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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/vdbalias_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/blast/vdb/vdbalias.cpp Source File

192 void x_ResolveDBList

(vector<string> & dblist,

char

prot_nucl, vector<string> & vdb_list);

216 void x_AppendSubNode

(

const string

& node,

char

prot_nucl,

bool

isVDB);

254 static void s_Tokenize

(

const string

& dbnames, vector<string> & db_list)

256

vector <CSeqDB_Substring>

tmp

;

259 for

(

unsigned int i

=0;

tmp

.size();

++) {

261 tmp

[

].GetString(

);

263

db_list.push_back(

);

267 static string s_Join

(

const

vector<string> & list,

unsigned int

max_size)

273

join_str.reserve(max_size + 1);

274 for

(

unsigned int i

=0;

< list.size();

++)

279

join_str += list[

];

283

join_str.resize(join_str.size() -1);

290

: m_ThisName (

"-"

292

m_ExpandLinks(expand_links),

294

m_VerifyVDBs(verify_vdbs)

296

vector<string> name_list;

297

vector<string> vdb_list;

298 if

(name_str.empty()) {

317 for

(

= 0;

< dblist.size();

++) {

318 _TRACE

(

"Input File :"

+ dblist[

]);

325 _TRACE

(

"Local db path db :"

+ resolved_path);

331 _TRACE

(

"Local alias db :"

+ resolved_path);

340 _TRACE

(

"Blast Alias File :"

+ resolved_path);

347 _TRACE

(

"Blast db :"

+ resolved_path);

350 _TRACE

(

"VDBs :"

+ resolved_path);

351

vdblist.push_back(dblist[

]);

360 for

(

=0;

< vdblist.size();

++) {

363 string

vdb = vdblist[

];

369 _TRACE

(

"VDB Local Alias File :"

+ resolved_path);

377 if

(local_file.

Exists

()) {

381 _TRACE

(

"VDB Local File :"

+ resolved_path);

390 _TRACE

(

"VDB Alias File :"

+ resolved_path);

399 file

.DereferenceLink();

402 _TRACE

(

"VDB File (blast config) :"

+ resolved_path);

470 const char

* spacep = p;

472 while

((spacep < ep) && ((*spacep !=

' '

) && (*spacep !=

'\t'

)))

478 while

((spacep < ep) && ((*spacep ==

' '

) || (*spacep ==

'\t'

)))

482 while

((spacep < ep) && ((ep[-1] ==

' '

) || (ep[-1] ==

'\t'

)))

487 for

(

size_t i

= 0;

value

.size();

++) {

488 if

(

value

[

] ==

'\t'

) {

517

bp = (

char

*) aliasFile.

Map

();

522

ep = bp + aliasFile.

GetSize

();

526 string

name_s, value_s;

530 while

((p < ep) && (*p ==

' '

)) {

534 const char

* eolp = p;

566

m_DBPath(m_ThisName.FindDirName()),

567

m_ExpandLinks(expand_links),

569

m_VerifyVDBs(verify_vdbs)

575

vector<string> db_list;

576

vector<string> vdb_list;

578 if

(vdb_alias && !db_list.empty()) {

584 if

(!vdb_list.empty()) {

599

vector<string> & node_vdbs = (*node)->GetNodeVDBs();

600

vdbs.

insert

( node_vdbs.begin(), node_vdbs.end());

601

vector<string> & node_db_list = (*node)->GetNodeDBList();

602

db_alias.

insert

(node_db_list.begin(), node_db_list.end());

603

vector<string> & node_vdb_list = (*node)->GetNodeVDBList();

604

vdb_alias.

insert

(node_vdb_list.begin(), node_vdb_list.end());

615

(*node)->GetExpandedPaths( vdbs, db_alias, vdb_alias);

622

vector<string> & paths,

623

vector<string> * db_alias_list ,

624

vector<string> * vdb_alias_list,

629 char

prot_nucl = (isProtein) ?

'p'

'n'

;

638

paths.insert(paths.begin(), vdbs.

begin

(), vdbs.

end

());

642

paths.insert(paths.begin(), vdbs.

begin

(), vdbs.

end

());

643

paths.insert(paths.end(), vdb_alias.

begin

(), vdb_alias.

end

());

644

paths.insert(paths.end(), db_alias.

begin

(), db_alias.

end

());

647 if

(db_alias_list !=

NULL

) {

648

db_alias_list->clear();

649

db_alias_list->insert(db_alias_list->begin(),db_alias.

begin

(), db_alias.

end

());

651 if

(vdb_alias_list !=

NULL

) {

652

vdb_alias_list->clear();

653

vdb_alias_list->insert(vdb_alias_list->begin(),vdb_alias.

begin

(), vdb_alias.

end

());

660

vector<string> & vdb_list,

661 string

& blastdb_list,

664 char

prot_nucl = (isProtein) ?

