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NCBI C++ ToolKit: src/app/splign/splign_app.cpp Source File

kDirSense[] =

;

kDirAntisense[] =

;

kDirBoth[] =

;

kDirAuto[] =

;

kDirDefault[] =

;

argdescr->AddOptionalKey

,

argdescr->AddOptionalKey

(

,

,

,

argdescr->AddOptionalKey

(

,

,

,

argdescr->AddOptionalKey

(

,

,

,

argdescr->AddOptionalKey

(

,

,

,

);

argdescr->AddOptionalKey

(

,

,

,

argdescr->AddOptionalKey

(

,

,

,

argdescr->AddOptionalKey

,

argdescr->AddOptionalKey

(

,

,

,

);

argdescr->AddDefaultKey

(

,

,

,

argdescr->AddOptionalKey

(

,

,

,

argdescr->AddDefaultKey

,

argdescr->AddDefaultKey(

,

,

,

argdescr->AddOptionalKey(

,

,

,

argdescr->AddOptionalKey(

,

,

,

->

(kDirDefault)

->

(kDirAntisense)

argdescr->SetConstraint(

, constrain_direction);

string::const_iterator ie = m8.end(), i0 = m8.begin(), i1 = i0;

(i1 != ie && *i1 !=

) ++i1;

string::const_iterator i2 = ++i1;

(i2 != ie && *i2 !=

) ++i2;

(find(i0, i1,

) == i1) {

strid = rv->GetQueryId()->GetSeqIdString(

);

rv->SetQueryId(seqid);

(find(i1, i2,

) == i2) {

strid = rv->GetSubjId()->GetSeqIdString(

);

rv->SetSubjId(seqid);

errmsg =

(

) + m8;

hitrefs_pair->resize(0);

dim = hitrefs.size();

&& hitrefs[

]->GetSubjId()->Match(*subj) )

= hitref->GetQueryId();

subj = hitref->GetSubjId();

ifs.getline(

,

,

);

(pos1 == pos0)

;

(

[0] ==

)

;

* p =

;

(*p ==

|| *p ==

) ++p;

(*p == 0)

;

(

.IsNull()) {

= hit->GetQueryId();

subj = hit->GetSubjId();

(hit->GetQueryStrand() ==

) {

(hit->GetSubjStop() == hit->GetSubjStart()) {

(hit->GetQueryId()->Match(*

) ==

||

hit->GetSubjId()->Match(*subj) ==

) {

(;

< pending_size; ++

) {

(h->GetQueryId()->Match(*

) ==

||

h->GetSubjId()->Match(*subj) ==

) {

hitrefs->resize(

);

hitrefs->size() > 0;

(phitrefs->empty())

;

;

phitrefs->push_back(h);

(!hitrefs_next.empty()) {

hitrefs.resize(hitrefs_next.size());

(hitrefs_next.begin(), hitrefs_next.end(), hitrefs.begin());

hitrefs_next.clear();

(smax !=

) {

(!hitrefs_next.empty()

&& hitrefs.front()->GetSubjStrand() == hitrefs_next.front()->GetSubjStrand()

&& hitrefs.front()->GetQueryId()->Match(*(hitrefs_next.front()->GetQueryId()))

&& hitrefs.front()->GetSubjId()->Match(*(hitrefs_next.front()->GetSubjId())))

hitrefs.back()->GetSubjMin());

hitrefs_next.back()->GetSubjMin());

hitrefs.back()->GetSubjMax());

hitrefs_next.back()->GetSubjMax());

( max1 > min1 && min2 < max1 ) {

ostr <<

<<hitrefs.front()->GetQueryId()->AsFastaString()

<<

<<hitrefs.front()->GetSubjId()->AsFastaString()

<<

<<

<< min1+1 <<

<< max1+1 <<

<<

<< min2+1 <<

<< max2+1 <<

;

