#include <ncbi_pch.hpp>#include <objects/seqfeat/BioSource.hpp>#include <objects/seqfeat/Org_ref.hpp>#include <objects/seqfeat/OrgName.hpp>#include <objects/seqfeat/seqfeat_macros.hpp>#include <objects/seqblock/GB_block.hpp>#include <objects/seq/Seqdesc.hpp>#include <objects/valid/Comment_rule.hpp>#include <objects/valid/Comment_set.hpp>#include <objects/general/User_object.hpp>#include <objects/general/general_macros.hpp>#include <util/xregexp/regexp.hpp>#include <objmgr/util/sequence.hpp>#include <objtools/cleanup/cleanup.hpp>#include <objtools/edit/field_handler.hpp>#include <gui/objutils/cmd_create_desc.hpp>#include <gui/objutils/cmd_create_feat.hpp>#include <gui/objutils/cmd_del_desc.hpp>#include <gui/objutils/descriptor_change.hpp>#include <gui/objutils/util_cmds.hpp>#include <gui/objutils/macro_util.hpp>#include <gui/objutils/macro_ex.hpp>#include <gui/objutils/macro_field_resolve.hpp>#include <gui/objutils/macro_fn_pubfields.hpp>#include <gui/objutils/macro_fn_aecr.hpp>
Include dependency graph for macro_fn_aecr.cpp:
Go to the source code of this file.
Go to the SVN repository for this file.
Functions | |
| USING_SCOPE (objects) | |
| static void | s_ResetModSubsrcQuals (CBioSource &bsrc) |
| DEFINE_MACRO_FUNCNAME (CMacroFunction_CopyFeatQual, "CopyFeatureQual") | |
| CopyFeatureQual(src_field, dest_feature_type, dest_feature_field, update_mrna, existing_text_opt, delimiter) The last parameter is optional The related mRNA is only updated if the action is successful and the destination feature is protein. More... | |
| DEFINE_MACRO_FUNCNAME (CMacroFunction_CopyRNARelQual, "CopyRnaRelQual") | |
| CopyRnaRelQual('rna'/'gene', src_field, 'gene'/'rna', dest_field, existing_text_opt, delimiter) The last parameter is optional Use this function when you need to copy from/to an RNA qualifier and a Gene qualifier Don't use this function to copy between two RNA qualifiers. More... | |
| DEFINE_MACRO_FUNCNAME (CMacroFunction_SetRelFeatQual,"SetRelatedFeatureQual") | |
| SetRelatedFeatureQual(feat_type, field_name, new_value, existing_text_option, delimiter, remove_blank, update_mrna) The last three parameters are optional. More... | |
| static void | s_SetBioSourceField (CRef< CBioSource > bsrc, CObjectInfo &oi, const string &field_name, CMQueryNodeValue::TObs &dest_objs) |
| static void | s_SetFeatField (CRef< CSeq_feat > feat, CObjectInfo &oi, const string &field_name, CMQueryNodeValue::TObs &result) |
| static string | s_GetEnumValue (CObjectInfo &obj) |
| static bool | s_SetEnumValue (CObjectInfo &obj, const string &str) |
| DEFINE_MACRO_FUNCNAME (CMacroFunction_ConvertFeatQual, "ConvertFeatureQual") | |
| class CMacroFunction_ConvertFeatQual ConvertFeatureQual(src_field, dest_feature_type, dest_feature_field, capitalization, strip_name, update_mrna, existing_text_opt, delimiter) The last parameter is optional The function will NOT delete the src_field. More... | |
| DEFINE_MACRO_FUNCNAME (CMacroFunction_ConvertRNARelQual, "ConvertRnaRelQual") | |
| ConvertRnaRelQual('rna'/'gene', src_field, 'gene'/'rna', dest_field, capitalization, strip_name, existing_text_opt, delimiter) The last parameter is optional Use this function when you need to convert from/to an RNA qualifier and a Gene qualifier Don't use this function to convert between two RNA qualifiers. More... | |
| DEFINE_MACRO_FUNCNAME (CMacroFunction_ParseStringQual, "ParseStringQual") | |
| class CMacroFunction_ParseStringQual - used when parsing SeqId ParseStringQual(from_field, to_field, capitalization, existing_text_opt, delimiter) // when all the text should be copied Last parameter is optional More... | |
| DEFINE_MACRO_FUNCNAME (CMacroFunction_ParseFeatQual, "ParseFeatureQual") | |
| class CMacroFunction_ParseFeatQual ParseFeatureQual(src_field, dest_feature_type, dest_feature_field, capitalization, update_mrna, existing_text_opt, delimiter) The last parameter is optional The related mRNA is only updated if the action is successful and the destination feature is protein More... | |
