--- /dev/null
+# This file was automatically generated by SWIG (http://www.swig.org).
+# Version 2.0.8
+#
+# 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;
+@EXPORT = qw();
+=head1 NAME
+
+RNA - interface to the Vienna RNA library (libRNA.a)
+Version 0.3
+
+=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 $iindx [int *]
+
+Array of indices for moving withing the C<pr> array. Better use
+L<get_pr|/get_pr>.
+
+
+=back
+
+=head2 Parsing and Comparing Structures
+
+from RNAstruct.h: these functions convert between strings
+representating secondary structures with various levels of coarse
+graining. See the documentation of the C library for details
+
+=over 4
+
+=item b2HIT STRUCTURE
+
+Full -> HIT [incl. root]
+
+=item b2C STRUCTURE
+
+Full -> Coarse [incl. root]
+
+=item b2Shapiro STRUCTURE
+
+Full -> weighted Shapiro [i.r.]
+
+=item add_root STRUCTURE
+
+{Tree} -> ({Tree}R)
+
+=item expand_Shapiro COARSE
+
+add S for stacks to coarse struct
+
+=item expand_Full STRUCTURE
+
+Full -> FFull
+
+=item unexpand_Full FSTRUCTURE
+
+FFull -> Full
+
+=item unweight WCOARSE
+
+remove weights from coarse struct
+
+=item unexpand_aligned_F ALIGN
+
+
+
+=item parse_structure STRUCTURE
+
+computes structure statistics, and fills the following global variables:
+
+$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, ($RNA::loops+1)*4);
+
+Warning: using these functions with wrong arguments will corrupt your
+memory and lead to a segmentation fault.
+
+=head1 AUTHOR
+
+Ivo L. Hofacker <ivo@tbi.univie.ac.at>
+
+=cut
+
+# ---------- BASE METHODS -------------
+
+package RNA;
+
+sub TIEHASH {
+ my ($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;
+*fold = *RNAc::fold;
+*fold_par = *RNAc::fold_par;
+*circfold = *RNAc::circfold;
+*energy_of_structure = *RNAc::energy_of_structure;
+*energy_of_struct_par = *RNAc::energy_of_struct_par;
+*energy_of_circ_structure = *RNAc::energy_of_circ_structure;
+*energy_of_circ_struct_par = *RNAc::energy_of_circ_struct_par;
+*energy_of_gquad_structure = *RNAc::energy_of_gquad_structure;
+*energy_of_structure_pt = *RNAc::energy_of_structure_pt;
+*energy_of_struct_pt_par = *RNAc::energy_of_struct_pt_par;
+*free_arrays = *RNAc::free_arrays;
+*parenthesis_structure = *RNAc::parenthesis_structure;
+*parenthesis_zuker = *RNAc::parenthesis_zuker;
+*letter_structure = *RNAc::letter_structure;
+*update_fold_params = *RNAc::update_fold_params;
+*update_fold_params_par = *RNAc::update_fold_params_par;
+*backtrack_fold_from_pair = *RNAc::backtrack_fold_from_pair;
+*energy_of_move = *RNAc::energy_of_move;
+*energy_of_move_pt = *RNAc::energy_of_move_pt;
+*loop_energy = *RNAc::loop_energy;
+*export_fold_arrays = *RNAc::export_fold_arrays;
+*export_fold_arrays_par = *RNAc::export_fold_arrays_par;
+*export_circfold_arrays = *RNAc::export_circfold_arrays;
+*export_circfold_arrays_par = *RNAc::export_circfold_arrays_par;
+*assign_plist_from_db = *RNAc::assign_plist_from_db;
+*LoopEnergy = *RNAc::LoopEnergy;
+*HairpinE = *RNAc::HairpinE;
+*initialize_fold = *RNAc::initialize_fold;
+*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;
+*cofold = *RNAc::cofold;
+*cofold_par = *RNAc::cofold_par;
+*free_co_arrays = *RNAc::free_co_arrays;
+*update_cofold_params = *RNAc::update_cofold_params;
+*update_cofold_params_par = *RNAc::update_cofold_params_par;
