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revision 1.4, Wed Feb 9 21:35:13 2005 UTC revision 1.11, Mon Jan 16 00:23:48 2006 UTC
# Line 1  Line 1 
1    #
2    # Copyright (c) 2003-2006 University of Chicago and Fellowship
3    # for Interpretations of Genomes. All Rights Reserved.
4    #
5    # This file is part of the SEED Toolkit.
6    #
7    # The SEED Toolkit is free software. You can redistribute
8    # it and/or modify it under the terms of the SEED Toolkit
9    # Public License.
10    #
11    # You should have received a copy of the SEED Toolkit Public License
12    # along with this program; if not write to the University of Chicago
13    # at info@ci.uchicago.edu or the Fellowship for Interpretation of
14    # Genomes at veronika@thefig.info or download a copy from
15    # http://www.theseed.org/LICENSE.TXT.
16    #
17    
18  use Frontier::RPC2;  use Frontier::RPC2;
19    
20  use FIG;  use FIG;
# Line 158  Line 175 
175      'all_subsystems'   => $wrapper->wrap_array_return("all_subsystems"),      'all_subsystems'   => $wrapper->wrap_array_return("all_subsystems"),
176      'assign_function' => $wrapper->wrap_scalar_return("assign_function"),      'assign_function' => $wrapper->wrap_scalar_return("assign_function"),
177      'assign_functionF' => $wrapper->wrap_scalar_return("assign_functionF"),      'assign_functionF' => $wrapper->wrap_scalar_return("assign_functionF"),
178        'assigned_pegs'   => $wrapper->wrap_array_return("assigned_pegs"),
179        'assigned_pegs_in_ss' => $wrapper->wrap_array_return("assigned_pegs_in_ss"),
180        'assigned_pegs_not_in_ss'   => $wrapper->wrap_array_return("assigned_pegs_not_in_ss"),
181      'assignments_made'   => $wrapper->wrap_array_return("assignments_made"),      'assignments_made'   => $wrapper->wrap_array_return("assignments_made"),
182      'auto_assign' => $wrapper->wrap_scalar_return("auto_assign"),      'auto_assign' => $wrapper->wrap_scalar_return("auto_assign"),
183      'auto_assignF' => $wrapper->wrap_scalar_return("auto_assignF"),      'auto_assignF' => $wrapper->wrap_scalar_return("auto_assignF"),
# Line 167  Line 187 
187      'blastit'   => $wrapper->wrap_array_return("blastit"),      'blastit'   => $wrapper->wrap_array_return("blastit"),
188      'boundaries_of' => $wrapper->wrap_scalar_return("boundaries_of"),      'boundaries_of' => $wrapper->wrap_scalar_return("boundaries_of"),
189      'build_tree_of_complete' => $wrapper->wrap_array_return("build_tree_of_complete"),      'build_tree_of_complete' => $wrapper->wrap_array_return("build_tree_of_complete"),
190      'by_alias'   => $wrapper->wrap_scalar_return("by_alias"),      'by_alias'   => $wrapper->wrap_array_return("by_alias"),
191        'by_raw_alias'   => $wrapper->wrap_array_return("by_raw_alias"),
192      'by_fig_id'   => $wrapper->wrap_scalar_return("by_fig_id"),      'by_fig_id'   => $wrapper->wrap_scalar_return("by_fig_id"),
193      'cas'   => $wrapper->wrap_scalar_return("cas"),      'cas'   => $wrapper->wrap_scalar_return("cas"),
194      'cas_to_cid'   => $wrapper->wrap_scalar_return("cas_to_cid"),      'cas_to_cid'   => $wrapper->wrap_scalar_return("cas_to_cid"),
# Line 199  Line 220 
220      'feature_annotations'   => $wrapper->wrap_array_return("feature_annotations"),      'feature_annotations'   => $wrapper->wrap_array_return("feature_annotations"),
221      'feature_location'   => $wrapper->wrap_scalar_return("feature_location"),      'feature_location'   => $wrapper->wrap_scalar_return("feature_location"),
222      'file2N'   => $wrapper->wrap_scalar_return("file_2N"),      'file2N'   => $wrapper->wrap_scalar_return("file_2N"),
223        'find_by_attribute'   => $wrapper->wrap_array_return("find_by_attribute"),
224      'ftype'   => $wrapper->wrap_scalar_return("ftype"),      'ftype'   => $wrapper->wrap_scalar_return("ftype"),
