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NCBI C++ ToolKit: src/algo/align/util/align_sort.cpp Source File

<

Container>

<

Container>

);

is_neg =

;

(*prev_it)->GetGenomic_start() -

(*it)->GetGenomic_end() - 1;

(*it)->GetGenomic_start() -

(*prev_it)->GetGenomic_end() - 1;

(

& chunk : (*it)->GetParts()) {

(chunk->Which()) {

key1.

.size() < key2.

.size();

(vector<string>, iter, key_toks) {

item.second =

.GetScore(align, *iter);

.items.push_back(item);

(

% 100000 == 0) {

<<

/ e <<

);

&tmp_path,

((*iter)[0] ==

) {

}

((*iter)[0] ==

) {

);

( &aligns_in == &aligns_out) {

);

list< CRef<CSeq_align> > TAlns;

( &aligns_in == &aligns_out) {

);

vector< CRef<CSeq_align> > TAlns;

vector<string> tmp_volumes;

aligns.push_back(

);

tmp_volumes.push_back(fname);

<<

<< aligns.size() <<

);

unique_ptr<CObjectOStream> tmp_os

);

*tmp_os << *it->second;

(tmp_volumes.size() && aligns.size()) {

tmp_volumes.push_back(fname);

<<

<< aligns.size() <<

);

unique_ptr<CObjectOStream> tmp_os

);

*tmp_os << *it->second;

(tmp_volumes.size()) {

sorted_output.

(*it);

sorted_output.

();

(vector<string>, it, tmp_volumes) {

remove_input_files,

vector< AutoPtr<CObjectIStream> > TFiles;

files.reserve(input_files.size());

(vector<string>, it, input_files) {

( !(*it)->EndOfData() ) {

kf.first.second = sa;

( !q.empty() ) {

sorted_output.

(kf.first);

( !(*files[kf.second]).EndOfData() ) {

(*files[kf.second]) >> *sa;

kf.first.second = sa;

files[kf.second].reset();

<< input_files[kf.second]);

( remove_input_files &&

<< input_files[kf.second]);

sorted_output.

();

bool IsReverse(ENa_strand s)

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.

static string s_GetCIGARForSort(CScope &, const CSeq_align &align)

bool Match(const objects::CSeq_align &align)

Match a single alignment.

virtual void Write(const TAlignment &aln)=0

SAlignExtractor m_Extractor

deque< TAlignment > TAlignments

CRef< CAlignFilter > m_Filter

CAlignSort(CScope &scope, string sorting_keys, CRef< CAlignFilter > filter=CRef< CAlignFilter >(), const string &tmp_path="/tmp", size_t memory_limit=0, size_t count_limit=0)

void MergeSortedFiles(const vector< string > &input_files, IAlignSortedOutput &sorted_output, bool remove_input_files=false, bool filtered=false)

void SortAlignments(IAlignSource &align_source, IAlignSortedOutput &sorted_output)

pair< SSortKey, CRef< CSeq_align > > TAlignment

pair< TAlignment, size_t > SKeyAndFile

SSortKey_Less m_Predicate

CLocalAlignSortedOutput(TList &sortedOutput)

virtual size_t GetCountProcessed() const

virtual size_t GetCountEmitted() const

virtual ~CLocalAlignSortedOutput()

virtual void Write(const CAlignSort::TAlignment &aln)

virtual bool EndOfData() const

virtual CRef< CSeq_align > GetNext()

CLocalAlignSource(const TList &aligns)

string GetTraceback(const CSeq_align &align, CSeq_align::TDim row)

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...

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

ENa_strand GetSeqStrand(TDim row) const

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

static Uint8 GetTotalPhysicalMemorySize(void)

Return the amount of actual/total physical memory, in bytes.

virtual bool EndOfData() const =0

virtual CRef< CSeq_align > GetNext()=0

std::ofstream out("events_result.xml")

main entry point for tests

static int lookup(const char *name, const struct lookup_int *table)

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.

@ eFollowLinks

Follow symbolic links.

#define LOG_POST(message)

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

void Error(CExceptionArgs_Base &args)

TErrCode GetErrCode(void) const

Get error code.

#define NCBI_THROW(exception_class, err_code, message)

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

void Info(CExceptionArgs_Base &args)

static string NormalizePath(const string &path, EFollowLinks follow_links=eIgnoreLinks)

Normalize a path.

static string CreateAbsolutePath(const string &path, ERelativeToWhat rtw=eRelativeToCwd)

Get an absolute path from some, possibly relative, path.

static string GetTmpNameEx(const string &dir=kEmptyStr, const string &prefix=kEmptyStr, ETmpFileCreationMode mode=eTmpFileGetName)

Get temporary file name.

bool CreatePath(TCreateFlags flags=fCreate_Default) const

Create the directory path recursively possibly more than one at a time.

virtual bool Remove(TRemoveFlags flags=eRecursive) const

Remove a directory entry.

virtual bool Exists(void) const

Check if directory "dirname" exists.

@ eSerial_AsnBinary

ASN.1 binary.

const string AsFastaString(void) const

CConstRef< CSeq_id > GetSeqId(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

static CObjectOStream * Open(ESerialDataFormat format, CNcbiOstream &outStream, bool deleteOutStream)

Create serial object writer and attach it to an output stream.

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

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

size_t total

Total memory usage.

static bool GetMemoryUsage(SMemoryUsage &usage)

Get current process memory usage.

position_type GetLength(void) const

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

Case-insensitive equality of a substring with another 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.

static string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

@ fSplit_MergeDelimiters

Merge adjacent delimiters.

double Restart(void)

Return time elapsed since first Start() or last Restart() call (in seconds).

double Elapsed(void) const

Return time elapsed since first Start() or last Restart() call (in seconds).

TGenomic_strand GetGenomic_strand(void) const

Get the Genomic_strand member data.

const TSpliced & GetSpliced(void) const

Get the variant data.

bool IsSetGenomic_strand(void) const

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

const TExons & GetExons(void) const

Get the Exons member data.

bool IsSpliced(void) const

Check if variant Spliced is selected.

const TSegs & GetSegs(void) const

Get the Segs member data.

@ e_Product_ins

insertion in product sequence (i.e. gap in the genomic sequence)

@ e_Diag

both sequences are represented, there is sufficient similarity between product and genomic sequences....

@ e_Genomic_ins

insertion in genomic sequence (i.e. gap in the product sequence)

@ e_Match

both sequences represented, product and genomic sequences match

@ e_Mismatch

both sequences represented, product and genomic sequences do not match

constexpr auto sort(_Init &&init)

double value_type

The numeric datatype used by the parser.

const struct ncbi::grid::netcache::search::fields::KEY key

Defines process management classes.

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

bool operator()(const TAlignment &k1, const TAlignment &k2) const

vector< ESortDir > sort_dirs

pair< string, double > TItem

Process memory usage information, in bytes.

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