ajmart.c

Function ajMartqueryNew

Initialise mart query object

Synopsis

Prototype
AjPMartquery ajMartqueryNew (
      void
);

TypeNameRead/WriteDescription
AjPMartquery RETURNMart query object

Returns
AjPMartquery:Mart query object

Description

Initialise mart query object

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartqueryDel

Delete Mart query object

Synopsis

Prototype
void ajMartqueryDel (
      AjPMartquery* thys
);

TypeNameRead/WriteDescription
AjPMartquery*thysModifyMary query object
void RETURN

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

Description

Delete Mart query object

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartquerySeqinFree

Delete Mart query object given a seqin object

Synopsis

Prototype
void ajMartquerySeqinFree (
      AjPSeqin thys
);

TypeNameRead/WriteDescription
AjPSeqinthysModifySeqin query object
void RETURN

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

Description

Delete Mart query object given a seqin object

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartLocNew

Create object for holding Mart location data read from XML

Synopsis

Prototype
AjPMartLoc ajMartLocNew (
      void
);

TypeNameRead/WriteDescription
AjPMartLoc RETURNMartLoc object

Returns
AjPMartLoc:MartLoc object

Description

Create object for holding Mart location data read from XML

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartLocDel

Delete a Mart Location object

Synopsis

Prototype
void ajMartLocDel (
      AjPMartLoc* thys
);

TypeNameRead/WriteDescription
AjPMartLoc*thysModifyMartLoc object
void RETURN

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

Description

Delete a Mart Location object

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartDatasetNew

Create object for holding Mart Dataset read from XML (or tab-sep list)

Synopsis

Prototype
AjPMartDataset ajMartDatasetNew (
      void
);

TypeNameRead/WriteDescription
AjPMartDataset RETURNMartDataset object

Returns
AjPMartDataset:MartDataset object

Description

Create object for holding Mart Dataset read from XML (or tab-sep list)

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartDatasetDel

Delete a Mart Dataset object

Synopsis

Prototype
void ajMartDatasetDel (
      AjPMartDataset* thys
);

TypeNameRead/WriteDescription
AjPMartDataset*thysModifyMartDataset object
void RETURN

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

Description

Delete a Mart Dataset object

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartAttributeNew

Create object for holding Mart Attributes read from XML (or tab-sep list)

Synopsis

Prototype
AjPMartAttribute ajMartAttributeNew (
      void
);

TypeNameRead/WriteDescription
AjPMartAttribute RETURNMartAttribute object

Returns
AjPMartAttribute:MartAttribute object

Description

Create object for holding Mart Attributes read from XML (or tab-sep list)

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartAttributeDel

Delete a Mart Attribute object

Synopsis

Prototype
void ajMartAttributeDel (
      AjPMartAttribute* thys
);

TypeNameRead/WriteDescription
AjPMartAttribute*thysModifyMartAttribute object
void RETURN

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

Description

Delete a Mart Attribute object

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartFilterNew

Create object for holding Mart Filters read from XML (or tab-sep list)

Synopsis

Prototype
AjPMartFilter ajMartFilterNew (
      void
);

TypeNameRead/WriteDescription
AjPMartFilter RETURNMartFilter object

Returns
AjPMartFilter:MartFilter object

Description

Create object for holding Mart Filters read from XML (or tab-sep list)

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartFilterDel

Delete a Mart Filter object

Synopsis

Prototype
void ajMartFilterDel (
      AjPMartFilter* thys
);

TypeNameRead/WriteDescription
AjPMartFilter*thysModifyMartFilter object
void RETURN

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

Description

Delete a Mart Filter object

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartDsinfoNew

Create object for query dataset info

Synopsis

Prototype
AjPMartdsinfo ajMartDsinfoNew (
      void
);

TypeNameRead/WriteDescription
AjPMartdsinfo RETURNMartdsinfo object

Returns
AjPMartdsinfo:Martdsinfo object

Description

Create object for query dataset info

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartDsinfoDel

Delete a Mart Dsinfo object

Synopsis

Prototype
void ajMartDsinfoDel (
      AjPMartdsinfo* thys
);

TypeNameRead/WriteDescription
AjPMartdsinfo*thysModifyMart Dsinfo object
void RETURN

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

Description

Delete a Mart Dsinfo object

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartQinfoNew

Create object for query info

Synopsis

Prototype
AjPMartqinfo ajMartQinfoNew (
      ajuint n
);

