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NCBI C++ ToolKit: src/objtools/edit/unit_test/unit_test_entry_edit.cpp Source File

CFileSorter(

* out_pMapFunctionToVecOfTests) : m_pMapFunctionToVecOfTests(out_pMapFunctionToVecOfTests) { }

operator()(

& dir_entry) {

( ! dir_entry.

() ) {

* arrAllowedExtensions[] = {

bHasAllowedExtension =

;

ii <

(arrAllowedExtensions)/

(arrAllowedExtensions[0]);

bHasAllowedExtension =

;

( ! bHasAllowedExtension ) {

vector<string> tokens;

( tokens.size() != 4u ) {

std::runtime_error(

+

.GetName());

& sFunction = tokens[0];

& sTestName = tokens[1];

& sStage = tokens[2];

& sSuffix = tokens[3];

( sSuffix !=

) {

cout <<

<<

.GetName() << endl;

bInsertSuccessful =

(*m_pMapFunctionToVecOfTests)[sFunction][sTestName].insert(

( ! bInsertSuccessful ) {

std::runtime_error(

+

.GetName() );

ifstream in_file(sFilename.c_str());

BOOST_REQUIRE(in_file.good());

s_AreSeqEntriesEqualAndPrintIfNot(

bEqual = entry1.

(entry2);

cerr <<

<< endl;

vector<string> kEmptyStringVec;

CFileSorter file_sorter(&s_mapFunctionToVecOfTests);

test_cases_dir(

);

kEmptyStringVec, kEmptyStringVec,

cout <<

<< endl;

s_mapFunctionToVecOfTests )

cout <<

<< func_to_vec_of_tests_it->first << endl;

func_to_vec_of_tests_it->second )

cout <<

<< test_name_to_files_it->first << endl;

cout <<

<< test_file_it->first <<

<< test_file_it->second.GetPath() <<

<< endl;

BOOST_CHECK_EQUAL(

,

);

num_user_descriptors_found = 0;

((*it)->IsUser()) {

BOOST_CHECK_EQUAL(usr.

()[0]->GetLabel().GetStr(),

);

num_user_descriptors_found++;;

BOOST_CHECK_EQUAL(num_user_descriptors_found, 1);

->Assign(collide);

(*it)->SetSeq().SetId().push_back(

);

BOOST_CHECK_EQUAL(entry1->

().

().front()->GetLocal().GetStr(),

);

BOOST_CHECK_EQUAL(entry2->

().

().front()->GetLocal().GetStr(),

);

BOOST_CHECK_EQUAL(entry1->

().

().front()->GetLocal().GetStr(),

);

BOOST_CHECK_EQUAL(entry2->

().

().front()->GetLocal().GetStr(),

);

BOOST_CHECK_EQUAL(entry3->

().

().front()->GetLocal().GetStr(),

);

count_users = 0;

BOOST_CHECK(count_users == 0);

->SetDdbj().SetAccession(

);

->SetEmbl().SetAccession(

);

->SetGenbank().SetAccession(

);

->SetOther().SetAccession(

);

->SetGeneral().SetDb(

);

->SetGeneral().SetTag().SetStr(

);

BOOST_CHECK_EQUAL(ds.

(),

);

seq_str =

;

(vector<string>, it, segs) {

orig_len = seq_str.length();

->Assign(*(entry->

().

().front()));

f1->

().SetImp().SetKey(

);

f1->

().SetInt().SetId().Assign(*

);

annot->

().SetFtable().push_back(f1);

brk->

().SetInt().SetId().Assign(*

);

brk->

().SetInt().SetFrom(54);

brk->

().SetInt().SetTo(56);

f2->

().SetCdregion().SetCode_break().push_back(brk);

f2->

().SetInt().SetId().Assign(*

);

annot->

().SetFtable().push_back(f2);

interval.

().Assign(*

);

(vector<string>, it, segs) {

(

(*it,

) == string::npos) {

l1->

().SetFrom(pos);

l1->

().SetTo(pos + it->length() - 1);

l1->

().SetId().Assign(*

);

CSeq_ext::TDelta::Tdata::const_iterator ds_it = inst.

().

().

().begin();

segs.push_back(

);

segs.push_back(

);

segs.push_back(

);

segs.push_back(

);

segs.push_back(

);

(vector<string>, it, segs) {

(

(*it,

) != string::npos) {

is_gap.push_back(

);

((*it).length() == 5) {

lens.push_back((*it).length());

is_gap.push_back(

);

lens.push_back((*it).length());

BOOST_CHECK_EQUAL(inst.

