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NCBI C++ ToolKit: src/gui/widgets/seq_graphic/bed_coverage_graph.cpp Source File

.AppendString(seq_id_str);

.AppendString(bed_id);

.AppendInteger(seq_len);

.AppendHost(remote_path);

lmd = last_modified;

.AppendString(lmd);

.ToString();

(cache_key.empty())

= field_seq_id.GetString();

field_id = field_seq_id.GetNextNeighbor();

field_len = field_id.GetNextNeighbor();

= (size_t)field_len.GetInteger();

field_path = field_len.GetNextNeighbor();

: m_SeqId(

.m_SeqId)

, m_BedId(

.m_BedId)

, m_SeqLen(

.m_SeqLen)

, m_RemotePath(

.m_RemotePath)

, m_LastModified(

.m_LastModified)

, m_DataKey(

.m_DataKey)

, m_DataBinCount(

.m_DataBinCount)

, m_Data(

.m_Data)

}

(exception& e) {

is.read((

*)&bin_count,

(

));

has_blob =

;

}

(exception& e) {

}

(exception& e) {

(

& data_url,

& chrom,

& from,

& to,

bin_count, vector<unsigned int>& data_points)

,

bin_count_str.c_str(),

sTmpFilename.c_str(),

(ExitCode == -1) {

data_points.push_back(v);

(

& data_url,

& chrom,

& from,

& to, vector<TSeqRange>& ranges)

,

sTmpFilename.c_str(),

start_s, end_s;

ranges.emplace_back(from, to);

w.write((

*)sv_lay.

(), sv_lay.

());

vector<unsigned int> data_points;

& data_r =

.GetRange();

(data_r.GetLength() > 0);

(data_r.GetLength() == 0) {

start = data_r.GetFrom()/bin_size;

stop = data_r.GetTo()/bin_size;

= (stop - start) + 1;

vector<unsigned int> temp_data(

, 0);

(data_r.GetFrom(), data_r.GetFrom() + bin_size - 1);

= temp_data[0];

(

= 1;

<

; ++

) {

from = data_r.GetFrom() +

* bin_size;

to = from + bin_size - 1;

(temp_data[

] ==

&& from ==

.GetToOpen()) {

= temp_data[

];

max_value = max<int>(max_value,

);

max_value = max<int>(max_value,

);

start = range.

()/bin_size;

stop = range.

()/bin_size;

= (stop - start) + 1;

vector<unsigned int> temp_data(

, 0);

(

= 0;

<

; ++

) {

(temp_data[

] == 0)

max_count = max<int>(max_count, temp_data[

]);

- empty_bins;

void s_GetBigBedFeats(const string &data_url, const string &chrom, const string &from, const string &to, vector< TSeqRange > &ranges)

static bool s_ReadData(ICache &icache, const string &data_key, int &bin_count, bm::sparse_vector< unsigned, bm::bvector<> > &sv, bm::word_t *tb)

void s_GetBigBedSummary(const string &data_url, const string &chrom, const string &from, const string &to, int bin_count, vector< unsigned int > &data_points)

#define BM_DECLARE_TEMP_BLOCK(x)

Serialization / compression of bvector<>. Set theoretical operations on compressed BLOBs.

Serialization for sparse_vector<>

Checksum and hash calculation classes.

void Save(TGraphCachePool &icache_pool)

void x_SaveData(ICache &icache)

size_t GetEstimatedFeatureCount(const TSeqRange &range, int &max_count)

static const int kMinBinSize

static string GetCacheKey(objects::CScope &scope, const objects::CSeq_id &seq_id, const string &bed_id, const string &remote_path, const string &last_modified=NcbiEmptyString)

CBedCoverageGraph.

mutex m_DataMutex

data access mutex

TSparseVector m_Data

map of sprasvectors, the key is used as a part of suffix of NetCache key (m_DataKey + "_" + this map ...

void Init(TGraphCachePool &icache_pool)

string m_RemotePath

path to remote data or srz accession

string m_LastModified

timestamp of the remote data last modified date as reported by www server

CBedCoverageGraph(const string &cache_key)

void GetData(CHistogramGlyph::TMap &data)

void x_InitData(ICache &icache)

CChecksum – Checksum calculator.

Pool of recycled CCompoundID objects.

CCompoundID NewID(ECompoundIDClass new_id_class)

Create and return a new CCompoundID objects.

CCompoundID FromString(const string &cid)

Unpack the base64-encoded ID and return a CCompoundID object for field extraction.

CCompoundIDField GetFirst(ECompoundIDFieldType field_type)

Return the first field of the specified type or NULL if this compound ID contains no fields of such t...

The result type for Spawn methods.

