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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/blastdbcheck_8cpp_source.html below:

NCBI C++ ToolKit: src/app/blastdb/blastdbcheck.cpp Source File

(

);

(

);

(

);

:

;

(

= 0;

<=

;

++) {

arg_desc->SetUsageContext(

().GetProgramBasename(),

);

arg_desc->SetCurrentGroup(

);

arg_desc->AddOptionalKey

,

arg_desc->AddDefaultKey(

,

,

,

,

,

));

arg_desc->AddOptionalKey

(

,

,

,

);

arg_desc->SetCurrentGroup(

);

arg_desc->AddOptionalKey

(

,

,

,

arg_desc->AddDefaultKey

(

,

,

arg_desc->SetConstraint(

,

(

)

,

));

arg_desc->SetCurrentGroup(

);

);

arg_desc->AddOptionalKey

(

,

,

,

arg_desc->AddOptionalKey

(

,

,

,

arg_desc->AddOptionalKey

(

,

,

,

);

);

(

,

);

(

,

);

tot_faults +=

.DoTest(db, seen);

num_failures = 0;

nv = vols.size();

(db,

) <<

<< endl;

(db,

) <<

<< endl;

(vector<string>, vol, vols) {

legacy_name.

(

);

(legacy_name.

((*entry)->GetExt())) {

(db,

) <<

<< (*entry)->GetPath() <<

((*entry)->IsFile() && (

((*entry)->GetPath()).

() <= 0)) {

(db,

) <<

<< (*entry)->GetPath() <<

<< endl;

((nseq > noid) || ((! tl) != (! noid)) || ((! vl) && tl)) {

(db,

) <<

<< endl;

(hs !=

) {

(db,

) <<

<< hs <<

<< endl;

}

(exception &e) {

(db,

) <<

<< endl;

(seen.

(oid) != seen.

()) {

list< CRef<CSeq_id> > seqids = db.

(oid);

* p =

;

((length == 0) || (p ==

)) {

runtime_error(

);

runtime_error(

);

align_format;

runtime_error(

);

where =

;

((! db.

(**iter, oid2)) || (oid != oid2)) {

<<

<< (**iter).AsFastaString();

}

(oid != oid2) {

<<

<< oid

<<

<< (**iter).AsFastaString();

details <<

<< where

<<

<< e.

() << endl;

(exception & e) {

<<

<< oid

<<

<< e.

() << endl;

minutiae <<

<< oid <<

<< (rv ?

:

) << endl;

(db,

) <<

<< m_N <<

<< endl;

(!

(db, seen, oid)) {

(db,

) <<

<< endl;

(

= 0;

< m_N;) {

oid = m_Rng.GetRand(0,

-1);

<<

<< oids.

()

<<

<< endl;

(!

(db, seen, *iter)) {

(db,

) <<

<< m_N <<

<< endl;

num_failures = 0;

dir(

.GetDir());

base(

.GetBase());

ext(

.GetExt());

(name,

) <<

<< endl;

++num_failures;

(

.GetLength() <= 0) {

(name,

) <<

<< endl;

++num_failures;

oidlist, gilist, nseq, mem_bit, first_oid, last_oid, maxoid, maxlen;

oidlist=gilist=nseq=mem_bit=first_oid=last_oid=maxoid=maxlen=-1;

vector <string> tokens;

(tokens.size() <= 1) {

(name,

) <<

<< tokens[0] << endl;

(tokens[0] ==

) {

}

(tokens[0] ==

) {

}

(tokens[0] ==

) {

}

(tokens[0] ==

) {

num_failures += x_CheckFile(name, dir, tokens);

}

(tokens[0] ==

) {

num_failures += x_CheckFile(name, dir, tokens);

}

(tokens[0] ==

) {

num_failures += x_CheckFile(name, dir, tokens);

}

(tokens[0] ==

) {

num_failures += x_CheckNumber(name, tokens, nseq);

}

(tokens[0] ==

) {

num_failures += x_CheckNumber8(name, tokens, length);

}

(tokens[0] ==

) {

num_failures += x_CheckNumber(name, tokens, mem_bit);

}

(tokens[0] ==

) {

num_failures += x_CheckNumber(name, tokens, first_oid);

}

(tokens[0] ==

) {

num_failures += x_CheckNumber(name, tokens, last_oid);

}

(tokens[0] ==

) {

num_failures += x_CheckNumber(name, tokens, maxoid);

}

(tokens[0] ==

) {

num_failures += x_CheckNumber(name, tokens, maxlen);

}

(tokens[0] ==

) {

}

(tokens[0] ==

) {

(name,

) <<

<< tokens[0] << endl;

}

(!line.

