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package Wurst; |
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# rcsid = "$Id: Wurst.pm,v 1.2 2008/01/18 15:05:59 margraf Exp $" |
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30851
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use strict; |
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use Carp; |
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use vars qw($VERSION @ISA @EXPORT @EXPORT_OK $AUTOLOAD); |
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require Exporter; |
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require DynaLoader; |
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require AutoLoader; |
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@ISA = qw(Exporter DynaLoader ); |
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# Items to export into callers namespace by default. Note: do not export |
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# names by default without a very good reason. Use EXPORT_OK instead. |
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# Do not simply export all your public functions/methods/constants. |
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# Please please delete "str_to_class" XXXX do not forget !!! |
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@EXPORT = qw( |
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aa_2_prob_vec |
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aa_strct_2_prob_vec |
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aa_strct_clssfcn_read |
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aa_strct_dump |
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aa_strct_nclass |
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aa_strct_size |
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ac_dump |
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ac_nclass |
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ac_read |
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ac_size |
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blst_chk_read |
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check_data_read |
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computeMembership |
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computeMembershipAA |
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computeMembershipAAProf |
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coord_get_sec_s |
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coord_has_sec_s |
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coord_c_n_dist |
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coord_calc_psi |
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coord_calc_phi |
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coord_psi |
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coord_phi |
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coord_deletion |
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coord_geo_gap |
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coord_get_seq |
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coord_name |
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coord_read |
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coord_rmsd |
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coord_size |
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coord_2_bin |
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coord_2_pdb |
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coord_2_pnlty |
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coord_2_spdb |
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dme_thresh |
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find_alt_path_score_simple |
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file_pre_read |
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file_un_read |
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func_int |
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func_float |
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func_char |
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funcs1_char |
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funcs2_char |
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get_clssfcn |
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get_nbor |
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get_rmsd |
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get_solv_data |
66
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get_torsion_data |
67
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get_seq_id_simple |
68
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make_model |
69
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model_pdb_num |
70
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make_model |
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merge_alignments |
72
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model_pdb_num |
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model_res_num |
74
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multal_string |
75
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split_multal |
76
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pair_set_chimera |
77
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pair_set_coverage |
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pair_set_gap |
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pair_set_string |
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pair_set_pretty_string |
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pair_set_score |
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pair_set_extend |
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param_fx_read |
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param_rs_read |
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pdb_read |
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prob_vec_info |
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prob_vec_read |
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prob_vec_size |
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prob_vec_length |
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prob_vec_copy |
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prob_vec_write |
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prof_aa_2_prob_vec |
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prof_aa_strct_2_prob_vec |
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pvec_avg |
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ReadRescoreParam |
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remove_seq |
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score_mat_add |
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score_mat_info |
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score_mat_diag_wipe |
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score_mat_double_matrix |
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score_mat_write_gnuplot |
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score_mat_new |
103
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score_mat_read |
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score_mat_scale |
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score_mat_shift |
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score_mat_string |
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score_mat_sum_smpl |
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score_mat_sum_sec |
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score_mat_sum_full |
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score_mat_write |
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sec_s_data_read |
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sec_s_data_string |
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seq_from_string |
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seq_get_1 |
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seq_num |
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seq_print_many |
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seq_print |
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seq_read |
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seq_read_many |
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seq_size |
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seqprof_get_seq |
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seqprof_str |
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scor_set_fromvec |
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scor_set_scale |
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scor_set_simpl |
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scor_set_to_vec |
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score_fx |
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score_fx_prof |
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score_prof_prof |
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score_pvec |
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score_rs |
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score_sec |
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score_smat |
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score_sprof |
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str_to_class |
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strct_2_prob_vec |
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struct_2_prob_vec |
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sub_mat_read |
