ajdas.c

Synopsis

Prototype

AjPDasServer ajDasServerNew (
      void
);

Type Name Read/Write Description

AjPDasServer RETURN DAS server object

Type	Name	Read/Write	Description
AjPDasServer		RETURN	DAS server object

Returns

AjPDasServer:

DAS server object

Description

Returns a new DasServer object

Availability

In release 6.4.0

Synopsis

Prototype

void ajDasServerDel (
      AjPDasServer* thys
);

Type Name Read/Write Description

AjPDasServer* thys Modify DASserver object

void RETURN

Type	Name	Read/Write	Description
AjPDasServer*	thys	Modify	DASserver object
void		RETURN

Input & Output

thys:

(Modify)

DASserver object

Returns

void:

No return value

Description

Delete DASserver object

Availability

In release 6.4.0

Function ajDasSegmentDel

Delete DAS segment objects returned by entry_points queries

Synopsis

Prototype

void ajDasSegmentDel (
      AjPDasSegment* Psegment
);

Type Name Read/Write Description

AjPDasSegment* Psegment Modify DAS segment object

void RETURN

Type	Name	Read/Write	Description
AjPDasSegment*	Psegment	Modify	DAS segment object
void		RETURN

Input & Output

Psegment:

(Modify)

DAS segment object

Returns

void:

No return value

Description

Delete DAS segment objects returned by entry_points queries

Availability

In release 6.4.0

Function ajDasParseRegistry

Parses XML list of DAS sources, either coming from dasregistry.org or from individual DAS servers supporting DAS 'sources' command

Synopsis

Prototype

AjBool ajDasParseRegistry (
      AjPFilebuff buff,
      AjPList sources
);

Type Name Read/Write Description

AjPFilebuff buff Modify XML input stream

AjPList sources Modify pointer to the data structure for storing parser results of DAS/XML 'source' objects

AjBool RETURN True on success

Type	Name	Read/Write	Description
AjPFilebuff	buff	Modify	XML input stream
AjPList	sources	Modify	pointer to the data structure for storing parser results of DAS/XML 'source' objects
AjBool		RETURN	True on success

Input & Output

buff:	(Modify)	XML input stream
sources:	(Modify)	pointer to the data structure for storing parser results of DAS/XML 'source' objects

Returns

AjBool:

True on success

Description

Parses XML list of DAS sources, either coming from dasregistry.org or from individual DAS servers supporting DAS 'sources' command

Availability

In release 6.4.0

Function ajDasParseEntrypoints

Parses XML list of DAS entry-points, either coming from dasregistry.org or from individual DAS servers supporting DAS 'entry_points' command

Synopsis

Prototype

AjBool ajDasParseEntrypoints (
      AjPFilebuff buff,
      AjPList segments
);

Type Name Read/Write Description

AjPFilebuff buff Modify XML input stream

AjPList segments Modify pointer to the data structure for storing parser results of DAS/XML 'segment' objects

AjBool RETURN True on success

Type	Name	Read/Write	Description
AjPFilebuff	buff	Modify	XML input stream
AjPList	segments	Modify	pointer to the data structure for storing parser results of DAS/XML 'segment' objects
AjBool		RETURN	True on success

Input & Output

buff:	(Modify)	XML input stream
segments:	(Modify)	pointer to the data structure for storing parser results of DAS/XML 'segment' objects

Returns

AjBool:

True on success

Description

Parses XML list of DAS entry-points, either coming from dasregistry.org or from individual DAS servers supporting DAS 'entry_points' command

Availability

In release 6.4.0

Function ajDasServerSethostS

Set the DAS server host name

Synopsis

Prototype

AjBool ajDasServerSethostS (
      AjPDasServer server,
      const AjPStr host
);

Type Name Read/Write Description

AjPDasServer server Modify DASserver object

const AjPStr host Input DAS server host name

AjBool RETURN True on success

Type	Name	Read/Write	Description
AjPDasServer	server	Modify	DASserver object
const AjPStr	host	Input	DAS server host name
AjBool		RETURN	True on success

Input

host:

(Input)

DAS server host name

Input & Output

server:

(Modify)

DASserver object

Returns

AjBool:

True on success

Description

Set the DAS server host name

Availability

In release 6.4.0

Function ajDasServerSetpathS

Set the DAS server URL path

Synopsis

Prototype

AjBool ajDasServerSetpathS (
      AjPDasServer server,
      const AjPStr path
);

Type Name Read/Write Description

AjPDasServer server Modify DASserver object

const AjPStr path Input DAS server URL path

AjBool RETURN True on success

Type	Name	Read/Write	Description
AjPDasServer	server	Modify	DASserver object
const AjPStr	path	Input	DAS server URL path
AjBool		RETURN	True on success

Input

path:

(Input)

DAS server URL path

Input & Output

server:

(Modify)

DASserver object

Returns

AjBool:

True on success

Description

Set the DAS server URL path

Availability

In release 6.4.0

Function ajDasServerSetport

Set the DAS server port

Synopsis

Prototype

AjBool ajDasServerSetport (
      AjPDasServer server,
      ajuint port
);

Type Name Read/Write Description

AjPDasServer server Modify DASserver object

ajuint port Input DAS server port

AjBool RETURN True on success

Type	Name	Read/Write	Description
AjPDasServer	server	Modify	DASserver object
ajuint	port	Input	DAS server port
AjBool		RETURN	True on success

