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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/align__tab__export__job_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/packages/pkg_alignment/align_tab_export_job.cpp Source File

:

(

), m_Params(params)

vector<CSeq_align::TDim> anchors;

anchors.push_back(

);

(anchors.empty()) {

(

level = 0; level <= 5 && anchors.empty(); ++level) {

anchors.push_back(

);

(anchors.empty()) {

);

defline =

.GenerateDefline(bsh);

out_label =

;

(out_label.length() > 20 && out_label.find(

) != string::npos) {

pos = out_label.find_last_of(

);

(pos != string::npos) {

out_label = out_label.substr(pos + 1);

(out_label.length() > 20) {

pos = out_label.rfind(

);

(pos != string::npos && pos > 0) {

pos = out_label.rfind(

, pos - 1);

(pos != string::npos) {

out_label = out_label.substr(pos + 1);

out_label =

;

pos = out_label.find(

);

(pos != string::npos) {

pos = out_label.find(

, pos + 7);

(pos != string::npos) {

out_label = out_label.substr(pos);

vector<bool> strands;

( !curr_text.empty() ) {

ids.push_back(

);

(num_rows > ids.size()) {

curr_text +=

;

fieldData[

] = curr_text;

(num_rows > ids.size()) {

is_protein =

;

(ids.size() == 2 && num_rows == 2 && anchorRow >= 0 && anchorRow < 2) {

curr_text = ids[anchorRow] +

;

fieldData[

] = curr_text;

fieldData[

] = curr_text;

(!is_protein && num_rows == 2 && strands.size() == 2) {

fieldData[

] = (strands[0] == strands[1]) ?

:

;

tag_name =

;

tag_name += is_protein ?

:

;

coverage = -1.0;

(coverage >= 0.0) {

(coverage < 100.0 && coverage > 99.9) {

curr_text =

;

sprintf(

,

, coverage);

fieldData[

] = curr_text;

(align_length < 1000000) {

(identities >= 0) {

identity = 0.0;

identity = identities * 100.0 / align_length;

(identity < 100.0 && identity > 99.9) {

curr_text =

;

sprintf(

,

, identity);

fieldData[

] = curr_text;

(mismatches >= 0) {

(vector<string>, it, fields)

exporter.

(*it);

(

align_iter(handle, range, sel); align_iter; ++align_iter) {

(vector<string>, it, fields)

exporter.

(fieldData[*it]);

err_msg =

;

(err_msg.empty()) {

User-defined methods of the data storage class.

static CFastMutex s_DFLock

USING_SCOPE(ncbi::objects)

static sequence::CDeflineGenerator s_DefGen

This class seems to be non-thread safe even as a stack var.

static CSeq_align::TDim sFindAnchorRow(CBioseq_Handle handle, const CSeq_align &align)

static string s_ShortenIdLabel(const string &label)

static void s_GetDefline(CBioseq_Handle bsh, string &defline)

static size_t s_CountSegments(const CSeq_align &align)

static string s_RemovePanfsBasePath(const string &label)

static map< string, string > sGenerateFields(CBioseq_Handle handle, const CSeq_align &align, CSeq_align::TDim anchorRow)

CAlignTabExportJob(const CAlignTabExportParams &params)

CAlignTabExportParams m_Params

virtual EJobState Run()

Function that does all the useful work, called by the Engine.

const SConstScopedObject & GetObject() const

wxString GetFileName() const

string GetAlignmentName() const

vector< string > GetFields() const

CAppJobError Default implementation for IAppJobError - encapsulates a text error message.

CAppJob - default implementation of IAppJob that could be used as a base class.

void Field(const string &value)

TSeqPos GetAlignLength(const CSeq_align &align, bool ungapped=false)

Compute the length of the alignment (= length of all segments, gaps + aligned)

int GetGapCount(const CSeq_align &align)

Compute the number of gaps in the alignment.

double GetPercentCoverage(CScope &scope, const CSeq_align &align, unsigned query=0)

Compute percent coverage of the query (sequence 0) (range 0-100)

int GetMismatchCount(CScope &scope, const CSeq_align &align)

Compute the number of mismatches in the alignment.

CRange< TSeqPos > GetSeqRange(TDim row) const

GetSeqRange NB: On a Spliced-seg, in case the product-type is protein, these only return the amin par...

TDim CheckNumRows(void) const

Validatiors.

const CSeq_id & GetSeq_id(TDim row) const

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

bool GetNamedScore(const string &id, int &score) const

Get score.

ENa_strand GetSeqStrand(TDim row) const

Get strand (the first one if segments have different strands).

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

#define NCBI_THROW(exception_class, err_code, message)

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

const string & GetMsg(void) const

Get message string.

void Info(CExceptionArgs_Base &args)

static objects::SAnnotSelector GetAnnotSelector(TAnnotFlags flags=0)

request an annotation selector for a given type

static void SetAnnot(objects::SAnnotSelector &sel, const string &annot)

help function for setting up an annotation.

static void SetResolveDepth(objects::SAnnotSelector &sel, bool adaptive, int depth=-1)

help function for setting selector resolve depth.

CRef< CAppJobError > m_Error

CRef< objects::CScope > scope

string m_Descr

mutex to sync our internals

virtual bool IsCanceled() const override

EJobState

Job states (describe FSM)

CConstRef< CObject > object

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

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

CConstRef< CSeq_id > GetSeqId(void) const

CConstRef< CSeq_id > GetSeqIdOrNull(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

@ eContent

Untagged human-readable accession or the like.

TRange GetTotalRange(void) const

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

@ eGetId_Best

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

bool IsProtein(void) const

bool ContainsSegment(const CSeq_id &id, size_t resolve_depth=kMax_Int, EFindSegment limit_flag=eFindSegment_NoLimit) const

Check if the seq-id describes a segment of the bioseq.

CScope & GetScope(void) const

Get scope this handle belongs to.

bool IsSynonym(const CSeq_id &id) const

Check if this id can be used to obtain this bioseq handle.

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

TObjectType & GetObject(void)

Get object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

static string SizetToString(size_t value, TNumToStringFlags flags=0, int base=10)

Convert size_t to string.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

@ fWithCommas

Use commas as thousands separator.

static const char label[]

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

E_Choice Which(void) const

Which variant is currently selected.

const TSpliced & GetSpliced(void) const

Get the variant data.

const TExons & GetExons(void) const

Get the Exons member data.

const TDisc & GetDisc(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

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

#define row(bind, expected)

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