embindex.c

Prototype

void embBtreeIndexEntry (
      EmbPBtreeEntry entry,
      ajuint dbno
);

Type Name Read/Write Description

EmbPBtreeEntry entry Modify Entry with id

ajuint dbno Input Database number for an identifier index field

void RETURN

Type	Name	Read/Write	Description
`EmbPBtreeEntry`	`entry`	Modify	Entry with id
`ajuint`	`dbno`	Input	Database number for an identifier index field
`void`		RETURN

From EMBOSS 6.4.0

Prototype

void embBtreeIndexField (
      EmbPBtreeField field,
      const EmbPBtreeEntry entry,
      ajuint dbno
);

Type Name Read/Write Description

EmbPBtreeField field Modify Field with list of data

const EmbPBtreeEntry entry Input Entry with id

ajuint dbno Input Database number for an identifier index field

void RETURN

Type	Name	Read/Write	Description
`EmbPBtreeField`	`field`	Modify	Field with list of data
`const EmbPBtreeEntry`	`entry`	Input	Entry with id
`ajuint`	`dbno`	Input	Database number for an identifier index field
`void`		RETURN

From EMBOSS 6.4.0

Function embBtreeParseEntry

Parse an entry ID from an input record

Prototype

void embBtreeParseEntry (
      const AjPStr readline,
      AjPRegexp regexp,
      EmbPBtreeEntry entry
);

Type Name Read/Write Description

const AjPStr readline Input INput record

AjPRegexp regexp Modify Regular expression to extract tokens

EmbPBtreeEntry entry Modify Entry

void RETURN

Type	Name	Read/Write	Description
`const AjPStr`	`readline`	Input	INput record
`AjPRegexp`	`regexp`	Modify	Regular expression to extract tokens
`EmbPBtreeEntry`	`entry`	Modify	Entry
`void`		RETURN

From EMBOSS 6.4.0

Function embBtreeParseField

Parse field tokens from an input record, iterating over a regular expression.

Prototype

void embBtreeParseField (
      const AjPStr readline,
      AjPRegexp regexp,
      EmbPBtreeField field
);

Type Name Read/Write Description

const AjPStr readline Input Input record

AjPRegexp regexp Modify Regular expression to extract tokens

EmbPBtreeField field Modify Field

void RETURN

Type	Name	Read/Write	Description
`const AjPStr`	`readline`	Input	Input record
`AjPRegexp`	`regexp`	Modify	Regular expression to extract tokens
`EmbPBtreeField`	`field`	Modify	Field
`void`		RETURN

From EMBOSS 6.4.0

Function embBtreeParseFieldSecond

Parse field tokens from an input record using the first and second matches to a regular expression.

Prototype

void embBtreeParseFieldSecond (
      const AjPStr readline,
      AjPRegexp regexp,
      EmbPBtreeField field
);

Type Name Read/Write Description

const AjPStr readline Input Input record

AjPRegexp regexp Modify Regular expression to extract tokens

EmbPBtreeField field Modify Field

void RETURN

Type	Name	Read/Write	Description
`const AjPStr`	`readline`	Input	Input record
`AjPRegexp`	`regexp`	Modify	Regular expression to extract tokens
`EmbPBtreeField`	`field`	Modify	Field
`void`		RETURN

From EMBOSS 6.4.0

Function embBtreeParseFieldThird

Parse field tokens from an input record using the first and third matches to a regular expression.

Prototype

void embBtreeParseFieldThird (
      const AjPStr readline,
      AjPRegexp regexp,
      EmbPBtreeField field
);

Type Name Read/Write Description

const AjPStr readline Input Input record

AjPRegexp regexp Modify Regular expression to extract tokens

EmbPBtreeField field Modify Field

void RETURN

Type	Name	Read/Write	Description
`const AjPStr`	`readline`	Input	Input record
`AjPRegexp`	`regexp`	Modify	Regular expression to extract tokens
`EmbPBtreeField`	`field`	Modify	Field
`void`		RETURN

From EMBOSS 6.4.0

Function embBtreeParseFieldTrim

Parse field tokens from an input record and trim any trailing whitespace, iterating over a regular expression.