TypeNameRead/WriteDescription
ajuintnInputnumber of datasets
AjPMartqinfo RETURNMartqinfo object

Input
n:(Input)number of datasets
Returns
AjPMartqinfo:Martqinfo object

Description

Create object for query info

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartQinfoDel

Delete a Mart qinfo object

Synopsis

Prototype
void ajMartQinfoDel (
      AjPMartqinfo* thys
);

TypeNameRead/WriteDescription
AjPMartqinfo*thysModifyMart Qinfo object
void RETURN

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

Description

Delete a Mart qinfo object

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartregistryParse

Read a mart registry file

Synopsis

Prototype
AjBool ajMartregistryParse (
      AjPSeqin seqin
);

TypeNameRead/WriteDescription
AjPSeqinseqinModifySeqin object holding mart info
AjBool RETURNTrue on success

Input & Output
seqin:(Modify)Seqin object holding mart info
Returns
AjBool:True on success

Description

Read a mart registry file

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartGetRegistry

Return contents of a mart registry

Synopsis

Prototype
AjBool ajMartGetRegistry (
      AjPSeqin seqin
);

TypeNameRead/WriteDescription
AjPSeqinseqinModify"Sequence" input object
AjBool RETURNtrue on success

Input & Output
seqin:(Modify)"Sequence" input object
Returns
AjBool:true on success

Description

Return contents of a mart registry

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartGetDatasets

Return datasets given a mart registry and a mart name within it

Synopsis

Prototype
AjBool ajMartGetDatasets (
      AjPSeqin seqin,
      const AjPStr mart
);

TypeNameRead/WriteDescription
AjPSeqinseqinModify"Sequence" input object
const AjPStrmartInput"Sequence" mart name
AjBool RETURNtrue on success

Input
mart:(Input)"Sequence" mart name
Input & Output
seqin:(Modify)"Sequence" input object
Returns
AjBool:true on success

Description

Return datasets given a mart registry and a mart name within it

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartdatasetParse

Read a mart dataset buffer

Synopsis

Prototype
AjBool ajMartdatasetParse (
      AjPSeqin seqin
);

TypeNameRead/WriteDescription
AjPSeqinseqinModifySeqin object holding mart info
AjBool RETURNTrue on success

Input & Output
seqin:(Modify)Seqin object holding mart info
Returns
AjBool:True on success

Description

Read a mart dataset buffer

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartGetAttributes

Return attributes given a mart dataset and a mart host/path/port

Synopsis

Prototype
AjBool ajMartGetAttributes (
      AjPSeqin seqin,
      const AjPStr dataset
);

TypeNameRead/WriteDescription
AjPSeqinseqinModify"Sequence" input object
const AjPStrdatasetInput"Sequence" mart dataset name
AjBool RETURNtrue on success

Input
dataset:(Input)"Sequence" mart dataset name
Input & Output
seqin:(Modify)"Sequence" input object
Returns
AjBool:true on success

Description

Return attributes given a mart dataset and a mart host/path/port

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartGetAttributesRetry

Retry an attribute fetch using the main biomart registry site This routine should only be called after an ajMartGetAttribute call followed by a ajMartattributesParse has returned an error. That typically means that an external server has not provided all the attributes fields, possibly due to outdated biomart software. As the main biomart registry site contains all the metadata for external marts (but not the marts themselves) it can be queried using the same dataset. The true mart server should always be tried first to minimise load on the main biomart site

Synopsis

Prototype
AjBool ajMartGetAttributesRetry (
      AjPSeqin seqin,
      const AjPStr dataset
);

TypeNameRead/WriteDescription
AjPSeqinseqinModify"Sequence" input object
const AjPStrdatasetInput"Sequence" mart dataset name
AjBool RETURNtrue on success

Input
dataset:(Input)"Sequence" mart dataset name
Input & Output
seqin:(Modify)"Sequence" input object
Returns
AjBool:true on success

Description

Retry an attribute fetch using the main biomart registry site This routine should only be called after an ajMartGetAttribute call followed by a ajMartattributesParse has returned an error. That typically means that an external server has not provided all the attributes fields, possibly due to outdated biomart software. As the main biomart registry site contains all the metadata for external marts (but not the marts themselves) it can be queried using the same dataset. The true mart server should always be tried first to minimise load on the main biomart site

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartGetAttributesSchema

Return attributes given a mart dataset, a mart host/path/port and a schemaname.

