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

.AppendSeqID(seq_id_str);

.AppendInteger(seq_len);

.AppendHost(remote_path);

.AppendCurrentTime();

session_tag =

.ToString();

runtime_error(

);

(

& old_data :

.m_Data) {

.emplace(old_data.first, unique_ptr<TSparseVector>(

(*old_data.second)));

missing_ranges.clear();

missing_ranges.emplace_back(range.

(), range.

());

vector<TSeqRange> mr;

(

< stop) {

(

== 0 ||

>= stop - 1) {

mr.emplace_back(

, stop - 1);

missing_ranges.push_back(mr.front());

(

= 1;

< mr.size(); ++

) {

(mr[

].GetFrom() - missing_ranges.back().GetFrom() < 20000) {

missing_ranges.back().SetTo(mr[

].GetTo());

missing_ranges.emplace_back(mr[

].GetFrom(), mr[

].GetTo());

unique_ptr<unsigned char> smem(new unsigned char[st.max_serialize_mem]);

cs.AddChars((const char*)smem.get(), slen);

has_blob =

;

}

(

exception& ) {

synced =

;

attempt = 1;

(attempt <= 3) {

last_modified;

time_t last_checked = 0;

x_ReadMap(*icache1,

, remote_path, last_modified, last_checked,

, data_map, tb);

must_sync =

!= m_SessionTag;

(my_MD5.empty()) {

lock_guard<mutex> guard(m_DataMutex);

must_sync = (my_MD5 !=

);

(must_sync ==

) {

lock_guard<mutex> guard(m_DataMutex);

m_LastSynced.SetCurrent();

(m_LastModified.empty()) {

m_LastModified = last_modified;

m_LastChecked =

(last_checked, m_LastChecked);

all_is_good =

;

(m_Data.size() > 1) {

vector<future<bool>> res;

(

&

: m_Data) {

temp_vectors.emplace(

.first, unique_ptr<TSparseVector>(

));

temp_vectors[

.first]->resize(

.second->size());

res.emplace_back(async(launch::async, [&]()->

{

data_key = m_NetCacheKey +

+

.first;

x_ReadData(*icache, data_key,

, *temp_vectors[

.first]); }));

all_is_good = all_of(res.begin(), res.end(), [](future<bool>&

) { return f.get(); });

&

= *m_Data.begin();

temp_vectors.emplace(

.first, unique_ptr<TSparseVector>(

));

temp_vectors[

.first]->resize(

.second->size());

data_key = m_NetCacheKey +

+

.first;

all_is_good = x_ReadData(*icache, data_key,

, *temp_vectors[

.first]);;

lock_guard<mutex> guard(m_DataMutex);

(!last_modified.empty()) {

m_LastModified = last_modified;

m_LastChecked =

(last_checked, m_LastChecked);

m_DataMap |= data_map;

m_LastSynced.SetCurrent();

(

&&

: m_Data) {

.second->join(*temp_vectors[

.first]);

}

(exception& e) {

chrono::milliseconds timespan(attempt * 50 + rand() % 100);

this_thread::sleep_for(timespan);

diag.

(

, attempt - 1);

diag.

(

, attempt - 1);

(!m_IsCacheGood) {

(

&&

: m_Data) {

data_key = m_NetCacheKey +

+

.first;

(diff_in_millisec > 250)

(

&

: update) {

(elapsed > 2000) {

diag.

(

, elapsed);

kRemoteDataCheckInterval = 600;

}

((

.GetTimeT() -

) > kRemoteDataCheckInterval) {

.second->set(0,

.second->size());

unique_ptr<unsigned char> smem(new unsigned char[st.max_serialize_mem]);

w(icache.GetWriteStream(m_NetCacheKey, 0, NcbiEmptyString), 0, 0, CRWStreambuf::fOwnWriter);

= static_cast<int>(m_SessionTag.size());

w.write((const char*)&val, sizeof(int));

(!w)

(CException, eUnknown, "Failed to write Session tag size: " + m_NetCacheKey);

w.write(m_SessionTag.c_str(), m_SessionTag.size());

(!w)

(CException, eUnknown, "Failed to write session tag: " + m_NetCacheKey);

