embindex.c


Function embBtreeIndexEntry

Add a term to an index entry cache

Prototype

void embBtreeIndexEntry (
      EmbPBtreeEntry entry,
      ajuint dbno
);

TypeNameRead/WriteDescription
EmbPBtreeEntryentryModifyEntry with id
ajuintdbnoInputDatabase number for an identifier index field
void RETURN

From EMBOSS 6.4.0


Function embBtreeIndexField

Add a term to an index field cache

Prototype

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

TypeNameRead/WriteDescription
EmbPBtreeFieldfieldModifyField with list of data
const EmbPBtreeEntryentryInputEntry with id
ajuintdbnoInputDatabase number for an identifier index field
void RETURN

From EMBOSS 6.4.0


Function embBtreeIndexPrimary

Add a term to an index field cache

Prototype

ajuint embBtreeIndexPrimary (
      EmbPBtreeField field,
      const EmbPBtreeEntry entry,
      ajuint dbno
);

TypeNameRead/WriteDescription
EmbPBtreeFieldfieldModifyField with list of data
const EmbPBtreeEntryentryInputEntry with id
ajuintdbnoInputDatabase number for an identifier index field
ajuint RETURNNumber of keys added

From EMBOSS 6.5.0


Function embBtreeIndexSecondary

Add a term to an index field cache

Prototype

ajuint embBtreeIndexSecondary (
      EmbPBtreeField field,
      const EmbPBtreeEntry entry
);

TypeNameRead/WriteDescription
EmbPBtreeFieldfieldModifyField with list of data
const EmbPBtreeEntryentryInputEntry identifier
ajuint RETURNNumber of keys added

From EMBOSS 6.5.0


Function embBtreeParseEntry

Parse an entry ID from an input record

Prototype

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

TypeNameRead/WriteDescription
const AjPStrreadlineInputINput record
AjPRegexpregexpModifyRegular expression to extract tokens
EmbPBtreeEntryentryModifyEntry
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
);

TypeNameRead/WriteDescription
const AjPStrreadlineInputInput record
AjPRegexpregexpModifyRegular expression to extract tokens
EmbPBtreeFieldfieldModifyField
void RETURN

From EMBOSS 6.4.0


Function embBtreeFieldGetdataS

Return the next field data value as a word

Prototype

AjBool embBtreeFieldGetdataS (
      EmbPBtreeField field,
      AjPStr* Pstr
);

TypeNameRead/WriteDescription
EmbPBtreeFieldfieldModifyField
AjPStr*PstrOutputData value field
AjBool RETURNTrue if data was found

From EMBOSS 6.5.0


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
);

TypeNameRead/WriteDescription
const AjPStrreadlineInputInput record
AjPRegexpregexpModifyRegular expression to extract tokens
EmbPBtreeFieldfieldModifyField
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
);

TypeNameRead/WriteDescription
const AjPStrreadlineInputInput record
AjPRegexpregexpModifyRegular expression to extract tokens
EmbPBtreeFieldfieldModifyField
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
);

TypeNameRead/WriteDescription
const AjPStrreadlineInputInput record
AjPRegexpregexpModifyRegular expression to extract tokens
EmbPBtreeFieldfieldModifyField
void RETURN

From EMBOSS 6.4.0


Function embBtreeReportEntry

Report on indexing of entries

Prototype

void embBtreeReportEntry (
      AjPFile outf,
      const EmbPBtreeEntry entry
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
const EmbPBtreeEntryentryInputEntry
void RETURN

From EMBOSS 6.4.0


Function embBtreeReportField

Report on indexing of field

Prototype

void embBtreeReportField (
      AjPFile outf,
      const EmbPBtreeField field
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
const EmbPBtreeFieldfieldInputField
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
);

TypeNameRead/WriteDescription
const AjPStrkwlineInputkeyword line
AjPListkwlistOutputlist of keywords
ajuintmaxlenInputmax 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
);