());

((first_oid+1)*(last_oid+1)==0) {

(first_oid+last_oid != -2) {

(name,

) <<

<< endl;

}

((nseq+1)*(nseq + first_oid -last_oid -1)!=0) {

(name,

) <<

<<

<< endl;

(oidlist + gilist >=0) {

(name,

) <<

<<

<< endl;

(oidlist!=-1 && (maxoid+1)*(length+1)*(nseq+1)==0) {

(name,

) <<

<<

<< endl;

}

(exception &e) {

(name,

) <<

<< endl;

ostream &

(

& name,

lvl)

(

&name,

&dir,

vector<string> &tokens)

num_failures = 0;

(

=1;

< tokens.size(); ++

) {

(tokens[0] ==

&&

.GetExt() !=

) {

(name,

) <<

<< tokens[

]

<<

<< endl;

(tokens[0] ==

&&

.GetExt() !=

) {

(name,

) <<

<< tokens[

]

<<

<< endl;

(name,

) <<

<< tokens[

]

<<

<< tokens[0]

<<

<< endl;

(

.GetLength() <=0) {

(name,

) <<

<< tokens[

]

<<

<< tokens[0]

<<

<< endl;

<<

<< tokens[0] << endl;

<<

<< tokens[0] << endl;

m_DbType (dbtype) { }

x_GetVolumeList(

vector <string> &dbs,

(vector<string>, iter, dbs) {

vector <string> paths;

vector <string> alias;

<<

<<

<< *iter <<

<< endl;

vlist.

(paths.begin(), paths.end());

alist.

(alias.begin(), alias.end());

tot_faults += x_GetVolumeList(dbs, seqtype, vol_list, ali_list);

total = vol_list.

(), passed = 0;

<<

<< total <<

<< endl;

m_Out.Log(

) <<

<< *iter << endl;

num_faults = action.

(*db, seen);

}

(exception &e) {

m_Out.Log(

) <<

<< *iter << endl;

m_Out.Log(

) << e.what() << endl;

(num_faults) tot_faults += num_faults;

(total == passed) {

<<

<< total <<

<< endl;

<<

<< (total-passed) <<

<< total <<

<< endl;

total = ali_list.

(), passed = 0;

<<

<< total <<

<< endl;

m_Out.Log(

) <<

<< *iter << endl;

num_faults = ali_test.

(*iter, seen);

(num_faults) tot_faults += num_faults;

(total == passed) {

<<

<< total <<

<< endl;

<<

<< (total-passed) <<

<< total <<

<< endl;

<<

<< tot_faults << endl;

(tot_faults == 0);

m_Recurse (recurse) { }

(vector<SSeqDBInitInfo>, iter, m_DBs) {

(iter->m_MoleculeType != stype)

;

vector <string> paths;

vector <string> alias;

<<

<<

<< iter->m_BlastDbName <<

<< endl;

vlist.

(paths.begin(), paths.end());

alist.

(alias.begin(), alias.end());

<<

<< endl;

m_DBs =

(m_Dir, m_DbType, m_Recurse,

);

total = prot_list.

() + nucl_list.

(), passed = 0;

<<

<< total <<

<< endl;

m_Out.Log(

) <<

<< *iter << endl;

num_faults = action.

(*db, seen);

}

(exception &e) {

m_Out.Log(

) <<

<< *iter << endl;

m_Out.Log(

) << e.what() << endl;

(num_faults) tot_faults += num_faults;

m_Out.Log(

) <<

<< *iter << endl;

num_faults = action.