This function will be deleted once virtual schemas are phased out. Use with caution.

Synopsis

Prototype
AjBool ajMartGetAttributesSchema (
      AjPSeqin seqin,
      const AjPStr dataset,
      const AjPStr schema
);

TypeNameRead/WriteDescription
AjPSeqinseqinModify"Sequence" input object
const AjPStrdatasetInput"Sequence" mart dataset name
const AjPStrschemaInputSchema name
AjBool RETURNtrue on success

Input
dataset:(Input)"Sequence" mart dataset name
schema:(Input)Schema name
Input & Output
seqin:(Modify)"Sequence" input object
Returns
AjBool:true on success

Description

Return attributes given a mart dataset, a mart host/path/port and a schemaname.

This function will be deleted once virtual schemas are phased out. Use with caution.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartattributesParse

Read a mart attributes buffer

Synopsis

Prototype
AjBool ajMartattributesParse (
      AjPSeqin seqin
);

TypeNameRead/WriteDescription
AjPSeqinseqinModifySeqin object holding mart info
AjBool RETURNTrue on success

Input & Output
seqin:(Modify)Seqin object holding mart info
Returns
AjBool:True on success

Description

Read a mart attributes buffer

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartGetFilters

Return filters given a mart dataset and a mart host/path/port

Synopsis

Prototype
AjBool ajMartGetFilters (
      AjPSeqin seqin,
      const AjPStr dataset
);

TypeNameRead/WriteDescription
AjPSeqinseqinModify"Sequence" input object
const AjPStrdatasetInput"Sequence" mart dataset name
AjBool RETURNtrue on success

Input
dataset:(Input)"Sequence" mart dataset name
Input & Output
seqin:(Modify)"Sequence" input object
Returns
AjBool:true on success

Description

Return filters given a mart dataset and a mart host/path/port

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartGetFiltersSchema

Return filters given a mart dataset, a mart host/path/port and a schema

Synopsis

Prototype
AjBool ajMartGetFiltersSchema (
      AjPSeqin seqin,
      const AjPStr dataset,
      const AjPStr schema
);

TypeNameRead/WriteDescription
AjPSeqinseqinModify"Sequence" input object
const AjPStrdatasetInput"Sequence" mart dataset name
const AjPStrschemaInput"Sequence" mart schema name
AjBool RETURNtrue on success

Input
dataset:(Input)"Sequence" mart dataset name
schema:(Input)"Sequence" mart schema name
Input & Output
seqin:(Modify)"Sequence" input object
Returns
AjBool:true on success

Description

Return filters given a mart dataset, a mart host/path/port and a schema

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartGetFiltersRetry

Retry a filters fetch using the main biomart registry site This routine should only be called after an ajMartGetFilters call followed by a ajMartfiltersParse has returned an error. That typically means that an external server has not provided all the filters fields, possibly due to outdated biomart software. As the main biomart registry site contains all the metadata for external marts (but not the marts themselves) it can be queried using the same dataset. The true mart server should always be tried first to minimise load on the main biomart site

Synopsis

Prototype
AjBool ajMartGetFiltersRetry (
      AjPSeqin seqin,
      const AjPStr dataset
);

TypeNameRead/WriteDescription
AjPSeqinseqinModify"Sequence" input object
const AjPStrdatasetInput"Sequence" mart dataset name
AjBool RETURNtrue on success

Input
dataset:(Input)"Sequence" mart dataset name
Input & Output
seqin:(Modify)"Sequence" input object
Returns
AjBool:true on success

Description

Retry a filters fetch using the main biomart registry site This routine should only be called after an ajMartGetFilters call followed by a ajMartfiltersParse has returned an error. That typically means that an external server has not provided all the filters fields, possibly due to outdated biomart software. As the main biomart registry site contains all the metadata for external marts (but not the marts themselves) it can be queried using the same dataset. The true mart server should always be tried first to minimise load on the main biomart site

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartfiltersParse

Parse a mart filters buffer

Synopsis

Prototype
AjBool ajMartfiltersParse (
      AjPSeqin seqin
);

TypeNameRead/WriteDescription
AjPSeqinseqinModifySeqin object holding mart info
AjBool RETURNTrue on success

Input & Output
seqin:(Modify)Seqin object holding mart info
Returns
AjBool:True on success