TypeNameRead/WriteDescription
const AjPStrtxlineInputtaxonomy line
AjPListtxlistOutputlist of taxons
ajuintmaxlenInputmax 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
);

TypeNameRead/WriteDescription
const AjPStraclineInputAC line
AjPListaclistOutputlist 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
);

TypeNameRead/WriteDescription
const AjPStridlineInputAC line
AjPListsvlistOutputlist 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
);

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

From EMBOSS 3.0.0


Function embBtreeParseEmblKw

Extract keywords from an EMBL KW line

Prototype

void embBtreeParseEmblKw (
      const AjPStr readline,
      EmbPBtreeField field
);

TypeNameRead/WriteDescription
const AjPStrreadlineInputkeyword line
EmbPBtreeFieldfieldModifylist of descriptions
void RETURN

From EMBOSS 6.5.0


Function embBtreeParseEmblTx

Extract keywords from an EMBL OC or OS line

Prototype

void embBtreeParseEmblTx (
      const AjPStr readline,
      EmbPBtreeField field
);

TypeNameRead/WriteDescription
const AjPStrreadlineInputtaxonomy line
EmbPBtreeFieldfieldModifylist of descriptions
void RETURN

From EMBOSS 6.5.0


Function embBtreeParseEmblAc

Extract accession numbers from an EMBL AC line

Prototype

void embBtreeParseEmblAc (
      const AjPStr readline,
      EmbPBtreeField field
);

TypeNameRead/WriteDescription
const AjPStrreadlineInputAC line
EmbPBtreeFieldfieldModifylist of descriptions
void RETURN

From EMBOSS 6.5.0


Function embBtreeFindEmblAc

Returns first accession number from an EMBL/UniProt AC line

Prototype

void embBtreeFindEmblAc (
      const AjPStr readline,
      EmbPBtreeField field,
      AjPStr* Pstr
);

TypeNameRead/WriteDescription
const AjPStrreadlineInputAC line
EmbPBtreeFieldfieldModifylist of descriptions
AjPStr*PstrOutputFirst accession
void RETURN

From EMBOSS 6.5.0


Function embBtreeParseEmblSv

Extract sequence version from an EMBL new format ID line

Prototype

void embBtreeParseEmblSv (
      const AjPStr readline,
      EmbPBtreeField field
);

TypeNameRead/WriteDescription
const AjPStrreadlineInputAC line
EmbPBtreeFieldfieldModifylist of descriptions
void RETURN

From EMBOSS 6.5.0


Function embBtreeParseEmblDe

Extract words from an EMBL DE line

Prototype

void embBtreeParseEmblDe (
      const AjPStr readline,
      EmbPBtreeField field
);

TypeNameRead/WriteDescription
const AjPStrreadlineInputdescription line
EmbPBtreeFieldfieldModifylist of descriptions
void RETURN

From EMBOSS 6.5.0


Function embBtreeParseGenbankAc

Extract accession numbers from a GenBank ACCESSION line

Prototype

void embBtreeParseGenbankAc (
      const AjPStr readline,
      EmbPBtreeField field
);

TypeNameRead/WriteDescription
const AjPStrreadlineInputAC line
EmbPBtreeFieldfieldModifyField with list of data
void RETURN

From EMBOSS 6.5.0


Function embBtreeParseGenbankDe

Extract keywords from a GenBank DESCRIPTION line

Prototype

void embBtreeParseGenbankDe (
      const AjPStr readline,
      EmbPBtreeField field
);

TypeNameRead/WriteDescription
const AjPStrreadlineInputAC line
EmbPBtreeFieldfieldModifyField with list of data
void RETURN

From EMBOSS 6.5.0


Function embBtreeParseGenbankKw

Extract keywords from a GenBank KEYWORDS line

Prototype

void embBtreeParseGenbankKw (
      const AjPStr readline,
      EmbPBtreeField field
);

TypeNameRead/WriteDescription
const AjPStrreadlineInputAC line
EmbPBtreeFieldfieldModifyField with list of data
void RETURN