= static_cast<int>(m_RemotePath.size());

w.write((const char*)&val, sizeof(int));

(!w)

(CException, eUnknown, "Failed to write remote path length: " + m_NetCacheKey);

w.write((const char*)m_RemotePath.c_str(), m_RemotePath.size());

(!w)

(CException, eUnknown, "Failed to write remote path length: " + m_NetCacheKey);

= static_cast<int>(m_LastModified.size());

w.write((const char*)&val, sizeof(int));

(!w)

(CException, eUnknown, "Failed to write last_modified: " + m_NetCacheKey);

w.write((const char*)m_LastModified.c_str(), val);

(!w)

(CException, eUnknown, "Failed to write last_modified: " + m_NetCacheKey);

w.write((const char*)&m_LastChecked, sizeof(time_t));

(!w)

(CException, eUnknown, "Failed to write last_checked: " + m_NetCacheKey);

w.write((const char*)smem.get(), slen);

(!w)

(CException, eUnknown, "Failed to write vector: " + m_NetCacheKey);

w.write((

*)&

,

(

));

w.write((

*)sv_lay.

(), sv_lay.

());

vector_offset = 0;

is.read((

*)&

,

(

));

vector_offset +=

(

);

vector_offset +=

.size();

is.read((

*)&

,

(

));

vector_offset +=

(

);

vector_offset +=

;

is.read((

*)&

,

(

));

vector_offset +=

(

);

last_modified.clear();

vector_offset +=

;

last_modified.append(&

[0],

);

is.read((

*)&last_checked,

(time_t));

vector_offset +=

(time_t);

vector<char>

(

- vector_offset, 0);

}

(exception& e) {

vector_offset = 0;

is.read((

*)&

,

(

));

vector_offset +=

(

);

vector_offset +=

.size();

.ToString();

(cache_key.empty())

(window < 1.0) window = 1.0;

num_pixels = (size_t)ceil(range.

() / window);

.resize(num_pixels);

start = range.

();

curr_pos = start;

(pos < stop && stat_idx < num_pixels) {

end_idx = (size_t)floor(curr_pos + 0.5);

max_mismatch = -1;

(pos < end_idx) {

index = pos -

;

mismatch =

(mismatches[index]);

=

(matches[index]);

gap =

(gaps[index]);

intron =

(introns[index]);

total = max<int>(total,

+ mismatch + gap + intron);

max_mismatch = max<int>(max_mismatch, mismatch);

max_gap = max<int>(max_gap, gap);

max_intron = max<int>(max_intron, intron);

max_error =

(max_gap,

(max_mismatch, max_intron));

vector<TValType> matches;

vector<TValType> mismatches;

vector<TValType> gaps;

vector<TValType> introns;

to = range.

();

matches.resize(

.GetLength());

mismatches.resize(

.GetLength());

gaps.resize(

.GetLength());

introns.resize(

.GetLength());

[

]->decode(&matches[0],

.GetFrom(),

.GetLength());

[

]->decode(&mismatches[0],

.GetFrom(),

.GetLength());

[

]->decode(&gaps[0],

.GetFrom(),

.GetLength());

[

]->decode(&introns[0],

.GetFrom(),

.GetLength());

(

= 0;

<

.GetLength(); ++

) {

sub_total = max<int>(sub_total,

(matches[

] + mismatches[

] + gaps[

] + introns[

]));

from =

.GetToOpen();

ncbi::TMaskedQueryRegions mask

#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.

@ eStat_Intron

intron (for mRNA-to-genome alignments)

@ eStat_Mismatch

mismatches (A+G+T+C - matches)

@ eStat_Total

total alignment count at this base (A+G+T+C+Gap)

vector< SStatStruct > TStatVec

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.

Base64-encoded ID string that contains extractable typed fields.

void AppendID(Uint8 id)

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

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

void UpdateAlignStats(const TSeqRange &range, float window, CAlnStatGlyph::TStatVec &stats)

CPileUpGraph(const string &data_key)

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

CPileUpGraph.

int GetNumberOfReads(const TSeqRange &range)

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

@ fOwnReader

Own the underlying reader.