(), orig_len - 5 + 100);

CSeq_ext::TDelta::Tdata::const_iterator ds_it = inst.

().

().

().begin();

vector<bool>::iterator is_gap_it = is_gap.begin();

vector<size_t>::iterator len_it = lens.begin();

((*it)->GetLiteral().GetSeq_data().IsGap()) {

((*it)->GetLiteral().GetSeq_data().IsGap()) {

& gap = (*it)->GetLiteral().GetSeq_data().GetGap();

((*it)->GetLiteral().GetSeq_data().IsGap()) {

& gap = (*it)->GetLiteral().GetSeq_data().GetGap();

((*it)->GetLiteral().GetSeq_data().IsGap()) {

& gap = (*it)->GetLiteral().GetSeq_data().GetGap();

BOOST_CHECK_EQUAL(interval.

(), 149);

BOOST_CHECK_EQUAL(interval.

(), 151);

BOOST_CHECK_EQUAL(interval.

(), 6);

BOOST_CHECK_EQUAL(interval.

(), 8);

( localid.

() ) {

localid.

() == sLocalid;

( id->

() ) {

->

() == gi;

cout <<

<< endl;

BOOST_CHECK( ! mapOfTests.empty() );

& sTestName = (test_it->first);

cout <<

<< sTestName << endl;

BOOST_REQUIRE( test_stage_map.size() == 2u );

& input_entry_file = test_stage_map[

];

& output_expected_file = test_stage_map[

];

( ; bioseq_ci; ++bioseq_ci ) {

cuts.push_back(cut1);

cuts.push_back(cut2);

BOOST_CHECK( s_AreSeqEntriesEqualAndPrintIfNot(

cout <<

<< endl;

BOOST_CHECK( ! mapOfTests.empty() );

& sTestName = (test_it->first);

cout <<

<< sTestName << endl;

BOOST_REQUIRE( test_stage_map.size() == 2u );

& input_entry_file = test_stage_map[

];

& output_expected_file = test_stage_map[

];

( ; bioseq_ci; ++bioseq_ci ) {

cuts.push_back(cut1);

(; graph_ci; ++graph_ci) {

cuts.push_back(cut1);

(; graph_ci; ++graph_ci) {

BOOST_CHECK( s_AreSeqEntriesEqualAndPrintIfNot(

cout <<

<< endl;

BOOST_CHECK( ! mapOfTests.empty() );

& sTestName = (test_it->first);

cout <<

<< sTestName << endl;

BOOST_REQUIRE( test_stage_map.size() == 2u );

& input_entry_file = test_stage_map[

];

& output_expected_file = test_stage_map[

];

( ; bioseq_ci; ++bioseq_ci ) {

cuts.push_back(cut1);

(; align_ci; ++align_ci) {

cuts.push_back(cut1);

(; align_ci; ++align_ci) {

cuts.push_back(cut1);

(; align_ci; ++align_ci) {

BOOST_CHECK( s_AreSeqEntriesEqualAndPrintIfNot(

pCds->SetData().SetCdregion();

& loc = pCds->SetLocation();

pId->SetLocal().SetStr(

);

loc.SetMix().AddInterval(*pId, 8964, 9089, strand);

loc.SetMix().AddInterval(*pId, 8520, 8760, strand);

loc.SetMix().AddInterval(*pId, 7605, 7633, strand);

isDeleted =

;

isTrimmed =

;

isPartialStart =

;

isPartialStop =

;

(pCds, cuts, isDeleted, isTrimmed, isPartialStart, isPartialStop);

BOOST_CHECK(! isPartialStart);

BOOST_CHECK(isPartialStop);

BOOST_CHECK(! isDeleted);

BOOST_CHECK(isTrimmed);

& loc = pCds->GetLocation();

cout <<

<< endl;

BOOST_CHECK( ! mapOfTests.empty() );

& sTestName = (test_it->first);

cout <<

<< sTestName << endl;

BOOST_REQUIRE( test_stage_map.size() == 2u );

& input_entry_file = test_stage_map[

];

& output_expected_file = test_stage_map[

];

( ; bioseq_ci; ++bioseq_ci ) {

cuts.push_back(cut1);

(; feat_ci; ++feat_ci) {

bFeatureDeleted =

;

bFeatureTrimmed =

;

isPartialStart =

;

isPartialStop =

;

BOOST_CHECK_NO_THROW(

(copy_feat, sorted_cuts, bFeatureDeleted, bFeatureTrimmed, isPartialStart, isPartialStop));

(bFeatureDeleted) {

(bFeatureTrimmed) {

feat_eh.

