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revision 1.6, Fri Feb 11 06:32:03 2005 UTC revision 1.10, Tue Jan 3 18:31:14 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 150  Line 167 
167      'all_constructs'   => $wrapper->wrap_array_return("all_constructs"),      'all_constructs'   => $wrapper->wrap_array_return("all_constructs"),
168      'all_exchangable_subsystems'   => $wrapper->wrap_array_return("all_exchangable_subsystems"),      'all_exchangable_subsystems'   => $wrapper->wrap_array_return("all_exchangable_subsystems"),
169      'all_features'   => $wrapper->wrap_array_return("all_features"),      'all_features'   => $wrapper->wrap_array_return("all_features"),
     'all_for_genome'   => $wrapper->wrap_array_return("all_for_genome"),  
170      'all_maps'   => $wrapper->wrap_array_return("all_maps"),      'all_maps'   => $wrapper->wrap_array_return("all_maps"),
171      'all_protein_families'   => $wrapper->wrap_array_return("all_protein_families"),      'all_protein_families'   => $wrapper->wrap_array_return("all_protein_families"),
172      'all_reactions'   => $wrapper->wrap_array_return("all_reactions"),      'all_reactions'   => $wrapper->wrap_array_return("all_reactions"),
# Line 159  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 168  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_fig_id'   => $wrapper->wrap_scalar_return("by_fig_id"),      'by_fig_id'   => $wrapper->wrap_scalar_return("by_fig_id"),
192      'cas'   => $wrapper->wrap_scalar_return("cas"),      'cas'   => $wrapper->wrap_scalar_return("cas"),
193      'cas_to_cid'   => $wrapper->wrap_scalar_return("cas_to_cid"),      'cas_to_cid'   => $wrapper->wrap_scalar_return("cas_to_cid"),
# Line 235  Line 254 
254      'names_of_compound'   => $wrapper->wrap_array_return("names_of_compund"),      'names_of_compound'   => $wrapper->wrap_array_return("names_of_compund"),
255      'neighborhood_of_role'   => $wrapper->wrap_scalar_return("neighborhood_of_role"),      'neighborhood_of_role'   => $wrapper->wrap_scalar_return("neighborhood_of_role"),
256      'org_of'   => $wrapper->wrap_scalar_return("org_of"),      'org_of'   => $wrapper->wrap_scalar_return("org_of"),
     'pegs_not_in_ss'   => $wrapper->wrap_array_return("pegs_not_in_ss"),  
257      'pegs_of'   => $wrapper->wrap_array_return("pegs_of"),      'pegs_of'   => $wrapper->wrap_array_return("pegs_of"),
258        'pegs_in_subsystem_cell' => $wrapper->wrap_array_return("pegs_in_subsystem_cell"),
259      'possibly_truncated'   => $wrapper->wrap_scalar_return("possibly_truncated"),      'possibly_truncated'   => $wrapper->wrap_scalar_return("possibly_truncated"),
260      'reaction2comp'   => $wrapper->wrap_scalar_return("reaction2comp"),      'reaction2comp'   => $wrapper->wrap_scalar_return("reaction2comp"),
261      '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 249  Line 268 
268      'sims'   => $wrapper->wrap_array_return("sims"),      'sims'   => $wrapper->wrap_array_return("sims"),
269      'sort_fids_by_taxonomy'   => $wrapper->wrap_array_return("sort_fids_by_taxonomy"),      'sort_fids_by_taxonomy'   => $wrapper->wrap_array_return("sort_fids_by_taxonomy"),
270      'sort_genomes_by_taxonomy'   => $wrapper->wrap_array_return("sort_genomes_by_taxonomy"),      'sort_genomes_by_taxonomy'   => $wrapper->wrap_array_return("sort_genomes_by_taxonomy"),
271        'subsystem_genomes' => $wrapper->wrap_array_return("subsystem_genomes"),
272        'subsystems_for_genome' => $wrapper->wrap_array_return("subsystems_for_genome"),
273      'subsystem_info' => $wrapper->wrap_array_return("subsystem_info"),      'subsystem_info' => $wrapper->wrap_array_return("subsystem_info"),
274        'subsystem_to_roles' => $wrapper->wrap_array_return("subsystem_to_roles"),
275      'subsystems_for_peg' => $wrapper->wrap_array_return("subsystems_for_peg"),      'subsystems_for_peg' => $wrapper->wrap_array_return("subsystems_for_peg"),
     'subsystems_for_genome' => $wrapper->wrap_array_return("subsystems_for_genome"),  
276      'sz_family'   => $wrapper->wrap_scalar_return("sz_family"),      'sz_family'   => $wrapper->wrap_scalar_return("sz_family"),
277      'taxonomic_groups_of_complete'   => $wrapper->wrap_array_return("taxonomic_groups_of_complete"),      'taxonomic_groups_of_complete'   => $wrapper->wrap_array_return("taxonomic_groups_of_complete"),
278      'taxonomy_of'   => $wrapper->wrap_scalar_return("taxonomy_of"),      'taxonomy_of'   => $wrapper->wrap_scalar_return("taxonomy_of"),

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