--- /dev/null
+#!/usr/bin/perl -Iblib/arch -Iblib/lib
+
+# Last changed Time-stamp: <2007-09-27 17:21:23 ivo>
+
+######################### We start with some black magic to print on failure.
+# (It may become useful if the test is moved to ./t subdirectory.)
+use strict;
+use Test;
+use lib qw|blib/arch blib/lib|;
+
+BEGIN { plan tests => 24; }
+
+use RNA;
+use warnings;
+
+######################### End of black magic.
+
+# Insert your test code below (better if it prints "ok 13"
+# (correspondingly "not ok 13") depending on the success of chunk 13
+# of the test code):
+
+
+my $seq1 ="CGCAGGGAUACCCGCG";
+my $struc1="(((.(((...))))))";
+my $seq2 ="GCGCCCAUAGGGACGC";
+my $struc2="((((((...))).)))";
+# calculate a hamming distance (from util.c)
+ok(RNA::hamming($seq1, $seq2), 16);
+
+# check a global variable
+ok($RNA::temperature, 37);
+
+# fold a sequence
+
+# old obsolete way of calling fold()
+my $struct = $seq1; # wierd way of allocating space
+my $mfe=RNA::fold($seq1, $struct);
+ok($struct, $struc1);
+
+# new better interface
+($struct, $mfe) = RNA::fold($seq1);
+ok($struct eq $struc1);
+# check energy
+ok(RNA::energy_of_struct($seq1,$struc1), $mfe);
+
+# check constrained folding
+$RNA::fold_constrained = 1;
+my($struct3, $cmfe) = RNA::fold($seq1, '....xx....xx...');
+ok($struct3, '(((..........)))');
+ok(RNA::energy_of_struct($seq1,$struct3), $cmfe);
+$RNA::fold_constrained = 0;
+
+# test cofold
+$RNA::cut_point = length($seq1)+1;
+my($costruct, $comfe) = RNA::cofold($seq1 . $seq2);
+ok($costruct, '(((.(((...))))))((((((...))).)))');
+$cmfe = RNA::energy_of_struct($seq1 . $seq2, $costruct);
+ok(abs($comfe-$cmfe)<1e-5);
+my ($x,$ac,$bc,$fcab,$cf) = RNA::co_pf_fold($seq1. $seq2, $struct);
+ok(($cf<$comfe)&&($comfe-$cf<1.3));
+#test concentration computation
+my $fcaa;
+my $fcbb;
+my ($usel1,$usel2, $usel3);
+($x,$usel1, $usel2, $fcaa, $usel3)= RNA::co_pf_fold($seq1. $seq1, $struct);
+$RNA::cut_point = length($seq2)+1;
+($x,$usel1, $usel2, $fcbb, $usel3)= RNA::co_pf_fold($seq2. $seq2, $struct);
+my ($AB,$AA,$BB,$A,$B)=RNA::get_concentrations($fcab, $fcaa, $fcbb,$ac, $bc, 1e-5, 1e-5);
+$AB/=2e-5;
+$AA/=2e-5;
+$BB/=2e-5;
+$A/=2e-5;
+$B/=2e-5;
+ok((abs($AB-0.0)+abs($AA-0.00578)+abs($BB-0.01100)+abs($A-0.48843)+abs($B-0.47801))<0.0001);
+$RNA::cut_point=-1;
+
+# pf_fold
+my $f = RNA::pf_fold($seq1, $struct);
+ok(($f<$mfe)&&($mfe-$f<0.8));
+
+# tree distance
+my $xstruc = RNA::expand_Full($struc1);
+my $T1 = RNA::make_tree($xstruc);
+$xstruc = RNA::expand_Full($struc2);
+my $T2 = RNA::make_tree($xstruc);
+$RNA::edit_backtrack = 1;
+my $tree_dist = RNA::tree_edit_distance($T1, $T2);
+# print RNA::get_aligned_line(0), RNA::get_aligned_line(1),"\n";
