embindex.c

Function embBtreeEmblKW

Extract keywords from an EMBL KW line

Synopsis

Prototype
void embBtreeEmblKW (
      const AjPStr kwline,
      AjPList kwlist,
      ajuint maxlen
);

TypeNameRead/WriteDescription
const AjPStrkwlineInputkeyword line
AjPListkwlistOutputlist of keywords
ajuintmaxlenInputmax keyword length
void RETURN

Input
kwline:(Input)keyword line
maxlen:(Input)max keyword length
Output
kwlist:(Output)list of keywords
Returns
void:No return value

Description

Extract keywords from an EMBL KW line

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function embBtreeEmblTX

Extract keywords from an EMBL OC or OS line

Synopsis

Prototype
void embBtreeEmblTX (
      const AjPStr txline,
      AjPList txlist,
      ajuint maxlen
);

TypeNameRead/WriteDescription
const AjPStrtxlineInputtaxonomy line
AjPListtxlistOutputlist of taxons
ajuintmaxlenInputmax taxon length
void RETURN

Input
txline:(Input)taxonomy line
maxlen:(Input)max taxon length
Output
txlist:(Output)list of taxons
Returns
void:No return value

Description

Extract keywords from an EMBL OC or OS line

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function embBtreeEmblAC

Extract accession numbers from an EMBL AC line

Synopsis

Prototype
void embBtreeEmblAC (
      const AjPStr acline,
      AjPList aclist
);

TypeNameRead/WriteDescription
const AjPStraclineInputAC line
AjPListaclistOutputlist of accession numbers
void RETURN

Input
acline:(Input)AC line
Output
aclist:(Output)list of accession numbers
Returns
void:No return value

Description

Extract accession numbers from an EMBL AC line

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function embBtreeEmblSV

Extract sequence version from an EMBL new format ID line

Synopsis

Prototype
void embBtreeEmblSV (
      const AjPStr idline,
      AjPList svlist
);

TypeNameRead/WriteDescription
const AjPStridlineInputAC line
AjPListsvlistOutputlist of accession numbers
void RETURN

Input
idline:(Input)AC line
Output
svlist:(Output)list of accession numbers
Returns
void:No return value

Description

Extract sequence version from an EMBL new format ID line

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function embBtreeEmblDE

Extract words from an EMBL DE line

Synopsis

Prototype
void embBtreeEmblDE (
      const AjPStr deline,
      AjPList delist,
      ajuint maxlen
);

TypeNameRead/WriteDescription
const AjPStrdelineInputdescription line
AjPListdelistOutputlist of descriptions
ajuintmaxlenInputmax keyword length
void RETURN

Input
deline:(Input)description line
maxlen:(Input)max keyword length
Output
delist:(Output)list of descriptions
Returns
void:No return value

Description

Extract words from an EMBL DE line

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function embBtreeGenBankAC

Extract accession numbers from a GenBank ACCESSION line

Synopsis

Prototype
void embBtreeGenBankAC (
      const AjPStr acline,
      AjPList aclist
);

TypeNameRead/WriteDescription
const AjPStraclineInputAC line
AjPListaclistOutputlist of accession numbers
void RETURN

Input
acline:(Input)AC line
Output
aclist:(Output)list of accession numbers
Returns
void:No return value

Description

Extract accession numbers from a GenBank ACCESSION line

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function embBtreeGenBankKW

Extract keywords from a GenBank KEYWORDS line

Synopsis

Prototype
void embBtreeGenBankKW (
      const AjPStr kwline,
      AjPList kwlist,
      ajuint maxlen
);

TypeNameRead/WriteDescription
const AjPStrkwlineInputkeyword line
AjPListkwlistOutputlist of keywords
ajuintmaxlenInputmax keyword length
void RETURN

Input
kwline:(Input)keyword line
maxlen:(Input)max keyword length
Output
kwlist:(Output)list of keywords
Returns
void:No return value

Description

Extract keywords from a GenBank KEYWORDS line

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function embBtreeGenBankDE

Extract keywords from a GenBank DESCRIPTION line

Synopsis

Prototype
void embBtreeGenBankDE (
      const AjPStr kwline,
      AjPList kwlist,
      ajuint maxlen
);