Prototype

void embBtreeParseFieldTrim (
      const AjPStr readline,
      AjPRegexp regexp,
      EmbPBtreeField field
);

Type Name Read/Write Description

const AjPStr readline Input Input record

AjPRegexp regexp Modify Regular expression to extract tokens

EmbPBtreeField field Modify Field

void RETURN

Type	Name	Read/Write	Description
`const AjPStr`	`readline`	Input	Input record
`AjPRegexp`	`regexp`	Modify	Regular expression to extract tokens
`EmbPBtreeField`	`field`	Modify	Field
`void`		RETURN

From EMBOSS 6.4.0

Function embBtreeReportEntry

Report on indexing of entries

Prototype

void embBtreeReportEntry (
      AjPFile outf,
      const EmbPBtreeEntry entry
);

Type Name Read/Write Description

AjPFile outf Modify Output file

const EmbPBtreeEntry entry Input Entry

void RETURN

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Modify	Output file
`const EmbPBtreeEntry`	`entry`	Input	Entry
`void`		RETURN

From EMBOSS 6.4.0

Function embBtreeReportField

Report on indexing of field

Prototype

void embBtreeReportField (
      AjPFile outf,
      const EmbPBtreeField field
);

Type Name Read/Write Description

AjPFile outf Modify Output file

const EmbPBtreeField field Input Field

void RETURN

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Modify	Output file
`const EmbPBtreeField`	`field`	Input	Field
`void`		RETURN

From EMBOSS 6.4.0

Function embBtreeEmblKW

Extract keywords from an EMBL KW line

Prototype

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

Type Name Read/Write Description

const AjPStr kwline Input keyword line

AjPList kwlist Output list of keywords

ajuint maxlen Input max keyword length

void RETURN

Type	Name	Read/Write	Description
`const AjPStr`	`kwline`	Input	keyword line
`AjPList`	`kwlist`	Output	list of keywords
`ajuint`	`maxlen`	Input	max keyword length
`void`		RETURN

From EMBOSS 3.0.0

Function embBtreeEmblTX

Extract keywords from an EMBL OC or OS line

Prototype

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

Type Name Read/Write Description

const AjPStr txline Input taxonomy line

AjPList txlist Output list of taxons

ajuint maxlen Input max taxon length

void RETURN

Type	Name	Read/Write	Description
`const AjPStr`	`txline`	Input	taxonomy line
`AjPList`	`txlist`	Output	list of taxons
`ajuint`	`maxlen`	Input	max taxon length
`void`		RETURN

From EMBOSS 3.0.0

Function embBtreeEmblAC

Extract accession numbers from an EMBL AC line

Prototype

void embBtreeEmblAC (
      const AjPStr acline,
      AjPList aclist
);

Type Name Read/Write Description

const AjPStr acline Input AC line

AjPList aclist Output list of accession numbers

void RETURN

Type	Name	Read/Write	Description
`const AjPStr`	`acline`	Input	AC line
`AjPList`	`aclist`	Output	list of accession numbers
`void`		RETURN

From EMBOSS 3.0.0

Function embBtreeEmblSV

Extract sequence version from an EMBL new format ID line

Prototype

void embBtreeEmblSV (
      const AjPStr idline,
      AjPList svlist
);

Type Name Read/Write Description

const AjPStr idline Input AC line

AjPList svlist Output list of accession numbers

void RETURN

Type	Name	Read/Write	Description
`const AjPStr`	`idline`	Input	AC line
`AjPList`	`svlist`	Output	list of accession numbers
`void`		RETURN

From EMBOSS 4.0.0

Function embBtreeEmblDE

Extract words from an EMBL DE line

Prototype

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

Type Name Read/Write Description

const AjPStr deline Input description line

AjPList delist Output list of descriptions

ajuint maxlen Input max keyword length

void RETURN

Type	Name	Read/Write	Description
`const AjPStr`	`deline`	Input	description line
`AjPList`	`delist`	Output	list of descriptions
`ajuint`	`maxlen`	Input	max keyword length
`void`		RETURN

From EMBOSS 3.0.0

Function embBtreeGenBankAC

Extract accession numbers from a GenBank ACCESSION line

Prototype

void embBtreeGenBankAC (
      const AjPStr acline,
      AjPList aclist
);

Type Name Read/Write Description

const AjPStr acline Input AC line

AjPList aclist Output list of accession numbers

void RETURN

Type	Name	Read/Write	Description
`const AjPStr`	`acline`	Input	AC line
`AjPList`	`aclist`	Output	list of accession numbers
`void`		RETURN