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sub_mat_string |
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sub_mat_shift |
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sub_mat_scale |
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sub_mat_get_by_c |
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sub_mat_get_by_i |
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sub_mat_set_by_c |
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sub_mat_set_by_i |
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wurstli_hello |
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$EXT_LONG |
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$EXT_SHORT |
149
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$N_AND_W |
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$S_AND_W |
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); |
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$VERSION = '0.01'; |
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use vars qw($EXT_LONG $EXT_SHORT $N_AND_W $S_AND_W); |
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252
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154
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*EXT_LONG = \0; |
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*EXT_SHORT = \1; |
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*N_AND_W = \0; |
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*S_AND_W = \1; |
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159
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bootstrap Wurst $VERSION; |
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161
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# Preloaded methods go here. |
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sub END { |
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10439
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free_scratch(); |
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} |
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use strict; |
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776
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168
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# ----------------------- score_mat_sum_smpl ------------------------ |
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# OK Mr Smartypants. There are two very nasty tricks here. |
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# 1. The first argument will be modified. $rmat is a matrix to be |
171
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# passed back to the interpreter. |
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# 2. On calling the score_m.. function, we pass in $$rmat, not $rmat. |
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# After exiting, $rmat will have been mutated into the correct class. |
174
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# More tricks |
175
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# * The C code expects some float arrays, but usually we do not |
176
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# want to use this feature. The magic below with the $null variable |
177
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# is simply to pass NULL pointers to the C code. |
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# * The last arguement is a "pair_set" - the result of a previous |
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# alignment calculation. It is optional, hence the two versions of |
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# of the call. |
181
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sub score_mat_sum_smpl (\$ $ $ $ $ $ $; $) |
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{ |
183
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1
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1
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0
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4564063
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my ($rmat, $scores, $pgap_open, $pgap_widen, $qgap_open, $qgap_widen, |
184
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$align_type, $bias_set) = @_; |
185
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1
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my $null = 0; |
186
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1
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bless (\$null, 'floatPtr'); |
187
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1
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my $ret; |
188
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1
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if ( ! defined ($bias_set)) { |
189
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1
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$ret = |
190
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score_mat_sum_full ($$rmat, $scores, $pgap_open, $pgap_widen, |
191
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$qgap_open, $qgap_widen, \$null, \$null, |
192
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$align_type); |
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194
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} else { |
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$ret = |
196
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score_mat_sum_full ($$rmat, $scores, $pgap_open, $pgap_widen, |
197
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$qgap_open, $qgap_widen, \$null, \$null, |
198
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$align_type, $bias_set); |
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} |
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1
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return $ret; |
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} |
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203
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204
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# ----------------------- wurstli_hello ------------------------ |
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sub wurstli_hello |
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{ |
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0
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0
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0
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print "wurstli wurstli\n"; |
208
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} |
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210
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# ----------------------- score_mat_sum_sec ------------------------ |
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sub score_mat_sum_sec ($ $ $ $ $ $ $ $ $; $) |
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{ |
213
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0
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0
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0
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my ($rmat, $scores, $coord, $sec_pnlty, |
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$pgap_open, $pgap_widen, $qgap_open, $qgap_widen, |
215
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$align_type, $bias_set) = @_; |
216
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0
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my $null = 0; |
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0
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bless (\$null, 'floatPtr'); |
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219
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0
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0
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if (! defined ($sec_pnlty)) { |
220
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0
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print STDERR "score_mat_sum_sec: called with \"sec_pnlty\" undef\n"; |
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0
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print STDERR "score_mat_sum_sec: setting to 1.0\n"; |
222
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0
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$sec_pnlty = 1; |
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} |
224
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0
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my $mult = coord_2_pnlty ($coord, $sec_pnlty); |
225
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0
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my $ret; |
226
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0
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0
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if ( ! defined ($bias_set)) { |
227
|
0
|
|
|
|
|
|
$ret = |
228
|
|
|
|
|
|
|
score_mat_sum_full ($rmat, $scores, $pgap_open, $pgap_widen, |
229
|
|
|
|
|
|
|
$qgap_open, $qgap_widen, $mult, \$null, |
230
|
|
|
|
|
|
|
$align_type); |
231
|
|
|
|
|
|
|
} else { |
232
|
0
|
|
|
|
|
|
$ret = |
233
|
|
|
|
|
|
|
score_mat_sum_full ($rmat, $scores, $pgap_open, $pgap_widen, |
234
|
|
|
|
|
|
|
$qgap_open, $qgap_widen, $mult, \$null, |
235
|
|
|
|
|
|
|
$align_type, $bias_set); |
236
|
|
|
|
|
|
|
} |
237
|
0
|
|
|
|
|
|
return $ret; |
238
|
|
|
|
|
|
|
} |
239
|
|
|
|
|
|
|
|
240
|
|
|
|
|
|
|
|
241
|
|
|
|
|
|
|
# Autoload methods go after =cut, and are processed by the autosplit program. |
242
|
|
|
|
|
|
|
|
243
|
|
|
|
|
|
|
1; |
244
|
|
|
|
|
|
|
__END__ |