(hitrefs.front()->GetSubjStart() < hitrefs_next.front()->GetSubjStart()) {

*psubj_min = smin !=

? smin: 0;

*psubj_max =

(hitrefs_next.front()->GetSubjMin(),

hitrefs_next.back()->GetSubjMin());

smin =

(hitrefs.front()->GetSubjMax(),

hitrefs.back()->GetSubjMax());

*psubj_min =

(hitrefs_next.front()->GetSubjMax(),

hitrefs_next.back()->GetSubjMax());

smax =

(hitrefs.front()->GetSubjMin(),

hitrefs.back()->GetSubjMin());

!hitrefs.empty();

TCompartment::eStatus_Ok: {

<<

<<

->GetSeqIdString(

)

<<

<< subj->GetSeqIdString(

)

TCompartment::eStatus_Error: {

<<

<<

->GetSeqIdString(

)

<<

<< subj->GetSeqIdString(

)

TCompartment::eStatus_Empty:

);

(blast_options_handle->

() ==

) {

);

blast_options_handle;

lds_db_dir = fasta_dir;

fds = fasta_dir.size();

(fds > 0 && fasta_dir[fds-1] != sep) {

lds_db_dir +=

;

scope->AddTopLevelSeqEntry(*se);

( args[

] && args[

] ) {

);

( args[

] && args[

] ) {

);

is_mklds = args[

];

is_hits = args[

];

is_query = args[

] || args[

];

is_subj = args[

] || args[

];

is_comps = args[

];

use_disc_megablast (args[

]);

fa_dir = args[

].AsString();

curdirsize = curdir.size();

(curdirsize && curdir[curdirsize-1] != sep) {

fa_dir = curdir + fa_dir;

dir(lds_db_dir);

(is_query && is_subj && !(is_hits || is_comps)) {

(is_hits && !(is_comps ||is_query || is_subj)) {

(is_comps && !(is_hits ||is_query || is_subj)) {

);

= args[

]? & args[

].AsOutputFile():

;

= args[

]? & args[

].AsOutputFile():

;

(args[

]) {

vector<string> TDbs;

(args[

].

()) {

blastdbstr = args[

].AsString();

<<

<< priority <<

);

(args[

].

()) {

ldsdbstr = args[

].AsString();

fasta_dir = *

;

(

<<

<< db <<

<< priority <<

);

(args[

]) {

}

(args[

]) {

& id_list = args[

].AsString();

);

(args[

]) {

}

(args[

]) {

& id_list = args[

].AsString();

);

(run_mode ==

) {

& hit_stream = args[

].AsInputFile();

(run_mode ==

) {

& hit_stream (args[

].AsInputFile());

(

(hit_stream, &hitrefs, &subj_min, &subj_max) ) {

(hitrefs.front()->GetScore() > 0) {

);

cout <<

<< endl;

phitrefs->reserve(100);

seqloc_query->

().Assign(*seqid_query);

seqloc_subj->

().Assign(*seqid_subj);

((*ii)->IsSet()) {

(hitref->GetQueryStrand() ==

) {

hitref->FlipStrands();

phitrefs->push_back(hitref);

psplign_results->push_back(ac);

top_matches (0);

matches (0), nc_count(0);

CSplign::TSegments::const_iterator

;

dnr [] = {0, 0, 0};

acc [] = {0, 0, 0};

exon_count (0);

* p (jj->m_details.data()), * pe (p +jj->m_details.size());

(; p != pe; ++p) {

(

== 0) ++matches;

(

> 0) matches +=

;

=

* 10 + *p -

;

(

== 0) ++matches;

(

> 0) matches +=

;

(exon_count > 0) {

(jj->m_annot[2] ==

) {

acc[0] = jj->m_annot[0];

acc[1] = jj->m_annot[1];

p = jj->m_annot.data();

(*p++ !=

);

(matches > top_matches) {

top_matches = matches;

:

;

:

;

:

;

:

;

raw_hits (!args[

]);

(hitrefs.size() == 0) {

(hitrefs.front()->GetScore() < 0) {

(args[

].