(*copy_feat);

BOOST_CHECK( s_AreSeqEntriesEqualAndPrintIfNot(

cout <<

<< endl;

BOOST_CHECK( ! mapOfTests.empty() );

& sTestName = (test_it->first);

cout <<

<< sTestName << endl;

BOOST_REQUIRE( test_stage_map.size() == 2u );

& input_entry_file = test_stage_map[

];

& output_expected_file = test_stage_map[

];

( ; bioseq_ci; ++bioseq_ci ) {

cuts.push_back(cut1);

cuts.push_back(cut2);

cuts.push_back(cut3);

cuts.push_back(cut4);

cuts.push_back(cut5);

cuts.push_back(cut6);

cuts.push_back(cut1);

cuts.push_back(cut2);

cuts.push_back(cut3);

cuts.push_back(cut4);

cuts.push_back(cut1);

cuts.push_back(cut2);

cuts.push_back(cut3);

cuts.push_back(cut4);

cuts.push_back(cut5);

cuts.push_back(cut1);

cuts.push_back(cut1);

cuts.push_back(cut1);

cuts.push_back(cut1);

cuts.push_back(cut1);

cuts.push_back(cut1);

BOOST_CHECK( s_AreSeqEntriesEqualAndPrintIfNot(

cout <<

<< endl;

& mapOfTests = s_mapFunctionToVecOfTests[

];

BOOST_CHECK( ! mapOfTests.empty() );

& sTestName = (test_it->first);

cout <<

<< sTestName << endl;

BOOST_REQUIRE( test_stage_map.size() == 1u );

& input_entry_file = test_stage_map[

];

( ; bioseq_ci; ++bioseq_ci ) {

submit->

().SetEntrys().push_back(wrapped);

BOOST_CHECK_EQUAL(entry->

(),

);

submit->

().SetEntrys().front()->Assign(*entry);

submit->

().SetEntrys().front()->Assign(*wrapped);

BOOST_CHECK_EQUAL(entry->

(),

);

submit->

().SetEntrys().front()->Assign(*entry);

BOOST_CHECK_EQUAL(

(

,

),

);

gene->

().SetGene().SetLocus(

);

->SetData().SetRna().SetRnaProductName(

, remainder);

imp->

().SetImp().SetKey(

);

imp->

().SetImp().SetKey(

);

imp->

().back()->SetVal(

);

BOOST_CHECK_EQUAL(seh.

().

().size(), 2);

BOOST_CHECK_EQUAL((*it)->GetSeq().GetDescr().Get().size(), 4);

BOOST_CHECK_EQUAL(seh.

(),

);

BOOST_CHECK_EQUAL((*it)->GetSeq().GetDescr().Get().size(), 6);

BOOST_CHECK_EQUAL(seh.

().

().size(), 3);

BOOST_CHECK_EQUAL((*it)->GetSeq().GetDescr().Get().size(), 3);

@ eExtreme_Positional

numerical value

@ eExtreme_Biological

5' and 3'

CLocalRange< TOffset > TRange

define for the fundamental building block of sequence ranges

TSeqPos GetLength(void) const

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

ESubtype GetSubtype(void) const

void ReassignConflictingIds(void)

CSeq_feat_EditHandle –.

namespace ncbi::objects::

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

void RemoveUnverifiedFeature()

void AddUnverifiedOrganism()

void AddUnverifiedContaminant()

void RemoveUnverifiedOrganism()

void AddUnverifiedMisassembled()

EObjectType GetObjectType() const

void AddUnverifiedFeature()

static DLIST_TYPE *DLIST_NAME() last(DLIST_LIST_TYPE *list)

static const char * expected[]

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

void FindFilesInDir(const CDir &dir, const vector< string > &masks, const vector< string > &masks_subdir, TFindFunc &find_func, TFindFiles flags=fFF_Default)

Find files in the specified directory.

bool IsFile(EFollowLinks follow=eFollowLinks) const

Check whether a directory entry is a file.

string GetName(void) const

Get the base entry name with extension (if any).

const string & GetPath(void) const

Get entry path.

