NCBI C++ ToolKit
util_cmds.hpp
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1 #ifndef GUI_OBJUTILS___UTIL_CMDS__HPP
2 #define GUI_OBJUTILS___UTIL_CMDS__HPP
3 
4 /* $Id: util_cmds.hpp 47378 2023-02-27 20:09:44Z asztalos $
5  * ===========================================================================
6  *
7  * PUBLIC DOMAIN NOTICE
8  * National Center for Biotechnology Information
9  *
10  * This software/database is a "United States Government Work" under the
11  * terms of the United States Copyright Act. It was written as part of
12  * the author's official duties as a United States Government employee and
13  * thus cannot be copyrighted. This software/database is freely available
14  * to the public for use. The National Library of Medicine and the U.S.
15  * Government have not placed any restriction on its use or reproduction.
16  *
17  * Although all reasonable efforts have been taken to ensure the accuracy
18  * and reliability of the software and data, the NLM and the U.S.
19  * Government do not and cannot warrant the performance or results that
20  * may be obtained by using this software or data. The NLM and the U.S.
21  * Government disclaim all warranties, express or implied, including
22  * warranties of performance, merchantability or fitness for any particular
23  * purpose.
24  *
25  * Please cite the author in any work or product based on this material.
26  *
27  * ===========================================================================
28  *
29  * Authors: Colleen Bollin
30  *
31  * File Description:
32  *
33  */
34 
35 
36 #include <corelib/ncbiobj.hpp>
37 #include <gui/gui_export.h>
38 
43 
44 
47  class CSeq_feat;
48  class CScope;
49  class CBioseq_Handle;
51 
52 
53 
59 
62 
65 NCBI_GUIOBJUTILS_EXPORT CRef<CCmdComposite> CleanupHugeFileCommand(objects::CSeq_entry_Handle orig_seh, bool extended, bool do_tax, objects::taxupdate_func_t& updater, bool rmv_user_object);
66 
74 
75 // This second GetRetranslateCDSCommand is for when you are making additional changes to the coding region
76 // before or after translation (such as truncating or extending for stop codon)
77 NCBI_GUIOBJUTILS_EXPORT CRef<CCmdComposite> GetRetranslateCDSCommand(objects::CScope& scope, objects::CSeq_feat& cds, bool& cds_change, bool create_general_only);
78 NCBI_GUIOBJUTILS_EXPORT CRef<CCmdComposite> GetRetranslateCDSCommand(objects::CScope& scope, objects::CSeq_feat& cds, bool& cds_change, int& offset, bool create_general_only);
79 
80 NCBI_GUIOBJUTILS_EXPORT CRef<CCmdComposite> SetTranslExcept(objects::CSeq_entry_Handle seh, const string& comment, bool strict, bool extend, bool adjust_gene);
82 
87 
88 // runs discrepancy autofix for a specific test
91 
93  bool retranslate, bool adjust_gene, const objects::CSeq_feat& orig_feat,
94  objects::CScope& scope, int& offset, bool create_general_only);
100 
102 
103 #endif // GUI_OBJUTILS___UTIL_CMDS__HPP
CBioseq_Handle –.
CConstRef –.
Definition: ncbiobj.hpp:1266
CObject –.
Definition: ncbiobj.hpp:180
CRef –.
Definition: ncbiobj.hpp:618
CScope –.
Definition: scope.hpp:92
CSeq_entry_Handle –.
CSeq_feat_Handle –.
namespace ncbi::objects::
Definition: Seq_feat.hpp:58
Definition: map.hpp:338
Definition: set.hpp:45
#define true
Definition: bool.h:35
static SQLCHAR output[256]
Definition: print.c:5
int offset
Definition: replacements.h:160
static char test_name[128]
Definition: utf8_2.c:34
#define END_NCBI_SCOPE
End previously defined NCBI scope.
Definition: ncbistl.hpp:103
#define END_SCOPE(ns)
End the previously defined scope.
Definition: ncbistl.hpp:75
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
Definition: ncbistl.hpp:100
#define BEGIN_SCOPE(ns)
Define a new scope.
Definition: ncbistl.hpp:72
#define kEmptyStr
Definition: ncbistr.hpp:123
#define NCBI_GUIOBJUTILS_EXPORT
Definition: gui_export.h:512
Defines to provide correct exporting from DLLs in Windows.
function< CRef< CTaxon3_reply >(const vector< CRef< COrg_ref > > &list)> taxupdate_func_t
Definition: itaxon3.hpp:60
Definition: fix_pub.hpp:45
Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.