()) {

mask_ranges_arg = args[

].AsString();

list<string> range_strs;

(list<string>, range_iter, range_strs) {

list<string> bound_strs;

Curr(NStr::StringToNumeric<TSeqPos>(bound_strs.front())-1,

NStr::StringToNumeric<TSeqPos>(bound_strs.back())-1);

(qidh && !MaskRanges.

()) {

subj (hitrefs.front()->GetSubjId());

strand (args[

].AsString());

(strand == kDirDefault) {

strand = (args[

].AsString() ==

)? kDirAuto: kDirBoth;

(strand == kDirSense) {

(raw_hits, &hitrefs, smin, smax, &splign_results);

(strand == kDirAntisense) {

(raw_hits, &hitrefs, smin, smax, &splign_results);

(strand == kDirBoth) {

hits0.push_back(h1);

mid (1);

mid_plus, mid_minus;

(raw_hits, &hitrefs, smin, smax, &splign_results);

(raw_hits, &hits0, smin, smax, &splign_results);

mid =

(mid_plus, mid_minus);

hits0.push_back(h1);

orf_sense (orfs.first.second - orfs.first.first);

orf_antisense (orfs.second.first - orfs.second.second);

sense_first (orf_sense >= orf_antisense);

mid (1);

mid_first, mid_second;

(raw_hits, &hitrefs, smin, smax, &splign_results);

polya_found (

);

(nc_count == 0) {

reverse (

.begin(),

.end());

polya_found = (0 < polya && polya <

.size());

(nc_count > 0 || polya_found) {

(raw_hits, &hits0, smin, smax, &splign_results);

mid =

(mid_first, mid_second);

(

argc,

* argv[])

rv (

().AppMain(argc, argv));

User-defined methods of the data storage class.

User-defined methods of the data storage class.

Data loader implementation that uses the blast databases.

Declares the CBl2Seq (BLAST 2 Sequences) class.

vector< CRef< objects::CSeq_align_set > > TSeqAlignVector

Vector of Seq-align-sets.

@ eMegablast

Nucl-Nucl (traditional megablast)

@ eDiscMegablast

Nucl-Nucl using discontiguous megablast.

void transform(Container &c, UnaryFunction *op)

Runs the BLAST algorithm between 2 sequences.

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, const string &dbname="nr", const EDbType dbtype=eUnknown, bool use_fixed_size_slices=true, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

EDbType

Describes the type of blast database to use.

@ eNucleotide

nucleotide database

@ eProtein

protein database

@ eUnknown

protein is attempted first, then nucleotide

Encapsulates ALL the BLAST algorithm's options.

Base class for reading FASTA sequences.

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CReader *reader=0, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

Argument-less loader - for compatibility only, unusable.

Class for managing LDS2 database and related data files.

void AddDataDir(const string &data_dir, EDirMode mode=eDir_Recurse)

Add data directory.

void UpdateData(void)

Rescan all indexed files, check for modifications, update the database.

@ eDir_Recurse

Automatically scan sub-directories (default).

Simple implementation of ILineReader for regions of memory (such as memory-mapped files).

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

void AddScore(CScope &scope, CSeq_align &align, CSeq_align::EScoreType score)

@ eScore_ConsensusSplices

CRef< blast::CBlastOptionsHandle > x_SetupBlastOptions(bool cross)

CSplign::THitRefs THitRefs

static THitRef s_ReadBlastHit(const string &m8)

bool x_GetNextComp(istream &ifs, THitRefs *hitrefs, THit::TCoord *psubj_min, THit::TCoord *psubj_max)

bool x_GetNextPair(istream &ifs, THitRefs *hitrefs)

CRef< objects::CSeq_id > x_ReadFastaSetId(const CArgValue &argval, CRef< objects::CScope >)

void x_RunSplign(bool raw_hits, THitRefs *phitrefs, THit::TCoord smin, THit::TCoord smax, CSplign::TResults *psplign_results)

CNcbiOstream * m_logstream

blast::EProgram m_BlastProgram

virtual void Init()

Initialize the application.