From EMBOSS 6.5.0


Function embBtreeParseGenbankTx

Extract keywords from a GenBank ORGANISM line

Prototype

void embBtreeParseGenbankTx (
      const AjPStr readline,
      EmbPBtreeField field
);

TypeNameRead/WriteDescription
const AjPStrreadlineInputAC line
EmbPBtreeFieldfieldModifyField with list of data
void RETURN

From EMBOSS 6.5.0


Function embBtreeGenBankAC

Extract accession numbers from a GenBank ACCESSION line

Prototype

void embBtreeGenBankAC (
      const AjPStr acline,
      AjPList aclist
);

TypeNameRead/WriteDescription
const AjPStraclineInputAC line
AjPListaclistOutputlist 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
);

TypeNameRead/WriteDescription
const AjPStrkwlineInputkeyword line
AjPListkwlistOutputlist of keywords
ajuintmaxlenInputmax 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
);

TypeNameRead/WriteDescription
const AjPStrkwlineInputkeyword line
AjPListkwlistOutputlist of keywords
ajuintmaxlenInputmax 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
);

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

From EMBOSS 3.0.0


Function embBtreeParseFastaDe

Extract keywords from a Fasta description

Prototype

void embBtreeParseFastaDe (
      const AjPStr readline,
      EmbPBtreeField field
);

TypeNameRead/WriteDescription
const AjPStrreadlineInputkeyword line
EmbPBtreeFieldfieldModifyField with list of data
void RETURN

From EMBOSS 6.5.0


Function embBtreeParseFastaAc

Extract sequence version keywords from a Fasta description

Prototype

void embBtreeParseFastaAc (
      const AjPStr readline,
      EmbPBtreeField field
);

TypeNameRead/WriteDescription
const AjPStrreadlineInputkeyword line
EmbPBtreeFieldfieldModifyField with list of data
void RETURN

From EMBOSS 6.5.0


Function embBtreeFastaDE

Extract keywords from a Fasta description

Prototype

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

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

From EMBOSS 3.0.0


Function embBtreeParseFastaSv

Extract sequence version keywords from a Fasta description

Prototype

void embBtreeParseFastaSv (
      const AjPStr readline,
      EmbPBtreeField field
);

TypeNameRead/WriteDescription
const AjPStrreadlineInputkeyword line
EmbPBtreeFieldfieldModifyField with list of data
void RETURN

From EMBOSS 6.5.0


Function embBtreeFastaSV

Extract sequence version keywords from a Fasta description

Prototype

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

TypeNameRead/WriteDescription
const AjPStrkwlineInputsequence version or GI string
AjPListkwlistOutputlist of sequence versions
ajuintmaxlenInputmax 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
);

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

From EMBOSS 2.8.0


Function embBtreeEntryNew

Construct a database entry object

Prototype

EmbPBtreeEntry embBtreeEntryNew (
      ajuint refcount
);

TypeNameRead/WriteDescription
ajuintrefcountInputNumber of reference file(s) per entry
EmbPBtreeEntry RETURNdb entry object pointer

From EMBOSS 3.0.0


Function embBtreeEntryDel

Delete a database entry object

Prototype

void embBtreeEntryDel (
      EmbPBtreeEntry* pthis
);

TypeNameRead/WriteDescription
EmbPBtreeEntry*pthisDeletedb 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
);

TypeNameRead/WriteDescription
EmbPBtreeEntryentryModifyDatabase entry information
void RETURN

From EMBOSS 6.4.0


Function embBtreeSetFields

Set database fields to index

Prototype

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

TypeNameRead/WriteDescription
EmbPBtreeEntryentryOutputDatabase entry information
AjPStr const*fieldsInputuser specified fields
ajuint RETURNnumber 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
);

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

From EMBOSS 3.0.0


Function embBtreeGetFieldC

Set database fields to index

Prototype

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

TypeNameRead/WriteDescription
EmbPBtreeEntryentryOutputDatabase entry information
const char*nametxtInputField name
EmbPBtreeField RETURNBtree index field definition