Guard that can be used to automatically return object to the pool after leaving some scope.

Extended exit information for waited process.

Note about the "buf_size" parameter for streams in this API.

@ fOwnReader

Own the underlying reader.

@ fOwnWriter

Own the underlying writer.

@ ESuggestedAction_Access

try to access the remote file

@ ESuggestedAction_Skip

do not access the file

static void Set(const string &sKey, ESuggestedAction KnownAccessibility)

static ESuggestedAction Check(const string &sKey)

Writer-based output stream.

BLOB cache read/write/maintenance interface.

virtual size_t GetSize(const string &key, TBlobVersion version, const string &subkey)=0

Check if BLOB exists, return BLOB size.

virtual IWriter * GetWriteStream(const string &key, TBlobVersion version, const string &subkey, unsigned int time_to_live=0, const string &owner=kEmptyStr)=0

Return sequential stream interface to write BLOB data.

virtual IReader * GetReadStream(const string &key, TBlobVersion version, const string &subkey)=0

Return sequential stream interface to read BLOB data.

succinct sparse vector with runtime compression using bit-slicing / transposition method

bool empty() const noexcept

return true if vector is empty

bvector_type::size_type size_type

void resize(size_type sz)

resize vector

size_type decode(value_type *arr, size_type idx_from, size_type dec_size, bool zero_mem=true) const

Bulk export list of elements to a C-style array.

void import(const value_type *arr, size_type arr_size, size_type offset=0, bool set_not_null=true)

Import list of elements from a C-style array.

void optimize(bm::word_t *temp_block=0, typename bvector_type::optmode opt_mode=bvector_type::opt_compress, typename sparse_vector< Val, BV >::statistics *stat=0)

run memory optimization for all vector planes

string GetHexSum(void) const

Return string with checksum in hexadecimal form.

void AddLine(const char *line, size_t len)

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

void Error(CExceptionArgs_Base &args)

#define NCBI_THROW(exception_class, err_code, message)

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

static CResult SpawnL(EMode mode, const char *cmdname, const char *argv,...)

Spawn a new process with specified command-line arguments.

TProcessHandle GetProcessHandle(void)

Get process handle/pid.

@ eNoWait

Continues to execute calling process concurrently with new process (asynchronous spawn).

static fstream * CreateTmpFile(const string &filename=kEmptyStr, ETextBinary text_binary=eBinary, EAllowRead allow_read=eAllowRead)

Create temporary file and return pointer to corresponding stream.

static string GetTmpName(ETmpFileCreationMode mode=eTmpFileGetName)

Get temporary file name.

@ eTmpFileCreate

Create empty file for each GetTmpName* call.

static void GetLastModified(const string &url, string &last_modified)

HTTP: Returns header's Last-Modified in the last_modified parameter FTP: Returns MD5 of first 512 byt...

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

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.

CSeq_id_Handle GetAccVer(const CSeq_id_Handle &idh, TGetFlags flags=0)

Get accession.version Seq-id Returns null CSeq_id_Handle if the sequence is not found or if it doesn'...

TSeqPos GetSequenceLength(const CSeq_id &id, TGetFlags flags=0)

Get sequence length Return kInvalidSeqPos if sequence is not found.

int Wait(unsigned long timeout=kInfiniteTimeoutMs, CExitInfo *info=0) const

Wait until process terminates.

int GetExitCode(void) const

Get process exit code.

@ eHandle

A process handle (MS Windows).

position_type GetLength(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

CNcbiIstream & NcbiGetline(CNcbiIstream &is, string &str, char delim, string::size_type *count=NULL)

Read from "is" to "str" up to the delimiter symbol "delim" (or EOF)

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

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

Convert string to int.

static double StringToDouble(const CTempStringEx str, TStringToNumFlags flags=0)

Convert string to double.

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

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.

@ fAllowTrailingSpaces

Ignore trailing whitespace characters.

@ fConvErr_NoThrow

Do not throw an exception on error.

@ fAllowLeadingSpaces

Ignore leading whitespace characters in converted string.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

unsigned int

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

void sparse_vector_serialize(const SV &sv, sparse_vector_serial_layout< SV > &sv_layout, bm::word_t *temp_block=0)

Serialize sparse vector into a memory buffer(s) structure.

int sparse_vector_deserialize(SV &sv, const unsigned char *buf, bm::word_t *temp_block=0)

Deserialize sparse vector.

const struct ncbi::grid::netcache::search::fields::SIZE size

Defines a portable execute class.

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

Reader-writer based streams.

layout class for serialization buffer structure

const unsigned char * buf() const noexcept

Return serialization buffer pointer.

size_t size() const noexcept

return current serialized size

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