture in their
-own directory. To do this, you must use a version of `make' that
-supports the `VPATH' variable, such as GNU `make'. `cd' to the
-directory where you want the object files and executables to go and run
-the `configure' script. `configure' automatically checks for the
-source code in the directory that `configure' is in and in `..'.
-
- If you have to use a `make' that does not supports the `VPATH'
-variable, you have to compile the package for one architecture at a time
-in the source code directory. After you have installed the package for
-one architecture, use `make distclean' before reconfiguring for another
-architecture.
-
-Installation Names
-==================
-
- By default, `make install' will install the package's files in
-`/usr/local/bin', `/usr/local/man', etc. You can specify an
-installation prefix other than `/usr/local' by giving `configure' the
-option `--prefix=PATH'.
-
- You can specify separate installation prefixes for
-architecture-specific files and architecture-independent files. If you
-give `configure' the option `--exec-prefix=PATH', the package will use
-PATH as the prefix for installing programs and libraries.
-Documentation and other data files will still use the regular prefix.
-
- In addition, if you use an unusual directory layout you can give
-options like `--bindir=PATH' to specify different values for particular
-kinds of files. Run `configure --help' for a list of the directories
-you can set and what kinds of files go in them.
-
- If the package supports it, you can cause programs to be installed
-with an extra prefix or suffix on their names by giving `configure' the
-option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'.
-
-Optional Features
-=================
-
- Some packages pay attention to `--enable-FEATURE' options to
-`configure', where FEATURE indicates an optional part of the package.
-They may also pay attention to `--with-PACKAGE' options, where PACKAGE
-is something like `gnu-as' or `x' (for the X Window System). The
-`README' should mention any `--enable-' and `--with-' options that the
-package recognizes.
-
- For packages that use the X Window System, `configure' can usually
-find the X include and library files automatically, but if it doesn't,
-you can use the `configure' options `--x-includes=DIR' and
-`--x-libraries=DIR' to specify their locations.
-
-Specifying the System Type
-==========================
-
- There may be some features `configure' can not figure out
-automatically, but needs to determine by the type of host the package
-will run on. Usually `configure' can figure that out, but if it prints
-a message saying it can not guess the host type, give it the
-`--host=TYPE' option. TYPE can either be a short name for the system
-type, such as `sun4', or a canonical name with three fields:
- CPU-COMPANY-SYSTEM
-
-See the file `config.sub' for the possible values of each field. If
-`config.sub' isn't included in this package, then this package doesn't
-need to know the host type.
-
- If you are building compiler tools for cross-compiling, you can also
-use the `--target=TYPE' option to select the type of system they will
-produce code for and the `--build=TYPE' option to select the type of
-system on which you are compiling the package.
-
-Sharing Defaults
-================
-
- If you want to set default values for `configure' scripts to share,
-you can create a site shell script called `config.site' that gives
-default values for variables like `CC', `cache_file', and `prefix'.
-`configure' looks for `PREFIX/share/config.site' if it exists, then
-`PREFIX/etc/config.site' if it exists. Or, you can set the
-`CONFIG_SITE' environment variable to the location of the site script.
-A warning: not all `configure' scripts look for a site script.
-
-Operation Controls
-==================
-
- `configure' recognizes the following options to control how it
-operates.
-
-`--cache-file=FILE'
- Use and save the results of the tests in FILE instead of
- `./config.cache'. Set FILE to `/dev/null' to disable caching, for
- debugging `configure'.
-
-`--help'
- Print a summary of the options to `configure', and exit.
-
-`--quiet'
-`--silent'
-`-q'
- Do not print messages saying which checks are being made. To
- suppress all normal output, redirect it to `/dev/null' (any error
- messages will still be shown).
-
-`--srcdir=DIR'
- Look for the package's source code in directory DIR. Usually
- `configure' can determine that directory automatically.
-
-`--version'
- Print the version of Autoconf used to generate the `configure'
- script, and exit.
-
-`configure' also accepts some other, not widely useful, options.
=====================================
src/Kinfold/configure deleted
=====================================
The diff for this file was not included because it is too large.
=====================================
src/Kinwalker/configure deleted
=====================================
The diff for this file was not included because it is too large.
=====================================
src/RNAforester/INSTALL deleted
=====================================
@@ -1,72 +0,0 @@
-Installation:
-
-This package uses GNU autoconf generated configure scripts, see the
-file INSTALL.configure for generic configure documentation.
-
-Requirements:
-----------
-
-You must have the g2 - graphic library V0.49a (C) 1999 Lj. Milanovic, H. Wagner
-installed on your system. If not the g2 graphics library
-is ditributed with RNAforester by the file g2-0.49a.tar.gz.
-
-If g2 is installed usually you'll just have to type:
- ./configure
- make
-and (as root)
- make install
-
-The Vienna RNA lib (libRNA) (C) I. Hofacker must be installed on your system.