CRef< blast::CBlastOptionsHandle > m_BlastOptionsHandle

CRef< CSplignFormatter > m_Formatter

virtual int Run()

Run the application.

void x_LogCompartmentStatus(const THit::TId &query, const THit::TId &subj, const CSplign::SAlignedCompartment &ac)

void x_GetBl2SeqHits(CRef< objects::CSeq_id > seqid_query, CRef< objects::CSeq_id > seqid_subj, CRef< objects::CScope > scope, THitRefs *phitrefs)

void x_ProcessPair(THitRefs &hitrefs, const CArgs &args, THit::TCoord smin=0, THit::TCoord smax=0)

CRef< objects::CObjectManager > m_ObjMgr

static void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup core splign argument descriptions for the application.

static void ArgsToSplign(CSplign *splign, const CArgs &args)

Translate command line arguments into splign algorithm core settings.

CRef< objects::CSeq_align_set > AsSeqAlignSet(const CSplign::TResults *results=0, int flags=eAF_SplicedSegWithParts) const

Format alignment as a seq-align-set.

void SetSeqIds(CConstRef< objects::CSeq_id > id1, CConstRef< objects::CSeq_id > id2)

string AsExonTable(const CSplign::TResults *results=0, int flags=eTF_None) const

string AsAlignmentText(CRef< objects::CScope > scope, const CSplign::TResults *results=0, size_t line_width=80, int segnum=-1) const

Format alignment as plain text.

@ eAF_SplicedSegWithParts

CSplign is the central library object for computing spliced cDNA-to-genomic alignments.

void Run(THitRefs *hitrefs)

void SetHardMaskRanges(objects::CSeq_id_Handle idh, const TSeqRangeColl &mask_ranges)

CRef< objects::CScope > & SetScope(void)

void SetStrand(bool strand)

const TResults & GetResult(void) const

bool AlignSingleCompartment(THitRefs *hitrefs, THit::TCoord range_left, THit::TCoord range_right, SAlignedCompartment *result)

static CVersionAPI & s_GetVersion(void)

Retrieve the library's version object.

CRef< objects::CScope > GetScope(void) const

Access the scope object that the library will use to retrieve the sequences.

void SetStartModelId(size_t model_id)

size_t GetNextModelId(void) const

vector< SAlignedCompartment > TResults

vector< THitRef > THitRefs

static size_t s_TestPolyA(const char *seq, size_t dim, size_t cds_stop=0)

TOrfPair GetCds(const THit::TId &id, const vector< char > *seq_data=0)

pair< TOrf, TOrf > TOrfPair

Simple implementation of ILineReader for i(o)streams.

Include a standard set of the NCBI C++ Toolkit most basic headers.

Operators to edit gaps in sequences.

static const char * str(char *buf, int n)

static bool s_IsConsensusSplice(const char *donor, const char *acceptor, bool semi_as_cons=false)

static CBlastOptionsHandle * Create(EProgram program, EAPILocality locality=CBlastOptions::eLocal)

Creates an options handle object configured with default options for the requested program,...

CBlastOptions & SetOptions()

Returns a reference to the internal options class which this object is a handle for.

virtual TSeqAlignVector Run()

Perform BLAST search Assuming N queries and M subjects, the structure of the returned vector is as fo...

bool Validate() const

Validate the options contained in this object.

CBlastOptionsHandle & SetOptionsHandle()

Set the options handle.

void SetMaskAtHash(bool val=true)

void SetDustFiltering(bool val=true)

virtual void SetDefaults()

Resets the state of the object to all default values.

void SetFullVersion(CRef< CVersionAPI > version)

Set version data for the program.

void HideStdArgs(THideStdArgs hide_mask)

Set the hide mask for the Hide Std Flags.