From EMBOSS 3.0.0

Function embBtreeGenBankKW

Extract keywords from a GenBank KEYWORDS line

Prototype

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

Type Name Read/Write Description

const AjPStr kwline Input keyword line

AjPList kwlist Output list of keywords

ajuint maxlen Input max keyword length

void RETURN

Type	Name	Read/Write	Description
`const AjPStr`	`kwline`	Input	keyword line
`AjPList`	`kwlist`	Output	list of keywords
`ajuint`	`maxlen`	Input	max keyword length
`void`		RETURN

From EMBOSS 3.0.0

Function embBtreeGenBankDE

Extract keywords from a GenBank DESCRIPTION line

Prototype

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

Type Name Read/Write Description

const AjPStr kwline Input keyword line

AjPList kwlist Output list of keywords

ajuint maxlen Input max keyword length

void RETURN

Type	Name	Read/Write	Description
`const AjPStr`	`kwline`	Input	keyword line
`AjPList`	`kwlist`	Output	list of keywords
`ajuint`	`maxlen`	Input	max keyword length
`void`		RETURN

From EMBOSS 3.0.0

Function embBtreeGenBankTX

Extract keywords from a GenBank ORGANISM line

Prototype

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

Type Name Read/Write Description

const AjPStr kwline Input keyword line

AjPList kwlist Output list of keywords

ajuint maxlen Input max keyword length

void RETURN

Type	Name	Read/Write	Description
`const AjPStr`	`kwline`	Input	keyword line
`AjPList`	`kwlist`	Output	list of keywords
`ajuint`	`maxlen`	Input	max keyword length
`void`		RETURN

From EMBOSS 3.0.0

Function embBtreeFastaDE

Extract keywords from a Fasta description

Prototype

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

Type Name Read/Write Description

const AjPStr kwline Input keyword line

AjPList kwlist Output list of keywords

ajuint maxlen Input max keyword length

void RETURN

Type	Name	Read/Write	Description
`const AjPStr`	`kwline`	Input	keyword line
`AjPList`	`kwlist`	Output	list of keywords
`ajuint`	`maxlen`	Input	max keyword length
`void`		RETURN

From EMBOSS 3.0.0

Function embBtreeFastaSV

Extract sequence version keywords from a Fasta description

Prototype

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

Type Name Read/Write Description

const AjPStr kwline Input sequence version or GI string

AjPList kwlist Output list of sequence versions

ajuint maxlen Input max sequence version length

void RETURN

Type	Name	Read/Write	Description
`const AjPStr`	`kwline`	Input	sequence version or GI string
`AjPList`	`kwlist`	Output	list of sequence versions
`ajuint`	`maxlen`	Input	max sequence version length
`void`		RETURN

From EMBOSS 6.0.0

Function embBtreeReadDir

Read files to index

Prototype

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

Type Name Read/Write Description

AjPStr** filelist Output list of files to read

const AjPStr fdirectory Input Directory to scan

const AjPStr files Input Filename to search for (or NULL)

const AjPStr exclude Input list of files to exclude

ajuint RETURN number of matching files

Type	Name	Read/Write	Description
`AjPStr**`	`filelist`	Output	list of files to read
`const AjPStr`	`fdirectory`	Input	Directory to scan
`const AjPStr`	`files`	Input	Filename to search for (or NULL)
`const AjPStr`	`exclude`	Input	list of files to exclude
`ajuint`		RETURN	number of matching files

From EMBOSS 2.8.0

Function embBtreeEntryNew

Construct a database entry object

Prototype

EmbPBtreeEntry embBtreeEntryNew (
      void
);

Type Name Read/Write Description

EmbPBtreeEntry RETURN db entry object pointer

Type	Name	Read/Write	Description
`EmbPBtreeEntry`		RETURN	db entry object pointer

From EMBOSS 3.0.0

Function embBtreeEntryDel

Delete a database entry object

Prototype

void embBtreeEntryDel (
      EmbPBtreeEntry* thys
);

Type Name Read/Write Description

EmbPBtreeEntry* thys Delete db entry object pointer

void RETURN

Type	Name	Read/Write	Description
`EmbPBtreeEntry*`	`thys`	Delete	db entry object pointer
`void`		RETURN

From EMBOSS 3.0.0

Function embBtreeEntrySetCompressed

Set database entry to be compressed on writing

Prototype

void embBtreeEntrySetCompressed (
      EmbPBtreeEntry entry
);

Type Name Read/Write Description

EmbPBtreeEntry entry Modify Database entry information

void RETURN

Type	Name	Read/Write	Description
`EmbPBtreeEntry`	`entry`	Modify	Database entry information
`void`		RETURN