| DEFINE_MACRO_FUNCNAME (CMacroFunction_ParseRNARelQual, "ParseRnaRelQual") | |
| ParseRnaRelQual('rna'/'gene', src_field, 'gene'/'rna', dest_field, capitalization, existing_text_opt, delimiter) The last parameter is optional Use this function when you need to convert from/to an RNA qualifier and a Gene qualifier Don't use this function to convert between two RNA qualifiers. More... | |
| DEFINE_MACRO_FUNCNAME (CMacroFunction_AddParsedText, "AddParsedText") | |
| class CMacroFunction_AddParsedText AddParsedText(parsed_text, to_field, capitalization, existing_text_opt, delimiter) Deprecated name: AECRParseStringQual when only the "text" portion is copied The capitalization change applies to the parsed text portion More... | |
| DEFINE_MACRO_FUNCNAME (CMacroFunction_AddParsedToFeatQual, "AddParsedTextToFeatureQual") | |
| AddParsedTextToFeatureQual(parsed_text, dest_feature_type, dest_feature_field, capitalization, update_mrna, existing_text_opt, delimiter) The last parameter is optional The related mRNA is only updated if the action is successful and the destination feature is protein. More... | |
| DEFINE_MACRO_FUNCNAME (CMacroFunction_ParsedText, "ParsedText") | |
| class CMacroFunction_ParsedText Obtains a portion of the text ParsedText(field_name(str/objects), left_del(str), include_left(b), right_del(str), include_right(b), case_sensitive(b), whole_word(b), rmv_from_parsed(b), rmv_left(b), rmv_right(b)); left_del and right_del can be free_text, "eDigits", "eLetters" the last three parameters are optional It may also modify the content of the field More... | |
| DEFINE_MACRO_FUNCNAME (CMacroFunction_ParsedTextFrom, "ParsedTextFromFeature") | |
| Obtains a portion of the text from a different feature that the current one ParsedTextFromFeature(feature_type, field_name(str/objects), left_del(str), include_left(b), right_del(str), include_right(b), case_sensitive(b), whole_word(b), rmv_from_parsed(b), rmv_left(b), rmv_right(b)); left_del and right_del can be free_text, "eDigits", "eLetters" the last three parameters are optional It may also modify the content of the field. More... | |
| static void | s_AddNewDBlinkValue (CUser_field &user_field, const string &newValue) |
| AddDBLink(dblink_type, newValue, existing_text, delimiter, remove_blank) The last parameter is optional. More... | |
| static void | s_SetVectorValue (CUser_field &user_field, const string &newValue, const string &del) |
| static bool | s_AddNewUserField (CRef< CSeqdesc > &user_object_desc, const string &dblink, const string &newValue) |
| static string | s_GatherExistingValues (CUser_field &user_field, const string &newValue, const string &del) |
| static void | s_AddUnverifiedType (CUser_object &user, NMacroUtil::EUnverifiedType type) |
| class CMacroFunction_AddUnverified AddUnverified("Features"); The user object will be added only to nucleotide sequences More... | |
| DEFINE_MACRO_FUNCNAME (CMacroFunction_AddorSetGbQual, "SetGBQualifier") | |
| class CMacroFunction_AddorSetContElement Usage: o = Resolve("org.orgname.mod") where o.subtype = "strain"; SetModifier(o, "org.orgname.mod", "strain", newvalue, existing_text, delimiter, remove_blank); SetGBQualifier(o, container_path, gb_qualifier, newvalue, existing_text, delimiter, remove_blank); The last two parameters are optional More... | |
| static bool | s_IsATGC (char ch) |
| CMacroFunction_SetCodonsRecognized SetCodonsRecognized(field_name) The field_name specifies one of the primer sequences. More... | |
| static const string | s_GetExpansion (const string &ch) |
| static vector< string > | ParseDegenerateCodons (string codon) |
| DEFINE_MACRO_FUNCNAME (CMacroFunction_ValueFromTable, "ValueFromTable") | |
| class CMacroFunction_ValueFromTable ValueFromTable(table_name, col_number(integer)) col_number - starts from 1 More... | |
| DEFINE_MACRO_FUNCNAME (CMacroFunction_GeneQual, "GeneQual") | |
| CMacroFunction_GeneQual GeneQual(gene_field_name);. More... | |
Variables | |
| static const string | kAmbiguities = "MRSVWYHKDBN" |
| static const string | kReplacements [] |
