macro_fn_do.cpp File Reference

#include <ncbi_pch.hpp>
#include <objects/valid/Comment_rule.hpp>
#include <objects/valid/Comment_set.hpp>
#include <objmgr/util/create_defline.hpp>
#include <objmgr/util/sequence.hpp>
#include <objtools/edit/cds_fix.hpp>
#include <objtools/writers/write_util.hpp>
#include <gui/objutils/utils.hpp>
#include <gui/objutils/report_trim.hpp>
#include <gui/objutils/cmd_del_desc.hpp>
#include <gui/objutils/cmd_create_desc.hpp>
#include <gui/objutils/descriptor_change.hpp>
#include <gui/objutils/util_cmds.hpp>
#include <gui/objutils/macro_util.hpp>
#include <gui/objutils/macro_field_resolve.hpp>
#include <gui/objutils/macro_ex.hpp>
#include <gui/objutils/macro_fn_do.hpp>
#include <objtools/edit/apply_object.hpp>

Include dependency graph for macro_fn_do.cpp:

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Functions
	USING_SCOPE (objects)
	DEFINE_MACRO_FUNCNAME (CMacroFunction_RemoveSequence, "RemoveSequence")
	class CMacroFunction_RemoveSequence RemoveSequence() More...
	DEFINE_MACRO_FUNCNAME (CMacroFunction_RemoveAlignment, "RemoveAlignment")
	class CMacroFunction_RemoveAlignment RemoveAlignment() More...
	DEFINE_MACRO_FUNCNAME (CMacroFunction_TrimStringQual, "TrimStringQual")
	class CMacroFunction_TrimStringQual TrimStringQual(fieldname, nr_start_chars) Trims nr_start_chars number of characters from the beginning of the field More...
	DEFINE_MACRO_FUNCNAME (CMacroFunction_CorrectGeneticCodes, "CorrectGeneticCode")
	class CMacroFunction_CorrectGeneticCodes CorrectGeneticCode() More...
	DEFINE_MACRO_FUNCNAME (CMacroFunction_RemoveOrgName, "RemoveOrgName")
	class CMacroFunction_RemoveOrgName RemoveOrgName(fieldname) - removes organism name words from the field More...
	DEFINE_MACRO_FUNCNAME (CMacroFunction_TrimJunkFromPrimers, "TrimJunkFromPrimerSeq")
	CMacroFunction_TrimJunkFromPrimerSeq TrimJunkFromPrimerSeq(field_name) The field_name specifies one of the primer sequences. More...
	DEFINE_MACRO_FUNCNAME (CMacroFunction_FixIInPrimers,"FixIInPrimerSeq")
	DEFINE_MACRO_FUNCNAME (CMacroFunction_FixUSAandStatesAbbrev, "FixUSAAndStateAbbreviations")
	class CMacroFunction_FixUSAandStatesAbbrev - fixes for USA country name and state abbreviations FixUSAAndStateAbbreviations() More...
	DEFINE_MACRO_FUNCNAME (CMacroFunction_FixMouseStrain, "FixMouseStrains")
	o = Resolve("org.orgname.mod") Where o.subtype = "strain"; FixMouseStrains(o); More...
	DEFINE_MACRO_FUNCNAME (CMacroFunction_FixAuthorCaps, "FixCapsAuthorLastName")
	obj = PUB_AUTHORS("last") WHERE ISUPPER(obj); FixCapsAuthorLastName(obj); More...
	DEFINE_MACRO_FUNCNAME (CMacroFunction_FixPubCapsTitle, "FixPubCapsTitle")
	class CMacroFunction_FixPubCaps - fixes the capitalization in publication title, authors, affiliation, affil-country obj = PUB_TITLE(); FixPubCapsTitle(obj, punct_only); - the second parameter is optional, it's default value is false affil_obj = PUB_AFFIL("country"); FixPubCapsAffilCountry(affil_obj, punct_only); affil_obj = PUB_AFFIL(); FixPubCapsAffiliation(affil_obj, punct_only); author_obj = PUB_AUTHORS(); FixPubCapsAuthors(author_obj, punct_only); obj = PUB_AFFIL(); FixPubCapsAffiliation_NOInstDept(obj, punct_only); - fixes caps in all affiliation fields except affil and div More...