From EMBOSS 6.4.0


Function embBtreeGetFieldS

Set database fields to index

Prototype

EmbPBtreeField embBtreeGetFieldS (
      EmbPBtreeEntry entry,
      const AjPStr name
);

TypeNameRead/WriteDescription
EmbPBtreeEntryentryOutputDatabase entry information
const AjPStrnameInputField name
EmbPBtreeField RETURNBtree 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
);

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

From EMBOSS 3.0.0


Function embBtreeWriteEntryFile

Put files to entry file

Prototype

AjBool embBtreeWriteEntryFile (
      const EmbPBtreeEntry entry
);

TypeNameRead/WriteDescription
const EmbPBtreeEntryentryInputdatabase data
AjBool RETURNtrue on success

From EMBOSS 3.0.0


Function embBtreeGetRsInfo

Get resource information for selected database

Prototype

void embBtreeGetRsInfo (
      EmbPBtreeEntry entry
);

TypeNameRead/WriteDescription
EmbPBtreeEntryentryModifydatabase data
void RETURN

From EMBOSS 3.0.0


Function embBtreeOpenCaches

Open index files for writing

Prototype

AjBool embBtreeOpenCaches (
      EmbPBtreeEntry entry
);

TypeNameRead/WriteDescription
EmbPBtreeEntryentryModifydatabase data
AjBool RETURNtrue on success

From EMBOSS 3.0.0


Function embBtreeCloseCaches

Close index files

Prototype

AjBool embBtreeCloseCaches (
      EmbPBtreeEntry entry
);

TypeNameRead/WriteDescription
EmbPBtreeEntryentryModifydatabase data
AjBool RETURNtrue on success

From EMBOSS 3.0.0


Function embBtreeProbeCaches

Close index files

Prototype

AjBool embBtreeProbeCaches (
      EmbPBtreeEntry entry
);

TypeNameRead/WriteDescription
EmbPBtreeEntryentryModifydatabase data
AjBool RETURNtrue on success

From EMBOSS 6.0.0


Function embBtreeDumpParameters

Write index parameter files

Prototype

AjBool embBtreeDumpParameters (
      EmbPBtreeEntry entry
);

TypeNameRead/WriteDescription
EmbPBtreeEntryentryModifydatabase data
AjBool RETURNtrue on success

From EMBOSS 3.0.0


Function embBtreeFieldNewC

Constructor for a Btree index field

Prototype

EmbPBtreeField embBtreeFieldNewC (
      const char* nametxt
);

TypeNameRead/WriteDescription
const char*nametxtInputName
EmbPBtreeField RETURNBtree field

From EMBOSS 6.4.0


Function embBtreeFieldNewS

Constructor for a Btree index field

Prototype

EmbPBtreeField embBtreeFieldNewS (
      const AjPStr name,
      ajuint refcount
);

TypeNameRead/WriteDescription
const AjPStrnameInputName
ajuintrefcountInputNumber of reference files
EmbPBtreeField RETURNBtree field

From EMBOSS 6.4.0


Function embBtreeFieldDel

Destructor for a Btree index field

Prototype

void embBtreeFieldDel (
      EmbPBtreeField* Pthis
);

TypeNameRead/WriteDescription
EmbPBtreeField*PthisDeleteBtree 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
);

TypeNameRead/WriteDescription
EmbPBtreeFieldfieldModifyDatabase 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
);

TypeNameRead/WriteDescription
EmbPBtreeFieldfieldModifyDatabase field information
void RETURN

From EMBOSS 6.4.0


Function embBtreeFieldSetSecondary

Set database field to be secondary on writing

Prototype

void embBtreeFieldSetSecondary (
      EmbPBtreeField field
);

TypeNameRead/WriteDescription
EmbPBtreeFieldfieldModifyDatabase field information
void RETURN

From EMBOSS 6.4.0


Function embIndexExit

Cleanup indexing internals on exit

Prototype

void embIndexExit (
      void
);

TypeNameRead/WriteDescription
void RETURN

From EMBOSS 6.0.0