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NCBI C++ ToolKit: src/objtools/blast/seqdb_reader/seqdbalias.hpp Source File

m_NodeNames.resize(4);

(

=0;

<m_Count;

++) {

(m_NodeNames[

] == name) {

(m_NodeNames.size() == m_Count) {

m_NodeNames.resize(m_NodeNames.size() * 2);

m_NodeNames[m_Count++].Assign(name.

());

(x_FindBlastDBPath(

.GetPathS(),

resolved.

(resolved_str);

(x_FindBlastDBPath(

.GetBasePathS(),

resolved.

(resolved_str);

x_FindBlastDBPath(

&

,

x_ReadAliasSetFile(

& group_fname,

& name_list,

FindVolumePaths(vector<string> & vols, vector<string> * alias,

recursive)

;

NeedTotalsScan(

& volset)

;

CompleteAliasFileValues(

& volset);

ComputeMasks(

& has_filters);

GetMaskList(vector <string> & mask_list);

GetOidMaskType(

& volset)

;

x_Tokenize(

& dbnames);

& name_list,

expand_links =

);

m_VolumeNames;

(vector<string> & vols, vector<string> * alias,

recursive)

vols = m_VolumeNames;

*alias = m_AliasNames;

m_Node->FindVolumePaths(vols, alias, recursive);

NeedTotalsScan(

& volset)

;

m_HasFilters;

GetAliasFileValues(TAliasFileValues & afv,

(m_Node->HasGiMask());

m_Node->GetMaskList(mask_list);

GetOidMaskType(

& volset)

;

m_Node->ComputeMasks(m_HasFilters);

CSeqDBAliasSets m_AliasSets

Combined alias files.

int m_MembBit

Membership bit.

bool HasGiMask() const

Is the top node alias file associated with Gi based masks?

TSeqDBAliasFileValues TAliasFileValues

Import type to allow shorter name.

bool m_HasTitle

True if we have the database title.

bool m_HasFilters

Are there filters for this database?

vector< string > m_AliasNames

The cached output of the topmost node's FindVolumePaths(recursive).

Int4 m_MinLength

Shortest sequence length.

void x_ComputeMasks()

Compute filtering options for all volumes.

bool m_IsProtein

True if this is a protein database.

void GetMaskList(vector< string > &mask_list)

Get Gi-based Mask Names From Alias Files.

Int8 m_TotalLength

Total length.

Int8 m_NumOIDs

Number of OIDs.

Int8 m_NumSeqs

Number of sequences.

int m_NumSeqsStats

Number of sequences for statistics purposes.

CRef< CSeqDB_FilterTree > m_TopTree

Filter tree representing all alias file filtering.

int m_NeedTotalsScan

1 if we need a totals scan, 0 if not, -1 if not known.

void FindVolumePaths(vector< string > &vols, vector< string > *alias, bool recursive) const

Find the base names of volumes.

CSeqDBAliasFile(const CSeqDBAliasFile &)

Disable copy constructor.

int m_OidMaskType

Oid Mask Type.

bool HasFilters()

Check if any volume filtering exists.

Int8 m_VolumeLength

Total length ignoring filtering.

const vector< string > & GetVolumeNames() const

Get the list of volume names.

string m_Title

Database title.

CRef< CSeqDBAliasNode > m_Node

This is the alias node tree's "artificial" topmost node, which aggregates the user provided database ...

vector< string > m_VolumeNames

The cached output of the topmost node's FindVolumePaths(recursive).

Int8 m_TotalLengthStats

Total length for statistics purposes.

TVolNames m_VolNames

Set of volume names associated with this node.

vector< bool > m_SkipLocal

Should we skip local DB search for this DBLIST?

map< string, string > TVarList

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

vector< CRef< CSeqDB_AliasMask > > m_NodeMasks

Mask objects for this node.

vector< CSeqDB_BasePath > TVolNames

Type used to store a set of volume names for each node.

bool m_HasGiMask

Do we have Gi masks for the top node? (only applicable to the top node)

bool HasGiMask() const

Is the top node alias file associated with Gi based masks?