(*db, seen);

}

(exception &e) {

m_Out.Log(

) <<

<< *iter << endl;

m_Out.Log(

) << e.what() << endl;

(num_faults) tot_faults += num_faults;

(total == passed) {

<<

<< total <<

<< endl;

<<

<< (total-passed) <<

<< total <<

<< endl;

total = ali_list.

(), passed = 0;

<<

<< total <<

<< endl;

m_Out.Log(

) <<

<< *iter << endl;

num_faults = ali_test.

(*iter, seen);

(num_faults) tot_faults += num_faults;

(total == passed) {

<<

<< total <<

<< endl;

<<

<< (total-passed) <<

<< total <<

<< endl;

<<

<< tot_faults << endl;

(tot_faults == 0);

x_GetHeader(

& db);

x_TestFreqRatios(

& db);

(x_GetHeader(db)) {

x_TestFreqRatios(db);

m_NumFailures;

m_Offsets.reserve(m_NumProfiles);

(

=0;

< m_NumProfiles;

++) {

(exception& e) {

(db,

) <<

(m_NumFailures == 0);

(db,

) <<

<< endl;

(db,

) <<

(

=0;

< m_NumProfiles;

++) {

(db,

) <<

<< endl;

(exception& e) {

(db,

) <<

<< endl;

(m_NumFailures == 0);

x_TestWeightedCounts(

& db);

x_TestObservations(

& db);

(x_GetHeader(db)) {

x_TestFreqRatios(db);

x_TestWeightedCounts(db);

x_TestObservations(db);

m_NumFailures;

(db,

) <<

<< endl;

(db,

) <<

(

=0;

< m_NumProfiles;

++) {

(db,

) <<

<< endl;

(exception& e) {

(db,

) <<

<< endl;

(m_NumFailures == 0);

(db,

) <<

<< endl;

(db,

) <<

(exception& e) {

(db,

) <<

<< endl;

(m_NumFailures == 0);

ostream*

= args[

] ? &args[

].AsOutputFile() : &cout;

= args[

].AsInteger();

(args[

]) {

<<

<< args[

].AsString() <<

;

<<

db(args[

] ? args[

].AsString() :

);

dir(args[

] ? args[

].AsString() :

);

dbtype(args[

].AsString());

recurse = !! args[

];

((db ==

) == (dir ==

)) {

<<

<< endl;

}

(db !=

) {

<<

<< (args[

] ?

:

) <<

<< endl;

<<

<< (args[

] ?

:

) <<

<< endl;

<<

<< (args[

] ?

:

) <<

<< endl;

default_set =

;

(args[

]) {

<<

<< endl;

default_set =

;

(args[

]) {

stride = args[

].HasValue() ? args[

].AsInteger() : 10000;

<<

<< stride <<

<< endl;

default_set =

;

(args[

]) {

random_sample = args[

].HasValue() ? args[

].AsInteger(): 200;

<<

<< random_sample <<

<< endl;

default_set =

;

(args[

]) {

end_amt = args[

].HasValue() ? args[

].AsInteger() : 200;

<<

<< end_amt

<<

<< end_amt <<

<< endl;

default_set =

;

random_sample = 200;

<<

<< random_sample <<

<< endl;

(args[

]) {

<<

<< endl;

status = okay ? 0 : 1;

(args[

].

()) {

(args[

].

()) {

(args[

].

()) {

(args[

].

()) {

(

argc,

* argv[])

Declares singleton objects to store the version and reference for the BLAST engine.

#define CATCH_ALL(exit_code)

Standard catch statement for all BLAST command line programs.

Interface for converting sources of sequence data into blast sequence input.

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

static string s_VerbosityText()

static string s_VerbosityString(int v)

int DoTest(const string &name, TSeen &)

int x_CheckNumber(const string &name, const vector< string > &tokens, int &n)

CAliasTest(CBlastDbCheckLog &log, int flags)

int x_CheckFile(const string &name, const string &dir, const vector< string > &tokens)

int x_CheckNumber8(const string &name, const vector< string > &tokens, Int8 &n)

ostream & Log(const string &name, int lvl)

static TTaxId GetTaxidForSeqid(const objects::CSeq_id &id, objects::CScope &scope)

return the tax id for a seqid

Class to constrain the values of an argument to those in between the values specified in the construc...

const CSeq_id * GetFirstId() const

TTaxId GetTaxId() const

Determine the tax-id for this bioseq.

