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NCBI C++ ToolKit: src/gui/core/prj_helper.cpp Source File

& score = **it;

new_align->

(align);

CSeq_align::TScore::iterator

= new_align->

().begin();

( ;

!= new_align->

().end(); ) {

new_aligns.push_back(new_align);

list<CConstRef<CSeq_id> > unresolved_subjects;

& rid(RemoteBlast->GetRID());

& rid_title(RemoteBlast->GetTitle());

TAlign& an_align =

.Set();

sProjectItemBaseName(rid_title.empty() ?

+ rid_title :

+ rid);

is_db_search = RemoteBlast->IsDbSearch();

write_local_seq =

;

report_total =

;

TAlignSetMap align_set_map;

( TAlign::iterator it = an_align.begin(); it != an_align.end(); ++it) {

(filter.

() && filter.

(target_id_str) == filter.

()) {

curr_set->

().push_back(*it);

list< CRef<CSeq_align> > new_aligns;

(new_aligns.size()) {

an_align.insert(it, new_aligns.begin(), new_aligns.end());

report_total =

;

(!is_db_search || !scope->GetBioseqHandle(target_id)) {

TAlignSetMap cleanup_align_set_map;

.SortInputsByScore(

);

.PreserveRows(

);

.FillUnaligned(

);

(TAlignSetMap, aln_set_iter, align_set_map) {

.Cleanup(aln_set_iter->second->Get(), aligns_out_tmp,

( !aligns_out_tmp.empty() && aligns_out_tmp.size() != aln_set_iter->second->Get().size() ) {

aln_set->

() = aligns_out_tmp;

cleanup_align_set_map.insert(

annot_base_name(sProjectItemBaseName +

+ aln_set_iter->first);

TAlignSetMap::iterator cleaned_iter = cleanup_align_set_map.find(aln_set_iter->first);

(cleaned_iter != cleanup_align_set_map.end()) {

annot->

().SetAlign() = cleaned_iter->second->Set();

annot->

(

+ annot_base_name);

annot->

().SetAlign() = aln_set_iter->second->Set();

found_in_scope =

;

(

seq_id : ids) {

(scope->GetBioseqHandle(*seq_id)) {

found_in_scope =

;

(found_in_scope)

;

(unresolved_subjects.size()) {

blast::CBlastScopeSource bss(bdlc, objMgr);

bss.AddDataLoaders(blast_scope);

list<CRef<CBioseq> > subjects = RemoteBlast->GetSubjectSequences();

entry->

(*bioseq_ref);

User-defined methods of the data storage class.

Declares CBlastScopeSource class to create properly configured CScope objects to invoke the BLAST dat...

class CAlignCleanup implements an alignment cleanup utility based on the C++ alignment manager.

list< CRef< CSeq_align > > TAligns

bool IsProtein() const

Returns true if the database is protein.

size_t GetNumQueries() const

Retrieve the number of queries in this object.

CDataLoadingAppJob - a base class for Jobs loading data into projects.

void AddProjectItem(objects::CProjectItem &item)

void AddTag(const string &tag)

void SetObject(CSerialObject &object)

wrapper for setting the object pointed to by this item

TSeqPos GetSeqStop(TDim row) const

const CSeq_id & GetSeq_id(TDim row) const

Get seq-id (the first one if segments have different ids).

TSeqPos GetSeqStart(TDim row) const

void SetNameDesc(const string &name)

void SetCreateDate(const CTime &dt)

void GetLabel(string *label, ELabelType type) const

Base class for all serializable objects.

const_iterator find(const key_type &key) const

const_iterator end() const

static void cleanup(void)

#define GI_FROM(T, value)

unsigned int TSeqPos

Type for sequence locations and lengths.

#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.

static void AddProjectItemsFromRID(CRef< objects::CScope > scope, CSeq_align_set &results, bool isFindComp, CRef< blast::CRemoteBlast > RemoteBlast, const set< string > &filter, CDataLoadingAppJob &job, SRIDStatInfo &RIDStatInfo)

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

Set object to copy of another one.

const string AsFastaString(void) const

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

TRange GetTotalRange(void) const

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

@ eCurrent

Use current time. See also CCurrentTime.

static const char label[]

bool IsSeq_loc_list(void) const

Check if variant Seq_loc_list is selected.

const TName & GetName(void) const

Get the Name member data.

TBioseq_set & SetBioseq_set(void)

Select the variant.

bool IsBioseq_set(void) const

Check if variant Bioseq_set is selected.

const TSeq_loc_list & GetSeq_loc_list(void) const

Get the variant data.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

void SetLabel(const TLabel &value)

Assign a value to Label data member.

bool IsStr(void) const

Check if variant Str is selected.

const TStr & GetStr(void) const

Get the variant data.

Tdata & Set(void)

Assign a value to data member.

TScore & SetScore(void)

Assign a value to Score data member.

E_Choice Which(void) const

Which variant is currently selected.

vector< CRef< CScore > > TScore

void SetSegs(TSegs &value)

Assign a value to Segs data member.

TInt GetInt(void) const

Get the variant data.

const TValue & GetValue(void) const

Get the Value member data.

bool IsSetScore(void) const

for whole alignment Check if a value has been assigned to Score data member.

const TScore & GetScore(void) const

Get the Score member data.

const TId & GetId(void) const

Get the Id member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

E_Choice Which(void) const

Which variant is currently selected.

bool IsWhole(void) const

Check if variant Whole is selected.

const TSeq & GetSeq(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

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.

void SetData(TData &value)

Assign a value to Data data member.

const TId & GetId(void) const

Get the Id member data.

list< CRef< CSeq_align > > TAlign

bool IsSetId(void) const

equivalent identifiers Check if a value has been assigned to Id data member.

double value_type

The numeric datatype used by the parser.

static void sPrepareSeqAlign(CSeq_align &align, list< CRef< CSeq_align > > &new_aligns)

static const string kBLASTProjectItemTag

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