+*export_cofold_arrays_gq = *RNAc::export_cofold_arrays_gq;
+*export_cofold_arrays = *RNAc::export_cofold_arrays;
+*zukersubopt = *RNAc::zukersubopt;
+*zukersubopt_par = *RNAc::zukersubopt_par;
+*get_monomere_mfes = *RNAc::get_monomere_mfes;
+*initialize_cofold = *RNAc::initialize_cofold;
+*pf_fold = *RNAc::pf_fold;
+*pf_fold_par = *RNAc::pf_fold_par;
+*pf_circ_fold = *RNAc::pf_circ_fold;
+*pbacktrack = *RNAc::pbacktrack;
+*pbacktrack_circ = *RNAc::pbacktrack_circ;
+*free_pf_arrays = *RNAc::free_pf_arrays;
+*update_pf_params = *RNAc::update_pf_params;
+*update_pf_params_par = *RNAc::update_pf_params_par;
+*export_bppm = *RNAc::export_bppm;
+*assign_plist_from_pr = *RNAc::assign_plist_from_pr;
+*assign_plist_gquad_from_pr = *RNAc::assign_plist_gquad_from_pr;
+*get_centroid_struct_gquad_pr = *RNAc::get_centroid_struct_gquad_pr;
+*get_pf_arrays = *RNAc::get_pf_arrays;
+*get_subseq_F = *RNAc::get_subseq_F;
+*get_centroid_struct_pl = *RNAc::get_centroid_struct_pl;
+*get_centroid_struct_pr = *RNAc::get_centroid_struct_pr;
+*mean_bp_distance = *RNAc::mean_bp_distance;
+*mean_bp_distance_pr = *RNAc::mean_bp_distance_pr;
+*bppm_to_structure = *RNAc::bppm_to_structure;
+*stackProb = *RNAc::stackProb;
+*bppm_symbol = *RNAc::bppm_symbol;
+*init_pf_fold = *RNAc::init_pf_fold;
+*centroid = *RNAc::centroid;
+*mean_bp_dist = *RNAc::mean_bp_dist;
+*expLoopEnergy = *RNAc::expLoopEnergy;
+*expHairpinEnergy = *RNAc::expHairpinEnergy;
+*co_pf_fold = *RNAc::co_pf_fold;
+*co_pf_fold_par = *RNAc::co_pf_fold_par;
+*export_co_bppm = *RNAc::export_co_bppm;
+*free_co_pf_arrays = *RNAc::free_co_pf_arrays;
+*update_co_pf_params = *RNAc::update_co_pf_params;
+*update_co_pf_params_par = *RNAc::update_co_pf_params_par;
+*get_concentrations = *RNAc::get_concentrations;
+*inverse_fold = *RNAc::inverse_fold;
+*inverse_pf_fold = *RNAc::inverse_pf_fold;
+*option_string = *RNAc::option_string;
+*set_model_details = *RNAc::set_model_details;
+*update_alifold_params = *RNAc::update_alifold_params;
+*circalifold = *RNAc::circalifold;
+*free_alifold_arrays = *RNAc::free_alifold_arrays;
+*get_mpi = *RNAc::get_mpi;
+*readribosum = *RNAc::readribosum;
+*energy_of_alistruct = *RNAc::energy_of_alistruct;
+*energy_of_ali_gquad_structure = *RNAc::energy_of_ali_gquad_structure;
+*encode_ali_sequence = *RNAc::encode_ali_sequence;
+*alloc_sequence_arrays = *RNAc::alloc_sequence_arrays;
+*free_sequence_arrays = *RNAc::free_sequence_arrays;
+*alipf_fold_par = *RNAc::alipf_fold_par;
+*alipf_fold = *RNAc::alipf_fold;
+*alipf_circ_fold = *RNAc::alipf_circ_fold;
+*export_ali_bppm = *RNAc::export_ali_bppm;
+*free_alipf_arrays = *RNAc::free_alipf_arrays;
+*alipbacktrack = *RNAc::alipbacktrack;
+*get_alipf_arrays = *RNAc::get_alipf_arrays;
+*alifold = *RNAc::alifold;
+*consensus = *RNAc::consensus;
+*consens_mis = *RNAc::consens_mis;
+*get_xy_coordinates = *RNAc::get_xy_coordinates;
+*subopt = *RNAc::subopt;
+*get_pr = *RNAc::get_pr;
+*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;
+*space = *RNAc::space;
+*xrealloc = *RNAc::xrealloc;
+*nrerror = *RNAc::nrerror;
+*warn_user = *RNAc::warn_user;
+*init_rand = *RNAc::init_rand;
+*urn = *RNAc::urn;
+*int_urn = *RNAc::int_urn;
+*filecopy = *RNAc::filecopy;
+*time_stamp = *RNAc::time_stamp;
+*random_string = *RNAc::random_string;
+*hamming = *RNAc::hamming;
+*hamming_bound = *RNAc::hamming_bound;