Description

Parse a mart filters buffer

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartFilterMatch

Associate filters with a given attribute table

Synopsis

Prototype
AjBool ajMartFilterMatch (
      AjPTable atab,
      const AjPMartFilter filt
);

TypeNameRead/WriteDescription
AjPTableatabModifyAttribute table
const AjPMartFilterfiltInputfilters
AjBool RETURNTrue on success

Input
filt:(Input)filters
Input & Output
atab:(Modify)Attribute table
Returns
AjBool:True on success

Description

Associate filters with a given attribute table

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartAssociate

Associate filters with attributes thgat can use them

Synopsis

Prototype
AjBool ajMartAssociate (
      AjPSeqin seqin
);

TypeNameRead/WriteDescription
AjPSeqinseqinModifySeqin object holding mart info
AjBool RETURNTrue on success

Input & Output
seqin:(Modify)Seqin object holding mart info
Returns
AjBool:True on success

Description

Associate filters with attributes thgat can use them

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartMakeQueryXml

Produce XML from an AjPMartqinfo object

Synopsis

Prototype
void ajMartMakeQueryXml (
      const AjPMartqinfo qinfo,
      AjPSeqin seqin
);

TypeNameRead/WriteDescription
const AjPMartqinfoqinfoInputMart qinfo object
AjPSeqinseqinModifySeqin object
void RETURN

Input
qinfo:(Input)Mart qinfo object
Input & Output
seqin:(Modify)Seqin object
Returns
void:No return value

Description

Produce XML from an AjPMartqinfo object

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartSendQuery

Send a query, given biomart query xml, to a mart server host/path/port

Synopsis

Prototype
AjBool ajMartSendQuery (
      AjPSeqin seqin
);

TypeNameRead/WriteDescription
AjPSeqinseqinModify"Sequence" input object
AjBool RETURNtrue on success

Input & Output
seqin:(Modify)"Sequence" input object
Returns
AjBool:true on success

Description

Send a query, given biomart query xml, to a mart server host/path/port

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartGetReghost

Return the Registry host name

Synopsis

Prototype
const AjPStr ajMartGetReghost (
      const AjPSeqin seqin
);

TypeNameRead/WriteDescription
const AjPSeqinseqinInputSeqin object
const AjPStr RETURNRegistry host name or NULL

Input
seqin:(Input)Seqin object
Returns
const AjPStr:Registry host name or NULL

Description

Return the Registry host name

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartGetRegpath

Return the Registry path name

Synopsis

Prototype
const AjPStr ajMartGetRegpath (
      const AjPSeqin seqin
);

TypeNameRead/WriteDescription
const AjPSeqinseqinInputSeqin object
const AjPStr RETURNRegistry host name or NULL

Input
seqin:(Input)Seqin object
Returns
const AjPStr:Registry host name or NULL

Description

Return the Registry path name

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartGetRegport

Return the Registry port

Synopsis

Prototype
ajuint ajMartGetRegport (
      const AjPSeqin seqin
);

TypeNameRead/WriteDescription
const AjPSeqinseqinInputSeqin object
ajuint RETURNRegistry port or 0

Input
seqin:(Input)Seqin object
Returns
ajuint:Registry port or 0

Description

Return the Registry port

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartGetMarthost

Return the Mart host name

Synopsis

Prototype
const AjPStr ajMartGetMarthost (
      const AjPSeqin seqin
);

TypeNameRead/WriteDescription
const AjPSeqinseqinInputSeqin object
const AjPStr RETURNMart host name or NULL

Input
seqin:(Input)Seqin object
Returns
const AjPStr:Mart host name or NULL

Description

Return the Mart host name

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartGetMartpath

Return the Mart path name

Synopsis

Prototype
const AjPStr ajMartGetMartpath (
      const AjPSeqin seqin
);

TypeNameRead/WriteDescription
const AjPSeqinseqinInputSeqin object
const AjPStr RETURNMart host name or NULL

Input
seqin:(Input)Seqin object
Returns
const AjPStr:Mart host name or NULL

Description

Return the Mart path name

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartGetMartport

Return the Mart port

Synopsis

Prototype
ajuint ajMartGetMartport (
      const AjPSeqin seqin
);

TypeNameRead/WriteDescription
const AjPSeqinseqinInputSeqin object
ajuint RETURNMart port or 0

