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NCBI C++ ToolKit: src/objtools/readers/descr_mod_apply.cpp Source File

(

)

= 0;

<

(

&)> f_verify,

<

(

&)> f_verify,

m_fReportError(fReportError),

m_SkippedMods(skipped_mods)

unordered_map<string,TMemFuncPtr>

it = s_MethodMap.find(mod_name);

(it != s_MethodMap.end()) {

mem_func_ptr = it->second;

(this->*mem_func_ptr)(mod_entry);

(name ==

) {

(it == s_GenomeStringToEnum.end()) {

(name ==

) {

(it == s_OriginStringToEnum.end()) {

(name ==

) {

(

&

: mod_entry.second) {

&

=

.GetValue();

(

.IsSetAttrib()) {

pSubSource->SetAttrib(

.GetAttrib());

->SetSubtype().push_back(std::move(pSubSource));

set_size = primer_set.

().size();

vector<string>

;

num_names =

.size();

it = primer_set.

().begin();

(

=0;

<num_names; ++

) {

(*it)->SetName().Set(

[

]);

pPrimer->SetName().Set(

[

]);

primer_set.

().push_back(std::move(pPrimer));

set_size = primer_set.

().size();

num_seqs = seqs.size();

it = primer_set.

().begin();

(

=0;

<num_seqs; ++

) {

(*it)->SetSeq().Set(seqs[

]);

pPrimer->SetSeq().Set(seqs[

]);

primer_set.

().push_back(std::move(pPrimer));

vector<string>

;

reaction_names.insert(reaction_names.end(),

.begin(),

.end());

(seqs.size() > 1) {

(seqs.front().front() ==

) {

seqs.front().erase(0,1);

(seqs.back().back() ==

) {

seqs.back().erase(seqs.back().size()-1,1);

(

& seq : seqs) {

(mod_name ==

) {

vector<string>

;

(

&

: mod_entry.second)

it = pcr_reaction_set.Set().begin();

(

& reaction_names :

) {

(it == pcr_reaction_set.Set().end()) {

pcr_reaction_set.Set().push_back(std::move(pPCRReaction));

(mod_name ==

) {

(

&

: mod_entry.second)

it = pcr_reaction_set.Set().begin();

(

& reaction_seqs : seqs) {

(it == pcr_reaction_set.Set().end()) {

pcr_reaction_set.Set().push_back(std::move(pPCRReaction));

(mod_name ==

)

vector<string>

;

(

&

: mod_entry.second) {

(!

.empty()) {

num_reactions = pcr_reaction_set.Get().size();

num_names =

.size();

(num_names <= num_reactions) {

it = pcr_reaction_set.Set().rbegin();

(

=num_names-1;

>=0; --

) {

it = pcr_reaction_set.Set().begin();

(

=0;

<num_reactions; ++

) {

(

=num_reactions;

<num_names; ++

) {

pcr_reaction_set.Set().push_back(std::move(pPCRReaction));

(mod_name ==

)

(

&

: mod_entry.second) {

num_reactions = pcr_reaction_set.Get().size();

num_seqs = seqs.size();

(num_seqs <= num_reactions) {

it = pcr_reaction_set.Set().rbegin();

(

=num_seqs-1;

>=0; --

) {

it = pcr_reaction_set.Set().begin();

(

=0;

<num_reactions; ++

) {

(

=num_reactions;

<num_seqs; ++

) {

pcr_reaction_set.Set().push_back(std::move(pPCRReaction));

(name ==

) {

(!preserve_taxid &&

(name ==

) {

taxid = NStr::StringToNumeric<TTaxId>(

);

preserve_taxid =

;

(name ==

) {

(name ==

) {

vector<CRef<CDbtag>> dbtags;

(

& value_attrib : mod_entry.second) {

&

= value_attrib.GetValue();

colon_pos =

.find(

);

(colon_pos < (

.length()-1)) {

pDbtag->SetTag().SetStr(

);

dbtags.push_back(std::move(pDbtag));

(name ==

) {

(name ==

) {

TFunction =

<void(

&,

)>;

unordered_map<string, TFunction>

s_GetCodeSetterMethods =

it = s_GetCodeSetterMethods.find(name);

(it != s_GetCodeSetterMethods.end()) {

(

&

: mod_entry.second) {

(

.IsSetAttrib()) {

pOrgMod->SetAttrib(

.GetAttrib());

unordered_map<string, string> s_NameToLabel =

{{

,

},

{

,

},

{

,

}};

&

= s_NameToLabel.at(name);

list<CTempString> value_list;

(

&

: mod_entry.second) {

list<CTempString> value_sublist;

& vals =

.GetValue();

value_list.splice(value_list.end(), value_sublist);

(value_list.empty()) {

list<CTempString>& vals,

(

pUserField : dblink.