TypeNameRead/WriteDescription
const AjPStrkwlineInputkeyword line
AjPListkwlistOutputlist of keywords
ajuintmaxlenInputmax keyword length
void RETURN

Input
kwline:(Input)keyword line
maxlen:(Input)max keyword length
Output
kwlist:(Output)list of keywords
Returns
void:No return value

Description

Extract keywords from a GenBank DESCRIPTION line

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function embBtreeGenBankTX

Extract keywords from a GenBank ORGANISM line

Synopsis

Prototype
void embBtreeGenBankTX (
      const AjPStr kwline,
      AjPList kwlist,
      ajuint maxlen
);

TypeNameRead/WriteDescription
const AjPStrkwlineInputkeyword line
AjPListkwlistOutputlist of keywords
ajuintmaxlenInputmax keyword length
void RETURN

Input
kwline:(Input)keyword line
maxlen:(Input)max keyword length
Output
kwlist:(Output)list of keywords
Returns
void:No return value

Description

Extract keywords from a GenBank ORGANISM line

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function embBtreeFastaDE

Extract keywords from a Fasta description

Synopsis

Prototype
void embBtreeFastaDE (
      const AjPStr kwline,
      AjPList kwlist,
      ajuint maxlen
);

TypeNameRead/WriteDescription
const AjPStrkwlineInputkeyword line
AjPListkwlistOutputlist of keywords
ajuintmaxlenInputmax keyword length
void RETURN

Input
kwline:(Input)keyword line
maxlen:(Input)max keyword length
Output
kwlist:(Output)list of keywords
Returns
void:No return value

Description

Extract keywords from a Fasta description

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function embBtreeReadDir

Read files to index

Synopsis

Prototype
ajuint embBtreeReadDir (
      AjPStr** filelist,
      const AjPStr fdirectory,
      const AjPStr files,
      const AjPStr exclude
);

TypeNameRead/WriteDescription
AjPStr**filelistOutputlist of files to read
const AjPStrfdirectoryInputDirectory to scan
const AjPStrfilesInputFilename to search for (or NULL)
const AjPStrexcludeInputlist of files to exclude
ajuint RETURNnumber of matching files

Input
fdirectory:(Input)Directory to scan
files:(Input)Filename to search for (or NULL)
exclude:(Input)list of files to exclude
Output
filelist:(Output)list of files to read
Returns
ajuint:number of matching files

Description

Read files to index

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function embBtreeEntryNew

Construct a database entry object

Synopsis

Prototype
EmbPBtreeEntry embBtreeEntryNew (
      void
);

TypeNameRead/WriteDescription
EmbPBtreeEntry RETURNdb entry object pointer

Returns
EmbPBtreeEntry:db entry object pointer

Description

Construct a database entry object

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function embBtreeEntryDel

Delete a database entry object

Synopsis

Prototype
void embBtreeEntryDel (
      EmbPBtreeEntry* thys
);

TypeNameRead/WriteDescription
EmbPBtreeEntry*thysDeletedb entry object pointer
void RETURN

Output
thys:(Delete)db entry object pointer
Returns
void:No return value

Description

Delete a database entry object

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function embBtreeSetFields

Set database fields to index

Synopsis

Prototype
ajuint embBtreeSetFields (
      EmbPBtreeEntry entry,
      AjPStr const* fields
);

TypeNameRead/WriteDescription
EmbPBtreeEntryentryOutputDatabase entry information
AjPStr const*fieldsInputuser specified fields
ajuint RETURNnumber of fields set

Input
fields:(Input)user specified fields
Output
entry:(Output)Database entry information
Returns
ajuint:number of fields set

Description

Set database fields to index

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function embBtreeSetDbInfo

Set general database information

Synopsis

Prototype
void embBtreeSetDbInfo (
      EmbPBtreeEntry entry,
      const AjPStr name,
      const AjPStr dbrs,
      const AjPStr date,
      const AjPStr release,
      const AjPStr type,
      const AjPStr directory,
      const AjPStr idirectory
);