'p'

'n'

;

668 CVDBAliasNode

node(input_list, prot_nucl,

true

, verify_vdbs);

673

vdb_list.insert(vdb_list.begin(), vdbs.

begin

(), vdbs.

end

());

CSeqDB_Substring GetDirNameSub() const

Get the directory name as a substring.

const string & GetPathS() const

Get the path as a string.

CVDBAliasNode(const string &name_list, char prot_nucl, bool expand_link, bool verify_vdbs)

Public Constructor.

void GetExpandedPaths(set< string > &vdbs, set< string > &db_alias, set< string > &vdb_alias)

map< string, string > TVarList

Type of set used for KEY/VALUE pairs within each node.

void x_ExpandAliases(char prot_nucl)

Expand a node of the alias node tree recursively.

vector< string > m_DBList

Alias Files from DBLIST.

CSeqDB_DirName m_DBPath

The common prefix for the DB paths.

void x_ReadLine(const char *bp, const char *ep, string &name_s, string &value_s)

Read one line of the alias file.

vector< string > & GetNodeVDBs()

vector< string > m_VDBNames

Set of vdb names associated with this node.

vector< CRef< CVDBAliasNode > > TSubNodeList

Type used to store the set of subnodes for this node.

CVDBAliasNode(const CVDBAliasNode &)

Disable copy constructor.

void x_ReadValues(const string &fn)

Read the alias file.

TVarList m_Values

List of KEY/VALUE pairs from this alias file.

vector< string > m_VDBList

Alias file from VDBLIST.

bool m_ExpandLinks

Do not expand link when resolving paths.

CSeqDB_Path m_ThisName

Filename of this alias file.

vector< string > & GetNodeDBList()

vector< string > & GetNodeVDBList()

void x_ResolveDBList(vector< string > &dblist, char prot_nucl, vector< string > &vdb_list)

Check for and resolve path for blast alias file(s)

void x_ResolveVDBList(const vector< string > &vdblist, char prot_nucl)

Resolve path for vdbs and vdb alias file(s)

void x_AppendSubNode(const string &node, char prot_nucl, bool isVDB)

Append a subnode to this alias node.

void GetNodePaths(set< string > &vdbs, set< string > &db_alias, set< string > &vdb_alias)

CVDBAliasNode & operator=(const CVDBAliasNode &)

Disable copy operator.

TSubNodeList m_SubNodes

List of subnodes contained by this node.

static void FindVDBPaths(const string &dbname, bool isProtein, vector< string > &paths, vector< string > *db_alias_list=NULL, vector< string > *vdb_alias_list=NULL, bool recursive=true, bool expand_links=true, bool verify_dbs=true)

Get the list of vdb names.

static void ProcessMixedDBsList(const string &input_list, bool isProtein, vector< string > &vdb_list, string &blastdb_list, bool verify_vdbs)

Process a list with mixed blast dbs and vdbs Expand all alais file to find and return vdbs with full ...

static void CheckVDBs(const vector< string > &vdbs)

Function to check a list of dbs if they can be opened Throw an exception if any of the db cannot be o...

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator end() const

The NCBI C++ standard methods for dealing with std::string.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define NCBI_THROW(exception_class, err_code, message)

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

size_t GetSize(void) const

Get length of the mapped region.

void * Map(TOffsetType offset=0, size_t length=0)

Map file.

void DereferenceLink(ENormalizePath normalize=eNormalizePath)

Dereference a link.

static char GetPathSeparator(void)

Get path separator symbol specific for the current platform.

const string & GetPath(void) const

Get entry path.

virtual bool Exists(void) const

Check existence of file.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

char * dbname(DBPROCESS *dbproc)

Get name of current database.

const GenericPointer< typename T::ValueType > T2 value

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

Defines exception class and several constants for SeqDB.

string SeqDB_ResolveDbPath(const string &filename)

Resolve a file path using SeqDB's path algorithms.

string SeqDB_ResolveDbPathNoExtension(const string &filename, char dbtype='-')

Resolve a file path using SeqDB's path algorithms.

File access objects for CSeqDB.

void SeqDB_SplitQuoted(const string &dbname, vector< CSeqDB_Substring > &dbs, bool keep_quote=false)

Combine and quote list of database names.

void SeqDB_CombinePath(const CSeqDB_Substring &path, const CSeqDB_Substring &file, const CSeqDB_Substring *extn, string &outp)

Combine a filesystem path and file name.

#define SEQDB_ISEOL(x)

Macro for EOL chars.

void s_SeqDB_QuickAssign(string &dst, const char *bp, const char *ep)

Higher Performance String Assignment.

void SeqDB_ConvertOSPath(string &dbs)

Change path delimiters to platform preferred kind in-place.

static string s_Join(const vector< string > &list, unsigned int max_size)

static void s_Tokenize(const string &dbnames, vector< string > &db_list)

static void s_SeqDB_ReadLine(const char *bp, const char *ep, string &name, string &value)

Parse a name-value pair.

Defines database alias file access classes.

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