Input
seqin:(Input)Seqin object
Returns
ajuint:Mart port or 0

Description

Return the Mart port

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartSetReghostC

Set the Registry host name

Synopsis

Prototype
AjBool ajMartSetReghostC (
      AjPSeqin seqin,
      const char* reghost
);

TypeNameRead/WriteDescription
AjPSeqinseqinModifySeqin object
const char*reghostInputRegistry name
AjBool RETURNTrue on success

Input
reghost:(Input)Registry name
Input & Output
seqin:(Modify)Seqin object
Returns
AjBool:True on success

Description

Set the Registry host name

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartSetRegpathC

Return the Registry path name

Synopsis

Prototype
AjBool ajMartSetRegpathC (
      AjPSeqin seqin,
      const char* regpath
);

TypeNameRead/WriteDescription
AjPSeqinseqinModifySeqin object
const char*regpathInputRegistry path
AjBool RETURNTrue on success

Input
regpath:(Input)Registry path
Input & Output
seqin:(Modify)Seqin object
Returns
AjBool:True on success

Description

Return the Registry path name

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartSetReghostS

Set the Registry host name

Synopsis

Prototype
AjBool ajMartSetReghostS (
      AjPSeqin seqin,
      const AjPStr reghost
);

TypeNameRead/WriteDescription
AjPSeqinseqinModifySeqin object
const AjPStrreghostInputRegistry name
AjBool RETURNTrue on success

Input
reghost:(Input)Registry name
Input & Output
seqin:(Modify)Seqin object
Returns
AjBool:True on success

Description

Set the Registry host name

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartSetRegpathS

Return the Registry path name

Synopsis

Prototype
AjBool ajMartSetRegpathS (
      AjPSeqin seqin,
      const AjPStr regpath
);

TypeNameRead/WriteDescription
AjPSeqinseqinModifySeqin object
const AjPStrregpathInputRegistry path
AjBool RETURNTrue on success

Input
regpath:(Input)Registry path
Input & Output
seqin:(Modify)Seqin object
Returns
AjBool:True on success

Description

Return the Registry path name

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartSetRegport

Return the Registry port

Synopsis

Prototype
AjBool ajMartSetRegport (
      AjPSeqin seqin,
      ajuint regport
);

TypeNameRead/WriteDescription
AjPSeqinseqinModifySeqin object
ajuintregportInputRegistry port
AjBool RETURNTrue on success

Input
regport:(Input)Registry port
Input & Output
seqin:(Modify)Seqin object
Returns
AjBool:True on success

Description

Return the Registry port

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartSetMarthostC

Set the Mart host name

Synopsis

Prototype
AjBool ajMartSetMarthostC (
      AjPSeqin seqin,
      const char* marthost
);

TypeNameRead/WriteDescription
AjPSeqinseqinModifySeqin object
const char*marthostInputMart name
AjBool RETURNTrue on success

Input
marthost:(Input)Mart name
Input & Output
seqin:(Modify)Seqin object
Returns
AjBool:True on success

Description

Set the Mart host name

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartSetMartpathC

Set the Mart path name

Synopsis

Prototype
AjBool ajMartSetMartpathC (
      AjPSeqin seqin,
      const char* martpath
);

TypeNameRead/WriteDescription
AjPSeqinseqinModifySeqin object
const char*martpathInputMart path
AjBool RETURNTrue on success

Input
martpath:(Input)Mart path
Input & Output
seqin:(Modify)Seqin object
Returns
AjBool:True on success

Description

Set the Mart path name

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartSetMarthostS

Set the Mart host name

Synopsis

Prototype
AjBool ajMartSetMarthostS (
      AjPSeqin seqin,
      const AjPStr marthost
);

TypeNameRead/WriteDescription
AjPSeqinseqinModifySeqin object
const AjPStrmarthostInputMart name
AjBool RETURNTrue on success

Input
marthost:(Input)Mart name
Input & Output
seqin:(Modify)Seqin object
Returns
AjBool:True on success

Description

Set the Mart host name

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartSetMartpathS

Set the Mart path name

Synopsis

Prototype
AjBool ajMartSetMartpathS (
      AjPSeqin seqin,
      const AjPStr martpath
);

TypeNameRead/WriteDescription
AjPSeqinseqinModifySeqin object
const AjPStrmartpathInputMart path
AjBool RETURNTrue on success

