NCBI C++ ToolKit
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#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>
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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" |