@ fOwnWriter

Own the underlying writer.

string m_RemotePath

path to remote data or srz accession

time_t m_LastChecked

timestamp: last time when m_LastModified was checked

void x_WriteMap(ICache &icache, bm::word_t *tb=0)

string m_NetCacheKey

data access key

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

CSparseGraph.

void x_Sync(TGraphCachePool &icache_pool)

void x_WriteData(ICache &icache, const string &data_key, TSparseVector &sv)

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 ...

void x_ReadMap(ICache &icache, string &tag, string &remote_path, string &last_modified, time_t &last_checked, string &md5, bm::bvector<> &bv, bm::word_t *tb=0)

string m_SeqId

NCBI seq_id, e.g. NC_000001.

size_t m_DataSize

size of each vector of m_Data

bm::bvector m_DataMap

bvector shows the regions m_Data exist

void InitFromCompoundID(CCompoundID id)

bool m_IsCacheGood

false value indicates that remote data were updated and the cache was reset

string m_SessionTag

A current session tag, used to separate session netcache blobs from the blobs saved by other sessions...

bool x_ReadData(ICache &icache, const string &data_key, const string &tag, TSparseVector &sv, bm::word_t *tb=0)

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

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.

void optimize(bm::word_t *temp_block=0, optmode opt_mode=opt_compress, statistics *stat=0)

Optimize memory bitvector's memory allocation.

size_type count_range(size_type left, size_type right, const rs_index_type &rs_idx) const noexcept

Returns count of 1 bits in the given range [left..right] Uses rank-select index to accelerate the sea...

bvector< Alloc > & set_range(size_type left, size_type right, bool value=true)

Sets all bits in the specified closed interval [left,right] Interval must be inside the bvector's siz...

void clear(const size_type *ids, size_type ids_size, bm::sort_order so=bm::BM_UNKNOWN)

clear list of bits in this bitset

void calc_stat(struct bm::bvector< Alloc >::statistics *st) const noexcept

Calculates bitvector statistics.

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

bvector_type::size_type size_type

static const int chunk_size

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

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

static void md5(const char *src, const char *out)

string GetHexSum(void) const

Return string with checksum in hexadecimal form.

void AddLine(const char *line, size_t len)

void GetMD5Digest(unsigned char digest[16]) const

Return calculated MD5 digest.

void AddChars(const char *str, size_t len)

Update current control sum with data provided.

CDiagContext_Extra & Print(const string &name, const string &value)

The method does not print the argument, but adds it to the string.

CDiagContext & GetDiagContext(void)

Get diag context instance.

CDiagContext_Extra Extra(void) const

Create a temporary CDiagContext_Extra object.

#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 bool IfModifiedSince(const string &url, string &last_modified)

Works with HTTP(s) protocol returns true if url was modified since last_modified date if true last_mo...

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.

static TPid GetPid(void)

Get process identifier (pid) for the current process.

position_type GetLength(void) const

position_type GetToOpen(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

@ eNocase

Case insensitive compare.

double Elapsed(void) const

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

double DiffNanoSecond(const CTime &t) const

Difference in nanoseconds from specified time.

CTime & AddHour(int hours=1, EDaylight adl=eDaylightDefault)

Add specified hours and adjust for daylight saving time.

@ eCurrent

Use current time. See also CCurrentTime.

@ eStart

Start timer immediately after creating.

size_t serialize(const BV &bv, unsigned char *buf, bm::word_t *temp_block=0, unsigned serialization_flags=0)

Saves bitvector into memory.

size_t deserialize(BV &bv, const unsigned char *buf, bm::word_t *temp_block=0, const bm::bv_ref_vector< BV > *ref_vect=0)

Bitvector deserialization from a memory BLOB.

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.

if(yy_accept[yy_current_state])

bm::id_t bvector_size_type

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

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

static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)

Reader-writer based streams.

static SLJIT_INLINE sljit_ins st(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

static void s_GenerateSessionTag(string &session_tag)

static void s_GetMD5Tag(bm::bvector<> &bv, string &tag, bm::word_t *tb=0)

Statistical information about bitset's memory allocation details.

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

string GetMD5Digest(const CChecksum &cs)

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