NCBI C++ ToolKit
Functions
util_cmds.hpp File Reference
#include <corelib/ncbiobj.hpp>
#include <gui/gui_export.h>
#include <objects/taxon3/itaxon3.hpp>
#include <objtools/edit/loc_edit.hpp>
#include <gui/objutils/cmd_composite.hpp>
#include <gui/objutils/cmd_change_seq_feat.hpp>
+ Include dependency graph for util_cmds.hpp:
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Go to the source code of this file.

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Functions

void GetProductToCDSMap (objects::CScope &scope, map< objects::CBioseq_Handle, set< objects::CSeq_feat_Handle > > &product_to_cds)
 
CRef< CCmdCompositeGetDeleteFeatureCommand (const objects::CSeq_feat_Handle &fh, bool remove_proteins=true)
 
CRef< CCmdCompositeGetDeleteFeatureCommand (const objects::CSeq_feat_Handle &fh, bool remove_proteins, map< objects::CBioseq_Handle, set< objects::CSeq_feat_Handle > > &product_to_cds)
 
CRef< CCmdCompositeGetDeleteSequenceCommand (objects::CBioseq_Handle bsh)
 
CRef< CCmdCompositeGetDeleteAllFeaturesCommand (objects::CSeq_entry_Handle seh, size_t &count, bool remove_proteins=true)
 
CRef< CCmdCompositeTaxonomyLookupCommand (objects::CSeq_entry_Handle seh)
 
CRef< CCmdCompositeCachedTaxonomyLookupCommand (objects::CSeq_entry_Handle seh, objects::taxupdate_func_t &updater)
 
CRef< CCmdCompositeSpecificHostCleanupCommand (objects::CSeq_entry_Handle seh)
 
CRef< CCmdCompositeCleanupCommand (objects::CSeq_entry_Handle orig_seh, bool extended, bool do_tax)
 
CRef< CCmdCompositeCleanupHugeFileCommand (objects::CSeq_entry_Handle orig_seh, bool extended, bool do_tax, objects::taxupdate_func_t &updater, bool rmv_user_object)
 
CRef< CCmdCompositeGetDisableStrainForwardingCommand (objects::CSeq_entry_Handle seh)
 
CRef< CCmdCompositeGetEnableStrainForwardingCommand (objects::CSeq_entry_Handle seh)
 
CRef< CCmdCompositeGetRmCultureNotesCommand (objects::CSeq_entry_Handle seh)
 
CRef< CCmdCompositeGetSynchronizeProductMolInfoCommand (objects::CScope &scope, const objects::CSeq_feat &cds)
 
CRef< CCmdCompositeGetSynchronizeProteinPartialsCommand (objects::CScope &scope, const objects::CSeq_feat &cds)
 
CRef< CCmdCompositeGetRetranslateCDSCommand (objects::CScope &scope, const objects::CSeq_feat &cds, bool create_general_only)
 
CRef< CCmdCompositeGetRetranslateCDSCommand (objects::CScope &scope, const objects::CSeq_feat &cds, int &offset, bool create_general_only)
 
CRef< CCmdCompositeGetRetranslateCDSCommand (objects::CScope &scope, objects::CSeq_feat &cds, bool &cds_change, bool create_general_only)
 
CRef< CCmdCompositeGetRetranslateCDSCommand (objects::CScope &scope, objects::CSeq_feat &cds, bool &cds_change, int &offset, bool create_general_only)
 
CRef< CCmdCompositeSetTranslExcept (objects::CSeq_entry_Handle seh, const string &comment, bool strict, bool extend, bool adjust_gene)
 
CRef< CCmdCompositeGetReverseComplimentSequenceCommand (objects::CBioseq_Handle bsh)
 
CRef< CCmdCompositeTrimStopsFromCompleteCDS (const objects::CSeq_feat &cds, objects::CScope &scope)
 
void SetProteinFeature (objects::CSeq_feat &prot, objects::CBioseq_Handle product, const objects::CSeq_feat &cds)
 
void AdjustProteinFeature (objects::CSeq_feat &prot, objects::CBioseq_Handle product, objects::CSeq_feat &cds, bool &cds_change)
 