From EMBOSS 6.4.0

Function embBtreeSetFields

Set database fields to index

Prototype

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

Type Name Read/Write Description

EmbPBtreeEntry entry Output Database entry information

AjPStr const* fields Input user specified fields

ajuint RETURN number of fields set

Type	Name	Read/Write	Description
`EmbPBtreeEntry`	`entry`	Output	Database entry information
`AjPStr const*`	`fields`	Input	user specified fields
`ajuint`		RETURN	number of fields set

From EMBOSS 3.0.0

Function embBtreeSetDbInfo

Set general database information

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
);

Type Name Read/Write Description

EmbPBtreeEntry entry Output Database entry information

const AjPStr name Input user specified name

const AjPStr dbrs Input user specified resource

const AjPStr date Input user specified date

const AjPStr release Input user specified release

const AjPStr type Input user specified type

const AjPStr directory Input user specified directory

const AjPStr idirectory Input user specified index directory

void RETURN

Type	Name	Read/Write	Description
`EmbPBtreeEntry`	`entry`	Output	Database entry information
`const AjPStr`	`name`	Input	user specified name
`const AjPStr`	`dbrs`	Input	user specified resource
`const AjPStr`	`date`	Input	user specified date
`const AjPStr`	`release`	Input	user specified release
`const AjPStr`	`type`	Input	user specified type
`const AjPStr`	`directory`	Input	user specified directory
`const AjPStr`	`idirectory`	Input	user specified index directory
`void`		RETURN

From EMBOSS 3.0.0

Function embBtreeGetFieldC

Set database fields to index

Prototype

EmbPBtreeField embBtreeGetFieldC (
      EmbPBtreeEntry entry,
      const char* nametxt
);

Type Name Read/Write Description

EmbPBtreeEntry entry Output Database entry information

const char* nametxt Input Field name

EmbPBtreeField RETURN Btree index field definition

Type	Name	Read/Write	Description
`EmbPBtreeEntry`	`entry`	Output	Database entry information
`const char*`	`nametxt`	Input	Field name
`EmbPBtreeField`		RETURN	Btree index field definition

From EMBOSS 6.4.0

Function embBtreeGetFieldS

Set database fields to index

Prototype

EmbPBtreeField embBtreeGetFieldS (
      EmbPBtreeEntry entry,
      const AjPStr name
);

Type Name Read/Write Description

EmbPBtreeEntry entry Output Database entry information

const AjPStr name Input Field name

EmbPBtreeField RETURN Btree index field definition

Type	Name	Read/Write	Description
`EmbPBtreeEntry`	`entry`	Output	Database entry information
`const AjPStr`	`name`	Input	Field name
`EmbPBtreeField`		RETURN	Btree index field definition

From EMBOSS 6.4.0

Function embBtreeGetFiles

Read files to index

Prototype

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

Type Name Read/Write Description

EmbPBtreeEntry entry Modify list of files to read

const AjPStr fdirectory Input Directory to scan

const AjPStr files Input Filename to search for (or NULL)

const AjPStr exclude Input list of files to exclude

ajuint RETURN number of matching files

Type	Name	Read/Write	Description
`EmbPBtreeEntry`	`entry`	Modify	list of files to read
`const AjPStr`	`fdirectory`	Input	Directory to scan
`const AjPStr`	`files`	Input	Filename to search for (or NULL)
`const AjPStr`	`exclude`	Input	list of files to exclude
`ajuint`		RETURN	number of matching files

From EMBOSS 3.0.0

Function embBtreeWriteEntryFile

Put files to entry file

Prototype

AjBool embBtreeWriteEntryFile (
      const EmbPBtreeEntry entry
);

Type Name Read/Write Description

const EmbPBtreeEntry entry Input database data

AjBool RETURN true on success

Type	Name	Read/Write	Description
`const EmbPBtreeEntry`	`entry`	Input	database data
`AjBool`		RETURN	true on success

From EMBOSS 3.0.0

Function embBtreeGetRsInfo

Get resource information for selected database

Prototype

void embBtreeGetRsInfo (
      EmbPBtreeEntry entry
);

Type Name Read/Write Description

EmbPBtreeEntry entry Modify database data

void RETURN

Type	Name	Read/Write	Description
`EmbPBtreeEntry`	`entry`	Modify	database data
`void`		RETURN

From EMBOSS 3.0.0

Function embBtreeOpenCaches

Open index files for writing

Prototype

AjBool embBtreeOpenCaches (
      EmbPBtreeEntry entry
);