()) {

pUserField->IsSetLabel() &&

pUserField->GetLabel().IsStr() &&

dblink.

().push_back(pField);

pField->

().SetStrs().assign(vals.begin(), vals.end());

(

&

: mod_entry.second) {

vals.push_back(

.GetValue());

= (mod_entry.first ==

) ?

;

(

: vals) {

pField->SetLabel().SetStr(

);

pField->SetData().SetStr(

);

user.SetData().push_back(pField);

list<CStringUTF8> accession_list;

(

&

: mod_entry.second) {

list<CTempString> value_sublist;

& vals =

.GetValue();

list<CStringUTF8> accession_sublist;

(value_sublist.begin(), value_sublist.end(), back_inserter(accession_sublist),

accession_list.splice(accession_list.end(), accession_sublist);

(accession_list.empty()) {

make_user_field = [](

& accession) {

pField->SetLabel().SetId(0);

pSubfield->SetLabel().SetStr(

);

pSubfield->SetData().SetStr(accession);

pField->SetData().SetFields().push_back(std::move(pSubfield));

user.SetData().resize(accession_list.size());

(accession_list.begin(), accession_list.end(),

user.SetData().begin(), make_user_field);

list<string> id_list;

(

&

: mod_entry.second) {

list<CTempString> value_sublist;

& vals =

.GetValue();

(

&

: value_sublist) {

id_list.insert(id_list.end(),idrange.

(), idrange.

());

id_list.push_back(

);

gb_block.SetExtra_accessions().assign(id_list.begin(), id_list.end());

list<CTempString> value_list;

(

&

: mod_entry.second) {

list<CTempString> value_sublist;

& vals =

.GetValue();

value_list.splice(value_list.end(), value_sublist);

(value_list.empty()) {

->SetGBblock().SetKeywords().assign(value_list.begin(), value_list.end());

(

&

: mod_entry.second) {

list<CTempString> value_sublist;

& vals =

.GetValue();

list<int> id_sublist;

(value_sublist.begin(), value_sublist.end(), back_inserter(id_sublist),

id_list.splice(id_list.end(), id_sublist);

(id_list.empty()) {

make_user_field = [](

& id) {

pField->SetLabel().SetId(0);

pSubfield->SetLabel().SetStr(

);

pSubfield->SetData().SetInt(

);

pField->SetData().SetFields().push_back(pSubfield);

pSubfield->SetLabel().SetStr(

);

pSubfield->SetData().SetInt(0);

pField->SetData().SetFields().push_back(pSubfield);

user.SetData().resize(id_list.size());

(id_list.begin(), id_list.end(),

user.SetData().begin(), make_user_field);

(

&

: mod_entry.second) {

(

&

: mod_entry.second)

&

=

.GetValue();

pmid = NStr::StringToNumeric<TEntrezId>(

);

pPub =

(

());

pPub->SetPmid().Set(pmid);

.push_back(std::move(pPub));

& add_msg)

& mod_name = mod_data.

();

& mod_value = mod_data.

();

=

+ mod_name +

+ mod_value +

;

+=

+ add_msg;

<

TObject>

pParentSet->IsSetClass() &&

& bioseq_set =

&

(*pParentSet);

!pDesc->

()) {

& pub_desc = pDesc->

();

pub_desc.

().Set().remove_if([](

& pPub) {

(pPub && pPub->

()); });

pub_desc.GetPub().Get().empty();

pDesc->SetPub();

pDesc->SetComment();

pDesc->SetGenbank();

pDesc->SetMolinfo();

<

(

&)> f_verify,

<

(

&)> f_verify,

it =

.find(eChoice);

*(it->second);

(pDescrContainer->

()) {

(

& pDesc : pDescrContainer->

().

()) {

(pDesc.NotEmpty() && f_verify(*pDesc)) {

.insert(make_pair(eChoice, pDesc));

pDesc = f_create();

.insert(make_pair(eChoice, pDesc));

pDescrContainer->

().

().push_back(pDesc);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

void transform(Container &c, UnaryFunction *op)

CConstRef< CBioseq_set > GetParentSet(void) const

CPCRReactionSet * m_pPCRReactionSet

CBioSource::TSubtype TSubtype

SDescrContainer_Base TDescrContainer

unique_ptr< TDescrContainer > m_pNucProtSetContainer

void x_SetUserType(const string &type, CUser_object &user_object)

CUser_object & SetFileTrack(void)

unordered_map< EChoice, CRef< CSeqdesc >, hash< underlying_type< EChoice >::type > > TMap

CPCRReactionSet & SetPCR_primers(void)

CDescrCache(CBioseq &bioseq)

CGB_block & SetGBblock(void)