225      'function_of'   => $wrapper->wrap_scalar_return("function_of"),      'function_of'   => $wrapper->wrap_scalar_return("function_of"),
226      'genes_in_region'   => $wrapper->wrap_array_return("genes_in_region"),      'genes_in_region'   => $wrapper->wrap_array_return("genes_in_region"),
# Line 207  Line 229 
229      'genome_counts'   => $wrapper->wrap_scalar_return("genome_counts"),      'genome_counts'   => $wrapper->wrap_scalar_return("genome_counts"),
230      'genome_version'   => $wrapper->wrap_scalar_return("genome_version"),      'genome_version'   => $wrapper->wrap_scalar_return("genome_version"),
231      'genus_species'   => $wrapper->wrap_scalar_return("genus_species"),      'genus_species'   => $wrapper->wrap_scalar_return("genus_species"),
232        'get_attributes'   => $wrapper->wrap_array_return("get_attributes"),
233        'get_cv_attributes'   => $wrapper->wrap_array_return("get_cv_attributes"),
234      'get_translation'   => $wrapper->wrap_scalar_return("get_translation"),      'get_translation'   => $wrapper->wrap_scalar_return("get_translation"),
235      'get_translations'   => $wrapper->wrap_array_return("get_translations"),      'get_translations'   => $wrapper->wrap_array_return("get_translations"),
236      'hypo'   => $wrapper->wrap_scalar_return("hypo"),      'hypo'   => $wrapper->wrap_scalar_return("hypo"),
# Line 235  Line 259 
259      'neighborhood_of_role'   => $wrapper->wrap_scalar_return("neighborhood_of_role"),      'neighborhood_of_role'   => $wrapper->wrap_scalar_return("neighborhood_of_role"),
260      'org_of'   => $wrapper->wrap_scalar_return("org_of"),      'org_of'   => $wrapper->wrap_scalar_return("org_of"),
261      'pegs_of'   => $wrapper->wrap_array_return("pegs_of"),      'pegs_of'   => $wrapper->wrap_array_return("pegs_of"),
262        'pegs_in_subsystem_cell' => $wrapper->wrap_array_return("pegs_in_subsystem_cell"),
263      'possibly_truncated'   => $wrapper->wrap_scalar_return("possibly_truncated"),      'possibly_truncated'   => $wrapper->wrap_scalar_return("possibly_truncated"),
264      'reaction2comp'   => $wrapper->wrap_scalar_return("reaction2comp"),      'reaction2comp'   => $wrapper->wrap_scalar_return("reaction2comp"),
265      'related_by_func_sim'   => $wrapper->wrap_array_return("related_by_func_sim"),      'related_by_func_sim'   => $wrapper->wrap_array_return("related_by_func_sim"),
# Line 247  Line 272 
272      'sims'   => $wrapper->wrap_array_return("sims"),      'sims'   => $wrapper->wrap_array_return("sims"),
273      'sort_fids_by_taxonomy'   => $wrapper->wrap_array_return("sort_fids_by_taxonomy"),      'sort_fids_by_taxonomy'   => $wrapper->wrap_array_return("sort_fids_by_taxonomy"),
274      'sort_genomes_by_taxonomy'   => $wrapper->wrap_array_return("sort_genomes_by_taxonomy"),      'sort_genomes_by_taxonomy'   => $wrapper->wrap_array_return("sort_genomes_by_taxonomy"),
275        'subsystem_genomes' => $wrapper->wrap_array_return("subsystem_genomes"),
276        'subsystems_for_genome' => $wrapper->wrap_array_return("subsystems_for_genome"),
277      'subsystem_info' => $wrapper->wrap_array_return("subsystem_info"),      'subsystem_info' => $wrapper->wrap_array_return("subsystem_info"),
278        'subsystem_to_roles' => $wrapper->wrap_array_return("subsystem_to_roles"),
279      'subsystems_for_peg' => $wrapper->wrap_array_return("subsystems_for_peg"),      'subsystems_for_peg' => $wrapper->wrap_array_return("subsystems_for_peg"),
280      'sz_family'   => $wrapper->wrap_scalar_return("sz_family"),      'sz_family'   => $wrapper->wrap_scalar_return("sz_family"),
281      'taxonomic_groups_of_complete'   => $wrapper->wrap_array_return("taxonomic_groups_of_complete"),      'taxonomic_groups_of_complete'   => $wrapper->wrap_array_return("taxonomic_groups_of_complete"),

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