Type Name Read/Write Description

EmbPBtreeEntry entry Modify database data

AjBool RETURN true on success

Type	Name	Read/Write	Description
`EmbPBtreeEntry`	`entry`	Modify	database data
`AjBool`		RETURN	true on success

From EMBOSS 3.0.0

Function embBtreeCloseCaches

Close index files

Prototype

AjBool embBtreeCloseCaches (
      EmbPBtreeEntry entry
);

Type Name Read/Write Description

EmbPBtreeEntry entry Modify database data

AjBool RETURN true on success

Type	Name	Read/Write	Description
`EmbPBtreeEntry`	`entry`	Modify	database data
`AjBool`		RETURN	true on success

From EMBOSS 3.0.0

Function embBtreeProbeCaches

Close index files

Prototype

AjBool embBtreeProbeCaches (
      EmbPBtreeEntry entry
);

Type Name Read/Write Description

EmbPBtreeEntry entry Modify database data

AjBool RETURN true on success

Type	Name	Read/Write	Description
`EmbPBtreeEntry`	`entry`	Modify	database data
`AjBool`		RETURN	true on success

From EMBOSS 6.0.0

Function embBtreeDumpParameters

Write index parameter files

Prototype

AjBool embBtreeDumpParameters (
      EmbPBtreeEntry entry
);

Type Name Read/Write Description

EmbPBtreeEntry entry Modify database data

AjBool RETURN true on success

Type	Name	Read/Write	Description
`EmbPBtreeEntry`	`entry`	Modify	database data
`AjBool`		RETURN	true on success

From EMBOSS 3.0.0

Function embBtreeFieldNewC

Constructor for a Btree index field

Prototype

EmbPBtreeField embBtreeFieldNewC (
      const char* nametxt
);

Type Name Read/Write Description

const char* nametxt Input Name

EmbPBtreeField RETURN Btree field

Type	Name	Read/Write	Description
`const char*`	`nametxt`	Input	Name
`EmbPBtreeField`		RETURN	Btree field

From EMBOSS 6.4.0

Function embBtreeFieldNewS

Constructor for a Btree index field

Prototype

EmbPBtreeField embBtreeFieldNewS (
      const AjPStr name
);

Type Name Read/Write Description

const AjPStr name Input Name

EmbPBtreeField RETURN Btree field

Type	Name	Read/Write	Description
`const AjPStr`	`name`	Input	Name
`EmbPBtreeField`		RETURN	Btree field

From EMBOSS 6.4.0

Function embBtreeFieldDel

Destructor for a Btree index field

Prototype

void embBtreeFieldDel (
      EmbPBtreeField* Pthis
);

Type Name Read/Write Description

EmbPBtreeField* Pthis Delete Btree index field object

void RETURN

Type	Name	Read/Write	Description
`EmbPBtreeField*`	`Pthis`	Delete	Btree index field object
`void`		RETURN

From EMBOSS 6.4.0

Function embBtreeFieldSetCompressed

Set database field to be compressed on writing

Prototype

void embBtreeFieldSetCompressed (
      EmbPBtreeField field
);

Type Name Read/Write Description

EmbPBtreeField field Modify Database field information

void RETURN

Type	Name	Read/Write	Description
`EmbPBtreeField`	`field`	Modify	Database field information
`void`		RETURN

From EMBOSS 6.4.0

Function embBtreeFieldSetIdtype

Set database field to be identifier type (not secondary) on writing

Prototype

void embBtreeFieldSetIdtype (
      EmbPBtreeField field
);

Type Name Read/Write Description

EmbPBtreeField field Modify Database field information

void RETURN

Type	Name	Read/Write	Description
`EmbPBtreeField`	`field`	Modify	Database field information
`void`		RETURN

From EMBOSS 6.4.0

Function embBtreeFieldSetSecondary

Set database field to be secondary on writing

Prototype

void embBtreeFieldSetSecondary (
      EmbPBtreeField field
);

Type Name Read/Write Description

EmbPBtreeField field Modify Database field information

void RETURN

Type	Name	Read/Write	Description
`EmbPBtreeField`	`field`	Modify	Database field information
`void`		RETURN

From EMBOSS 6.4.0

Function embIndexExit

Cleanup indexing internals on exit

Prototype

void embIndexExit (
      void
);

Type Name Read/Write Description

void RETURN

Type	Name	Read/Write	Description
`void`		RETURN

From EMBOSS 6.0.0