CBlastDbCheckApplication: the main application class.

~CBlastDbCheckApplication()

CBlastUsageReport m_UsageReport

virtual void Init(void)

@inheritDoc

virtual int Run(void)

@inheritDoc

CBlastDbCheckApplication()

@inheritDoc

virtual void Exit(void)

@inheritDoc

CBlastDbCheckLog(ostream &outp, int max_level)

CNcbiOstrstream m_DevNull

CBlastDbCheckLog(const CBlastDbCheckLog &)

CBlastDbCheckLog & operator=(const CBlastDbCheckLog &)

Wrapper class to manage the BlastRPSInfo structure, as currently there aren't any allocation or deall...

void AddParam(EUsageParams p, int val)

Keeps track of the version of the BLAST engine in the NCBI C++ toolkit.

CDbTest(CBlastDbCheckLog &outp, string db, string dbtype)

virtual bool Test(CTestActionList &action)

int x_GetVolumeList(const vector< string > &dbs, CSeqDB::ESeqType stype, set< string > &vlist, set< string > &alist) const

vector< SSeqDBInitInfo > m_DBs

CDirTest(CBlastDbCheckLog &outp, string dir, string dbtype, int threads, bool recurse)

int x_GetVolumeList(CSeqDB::ESeqType stype, set< string > &vlist, set< string > &alist) const

virtual bool Test(CTestActionList &action)

CEndsTest(CBlastDbCheckLog &log, int n, int flags)

virtual int DoTest(CSeqDB &db, TSeen &seen)

int m_N

Test m_N elements from the start, m_N elements from the end.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

virtual int DoTest(CSeqDB &db, TSeen &seen)

CSampleTest(CBlastDbCheckLog &log, int n, int flags)

static void FindVolumePaths(const string &dbname, ESeqType seqtype, vector< string > &paths, vector< string > *alias_paths=NULL, bool recursive=true, bool expand_links=true)

Find volume paths.

Uint8 GetTotalLength() const

Returns the sum of the lengths of all available sequences.

int GetNumOIDs() const

Returns the size of the (possibly sparse) OID range.

Uint8 GetVolumeLength() const

Returns the sum of the lengths of all volumes.

const string & GetDBNameList() const

Get list of database names.

list< CRef< CSeq_id > > GetSeqIDs(int oid) const

Gets a list of sequence identifiers.

ESeqType

Sequence types (eUnknown tries protein, then nucleotide).

bool SeqidToOid(const CSeq_id &seqid, int &oid) const

Translate a Seq-id to any matching OID.

CRef< CBioseq > GetBioseq(int oid, TGi target_gi=ZERO_GI, const CSeq_id *target_seq_id=NULL) const

Get a CBioseq for a sequence.

void RetSequence(const char **buffer) const

Returns any resources associated with the sequence.

string GetTitle() const

Returns the database title.

int GetNumSeqs() const

Returns the number of sequences available.

int GetSequence(int oid, const char **buffer) const

Get a pointer to raw sequence data.

bool CheckOrFindOID(int &next_oid) const

Find an included OID, incrementing next_oid if necessary.

string GetDate() const

Returns the construction date of the database.

static void GetTaxInfo(TTaxId taxid, SSeqDBTaxInfo &info)

Get taxonomy information.