+*get_line = *RNAc::get_line;
+*skip_comment_lines = *RNAc::skip_comment_lines;
+*get_input_line = *RNAc::get_input_line;
+*get_multi_input_line = *RNAc::get_multi_input_line;
+*read_record = *RNAc::read_record;
+*extract_record_rest_structure = *RNAc::extract_record_rest_structure;
+*pack_structure = *RNAc::pack_structure;
+*unpack_structure = *RNAc::unpack_structure;
+*make_pair_table = *RNAc::make_pair_table;
+*make_pair_table_pk = *RNAc::make_pair_table_pk;
+*copy_pair_table = *RNAc::copy_pair_table;
+*alimake_pair_table = *RNAc::alimake_pair_table;
+*make_pair_table_snoop = *RNAc::make_pair_table_snoop;
+*make_loop_index_pt = *RNAc::make_loop_index_pt;
+*bp_distance = *RNAc::bp_distance;
+*print_tty_input_seq = *RNAc::print_tty_input_seq;
+*print_tty_input_seq_str = *RNAc::print_tty_input_seq_str;
+*print_tty_constraint_full = *RNAc::print_tty_constraint_full;
+*print_tty_constraint = *RNAc::print_tty_constraint;
+*str_DNA2RNA = *RNAc::str_DNA2RNA;
+*str_uppercase = *RNAc::str_uppercase;
+*get_iindx = *RNAc::get_iindx;
+*get_indx = *RNAc::get_indx;
+*getConstraint = *RNAc::getConstraint;
+*constrain_ptypes = *RNAc::constrain_ptypes;
+*make_referenceBP_array = *RNAc::make_referenceBP_array;
+*compute_BPdifferences = *RNAc::compute_BPdifferences;
+*read_parameter_file = *RNAc::read_parameter_file;
+*write_parameter_file = *RNAc::write_parameter_file;
+*deref_any = *RNAc::deref_any;
+*scale_parameters = *RNAc::scale_parameters;
+*copy_parameters = *RNAc::copy_parameters;
+*set_parameters = *RNAc::set_parameters;
+*get_aligned_line = *RNAc::get_aligned_line;
+*make_loop_index = *RNAc::make_loop_index;
+*duplexfold = *RNAc::duplexfold;
+*aliduplexfold = *RNAc::aliduplexfold;
+*encode_seq = *RNAc::encode_seq;
+*Lfold = *RNAc::Lfold;
+*Lfoldz = *RNAc::Lfoldz;
+*aliLfold = *RNAc::aliLfold;
+*simple_xy_coordinates = *RNAc::simple_xy_coordinates;
+*simple_circplot_coordinates = *RNAc::simple_circplot_coordinates;
+*PS_rna_plot_snoop_a = *RNAc::PS_rna_plot_snoop_a;
+*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;
+*gmlRNA = *RNAc::gmlRNA;
+*ssv_rna_plot = *RNAc::ssv_rna_plot;
+*svg_rna_plot = *RNAc::svg_rna_plot;
+*xrna_plot = *RNAc::xrna_plot;
+*PS_color_dot_plot = *RNAc::PS_color_dot_plot;
+*PS_color_dot_plot_turn = *RNAc::PS_color_dot_plot_turn;
+*PS_dot_plot_list = *RNAc::PS_dot_plot_list;
+*PS_dot_plot_turn = *RNAc::PS_dot_plot_turn;
+*PS_color_aln = *RNAc::PS_color_aln;
+*aliPS_color_aln = *RNAc::aliPS_color_aln;
+*PS_dot_plot = *RNAc::PS_dot_plot;
+*find_saddle = *RNAc::find_saddle;
+*get_path = *RNAc::get_path;
+*free_path = *RNAc::free_path;
+
+############# Class : RNA::intArray ##############
+
+package RNA::intArray;
+use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
+@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);
+@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);
+@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::COORDINATE ##############
+
+package RNA::COORDINATE;
+use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
+@ISA = qw( RNA );
+%OWNER = ();
+%ITERATORS = ();
+*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;
+*get = *RNAc::COORDINATE_get;
+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::SOLUTION ##############
+
+package RNA::SOLUTION;
+use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
