ajdas.c


Function ajDasServerNew

Returns a new DasServer object

Synopsis

Prototype
AjPDasServer ajDasServerNew (
      void
);

TypeNameRead/WriteDescription
AjPDasServer RETURNDAS server object

Returns
AjPDasServer:DAS server object

Description

Returns a new DasServer object

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajDasServerDel

Delete DASserver object

Synopsis

Prototype
void ajDasServerDel (
      AjPDasServer* thys
);

TypeNameRead/WriteDescription
AjPDasServer*thysModifyDASserver object
void RETURN

Input & Output
thys:(Modify)DASserver object
Returns
void:No return value

Description

Delete DASserver object

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajDasSegmentDel

Delete DAS segment objects returned by entry_points queries

Synopsis

Prototype
void ajDasSegmentDel (
      AjPDasSegment* Psegment
);

TypeNameRead/WriteDescription
AjPDasSegment*PsegmentModifyDAS 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

See Also

See other functions in this section

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
);

TypeNameRead/WriteDescription
AjPFilebuffbuffModifyXML input stream
AjPListsourcesModifypointer to the data structure for storing parser results of DAS/XML 'source' objects
AjBool RETURNTrue 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

See Also

See other functions in this section

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
);

TypeNameRead/WriteDescription
AjPFilebuffbuffModifyXML input stream
AjPListsegmentsModifypointer to the data structure for storing parser results of DAS/XML 'segment' objects
AjBool RETURNTrue 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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajDasServerSethostS

Set the DAS server host name

Synopsis

Prototype
AjBool ajDasServerSethostS (
      AjPDasServer server,
      const AjPStr host
);

TypeNameRead/WriteDescription
AjPDasServerserverModifyDASserver object
const AjPStrhostInputDAS server host name
AjBool RETURNTrue 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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajDasServerSetpathS

Set the DAS server URL path

Synopsis

Prototype
AjBool ajDasServerSetpathS (
      AjPDasServer server,
      const AjPStr path
);

TypeNameRead/WriteDescription
AjPDasServerserverModifyDASserver object
const AjPStrpathInputDAS server URL path
AjBool RETURNTrue 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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajDasServerSetport

Set the DAS server port

Synopsis

Prototype
AjBool ajDasServerSetport (
      AjPDasServer server,
      ajuint port
);

TypeNameRead/WriteDescription
AjPDasServerserverModifyDASserver object
ajuintportInputDAS server port
AjBool RETURNTrue 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

See Also

See other functions in this section

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
);

TypeNameRead/WriteDescription
AjPDasServerserverModifyDAS server object
const AjPStrcmdInputDAS '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

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

See Also

See other functions in this section

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
);

TypeNameRead/WriteDescription
const AjPQueryqryInputsequence query object
const AjPStrsourceURIorTitleInputDAS source URI or title specified in current query
AjPStr RETURNsequence-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.

See Also

See other functions in this section

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
);

TypeNameRead/WriteDescription
const AjPDasSourcesourceInputDAS source object
AjBooltitleAndURIInputInclude URI in name
AjPStr RETURNDB 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

See Also

See other functions in this section

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
);

TypeNameRead/WriteDescription
const AjPDasServerserverInputDAS server object
AjPFilecachefOutputserver 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

See Also

See other functions in this section

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
);

TypeNameRead/WriteDescription
const AjPStrtestrangeInputDAS test_range string
AjPStr*idOutputsequence identifier
ajint*ibeginOutputsequence begin position
ajint*iendOutputsequence end position
AjPStr RETURNreturns 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.

See Also

See other functions in this section

Availability

In release 6.4.0