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

nested_id.AppendInteger(data_type);

lmd = last_modified;

nested_id.AppendString(lmd);

.AppendNestedCID(nested_id);

.ToString();

(cache_key.empty())

data_type = nested_cid.GetFirst(

).GetInteger();

, m_WigId(

.m_WigId)

, m_DataType(

.m_DataType)

, m_SummaryBinCount(

.m_SummaryBinCount)

}

(exception& e) {

summary_size = 0;

is.read((

*)&summary_size,

(

));

has_blob =

;

}

(exception& e) {

}

(exception& e) {

request_type =

;

request_type =

;

,

request_type.c_str(),

bin_count_pct = 0.9f;

(exit_code != 0) {

err_msg = (exit_code == -1) ?

:

+

(exit_code);

bin_count_pct -= 0.1;

val_max, val_min;

vector<TValType> data_points;

constexpr

buf_len = 64000;

data_points.resize(buf_len, 0);

(

(summary_is, summary,

)) {

v_max = NStr::StringToNumeric<float>(val_max, convFlags);

v_min = NStr::StringToNumeric<float>(val_min, convFlags);

v = (

(v_min) >

(v_max)) ? v_min : v_max;

summary_sv.

(&data_points[0], batch_size, start);

fill_n(data_points.begin(), buf_len, 0);

summary_sv.

(&data_points[0], batch_size, start);

= v_in.size();

v_out.resize(

, 0);

(

pos = 0; pos <

; ++pos) {

= (range.

() - from) + 1;

vector<TValType> v_in(

, 0);

(

= 0;

<

; ++

) {

vector<float> raw_data(range.

(), 0);

(exit_code != 0) {

err_msg = (exit_code == -1) ?

:

+

(exit_code);

(curr_line.empty() || curr_line[0] ==

)

start = max<int>(NStr::StringToNumeric<int>(

[1]), range.

());

stop = NStr::StringToNumeric<int>(

[2]);

span = stop - start;

= NStr::StringToNumeric<float>(

[3]);

fill_n(raw_data.begin() + pos, span,

);

=

(sv_lay.

());

w.write((

*)&

,

(

));

w.write((

*)sv_lay.

(),

);

runtime_error(

);

stop = range.

();

(start <= stop) {

res.emplace_back(start, min<int>(start + (

- 1), stop));

it =

.begin();

to = from +

(

.size() - 1);

(++it !=

.end()) {

& 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;

from = data_r.GetFrom();

vector<TSparseVector::value_type> data_points;

constexpr

buf_len = 64000;

data_points.resize(buf_len, 0);

batch_size = min<int>(buf_len, (stop + 1) - start);

[

]->decode(&data_points[0], start, batch_size);

(

= 0;

< batch_size; ++

) {

= from +

* bin_size;

.AddRange(

, v);

from += (batch_size * bin_size);

vector<TSeqRange> chunks;

(

& chunk : chunks) {

vector<float> data_points;

(chunk.GetLength() == data_points.size());

vector<TSeqRange> missing_ranges;

(

&

: missing_ranges) {

-=

.GetLength();

coverage =

;

vector<TSeqRange> missing_ranges;

update_data = !missing_ranges.empty();

(update_data ==

)

vector<TSeqRange> normalized_ranges;

normalized_ranges.emplace_back(from, to);

(

= 1;

< missing_ranges.size(); ++

) {

&

= missing_ranges[

];

(

.GetFrom() > normalized_ranges.back().GetTo()) {

normalized_ranges.emplace_back(from, to);

}

(

.GetTo() > normalized_ranges.back().GetTo()) {

normalized_ranges.back().SetTo(to);

(

& range : normalized_ranges) {

.emplace(range, async(std::launch::async, [range,

]{

(!pending_data.

()) {

(

&

: pending_data) {

(d->range, update);

Compressed bit-vector bvector<> container, set algebraic methods, traversal iterators.

Debugging functions (internal). Poorly documented, not well written.

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

Serialization for sparse_vector<>

Checksum and hash calculation classes.

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.

void AppendSeqID(const string &seq_id)

Append an eCIT_SeqID field at the end of this compound ID.