TypeNameRead/WriteDescription
EmbPBtreeEntryentryOutputDatabase entry information
const AjPStrnameInputuser specified name
const AjPStrdbrsInputuser specified resource
const AjPStrdateInputuser specified date
const AjPStrreleaseInputuser specified release
const AjPStrtypeInputuser specified type
const AjPStrdirectoryInputuser specified directory
const AjPStridirectoryInputuser specified index directory
void RETURN

Input
name:(Input)user specified name
dbrs:(Input)user specified resource
date:(Input)user specified date
release:(Input)user specified release
type:(Input)user specified type
directory:(Input)user specified directory
idirectory:(Input)user specified index directory
Output
entry:(Output)Database entry information
Returns
void:No return value

Description

Set general database information

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function embBtreeGetFiles

Read files to index

Synopsis

Prototype
ajuint embBtreeGetFiles (
      EmbPBtreeEntry entry,
      const AjPStr fdirectory,
      const AjPStr files,
      const AjPStr exclude
);

TypeNameRead/WriteDescription
EmbPBtreeEntryentryModifylist of files to read
const AjPStrfdirectoryInputDirectory to scan
const AjPStrfilesInputFilename to search for (or NULL)
const AjPStrexcludeInputlist of files to exclude
ajuint RETURNnumber of matching files

Input
fdirectory:(Input)Directory to scan
files:(Input)Filename to search for (or NULL)
exclude:(Input)list of files to exclude
Input & Output
entry:(Modify)list of files to read
Returns
ajuint:number of matching files

Description

Read files to index

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function embBtreeWriteEntryFile

Put files to entry file

Synopsis

Prototype
AjBool embBtreeWriteEntryFile (
      const EmbPBtreeEntry entry
);

TypeNameRead/WriteDescription
const EmbPBtreeEntryentryInputdatabase data
AjBool RETURNtrue on success

Input
entry:(Input)database data
Returns
AjBool:true on success

Description

Put files to entry file

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function embBtreeGetRsInfo

Get resource information for selected database

Synopsis

Prototype
void embBtreeGetRsInfo (
      EmbPBtreeEntry entry
);

TypeNameRead/WriteDescription
EmbPBtreeEntryentryModifydatabase data
void RETURN

Input & Output
entry:(Modify)database data
Returns
void:No return value

Description

Get resource information for selected database

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function embBtreeOpenCaches

Open index files

Synopsis

Prototype
AjBool embBtreeOpenCaches (
      EmbPBtreeEntry entry
);

TypeNameRead/WriteDescription
EmbPBtreeEntryentryModifydatabase data
AjBool RETURNtrue on success

Input & Output
entry:(Modify)database data
Returns
AjBool:true on success

Description

Open index files

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function embBtreeCloseCaches

Close index files

Synopsis

Prototype
AjBool embBtreeCloseCaches (
      EmbPBtreeEntry entry
);

TypeNameRead/WriteDescription
EmbPBtreeEntryentryModifydatabase data
AjBool RETURNtrue on success

Input & Output
entry:(Modify)database data
Returns
AjBool:true on success

Description

Close index files

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function embBtreeProbeCaches

Close index files

Synopsis

Prototype
AjBool embBtreeProbeCaches (
      EmbPBtreeEntry entry
);

TypeNameRead/WriteDescription
EmbPBtreeEntryentryModifydatabase data
AjBool RETURNtrue on success

Input & Output
entry:(Modify)database data
Returns
AjBool:true on success

Description

Close index files

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function embBtreeDumpParameters

Write index parameter files

Synopsis

Prototype
AjBool embBtreeDumpParameters (
      EmbPBtreeEntry entry
);

TypeNameRead/WriteDescription
EmbPBtreeEntryentryModifydatabase data
AjBool RETURNtrue on success

Input & Output
entry:(Modify)database data
Returns
AjBool:true on success

Description

Write index parameter files

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function embIndexExit

Cleanup indexing internals on exit

Synopsis

Prototype
void embIndexExit (
      void
);

TypeNameRead/WriteDescription
void RETURN

Returns
void:No return value

Description

Cleanup indexing internals on exit

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0