CRef< CCmdComposite > AutofixCommand(objects::CSeq_entry_Handle seh, const string &test_name, string *output, const string &suspect_rules=kEmptyStr)
CRef< CCmdChangeSeq_feat > AdjustGene(const objects::CSeq_feat &orig_feat, const objects::CSeq_feat &new_feat, objects::CScope &scope)
CRef< CCmdComposite > GetRemoveDuplicateGOTermsCommand(objects::CSeq_entry_Handle seh)
CRef< CCmdComposite > GetSynchronizeProteinPartialsCommand(objects::CScope &scope, const objects::CSeq_feat &cds)
CRef< CCmdComposite > CleanupCommand(objects::CSeq_entry_Handle orig_seh, bool extended, bool do_tax)
CRef< CCmdComposite > GetRetranslateCDSCommand(objects::CScope &scope, const objects::CSeq_feat &cds, bool create_general_only)
void GetProductToCDSMap(objects::CScope &scope, map< objects::CBioseq_Handle, set< objects::CSeq_feat_Handle > > &product_to_cds)
CRef< CCmdComposite > GetDisableStrainForwardingCommand(objects::CSeq_entry_Handle seh)
CRef< CCmdComposite > CachedTaxonomyLookupCommand(objects::CSeq_entry_Handle seh, objects::taxupdate_func_t &updater)
CRef< CCmdComposite > TrimStopsFromCompleteCDS(const objects::CSeq_feat &cds, objects::CScope &scope)
void AdjustProteinFeature(objects::CSeq_feat &prot, objects::CBioseq_Handle product, objects::CSeq_feat &cds, bool &cds_change)
CRef< CCmdComposite > GetRmCultureNotesCommand(objects::CSeq_entry_Handle seh)
CRef< CCmdComposite > SetTranslExcept(objects::CSeq_entry_Handle seh, const string &comment, bool strict, bool extend, bool adjust_gene)
CRef< CCmdComposite > GetDeleteAllFeaturesCommand(objects::CSeq_entry_Handle seh, size_t &count, bool remove_proteins=true)
CRef< CCmdComposite > AutofixCommandHugeMode(objects::CSeq_entry_Handle seh, const string &test_name, map< string, size_t > &report, const string &suspect_rules=kEmptyStr)
CRef< CCmdComposite > SpecificHostCleanupCommand(objects::CSeq_entry_Handle seh)
CRef< CCmdComposite > CleanupHugeFileCommand(objects::CSeq_entry_Handle orig_seh, bool extended, bool do_tax, objects::taxupdate_func_t &updater, bool rmv_user_object)
CRef< CCmdComposite > GetNormalizeGeneQualsCommand(objects::CSeq_entry_Handle seh)
CRef< CCmdComposite > GetSynchronizeProductMolInfoCommand(objects::CScope &scope, const objects::CSeq_feat &cds)
CRef< CCmdComposite > GetEnableStrainForwardingCommand(objects::CSeq_entry_Handle seh)
CRef< CCmdComposite > TaxonomyLookupCommand(objects::CSeq_entry_Handle seh)
CRef< CCmdComposite > GetDeleteSequenceCommand(objects::CBioseq_Handle bsh)
CRef< CCmdComposite > GetDeleteFeatureCommand(const objects::CSeq_feat_Handle &fh, bool remove_proteins=true)
CRef< CCmdComposite > GetEditLocationCommand(const objects::edit::CLocationEditPolicy &policy, bool retranslate, bool adjust_gene, const objects::CSeq_feat &orig_feat, objects::CScope &scope, int &offset, bool create_general_only)
CRef< CCmdComposite > UpdatemRNAProduct(const objects::CSeq_feat &protein, objects::CScope &scope, string &message)
CRef< CCmdComposite > CreateOrAdjustProteinFeature(objects::CBioseq_Handle product, objects::CSeq_feat &cds, bool &cds_change)
CRef< CCmdComposite > GetReverseComplimentSequenceCommand(objects::CBioseq_Handle bsh)
void SetProteinFeature(objects::CSeq_feat &prot, objects::CBioseq_Handle product, const objects::CSeq_feat &cds)
#define const
Definition: zconf.h:232
Modified on Tue Jun 18 13:35:36 2024 by modify_doxy.py rev. 669887