The result type for Spawn methods.

void SaveData(CRef< TData > data)

Clones TData, puts it into Save Queue for asynchroneous storage operation.

static CGraphCache & GetInstance()

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)

string m_RemotePath

path to remote data or srz accession

time_t m_LastChecked

timestamp: last time when m_LastModified was checked

string m_NetCacheKey

data access key

static CCompoundID CreateCompoundID(objects::CScope &scope, const objects::CSeq_id &seq_id, const string &remote_path)

CSparseGraph.

virtual void Init(TGraphCachePool &icache_pool)

string m_LastModified

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

void Update(const TSeqRange &range, const TUpdateMap &update)

virtual void Save(TGraphCachePool &icache_pool)

mutex m_DataMutex

data access mutex

map< string, unique_ptr< TSparseVector > > m_Data

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

string m_SeqId

NCBI seq_id, e.g. NC_000001.

size_t m_DataSize

size of each vector of m_Data

void InitFromCompoundID(CCompoundID id)

void GetMissingRegions(const TSeqRange &range, vector< TSeqRange > &missing_ranges)

Writer-based output stream.

int64_t x_DecodeSign(uint64_t v)

map< TSeqRange, future< TPrefetchData > > m_PendingData

void Prefetch(const TSeqRange &range)

virtual void Save(TGraphCachePool &icache_pool) override

GetData serializes the data into CDensityMap for the range provided in @data.

void x_CreateNetCacheKey()

virtual void Init(TGraphCachePool &icache_pool) override

Save is invoked by CGraphCache when cached data needs to be permanently saved into NetCache.

CWigGraph(const string &cache_key)

Copy constructor is invoked by CGraphCache which clones the data for aynchroneous saving operation.

void x_GetBigWigData(const TSeqRange &range, vector< TValType > &v_out)

void x_DecodeDelta(const TSeqRange &range, vector< float > &v_out)

float GetDataCoverage(const TSeqRange &range)

bool x_ReadSummary(ICache &icache, TSparseVector &sv)

void GetData(CHistogramGlyph::TMap &data)

GetDataCoverage returns fraction (0.

int x_RunBigWigScript(const TSeqRange &range, const string tmp_file)

void x_UnPackFloat(TSparseVector::value_type v_in, float &v_out)

void x_AddDataToMap(const vector< float > &data, const TSeqPos from, CHistogramGlyph::TMap &the_map)

future< TPrefetchSummary > m_PendingSummary

unique_ptr< TSparseVector > TPrefetchSummary

void x_SaveSummary(ICache &icache, TSparseVector &sv)

string m_WigId

WigFile id, e.g. chr1.

void x_GetBigWigSummary(TSparseVector &summary_sv)

void x_EncodeDelta(const TSeqRange &range, const vector< float > &v_in, vector< TValType > &v_out)

atomic< bool > m_PrefetchRequested

Number od data points in one Summary point.

static constexpr float kFract

CWigGraph data come in two flavors Summary - low-res representation for the whole sequence length and...

unique_ptr< TPrefetchRequest > TPrefetchData

uint64_t x_EncodeSign(int64_t v)

Encode/Decode negtaive vaues to positive ones.

static const int kMinBinSize

void x_PackFloat(float v_in, TSparseVector::value_type &v_out)

Float values are packed with precision loss (3 decimal places retained) values are conveeted to posti...

struct { TSeqRange range TPrefetchRequest

static string GetCacheKey(objects::CScope &scope, const objects::CSeq_id &seq_id, const string &wig_id, const string &remote_path, const string &last_modified, EDataType data_type)

CWigGraph.

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

bvector_type::size_type size_type

void resize(size_type sz)

resize vector

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

static const int chunk_size

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

static const column_t columns[]

unsigned int TSeqPos

Type for sequence locations and lengths.

int TSignedSeqPos

Type for signed sequence position.

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.

virtual void AddRange(TSeqRange range, CntType score=1, bool expand=false)

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...

CRef< C > Ref(C *object)

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

int GetSignal(void) const

Get the signal number that has caused the process to terminate (UNIX only).

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

Wait until process terminates.

bool IsSignaled(void) const

TRUE if the process terminated by a signal (UNIX only).

int GetExitCode(void) const

Get process exit code.

@ eHandle

A process handle (MS Windows).

position_type GetLength(void) const

position_type GetToOpen(void) const

CRange< TSeqPos > TSeqRange

typedefs for sequence ranges

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

CNcbiIstream & NcbiGetlineEOL(CNcbiIstream &is, string &str, string::size_type *count=NULL)

Read from "is" to "str" the next line (taking into account platform specifics of End-of-Line)

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 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 void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

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.

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

time_t GetTimeT(void) const

Get time in time_t format.

@ eCurrent

Use current time. See also CCurrentTime.

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.

constexpr bool empty(list< Ts... >) noexcept

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

const GenericPointer< typename T::ValueType > T2 value

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

static const int kDeltaFrameSize

static TSeqPos s_AlignToFrame(TSeqPos pos)

static void s_SplitRange(const TSeqRange &range, int frames, vector< TSeqRange > &res)

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