+ok($tree_dist,2);
+
+# check access to a C array
+#ok(RNA::ptrvalue($RNA::iindx,3),108);
+ok(RNA::intP_getitem($RNA::iindx,3),108);
+
+# memmove does not work in current swig versions
+# RNA::memmove($RNA::xsubi, pack('S3', 171,42,93));
+# use shortP_setitem instead
+RNA::ushortP_setitem($RNA::xsubi, 0, 171);
+RNA::ushortP_setitem($RNA::xsubi, 1, 42);
+RNA::ushortP_setitem($RNA::xsubi, 2, 93);
+ok(RNA::cdata($RNA::xsubi, 6),pack('S3', 171,42,93));
+
+# get a bp prob in two different ways
+my $p1 = RNA::get_pr(2,15);
+my $ii = RNA::intP_getitem($RNA::iindx, 2);
+my $p2 = RNA::doubleP_getitem($RNA::pr, $ii-15);
+ok(($p1<0.999) && ($p1>0.99) && (abs($p1-$p2)<1.2e-7));
+
+my $bpf = RNA::Make_bp_profile(length($seq1));
+my @bpf = unpack("f*",RNA::cdata($bpf, length($seq1)*4*3));
+ok (($bpf[2*3]+$bpf[2*3+1]>.99999)&&$bpf[2*3+2]==0 &&
+ ($bpf[2*3+1]>=$p1));
+
+my $pack = RNA::pack_structure($struc1);
+ok (RNA::unpack_structure($pack), $struc1);
+
+
+RNA::parse_structure($struc1);
+ok(($RNA::loops==2) && ($RNA::pairs==6)&&($RNA::unpaired==4) &&
+ (RNA::intP_getitem($RNA::loop_degree,1)==2));
+
+
+RNA::PS_rna_plot($seq1, $struc1, "test_ss.ps");
+my $anote = "2 15 1 gmark\n" . "3 cmark\n";
+RNA::PS_rna_plot_a($seq1, $struc1, "test_ss_a.ps", undef, $anote);
+RNA::PS_dot_plot($seq1, "test_dp.ps");
+RNA::ssv_rna_plot($seq1, $struct, "test.coord");
+# print "$seq1, $struct, $mfe, $f\n";
+print "please check the two postscript files test_ss.ps and test_dp.ps\n";
+RNA::write_parameter_file("test.par");
+
+$RNA::symbolset = "GC";
+my $start = RNA::random_string(length $struc1, "GC");
+my ($sinv, $cost) = RNA::inverse_fold($start, $struc1);
+my ($ss, $en) = RNA::fold($sinv);
+ok($ss, $struc1);
+
+RNA::free_pf_arrays();
+RNA::free_arrays();
+RNA::free_co_arrays();
+
+$RNA::subopt_sorted = 1;
+$RNA::noLonelyPairs = 1;
+my $solution = RNA::subopt($seq1, undef, 500, undef);
+
+printf "%d suboptimals\n", $solution->size();
+for (0..$solution->size()) {
+ # the last access should produce a "value out of range" warning
+ printf "%s %6.2f\n", $solution->get($_)->{structure},
+ $solution->get($_)->{energy}
+ if defined $solution->get($_)->{structure};
+}
+$RNA::cut_point = 3;
+my $e = RNA::energy_of_struct("GCGC", "(())");
+ok(int($e*100+0.5), 70);
+
+my $duplex = RNA::duplexfold($seq1, $seq2);
+
+ok($duplex->{structure}, "(.(.(((.....(((.&))))))...).).");
+undef $duplex;
+
+my @align = ("GCCAUCCGAGGGAAAGGUU", "GAUCGACAGCGUCU-AUCG", "CCGUCUUUAUGAGUCCGGC");
+my ($css, $cen) = RNA::alifold(\@align);
+ok($css,"(((.(((...)))..))).");
+ok(RNA::consens_mis(\@align), "SMBHBHYDRBGDVWmVKBB");
+RNA::free_alifold_arrays();
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