Simple implementation of ILineReader for i(o)streams.

virtual int DoTest(CSeqDB &db, TSeen &seen)

CStrideTest(CBlastDbCheckLog &log, int n, int flags)

int DoTests(CSeqDB &db, TSeen &seen)

vector< CRef< CTestAction > > m_List

void Add(CTestAction *action)

CTestAction(CBlastDbCheckLog &log, const string &nm, int flags)

ostream & Log(CSeqDB &db, int lvl)

virtual int DoTest(CSeqDB &db, TSeen &seen)=0

bool TestOID(CSeqDB &db, TSeen &seen, int oid)

ostream & LogMore(int lvl)

CTestData(CBlastDbCheckLog &outp, string dbtype)

virtual bool Test(CTestActionList &action)=0

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

void Print(const CCompactSAMApplication::AlignInfo &ai)

#define test(a, b, c, d, e)

static void Test(const char *bind1, SQLSMALLINT type1, const char *bind2, SQLSMALLINT type2)

static SQLCHAR output[256]

static DbTestEntry * tests

@ fFrequenciesFile

Open residue frequencies file.

@ fFreqRatiosFile

Open file with frequency ratios.

@ fObservationsFile

Open file with numbers of independent observations.

@ fRpsBlast

Flags set for RPS-BLAST.

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.

int AppMain(int argc, const char *const *argv, const char *const *envp=0, EAppDiagStream diag=eDS_Default, const char *conf=NcbiEmptyCStr, const string &name=NcbiEmptyString)

Main function (entry point) for the NCBI application.

CVersionInfo GetVersion(void) const

Get the program version information.

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.

@ fHideFullVersion

Hide full version description.

@ fHideDryRun

Hide dryrun description.

@ fHideConffile

Hide configuration file description.

@ eExcludes

One argument excludes another.

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

@ eInteger

Convertible into an integer number (int or Int8)

void SetDiagPostPrefix(const char *prefix)

Specify a string to prefix all subsequent error postings with.

void SetDiagStream(CNcbiOstream *os, bool quick_flush=true, FDiagCleanup cleanup=0, void *cleanup_data=0, const string &stream_name="")

Set diagnostic stream.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

TEntries GetEntries(const string &mask=kEmptyStr, TGetEntriesFlags flags=0) const

Get directory entries based on the specified "mask".

string GetDir(EIfEmptyPath mode=eIfEmptyPath_Current) const

Get the directory component for this directory entry.

Int8 GetLength(void) const

Get size of file.

static string MakePath(const string &dir=kEmptyStr, const string &base=kEmptyStr, const string &ext=kEmptyStr)

Assemble a path from basic components.

string GetName(void) const

Get the base entry name with extension (if any).

bool AtEOF(void) const

Indicates (negatively) whether there is any more input.

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

int32_t Int4

4-byte (32-bit) signed integer

int64_t Int8

8-byte (64-bit) signed integer

uint64_t Uint8

8-byte (64-bit) unsigned integer

Uint4 TValue

Type of the generated integer value and/or the seed value.

bool IsEnabled(void)

Indicates whether application usage statistics collection is enabled for a current reporter instance.

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 Int8 StringToInt8(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to Int8.

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 IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

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

Check if a string starts with a specified prefix value.

@ fSplit_Tokenize

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

double Elapsed(void) const

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

time_t GetTimeT(void) const

Get time in time_t format.

void Start(void)

Start the timer.

@ eCurrent

Use current time. See also CCurrentTime.

bool Match(CTempString str, NStr::ECase use_case=NStr::eCase) const

Match a string.

void Add(const string &mask)

Add an inclusion mask.

char * dbname(DBPROCESS *dbproc)

Get name of current database.

Lightweight interface for getting lines of data with minimal memory copying.

const string version

version string

Classes to match a string against a set of masks.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

#define GetArgs

Avoid preprocessor name clash with the NCBI C Toolkit.

Defines command line argument related classes.

Defines unified interface to application:

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

Declares auxiliary classes to manage RPS-BLAST related C-structures.

Defines BLAST database access classes.

CSeqDB::ESeqType ParseMoleculeTypeString(const string &str)

Convert a string to a CSeqDB ESeqType object.

vector< SSeqDBInitInfo > FindBlastDBs(const string &path, const string &dbtype, bool recurse, bool include_alias_files=false, bool remove_redundant_dbs=false)

Find BLAST DBs in the directory specified.

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

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

string scientific_name

Scientific name, such as "Aotus vociferans".

static wxAcceleratorEntry entries[3]

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