CRef< CCmdCompositeCreateOrAdjustProteinFeature (objects::CBioseq_Handle product, objects::CSeq_feat &cds, bool &cds_change)
 
CRef< CCmdCompositeAutofixCommand (objects::CSeq_entry_Handle seh, const string &test_name, string *output, const string &suspect_rules=kEmptyStr)
 
CRef< CCmdCompositeAutofixCommandHugeMode (objects::CSeq_entry_Handle seh, const string &test_name, map< string, size_t > &report, const string &suspect_rules=kEmptyStr)
 
CRef< CCmdCompositeGetEditLocationCommand (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< CCmdChangeSeq_featAdjustGene (const objects::CSeq_feat &orig_feat, const objects::CSeq_feat &new_feat, objects::CScope &scope)
 
CRef< CCmdCompositeGetNormalizeGeneQualsCommand (objects::CSeq_entry_Handle seh)
 
CRef< CCmdCompositeGetRemoveDuplicateGOTermsCommand (objects::CSeq_entry_Handle seh)
 
CRef< CCmdCompositeUpdatemRNAProduct (const objects::CSeq_feat &protein, objects::CScope &scope, string &message)
 
CRef< CCmdCompositeUpdatemRNAProduct (const string &prot_product, CConstRef< CObject > object, objects::CScope &scope)
 

Function Documentation

◆ AdjustGene()

CRef<CCmdChangeSeq_feat> AdjustGene ( const objects::CSeq_feat &  orig_feat,
const objects::CSeq_feat &  new_feat,
objects::CScope &  scope 
)

◆ AdjustProteinFeature()

void AdjustProteinFeature ( objects::CSeq_feat &  prot,
objects::CBioseq_Handle  product,
objects::CSeq_feat &  cds,
bool cds_change 
)

◆ AutofixCommand()

CRef<CCmdComposite> AutofixCommand ( objects::CSeq_entry_Handle  seh,
const string test_name,
string output,
const string suspect_rules = kEmptyStr 
)

◆ AutofixCommandHugeMode()

CRef<CCmdComposite> AutofixCommandHugeMode ( objects::CSeq_entry_Handle  seh,
const string test_name,
map< string, size_t > &  report,
const string suspect_rules = kEmptyStr 
)

◆ CachedTaxonomyLookupCommand()

CRef<CCmdComposite> CachedTaxonomyLookupCommand ( objects::CSeq_entry_Handle  seh,
objects::taxupdate_func_t updater 
)

◆ CleanupCommand()

CRef<CCmdComposite> CleanupCommand ( objects::CSeq_entry_Handle  orig_seh,
bool  extended,
bool  do_tax 
)

◆ CleanupHugeFileCommand()

CRef<CCmdComposite> CleanupHugeFileCommand ( objects::CSeq_entry_Handle  orig_seh,
bool  extended,
bool  do_tax,
objects::taxupdate_func_t updater,
bool  rmv_user_object 
)

◆ CreateOrAdjustProteinFeature()

CRef<CCmdComposite> CreateOrAdjustProteinFeature ( objects::CBioseq_Handle  product,
objects::CSeq_feat &  cds,
bool cds_change 
)

◆ GetDeleteAllFeaturesCommand()

CRef<CCmdComposite> GetDeleteAllFeaturesCommand ( objects::CSeq_entry_Handle  seh,
size_t &  count,
bool  remove_proteins = true 
)

◆ GetDeleteFeatureCommand() [1/2]

CRef<CCmdComposite> GetDeleteFeatureCommand ( const objects::CSeq_feat_Handle &  fh,
bool  remove_proteins,
map< objects::CBioseq_Handle, set< objects::CSeq_feat_Handle > > &  product_to_cds 
)

◆ GetDeleteFeatureCommand() [2/2]

CRef<CCmdComposite> GetDeleteFeatureCommand ( const objects::CSeq_feat_Handle &  fh,
bool  remove_proteins = true 
)

◆ GetDeleteSequenceCommand()

CRef<CCmdComposite> GetDeleteSequenceCommand ( objects::CBioseq_Handle  bsh)