Input
martpath:(Input)Mart path
Input & Output
seqin:(Modify)Seqin object
Returns
AjBool:True on success

Description

Set the Mart path name

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartSetMartport

Set the Mart port

Synopsis

Prototype
AjBool ajMartSetMartport (
      AjPSeqin seqin,
      ajuint martport
);

TypeNameRead/WriteDescription
AjPSeqinseqinModifySeqin object
ajuintmartportInputMart port
AjBool RETURNTrue on success

Input
martport:(Input)Mart port
Input & Output
seqin:(Modify)Seqin object
Returns
AjBool:True on success

Description

Set the Mart port

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartFixRegistry

Try to fill in missing registry fields

Synopsis

Prototype
void ajMartFixRegistry (
      AjPSeqin seqin
);

TypeNameRead/WriteDescription
AjPSeqinseqinModifySeqin object
void RETURN

Input & Output
seqin:(Modify)Seqin object
Returns
void:No return value

Description

Try to fill in missing registry fields

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartFixMart

Try to fill in missing mart fields

Synopsis

Prototype
void ajMartFixMart (
      AjPSeqin seqin
);

TypeNameRead/WriteDescription
AjPSeqinseqinModifySeqin object
void RETURNTrue if valid

Input & Output
seqin:(Modify)Seqin object
Returns
void:No return value

Description

Try to fill in missing mart fields

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartAttachMartquery

Add a mart query object to a seqin object

Synopsis

Prototype
void ajMartAttachMartquery (
      AjPSeqin seqin,
      AjPMartquery mq
);

TypeNameRead/WriteDescription
AjPSeqinseqinModifySeqin object
AjPMartquerymqModifyMartquery object
void RETURN

Input & Output
seqin:(Modify)Seqin object
mq:(Modify)Martquery object
Returns
void:No return value

Description

Add a mart query object to a seqin object

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartGetMartqueryPtr

Return a seqin Query pointer

Synopsis

Prototype
AjPMartquery ajMartGetMartqueryPtr (
      const AjPSeqin seqin
);

TypeNameRead/WriteDescription
const AjPSeqinseqinInputSeqin object
AjPMartquery RETURNMartquery

Input
seqin:(Input)Seqin object
Returns
AjPMartquery:Martquery

Description

Return a seqin Query pointer

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajStrtokQuotR

Reentrant strtok that disallows tokenisation at delimiter characters if they are within quotation chracters e.g. tokenisation of -token1="a,b,c",-token2 will yield -token1="a,b,c" and -token2 if the delimstr contains ',' and the quotstr contains '"'

The source string is unchanged

Synopsis

Prototype
char* ajStrtokQuotR (
      const char* srcstr,
      const char* delimstr,
      const char* quotstr,
      const char** ptrptr,
      AjPStr* buf
);

TypeNameRead/WriteDescription
const char*srcstrInputSource string
const char*delimstrInputDelimiter string
const char*quotstrInputAllowable quotes(s)
const char**ptrptrInputSaved position in srcstr
AjPStr*bufOutputResults buffer (the token)
char* RETURNPointer to start of token (in buf) or NULL

Input
srcstr:(Input)Source string
delimstr:(Input)Delimiter string
quotstr:(Input)Allowable quotes(s)
ptrptr:(Input)Saved position in srcstr
Output
buf:(Output)Results buffer (the token)
Returns
char*:Pointer to start of token (in buf) or NULL

Description

Reentrant strtok that disallows tokenisation at delimiter characters if they are within quotation chracters e.g. tokenisation of -token1="a,b,c",-token2 will yield -token1="a,b,c" and -token2 if the delimstr contains ',' and the quotstr contains '"'

The source string is unchanged

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartParseParameters

Parses attribute and filter strings and load a given Qinfo object with them

Synopsis

Prototype
AjBool ajMartParseParameters (
      AjPMartqinfo qinfo,
      const AjPStr atts,
      const AjPStr filts,
      ajuint idx
);

TypeNameRead/WriteDescription
AjPMartqinfoqinfoModifyQuery object
const AjPStrattsInputAttributes
const AjPStrfiltsInputFilters
ajuintidxInputdataset index
AjBool RETURNFalse on parsing or loading error

Input
atts:(Input)Attributes
filts:(Input)Filters
idx:(Input)dataset index
Input & Output
qinfo:(Modify)Query object
Returns
AjBool:False on parsing or loading error