Input

port:

(Input)

DAS server port

Input & Output

server:

(Modify)

DASserver object

Returns

AjBool:

True on success

Description

Set the DAS server port

Availability

In release 6.4.0

Function ajDasServerGetSources

Makes an http request for getting either list of all DAS sources or a particular DAS source on a given DAS server. Http response is parsed and results are stored in server object's 'sources' attribute

Synopsis

Prototype

void ajDasServerGetSources (
      AjPDasServer server,
      const AjPStr cmd
);

Type Name Read/Write Description

AjPDasServer server Modify DAS server object

const AjPStr cmd Input DAS 'sources' command, queries either all DAS sources or a particular DAS source

void RETURN

Type	Name	Read/Write	Description
AjPDasServer	server	Modify	DAS server object
const AjPStr	cmd	Input	DAS 'sources' command, queries either all DAS sources or a particular DAS source
void		RETURN

Input

cmd:

(Input)

DAS 'sources' command, queries either all DAS sources or a particular DAS source

Input & Output

server:

(Modify)

DAS server object

Returns

void:

No return value

Description

Availability

In release 6.4.0

Function ajDasGetSequenceQueryURI

Given a DAS server URL, returns sequence query URI for the DAS source specified in user query.

It first makes a DAS source command/query for the specific DAS source. If above fails then makes another query for all DAS sources and checks them against the current DAS source.

Synopsis

Prototype

AjPStr ajDasGetSequenceQueryURI (
      const AjPQuery qry,
      const AjPStr sourceURIorTitle
);

Type Name Read/Write Description

const AjPQuery qry Input sequence query object

const AjPStr sourceURIorTitle Input DAS source URI or title specified in current query

AjPStr RETURN sequence-query URI, null if not found

Type	Name	Read/Write	Description
const AjPQuery	qry	Input	sequence query object
const AjPStr	sourceURIorTitle	Input	DAS source URI or title specified in current query
AjPStr		RETURN	sequence-query URI, null if not found

Input

qry:	(Input)	sequence query object
sourceURIorTitle:	(Input)	DAS source URI or title specified in current query

Returns

AjPStr:

sequence-query URI, null if not found

Description

Given a DAS server URL, returns sequence query URI for the DAS source specified in user query.

It first makes a DAS source command/query for the specific DAS source. If above fails then makes another query for all DAS sources and checks them against the current DAS source.

Availability

In release 6.4.0

Function ajDasSourceGetDBname

Returns an EMBOSS DB name for a given DAS source

Synopsis

Prototype

AjPStr ajDasSourceGetDBname (
      const AjPDasSource source,
      AjBool titleAndURI
);

Type Name Read/Write Description

const AjPDasSource source Input DAS source object

AjBool titleAndURI Input Include URI in name

AjPStr RETURN DB name

Type	Name	Read/Write	Description
const AjPDasSource	source	Input	DAS source object
AjBool	titleAndURI	Input	Include URI in name
AjPStr		RETURN	DB name

Input

source:	(Input)	DAS source object
titleAndURI:	(Input)	Include URI in name

Returns

AjPStr:

DB name

Description

Returns an EMBOSS DB name for a given DAS source

Availability

In release 6.4.0

Function ajDasPrintCachefile

Prints DB definition for the specified DAS server object

Synopsis

Prototype

void ajDasPrintCachefile (
      const AjPDasServer server,
      AjPFile cachef
);

Type Name Read/Write Description

const AjPDasServer server Input DAS server object

AjPFile cachef Output server cachefile with DB definitions

void RETURN

Type	Name	Read/Write	Description
const AjPDasServer	server	Input	DAS server object
AjPFile	cachef	Output	server cachefile with DB definitions
void		RETURN

Input

server:

(Input)

DAS server object

Output

cachef:

(Output)

server cachefile with DB definitions

Returns

void:

No return value

Description

Prints DB definition for the specified DAS server object

Availability

In release 6.4.0

Function ajDasTestrangeParse

Parses a DAS test_range attribute and returns sequence identifier, and 'begin' and 'end' positions if any.

Synopsis

Prototype

AjPStr ajDasTestrangeParse (
      const AjPStr testrange,
      AjPStr* id,
      ajint* ibegin,
      ajint* iend
);

Type Name Read/Write Description

const AjPStr testrange Input DAS test_range string

AjPStr* id Output sequence identifier

ajint* ibegin Output sequence begin position

ajint* iend Output sequence end position

AjPStr RETURN returns the example query in EMBOSS USA syntax

Type	Name	Read/Write	Description
const AjPStr	testrange	Input	DAS test_range string
AjPStr*	id	Output	sequence identifier
ajint*	ibegin	Output	sequence begin position
ajint*	iend	Output	sequence end position
AjPStr		RETURN	returns the example query in EMBOSS USA syntax

Input

testrange:

(Input)

DAS test_range string

Output

id:	(Output)	sequence identifier
ibegin:	(Output)	sequence begin position
iend:	(Output)	sequence end position

Returns

AjPStr:

returns the example query in EMBOSS USA syntax

Description

Parses a DAS test_range attribute and returns sequence identifier, and 'begin' and 'end' positions if any.

Availability

In release 6.4.0

ajdas.c

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