@ fFF_Recursive

descend into sub-dirs

@ fFF_Default

default behavior

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

#define MSerial_AsnText

I/O stream manipulators –.

virtual bool Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) const

Check if both objects contain the same values.

CConstRef< CSeq_id > GetSeqIdOrNull(void) const

TRange GetRange(void) const

Get the range.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

void RemoveTopLevelSeqEntry(const CTSE_Handle &entry)

Revoke TSE previously added using AddTopLevelSeqEntry() or AddBioseq().

vector< CSeq_id_Handle > TId

const TDescr & GetDescr(void) const

const CSeqFeatData & GetData(void) const

void Replace(const CSeq_align &new_obj) const

Replace the Seq-align with new Seq-align object.

void SetInst(TInst &v) const

CBioseq_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

bool IsSetDescr(void) const

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

void Replace(const CSeq_feat &new_feat) const

Replace the feature with new Seq-feat object.

const TId & GetId(void) const

void Replace(const CSeq_graph &new_obj) const

Replace the Seq-graph with new Seq-graph object.

const TInst & GetInst(void) const

const string & GetTitle(void) const

bool IsSetTitle(void) const

const CSeq_align & GetOriginalSeq_align(void) const

Get original alignment.

const CSeq_loc & GetLocation(void) const

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

const CSeq_graph & GetOriginalGraph(void) const

Get original graph with unmapped location/product.

vector< CSeqdesc::E_Choice > TDescChoices

CSeq_align_Handle GetSeq_align_Handle(void) const

Get original alignment handle.

CSeq_graph_Handle GetSeq_graph_Handle(void) const

Get original graph handle.

CRef< C > Ref(C *object)

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

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

#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 int CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another string.

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 EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

bool IsStr(void) const

Check if variant Str is selected.

const TTag & GetTag(void) const

Get the Tag member data.

const TDb & GetDb(void) const

Get the Db member data.

const TStr & GetStr(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const TAnticodon & GetAnticodon(void) const

Get the Anticodon member data.

const TExt & GetExt(void) const

Get the Ext member data.

const TTRNA & GetTRNA(void) const

Get the variant data.

bool CanGetDim(void) const

Check if it is safe to call GetDim method.

const TDenseg & GetDenseg(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

bool CanGetNumseg(void) const

Check if it is safe to call GetNumseg method.

bool CanGetIds(void) const

Check if it is safe to call GetIds method.

bool CanGetSegs(void) const

Check if it is safe to call GetSegs method.

bool CanGetStarts(void) const

Check if it is safe to call GetStarts method.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool CanGetLens(void) const

Check if it is safe to call GetLens method.

void SetLocation(TLocation &value)

Assign a value to Location data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

void SetComment(const TComment &value)

Assign a value to Comment data member.

void SetData(TData &value)

Assign a value to Data data member.

const TCdregion & GetCdregion(void) const

Get the variant data.

void SetLoc(TLoc &value)

Assign a value to Loc data member.

const TRna & GetRna(void) const

Get the variant data.

TQual & SetQual(void)

Assign a value to Qual data member.

const TCode_break & GetCode_break(void) const

Get the Code_break member data.

void SetTo(TTo value)

Assign a value to To data member.

ENa_strand

strand of nucleic acid

void SetId(TId &value)

Assign a value to Id data member.

TFrom GetFrom(void) const

Get the From member data.

bool IsGeneral(void) const

Check if variant General is selected.

E_Choice Which(void) const

Which variant is currently selected.

E_Choice Which(void) const

Which variant is currently selected.

void SetFrom(TFrom value)

Assign a value to From data member.

TGi GetGi(void) const

Get the variant data.

const TLocal & GetLocal(void) const

Get the variant data.

bool IsLocal(void) const

Check if variant Local is selected.

const TGeneral & GetGeneral(void) const

Get the variant data.

bool IsGi(void) const

Check if variant Gi is selected.

TTo GetTo(void) const

Get the To member data.

const TInt & GetInt(void) const

Get the variant data.

@ e_General

for other databases

const TSeq & GetSeq(void) const

Get the variant data.

const TDescr & GetDescr(void) const

Get the Descr member data.