-Refer to http://www.tbi.univie.ac.at/~ivo/RNA/ for download and further
-instructions.
-
-Quickstart for users that do not have administrator rights
-----------------------------------------------------------
-
-Say your home directory is /home/user.
-If the g2 library is not installed on your system you'll have to type:
-
-tar xvzf g2-0.49a.tar.gz
-cd g2-0.49a
-./configure --prefix=/home/user
-make
-make install
-cd ..
-
-Make sure the Vienna RNA package is installed on your system.
-
-To install RNAforester type:
-
-./configure --prefix=/home/user
-make
-make install
-
-If the includes files of the g2 library cannot be found you can add
-the path including the headers as follows:
-CPPFLAGS=-I/home/user/include ./configure --prefix=/home/user
-(of course, your include path can differ)
-
-Installation Paths:
--------------
-The main programs, library and man are
-installed in the usual places by default
-(i.e. /usr/local/{bin,lib,man}).
-
-All these locations can be changed by calling ./configure with
-appropriate options.
-
-
-Microsoft Visual C++
------------------------
-
-RNAforester uses the getline function of STL. There is a bug in some VC versions
-in this function. If you must hit the return key twice to confirm your input,
- open file <string> and change the code as indicated by the comment:
-
- else if (_Tr::eq(_C, _D))
- {_Chg = true;
- _I.rdbuf()->snextc(); // replace snextc with sbumpc
- break; }
-
-
-
=====================================
src/RNAforester/configure deleted
=====================================
The diff for this file was not included because it is too large.
=====================================
src/RNAforester/g2-0.72/configure deleted
=====================================
The diff for this file was not included because it is too large.
=====================================
src/RNAlocmin/configure deleted
=====================================
The diff for this file was not included because it is too large.
=====================================
src/ViennaRNA/static/energy_parameter_sets.h deleted
=====================================
@@ -1,36 +0,0 @@
-#ifndef VIENNA_RNA_PACKAGE_ENERGY_PARAMETER_SETS_H
-#define VIENNA_RNA_PACKAGE_ENERGY_PARAMETER_SETS_H
-
-/* The strings below are automatically generated from corresponding .par files */
-
-
-static const char parameter_set_dna_mathews1999[] = {
-#include "misc/dna_mathews1999.hex"
-};
-
-static const char parameter_set_dna_mathews2004[] = {
-#include "misc/dna_mathews2004.hex"
-};
-
-static const char parameter_set_rna_andronescu2007[] = {
-#include "misc/rna_andronescu2007.hex"
-};
-
-static const char parameter_set_rna_langdon2018[] = {
-#include "misc/rna_langdon2018.hex"
-};
-
-static const char parameter_set_rna_misc_special_hairpins[] = {
-#include "misc/rna_misc_special_hairpins.hex"
-};
-
-static const char parameter_set_rna_turner1999[] = {
-#include "misc/rna_turner1999.hex"
-};
-
-static const char parameter_set_rna_turner2004[] = {
-#include "misc/rna_turner2004.hex"
-};
-
-
-#endif
=====================================
src/ViennaRNA/static/templates_postscript.h deleted
=====================================
@@ -1,44 +0,0 @@
-#ifndef VIENNA_RNA_PACKAGE_PLOT_PS_TEMPLATES_H
-#define VIENNA_RNA_PACKAGE_PLOT_PS_TEMPLATES_H
-
-/* The strings below are automatically generated from corresponding .ps files */
-
-
-static const char PS_structure_plot_macro_base[] = {
-#include "postscript/structure_plot_macro_base.hex"
-};
-
-static const char PS_structure_plot_macro_extras[] = {
-#include "postscript/structure_plot_macro_extras.hex"
-};
-
-static const char PS_dot_plot_macro_base[] = {
-#include "postscript/dot_plot_macro_base.hex"
-};
-
-static const char PS_dot_plot_macro_turn[] = {
-#include "postscript/dot_plot_macro_turn.hex"
-};
-
-static const char PS_dot_plot_macro_sd[] = {
-#include "postscript/dot_plot_macro_sd.hex"
-};
-
-static const char PS_dot_plot_macro_ud[] = {
-#include "postscript/dot_plot_macro_ud.hex"
-};
-
-static const char PS_dot_plot_macro_sc_motifs[] = {
-#include "postscript/dot_plot_macro_sc_motifs.hex"
-};
-
-static const char PS_dot_plot_macro_linear_data[] = {
-#include "postscript/dot_plot_macro_linear_data.hex"
-};
-
-static const char PS_aln_macro_base[] = {
-#include "postscript/aln_macro_base.hex"
-};
-
-
-#endif
View it on GitLab: https://salsa.debian.org/med-team/vienna-rna/-/commit/bbc579f52ad84dbd43d674e3dd09e5b3450d2a0e
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View it on GitLab: https://salsa.debian.org/med-team/vienna-rna/-/commit/bbc579f52ad84dbd43d674e3dd09e5b3450d2a0e
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