CSeqdesc & x_SetDescriptor(const EChoice eChoice, function< bool(const CSeqdesc &)> f_verify, function< CRef< CSeqdesc >(void)> f_create)

unique_ptr< TDescrContainer > m_pBioseqContainer

CMolInfo & SetMolInfo(void)

TDescrContainer * m_pPrimaryContainer

CUser_object & SetDBLink(void)

CBioSource & SetBioSource(void)

CPubdesc & SetPubdesc(void)

CUser_object & SetGenomeProjects(void)

string & SetComment(void)

CUser_object & SetTpaAssembly(void)

TSubtype & SetSubtype(void)

TOrgMods & SetOrgMods(void)

CDescrContainer(TObject &object)

CSeq_descr & SetDescr(void)

void x_SetMolInfoType(const TModEntry &mod_entry)

void x_SetOrgMod(const TModEntry &mod_entry)

CDescrModApply(CBioseq &bioseq, FReportError fReportError, TSkippedMods &skipped_mods)

void x_SetMolInfoCompleteness(const TModEntry &mod_entry)

bool x_TryBioSourceMod(const TModEntry &mod_entry, bool &preserve_taxid)

bool x_TryOrgNameMod(const TModEntry &mod_entry)

virtual ~CDescrModApply()

bool x_TryOrgRefMod(const TModEntry &mod_entry, bool &preserve_taxid)

TSkippedMods & m_SkippedMods

void x_SetTpaAssembly(const TModEntry &mod_entry)

bool x_TryPCRPrimerMod(const TModEntry &mod_entry)

CModAdder::FReportError FReportError

void x_SetFileTrack(const TModEntry &mod_entry)

CModAdder::TSkippedMods TSkippedMods

void x_SetPMID(const TModEntry &mod_entry)

void x_SetComment(const TModEntry &mod_entry)

CModHandler::TMods::value_type TModEntry

void x_SetGBblockKeywords(const TModEntry &mod_entry)

void x_SetGBblockIds(const TModEntry &mod_entry)

static const string & x_GetModValue(const TModEntry &mod_entry)

void x_SetDBLink(const TModEntry &mod_entry)

FReportError m_fReportError

unique_ptr< CDescrCache > m_pDescrCache

void x_SetDBLinkFieldVals(const string &label, const list< CTempString > &vals, CUser_object &db_link)

void x_SetDBLinkField(const string &label, const TModEntry &mod_entry, CDescrCache &descr_cache)

void x_SetDBxref(const TModEntry &mod_entry)

static const string & x_GetModName(const TModEntry &mod_entry)

void x_SetMolInfoTech(const TModEntry &mod_entry)

void x_ReportInvalidValue(const CModData &mod_data, const string &add_msg="")

void x_SetSubtype(const TModEntry &mod_entry)

bool Apply(const TModEntry &mod_entry)

void x_SetGenomeProjects(const TModEntry &mod_entry)

const string & GetValue(void) const

const string & GetName(void) const

static const string & GetCanonicalName(const TModEntry &mod_entry)

static const string & AssertReturnSingleValue(const TModEntry &mod_entry)

@OrgMod.hpp User-defined methods of the data storage class.

@Pubdesc.hpp User-defined methods of the data storage class.

@Seq_descr.hpp User-defined methods of the data storage class.

static bool NeedsNoText(const TSubtype &subtype)

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

Include a standard set of the NCBI C++ Toolkit most basic headers.

static const auto s_OrgModStringToEnum

static const unordered_map< string, CMolInfo::TTech > s_TechStringToEnum

static bool s_EmptyAfterRemovingPMID(CRef< CSeqdesc > &pDesc)

static const auto s_SubSourceStringToEnum

static void s_SetPrimerNames(const string &primer_names, CPCRPrimerSet &primer_set)

static const unordered_map< string, CMolInfo::TCompleteness > s_CompletenessStringToEnum

static bool s_IsUserType(const CUser_object &user_object, const string &type)

static void s_AppendPrimerNames(const string &mod, vector< string > &reaction_names)

static void s_AppendPrimerSeqs(const string &mod, vector< string > &reaction_seqs)

static void s_SetPrimerSeqs(const string &primer_seqs, CPCRPrimerSet &primer_set)

static const struct name_t names[]

SStrictId_Entrez::TId TEntrezId

TEntrezId type for entrez ids which require the same strictness as TGi.

SStrictId_Tax::TId TTaxId

Taxon id type.

@ eDiag_Error

Error message.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

const_iterator end(void) const

const_iterator begin(void) const

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static CTempString TruncateSpaces_Unsafe(const CTempString str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static CStringUTF8 AsUTF8(const CTempString &src, EEncoding encoding, EValidate validate=eNoValidate)

Convert into UTF8 from a C/C++ string.

static unsigned int StringToUInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to unsigned int.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

static string & ToLower(string &str)

Convert string to lower case – string& version.