CSeqDBAliasNode(const CSeqDBAliasNode &)

Disable copy constructor.

CSeqDB_DirName m_DBPath

The common prefix for the DB paths.

vector< CSeqDB_BasePath > m_DBList

Tokenized version of DBLIST.

CSeqDBAtlas & m_Atlas

The memory management layer for this SeqDB instance.

TVarList m_Values

List of KEY/VALUE pairs from this alias file.

TSeqDBAliasFileValues TAliasFileValues

Import type to allow shorter name.

TSubNodeList m_SubNodes

List of subnodes contained by this node.

vector< CRef< CSeqDBAliasNode > > TSubNodeList

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

bool m_ExpandLinks

Do not expand link when resolving paths.

void SetMasks(CSeqDBVolSet &volset)

Set filtering options for all volumes.

CSeqDBAliasSets & m_AliasSets

Combined alias files.

CSeqDB_Path m_ThisName

Filename of this alias file.

bool FindBlastDBPath(const CSeqDB_Path &dbname, CSeqDB_Path &resolved)

Find a file given a partial path and name.

bool FindBlastDBPath(const CSeqDB_BasePath &dbname, char dbtype, CSeqDB_BasePath &resolved)

Find a file given a partial path and name.

map< string, string > TAliasGroup

Aggregated alias file - maps filename to file contents.

CSeqDBAliasSets(const CSeqDBAliasSets &)

Disable copy constructor.

CSeqDBAtlas & m_Atlas

Reference to the memory management layer.

map< string, TAliasGroup > TAliasGroupMap

Full index filename to aggregated alias file.

CSeqDBAliasSets(CSeqDBAtlas &atlas)

Constructor.

map< string, string > m_PathLookup

Caches results of FindBlastDBPath.

TAliasGroupMap m_Groups

Alias groups.

bool Exists(const CSeqDB_Path &name)

Check whether the stack contains the specified string.

void Push(const CSeqDB_Path &name)

Push a new string onto to the stack.

vector< CSeqDB_Path > m_NodeNames

List of node names.

CSeqDBAliasStack()

Constructor.

CSeqDBAliasStack(const CSeqDBAliasStack &)

Disable copy constructor.

void Pop()

Remove the top element of the stack.

unsigned Size()

Return the number of in-use elements.

unsigned m_Count

Number of in-use node names.

CSeqDBAliasExplorer class.

virtual bool Explore(const TVarList &values)=0

This will be called with the map of key/value pairs associated with this alias file.

map< string, string > TVarList

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

virtual void Accumulate(const CSeqDBVol &volumes)=0

This will be called with each CVolume that is in the alias file tree structure (in order of traversal...

virtual ~CSeqDB_AliasExplorer()

Destructor.

virtual void AddString(const string &)=0

This will be called with the value associated with this key in the alias file.

virtual void Accumulate(const CSeqDBVol &)=0

This will be called with each CVolume that is in the alias file tree structure (in order of traversal...

virtual const char * GetFileKey() const =0

Override to provide the alias file KEY name for the type of summary data you want to gather,...

virtual ~CSeqDB_AliasWalker()

Destructor.

void Assign(const CSeqDB_Substring &sub)

Assign the value from a substring.

Tree of nodes describing filtering of database sequences.

const string & GetPathS() const

Get the path as a string.

void Assign(const string &path)

Assigns the provided value to this path.

static unsigned char depth[2 *(256+1+29)+1]

NCBI_XOBJUTIL_EXPORT string GetTitle(const CBioseq_Handle &hnd, TGetTitleFlags flags=0)

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

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

char * dbname(DBPROCESS *dbproc)

Get name of current database.

static const char * x_ReadLine(const char *path, char *line, size_t size)

Defines BLAST database access classes.

Defines exception class and several constants for SeqDB.

File access objects for CSeqDB.

This file defines several SeqDB utility functions related to byte order and file system portability.

The SeqDB oid filtering layer.

Defines database volume access classes.

Manages a set of database volumes.

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