◆ GetDisableStrainForwardingCommand()

CRef<CCmdComposite> GetDisableStrainForwardingCommand ( objects::CSeq_entry_Handle  seh)

◆ GetEditLocationCommand()

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 
)

◆ GetEnableStrainForwardingCommand()

CRef<CCmdComposite> GetEnableStrainForwardingCommand ( objects::CSeq_entry_Handle  seh)

◆ GetNormalizeGeneQualsCommand()

CRef<CCmdComposite> GetNormalizeGeneQualsCommand ( objects::CSeq_entry_Handle  seh)

◆ GetProductToCDSMap()

void GetProductToCDSMap ( objects::CScope &  scope,
map< objects::CBioseq_Handle, set< objects::CSeq_feat_Handle > > &  product_to_cds 
)

◆ GetRemoveDuplicateGOTermsCommand()

CRef<CCmdComposite> GetRemoveDuplicateGOTermsCommand ( objects::CSeq_entry_Handle  seh)

◆ GetRetranslateCDSCommand() [1/4]

CRef<CCmdComposite> GetRetranslateCDSCommand ( objects::CScope &  scope,
const objects::CSeq_feat &  cds,
bool  create_general_only 
)

◆ GetRetranslateCDSCommand() [2/4]

CRef<CCmdComposite> GetRetranslateCDSCommand ( objects::CScope &  scope,
const objects::CSeq_feat &  cds,
int offset,
bool  create_general_only 
)

◆ GetRetranslateCDSCommand() [3/4]

CRef<CCmdComposite> GetRetranslateCDSCommand ( objects::CScope &  scope,
objects::CSeq_feat &  cds,
bool cds_change,
bool  create_general_only 
)

◆ GetRetranslateCDSCommand() [4/4]

CRef<CCmdComposite> GetRetranslateCDSCommand ( objects::CScope &  scope,
objects::CSeq_feat &  cds,
bool cds_change,
int offset,
bool  create_general_only 
)

◆ GetReverseComplimentSequenceCommand()

CRef<CCmdComposite> GetReverseComplimentSequenceCommand ( objects::CBioseq_Handle  bsh)

◆ GetRmCultureNotesCommand()

CRef<CCmdComposite> GetRmCultureNotesCommand ( objects::CSeq_entry_Handle  seh)

◆ GetSynchronizeProductMolInfoCommand()

CRef<CCmdComposite> GetSynchronizeProductMolInfoCommand ( objects::CScope &  scope,
const objects::CSeq_feat &  cds 
)

◆ GetSynchronizeProteinPartialsCommand()

CRef<CCmdComposite> GetSynchronizeProteinPartialsCommand ( objects::CScope &  scope,
const objects::CSeq_feat &  cds 
)

◆ SetProteinFeature()

void SetProteinFeature ( objects::CSeq_feat &  prot,
objects::CBioseq_Handle  product,
const objects::CSeq_feat &  cds 
)

◆ SetTranslExcept()

CRef<CCmdComposite> SetTranslExcept ( objects::CSeq_entry_Handle  seh,
const string comment,
bool  strict,
bool  extend,
bool  adjust_gene 
)

◆ SpecificHostCleanupCommand()

CRef<CCmdComposite> SpecificHostCleanupCommand ( objects::CSeq_entry_Handle  seh)

◆ TaxonomyLookupCommand()

CRef<CCmdComposite> TaxonomyLookupCommand ( objects::CSeq_entry_Handle  seh)

◆ TrimStopsFromCompleteCDS()

CRef<CCmdComposite> TrimStopsFromCompleteCDS ( const objects::CSeq_feat &  cds,
objects::CScope &  scope 
)

◆ UpdatemRNAProduct() [1/2]

CRef<CCmdComposite> UpdatemRNAProduct ( const objects::CSeq_feat &  protein,
objects::CScope &  scope,
string message 
)

◆ UpdatemRNAProduct() [2/2]

CRef<CCmdComposite> UpdatemRNAProduct ( const string prot_product,
CConstRef< CObject object,
objects::CScope &  scope 
)
Modified on Tue May 28 05:54:10 2024 by modify_doxy.py rev. 669887