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

static const char label[]

const Tdata & Get(void) const

Get the member data.

list< CRef< CSubSource > > TSubtype

void SetPcr_primers(TPcr_primers &value)

Assign a value to Pcr_primers data member.

void SetOrg(TOrg &value)

Assign a value to Org data member.

Tdata & Set(void)

Assign a value to data member.

TSubtype & SetSubtype(void)

Assign a value to Subtype data member.

bool IsSetData(void) const

the object itself Check if a value has been assigned to Data data member.

bool IsStr(void) const

Check if variant Str is selected.

bool IsSetType(void) const

type of object within class Check if a value has been assigned to Type data member.

TData & SetData(void)

Assign a value to Data data member.

const TStr & GetStr(void) const

Get the variant data.

void SetLabel(TLabel &value)

Assign a value to Label data member.

void SetType(TType &value)

Assign a value to Type data member.

void SetData(TData &value)

Assign a value to Data data member.

const TType & GetType(void) const

Get the Type member data.

TMgcode & SetMgcode(void)

Assign a value to Mgcode data member.

TPgcode & SetPgcode(void)

Assign a value to Pgcode data member.

list< CRef< COrgMod > > TMod

TGcode & SetGcode(void)

Assign a value to Gcode data member.

bool IsPmid(void) const

Check if variant Pmid is selected.

@ eClass_nuc_prot

nuc acid and coded proteins

bool IsGenbank(void) const

Check if variant Genbank is selected.

const TUser & GetUser(void) const

Get the variant data.

bool IsMolinfo(void) const

Check if variant Molinfo is selected.

void SetPub(TPub &value)

Assign a value to Pub data member.

TPub & SetPub(void)

Select the variant.

bool IsComment(void) const

Check if variant Comment is selected.

bool IsSource(void) const

Check if variant Source is selected.

bool IsPub(void) const

Check if variant Pub is selected.

Tdata & Set(void)

Assign a value to data member.

bool IsUser(void) const

Check if variant User is selected.

@ eCompleteness_has_left

5' or NH3 end present

@ eCompleteness_complete

complete biological entity

@ eCompleteness_has_right

3' or COOH end present

@ eCompleteness_no_left

missing 5' or NH3 end

@ eCompleteness_partial

partial but no details given

@ eCompleteness_no_right

missing 3' or COOH end

@ eCompleteness_no_ends

missing both ends

@ eTech_htgs_2

ordered High Throughput sequence contig

@ eTech_physmap

from physical mapping techniques

@ eTech_htc

high throughput cDNA

@ eTech_both

concept transl. w/ partial pept. seq.

@ eTech_targeted

targeted locus sets/studies

@ eTech_seq_pept_homol

sequenced peptide, ordered by homology

@ eTech_composite_wgs_htgs

composite of WGS and HTGS

@ eTech_sts

Sequence Tagged Site.

@ eTech_htgs_3

finished High Throughput sequence

@ eTech_seq_pept_overlap

sequenced peptide, ordered by overlap

@ eTech_htgs_1

unordered High Throughput sequence contig

@ eTech_concept_trans

conceptual translation

@ eTech_tsa

transcriptome shotgun assembly

@ eTech_standard

standard sequencing

@ eTech_wgs

whole genome shotgun sequencing

@ eTech_seq_pept

peptide was sequenced

@ eTech_survey

one-pass genomic sequence

@ eTech_barcode

barcode of life project

@ eTech_htgs_0

single genomic reads for coordination

@ eTech_derived

derived from other data, not a primary entity

@ eTech_fli_cdna

full length insert cDNA

@ eTech_est

Expressed Sequence Tag.

@ eTech_concept_trans_a

conceptual transl. supplied by author

@ eTech_genemap

from genetic mapping techniques

unsigned int

A callback function used to compare two keys in a database.

use only n Cassandra database for the lookups</td > n</tr > n< tr > n< td > yes</td > n< td > do not use tables BIOSEQ_INFO and BLOB_PROP in the Cassandra database

const TStringToEnumMap< CMolInfo::TBiomol > g_BiomolStringToEnum

TStringToEnumMap< CSubSource::ESubtype > g_InitModNameSubSrcSubtypeMap(void)

TStringToEnumMap< COrgMod::ESubtype > g_InitModNameOrgSubtypeMap(void)

string g_GetNormalizedModVal(const string &unnormalized)

TStringToEnumMap< CBioSource::EGenome > g_InitModNameGenomeMap(void)

TStringToEnumMap< CBioSource::EOrigin > g_InitModNameOriginMap(void)

const GenericPointer< typename T::ValueType > T2 value

@ eModSubcode_InvalidValue

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

virtual ~SDescrContainer_Base(void)=default

virtual bool IsSet(void) const =0

virtual CSeq_descr & SetDescr(void)=0

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