+@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::duplexT ##############
+
+package RNA::duplexT;
+use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
+@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 new {
+ my $pkg = shift;
+ my $self = RNAc::new_duplexT(@_);
+ 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_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;
+}
+
+
+# ------- VARIABLE STUBS --------
+
+package RNA;
+
+*VERSION = *RNAc::VERSION;
+*logML = *RNAc::logML;
+*uniq_ML = *RNAc::uniq_ML;
+*cut_point = *RNAc::cut_point;
+*eos_debug = *RNAc::eos_debug;
+*st_back = *RNAc::st_back;
+*mirnatog = *RNAc::mirnatog;
+*F_monomer = *RNAc::F_monomer;
+*symbolset = *RNAc::symbolset;
+*final_cost = *RNAc::final_cost;
+*give_up = *RNAc::give_up;
+*inv_verbose = *RNAc::inv_verbose;
+*fold_constrained = *RNAc::fold_constrained;
+*noLonelyPairs = *RNAc::noLonelyPairs;
+*dangles = *RNAc::dangles;
+*noGU = *RNAc::noGU;
+*no_closingGU = *RNAc::no_closingGU;
+*tetra_loop = *RNAc::tetra_loop;
+*energy_set = *RNAc::energy_set;
+*circ = *RNAc::circ;
+*csv = *RNAc::csv;
+*oldAliEn = *RNAc::oldAliEn;
+*ribo = *RNAc::ribo;
+*RibosumFile = *RNAc::RibosumFile;
+*nonstandards = *RNAc::nonstandards;
+*temperature = *RNAc::temperature;
+*james_rule = *RNAc::james_rule;
+*base_pair = *RNAc::base_pair;
+*pr = *RNAc::pr;
+*iindx = *RNAc::iindx;
+*pf_scale = *RNAc::pf_scale;
+*do_backtrack = *RNAc::do_backtrack;
+*backtrack_type = *RNAc::backtrack_type;
+*gquad = *RNAc::gquad;
+*cv_fact = *RNAc::cv_fact;
+*nc_fact = *RNAc::nc_fact;
+*subopt_sorted = *RNAc::subopt_sorted;
+*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;
+*VRNA_INPUT_ERROR = *RNAc::VRNA_INPUT_ERROR;
+*VRNA_INPUT_QUIT = *RNAc::VRNA_INPUT_QUIT;
+*VRNA_INPUT_MISC = *RNAc::VRNA_INPUT_MISC;
+*VRNA_INPUT_FASTA_HEADER = *RNAc::VRNA_INPUT_FASTA_HEADER;
+*VRNA_INPUT_SEQUENCE = *RNAc::VRNA_INPUT_SEQUENCE;
+*VRNA_INPUT_CONSTRAINT = *RNAc::VRNA_INPUT_CONSTRAINT;
+*VRNA_INPUT_NO_TRUNCATION = *RNAc::VRNA_INPUT_NO_TRUNCATION;
+*VRNA_INPUT_NO_REST = *RNAc::VRNA_INPUT_NO_REST;
+*VRNA_INPUT_NO_SPAN = *RNAc::VRNA_INPUT_NO_SPAN;
+*VRNA_INPUT_NOSKIP_BLANK_LINES = *RNAc::VRNA_INPUT_NOSKIP_BLANK_LINES;
+*VRNA_INPUT_BLANK_LINE = *RNAc::VRNA_INPUT_BLANK_LINE;
+*VRNA_INPUT_NOSKIP_COMMENTS = *RNAc::VRNA_INPUT_NOSKIP_COMMENTS;
+*VRNA_INPUT_COMMENT = *RNAc::VRNA_INPUT_COMMENT;
+*VRNA_CONSTRAINT_PIPE = *RNAc::VRNA_CONSTRAINT_PIPE;
+*VRNA_CONSTRAINT_DOT = *RNAc::VRNA_CONSTRAINT_DOT;
+*VRNA_CONSTRAINT_X = *RNAc::VRNA_CONSTRAINT_X;
+*VRNA_CONSTRAINT_ANG_BRACK = *RNAc::VRNA_CONSTRAINT_ANG_BRACK;
+*VRNA_CONSTRAINT_RND_BRACK = *RNAc::VRNA_CONSTRAINT_RND_BRACK;
+*VRNA_CONSTRAINT_MULTILINE = *RNAc::VRNA_CONSTRAINT_MULTILINE;
+*VRNA_CONSTRAINT_NO_HEADER = *RNAc::VRNA_CONSTRAINT_NO_HEADER;
+*VRNA_CONSTRAINT_ALL = *RNAc::VRNA_CONSTRAINT_ALL;
+*VRNA_CONSTRAINT_G = *RNAc::VRNA_CONSTRAINT_G;
+*VRNA_OPTION_MULTILINE = *RNAc::VRNA_OPTION_MULTILINE;
+*FILENAME_MAX_LENGTH = *RNAc::FILENAME_MAX_LENGTH;
+*FILENAME_ID_LENGTH = *RNAc::FILENAME_ID_LENGTH;
+*xsubi = *RNAc::xsubi;
+*PI = *RNAc::PI;
+*PIHALF = *RNAc::PIHALF;
+*VRNA_PLOT_TYPE_SIMPLE = *RNAc::VRNA_PLOT_TYPE_SIMPLE;
+*VRNA_PLOT_TYPE_NAVIEW = *RNAc::VRNA_PLOT_TYPE_NAVIEW;
+*VRNA_PLOT_TYPE_CIRCULAR = *RNAc::VRNA_PLOT_TYPE_CIRCULAR;
+*rna_plot_type = *RNAc::rna_plot_type;
+1;
git://source.jalview.org / jabaws.git / blobdiff