TSet & SetSet(void)

Select the variant.

const TSet & GetSet(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

bool IsSet(void) const

Check if variant Set is selected.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

void SetClass(TClass value)

Assign a value to Class data member.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

list< CRef< CSeq_entry > > TSeq_set

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

@ eClass_phy_set

phylogenetic study

bool IsSetLinkage(void) const

Check if a value has been assigned to Linkage data member.

TRepr GetRepr(void) const

Get the Repr member data.

void SetData(TData &value)

Assign a value to Data data member.

list< CRef< CSeqdesc > > Tdata

TLinkage GetLinkage(void) const

Get the Linkage member data.

const TInst & GetInst(void) const

Get the Inst member data.

void SetExt(TExt &value)

Assign a value to Ext data member.

TType GetType(void) const

Get the Type member data.

const TLiteral & GetLiteral(void) const

Get the variant data.

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

const TId & GetId(void) const

Get the Id member data.

const Tdata & Get(void) const

Get the member data.

TLength GetLength(void) const

Get the Length member data.

TLength GetLength(void) const

Get the Length member data.

const TLinkage_evidence & GetLinkage_evidence(void) const

Get the Linkage_evidence member data.

TComment & SetComment(void)

Select the variant.

void SetInst(TInst &value)

Assign a value to Inst data member.

const TExt & GetExt(void) const

Get the Ext member data.

bool IsSetDescr(void) const

descriptors Check if a value has been assigned to Descr data member.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

const TDelta & GetDelta(void) const

Get the variant data.

TUser & SetUser(void)

Select the variant.

const Tdata & Get(void) const

Get the member data.

bool IsLiteral(void) const

Check if variant Literal is selected.

bool IsSetSeq_data(void) const

may have the data Check if a value has been assigned to Seq_data data member.

void SetLength(TLength value)

Assign a value to Length data member.

list< CRef< CDelta_seq > > Tdata

bool IsGap(void) const

Check if variant Gap is selected.

void SetSeq_data(TSeq_data &value)

Assign a value to Seq_data data member.

const TDescr & GetDescr(void) const

Get the Descr member data.

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

bool IsSetLinkage_evidence(void) const

Check if a value has been assigned to Linkage_evidence data member.

@ eRepr_delta

sequence made by changes (delta) to others

@ eMol_na

just a nucleic acid

void SetSub(TSub &value)

Assign a value to Sub data member.

const TEntrys & GetEntrys(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

double value_type

The numeric datatype used by the parser.

Portable class to work with a spawned process via pipes.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

void TrimSeqAlign(CBioseq_Handle bsh, CRef< CSeq_align > align, const TCuts &sorted_cuts)

Trim Seq-align annotation.

void SetLinkageType(CSeq_ext &ext, CSeq_gap::TType linkage_type)

SetLinkageType A function to set the linkage_type for gaps in a delta sequence.

void TrimSequenceAndAnnotation(CBioseq_Handle bsh, const TCuts &cuts, EInternalTrimType internal_cut_conversion=eTrimToClosestEnd)

Trim sequence data and all associated annotation.

void TrimSeqData(CBioseq_Handle bsh, CRef< CSeq_inst > inst, const TCuts &sorted_cuts)

Trim sequence data.

TLocAdjustmentVector NormalizeUnknownLengthGaps(CSeq_inst &inst, TSeqPos unknown_length=100)

NormalizeUnknownLengthGaps A function to adjust the length of unknown-length gaps to a specific lengt...

CRef< CSeqdesc > FindUnverified(const CBioseq &seq)

void TrimSeqGraph(CBioseq_Handle bsh, CRef< CSeq_graph > graph, const TCuts &sorted_cuts)

Trim Seq-graph annotation.

bool IsUnverifiedMisassembled(const CBioseq &seq)

string GetTargetedLocusName(const CSeq_feat &feat)

void AddLocalIdUserObjects(CSeq_entry &entry)

Creates a User-object descriptor on every sequence that has a local ID Contains the original local ID...