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

#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.

const CNcbiArguments & GetArguments(void) const

Get the application's cached unprocessed command-line arguments.

@ fHideXmlHelp

Hide XML help description.

@ fHideLogfile

Hide log file description.

@ fHideFullHelp

Hide full help description.

@ fHideFullVersion

Hide full version description.

@ fHideDryRun

Hide dryrun description.

@ fHideConffile

Hide configuration file description.

@ fHideHelp

Hide help description.

@ fHideVersion

Hide version description.

@ eTakeOwnership

An object can take ownership of another.

virtual const string & AsString(void) const =0

Get the argument's string value.

virtual CNcbiIstream & AsInputFile(TFileFlags flags=0) const =0

Get the argument as an input file stream.

CArgAllow_Strings * Allow(const string &value)

Add allowed string values.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

@ eInteger

Convertible into an integer number (int or Int8)

#define ERR_POST(message)

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

#define LOG_POST(message)

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

@ eDiag_Fatal

Fatal error – guarantees exit(or abort)

#define NCBI_THROW(exception_class, err_code, message)

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

string ReportAll(TDiagPostFlags flags=eDPF_Exception) const

Report all exceptions.

#define NCBI_THROW2(exception_class, err_code, message, extra)

Throw exception with extra parameter.

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 bool IsAbsolutePath(const string &path)

Check if a "path" is absolute for the current OS.

static char GetPathSeparator(void)

Get path separator symbol specific for the current platform.

static string ConcatPath(const string &first, const string &second)

Concatenate two parts of the path for the current OS.

bool Create(TCreateFlags flags=fCreate_Default) const

Create the directory using "dirname" passed in the constructor.

static string GetCwd(void)

Get the current working directory.

#define MSerial_AsnText

I/O stream manipulators –.

virtual CRef< CSeq_entry > ReadOneSeq(ILineErrorListener *pMessageListener=nullptr)

Read a single effective sequence, which may turn out to be a segmented set.

@ fAssumeNuc

Assume nucs unless accns indicate otherwise.

@ fOneSeq

Just read the first sequence found.

static SIZE_TYPE ParseFastaIds(CBioseq::TId &ids, const CTempString &s, bool allow_partial_failure=false)

Parse an entire set of |-delimited FASTA-style IDs, appending the results to IDS.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

TObjectType * GetNonNullPointer(void)

Get pointer value and throw a null pointer exception if pointer is null.

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

CRef< C > Ref(C *object)

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

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define USING_SCOPE(ns)

Use the specified namespace.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

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

Check if a string starts with a specified prefix value.

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

Truncate whitespace in a string.

@ eNocase

Case insensitive compare.

C::value_type FindBestChoice(const C &container, F score_func)

Find the best choice (lowest score) for values in a container.

Tdata & Set(void)

Assign a value to data member.

list< CRef< CSeq_align > > Tdata

const TSeq & GetSeq(void) const

Get the variant data.

const TId & GetId(void) const

Get the Id member data.

list< CRef< CSeq_id > > TId

Main class to perform a BLAST search on the local machine.

Declares class which provides internal BLAST database representations to the internal BLAST APIs.

vector< CSeq_align const * >::const_iterator TIterator

const string version

version string

#define GetProgramName

Avoid name clash with the NCBI C Toolkit.

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...

static const float kUndef

string GetLdsDbDir(const string &fasta_dir)

void ReadCompartment(istream &istr, CSplign::THitRefs *phitrefs)

size_t GetNonConsensusSpliceCount(const CSplign::TResults &splign_results)

int main(int argc, const char *argv[])

const char kSplignLdsDb[]

ECompartmentStatus m_Status

Structure to represent a single sequence to be fed to BLAST.

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