	DEFINE_MACRO_FUNCNAME (CMacroFunction_FixPubCapsAuthor, "FixPubCapsAuthors")
	DEFINE_MACRO_FUNCNAME (CMacroFunction_FixPubCapsAffil, "FixPubCapsAffiliation")
	DEFINE_MACRO_FUNCNAME (CMacroFunction_FixPubCapsAffilWithExcept, "FixPubCapsAffiliation_NOInstDept")
	DEFINE_MACRO_FUNCNAME (CMacroFunction_FixPubCapsAffilCountry, "FixPubCapsAffilCountry")
	DEFINE_MACRO_FUNCNAME (CMacroFunction_FixFormat, "FixFormat")
	class CMacroFunction_FixFormat - fixes the format of lat-lon, collection-date, altitude FixFormat(obj) - obj - run-time variable More...
	DEFINE_MACRO_FUNCNAME (CMacroFunction_Resolve, "Resolve")
	class CMacroFunction_Resolve Resolves an existing field More...
	DEFINE_MACRO_FUNCNAME (CMacroFunction_ResolveBioSourceQuals, "ResolveBsrcQuals")
	class CMacroFunction_ResolveBioSourceQuals Resolves all string qualifiers except the subsource and orgmod modifiers More...
	DEFINE_MACRO_FUNCNAME (CMacroFunction_ResolveNASeq, "ResolveNASeq")
	class CMacroFunction_ResolveNA Resolves an existing field within the Bioseq More...
	DEFINE_MACRO_FUNCNAME (CMacroFunction_ChangeSeqInst, "ChangeSeqInst")
	class CMacroFunction_ChangeSeqInst ChangeSeqInst(fieldname, value); More...
	DEFINE_MACRO_FUNCNAME (CMacroFunction_RemoveLineageSourceNotes, "RemoveLineageSourceNotes")
	class CMacroFunction_RemoveLineageNotes Removes orgmod and subsource notes that are exclusively composed from special words, appearing in a list, in the lineage or in the taxname More...
	DEFINE_MACRO_FUNCNAME (CMacroFunction_RemoveSegGaps, "RemoveSegGaps")
	class CMacroFunction_RemoveSegGaps RemoveSegGaps(); More...
	DEFINE_MACRO_FUNCNAME (CMacroFunction_RmvDuplStructComments, "RemoveDuplicateStructComments")
	class CMacroFunction_RmvDuplStructComments Usage: RemoveDuplicateStructComments() More...
	DEFINE_MACRO_FUNCNAME (CMacroFunction_ReorderStructComment, "ReorderStructuredComment")
	class CMacroFunction_ReorderStructComment ReorderStructuredComment(); More...
	DEFINE_MACRO_FUNCNAME (CMacroFunction_MakeBoldXrefs, "MakeBOLDXrefs")
	class CMacroFunction_MakeBoldXrefs MakeBOLDXrefs(); More...
	DEFINE_MACRO_FUNCNAME (CMacroFunction_AddProteinTitles, "AddProteinTitles")
	class CMacroFunction_AddProteinTitles AddProteinTitles(); More...
	DEFINE_MACRO_FUNCNAME (CMacroFunction_TrimTerminalNs, "TrimTerminalNs")
	class CMacroFunction_TrimTerminalNs TrimTerminalNs() Trim ambiguous characters from the ends of the sequences More...
static string	s_GetModifierName (const string &name)
	class CMacroFunction_PrintBankit PrintBankit(field_name|object, multiple_del, append_del) The last two parameters are optional More...
static bool	s_PrintContainer (const CMQueryNodeValue::TObs &res_oi, const string &append_del, const string &multiple_del, CNcbiOstream &ostr)

Variables
static const char *	kBOLDDb = "BOLD"