CRef< CSeq_entry > SeqEntryFromSeqSubmit(const CSeq_submit &submit)

Create a Seq-entry from a Seq-submit.

void BioseqSetDescriptorPropagateDown(const CBioseq_set_Handle &bioseq_set_h, const vector< CSeqdesc::E_Choice > &choices_to_delete=vector< CSeqdesc::E_Choice >())

Moves descriptors down to children of the given bioseq-set.

bool HasRepairedIDs(const CSeq_entry &entry)

Detects whether colliding IDs were fixed by comparing sequence IDs to the contents of the OriginalID ...

void RemoveUserObjectType(CSeq_entry &entry, CUser_object::EObjectType type)

Removes User-object descriptors of a certain type from the seq-entry.

bool IsUnverifiedOrganism(const CBioseq &seq)

void SetLinkageTypeLinkedRepeat(CSeq_ext &ext, CLinkage_evidence::TType evidence_type)

void DeleteProteinAndRenormalizeNucProtSet(const CSeq_feat_Handle &feat_h)

Secondary function needed after trimming Seq-feat.

void ConvertRawToDeltaByNs(CSeq_inst &inst, size_t min_unknown, int max_unknown, size_t min_known, int max_known, bool is_assembly_gap=false, int gap_type=CSeq_gap::eType_unknown, int linkage=-1, int linkage_evidence=-1)

ConvertRawToDeltaByNs A function to convert a raw sequence to a delta sequence, using runs of Ns to d...

string GetTargetedLocusNameConsensus(const string &tls1, const string &tls2)

void TrimSeqFeat(CRef< CSeq_feat > feat, const TCuts &sorted_cuts, bool &bFeatureDeleted, bool &bFeatureTrimmed, bool &partial_start, bool &partial_stop)

Trim Seq-feat annotation.

void GetSortedCuts(CBioseq_Handle bsh, const TCuts &cuts, TCuts &sorted_cuts, EInternalTrimType internal_cut_conversion=eTrimToClosestEnd)

1) Merge abutting and overlapping cuts.

bool IsUnverifiedContaminant(const CBioseq &seq)

bool IsUnverifiedFeature(const CBioseq &seq)

string GenerateTargetedLocusName(CBioseq_Handle seq)

void BioseqSetDescriptorPropagateUp(CBioseq_set_Handle set)

Moves descriptors up from children of the given bioseq-set if each child has an identical copy of the...

#define FOR_EACH_SEQDESC_ON_SEQENTRY(Itr, Var)

FOR_EACH_SEQDESC_ON_SEQENTRY EDIT_EACH_SEQDESC_ON_SEQENTRY.

Utility stuff for more convenient using of Boost.Test library.

void s_IntervalsMatchGaps(const CSeq_loc &loc, const CSeq_inst &inst)

void s_CheckSeg(const CDelta_seq &ds, bool expect_gap, size_t expect_length)

void CheckTargetedLocusEntry(CRef< CSeq_entry > entry, const string &expected)

BOOST_AUTO_TEST_CASE(FixCollidingIds)

CRef< CSeq_entry > MakeEntryForDeltaConversion(vector< string > segs)

std::map< string, TMapTestNameToTestFiles > TMapFunctionToVecOfTests

void TestCollidingAccessionFixes(const CSeq_id &collide, const string &last)

std::map< string, CFile > TMapTestFiles

void CheckLocalId(const CBioseq &seq, const string &expected)

static bool s_FindGi(const CBioseq_Handle &bsh, const TGi &gi)

std::map< string, TMapTestFiles > TMapTestNameToTestFiles

static bool s_FindLocalId(const CBioseq_Handle &bsh, const string &sLocalid)

CRef< objects::CSeq_feat > MakeGeneForFeature(CRef< objects::CSeq_feat > feat)

CRef< objects::CAuthor > BuildGoodAuthor()

void SetDrosophila_melanogaster(CRef< objects::CSeq_entry > entry)

CRef< objects::CSeq_feat > GetCDSFromGoodNucProtSet(CRef< objects::CSeq_entry > entry)

void SetSebaea_microphylla(CRef< objects::CSeq_entry > entry)

CRef< objects::CSeq_annot > AddFeat(CRef< objects::CSeq_feat > feat, CRef< objects::CSeq_entry > entry)

CRef< objects::CSeq_entry > BuildGoodSeq(void)

CRef< objects::CSeq_feat > AddMiscFeature(CRef< objects::CSeq_entry > entry)

CRef< objects::CSeq_entry > BuildGoodEcoSet()

CRef< objects::CSeq_feat > GetProtFeatFromGoodNucProtSet(CRef< objects::CSeq_entry > entry)

CRef< objects::CSeq_entry > BuildGoodNucProtSet(void)

CRef< objects::CSeq_entry > GetNucleotideSequenceFromGoodNucProtSet(CRef< objects::CSeq_entry > entry)

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