Description

Parses attribute and filter strings and load a given Qinfo object with them

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartSetQuerySchemaC

Set the Qinfo Virtual Schema field

Synopsis

Prototype
void ajMartSetQuerySchemaC (
      AjPMartqinfo qinfo,
      const char* schema
);

TypeNameRead/WriteDescription
AjPMartqinfoqinfoModifySeqin object
const char*schemaInputVirtual schema
void RETURN

Input
schema:(Input)Virtual schema
Input & Output
qinfo:(Modify)Seqin object
Returns
void:No return value

Description

Set the Qinfo Virtual Schema field

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartSetQueryVersionC

Set the Qinfo Software Version field

Synopsis

Prototype
void ajMartSetQueryVersionC (
      AjPMartqinfo qinfo,
      const char* version
);

TypeNameRead/WriteDescription
AjPMartqinfoqinfoModifySeqin object
const char*versionInputVersion
void RETURN

Input
version:(Input)Version
Input & Output
qinfo:(Modify)Seqin object
Returns
void:No return value

Description

Set the Qinfo Software Version field

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartSetQueryFormatC

Set the Qinfo Format field

Synopsis

Prototype
void ajMartSetQueryFormatC (
      AjPMartqinfo qinfo,
      const char* format
);

TypeNameRead/WriteDescription
AjPMartqinfoqinfoModifySeqin object
const char*formatInputFormat
void RETURN

Input
format:(Input)Format
Input & Output
qinfo:(Modify)Seqin object
Returns
void:No return value

Description

Set the Qinfo Format field

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartSetQueryCount

Set the Qinfo Count (unique ID count only) field

Synopsis

Prototype
void ajMartSetQueryCount (
      AjPMartqinfo qinfo,
      AjBool count
);

TypeNameRead/WriteDescription
AjPMartqinfoqinfoModifySeqin object
AjBoolcountInputcount
void RETURN

Input
count:(Input)count
Input & Output
qinfo:(Modify)Seqin object
Returns
void:No return value

Description

Set the Qinfo Count (unique ID count only) field

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartSetQueryHeader

Set the Qinfo Header (column title) field

Synopsis

Prototype
void ajMartSetQueryHeader (
      AjPMartqinfo qinfo,
      AjBool header
);

TypeNameRead/WriteDescription
AjPMartqinfoqinfoModifySeqin object
AjBoolheaderInputHeader
void RETURN

Input
header:(Input)Header
Input & Output
qinfo:(Modify)Seqin object
Returns
void:No return value

Description

Set the Qinfo Header (column title) field

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartSetQueryUnique

Set the Qinfo Unique rows field

Synopsis

Prototype
void ajMartSetQueryUnique (
      AjPMartqinfo qinfo,
      AjBool unique
);

TypeNameRead/WriteDescription
AjPMartqinfoqinfoModifySeqin object
AjBooluniqueInputUnique
void RETURN

Input
unique:(Input)Unique
Input & Output
qinfo:(Modify)Seqin object
Returns
void:No return value

Description

Set the Qinfo Unique rows field

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartSetQueryStamp

Set the Qinfo Completion Stamp ([success]) field

Synopsis

Prototype
void ajMartSetQueryStamp (
      AjPMartqinfo qinfo,
      AjBool stamp
);

TypeNameRead/WriteDescription
AjPMartqinfoqinfoModifySeqin object
AjBoolstampInputStamp
void RETURN

Input
stamp:(Input)Stamp
Input & Output
qinfo:(Modify)Seqin object
Returns
void:No return value

Description

Set the Qinfo Completion Stamp ([success]) field

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartSetQueryVerify

Set the Qinfo verification field to test that given atts & filts exist in the dataset

Synopsis

Prototype
void ajMartSetQueryVerify (
      AjPMartqinfo qinfo,
      AjBool verify
);

TypeNameRead/WriteDescription
AjPMartqinfoqinfoModifySeqin object
AjBoolverifyInputverify flag
void RETURN

Input
verify:(Input)verify flag
Input & Output
qinfo:(Modify)Seqin object
Returns
void:No return value

Description

Set the Qinfo verification field to test that given atts & filts exist in the dataset

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartSetQueryDatasetName

Set a Qinfo dataset name field

Synopsis

Prototype
void ajMartSetQueryDatasetName (
      AjPMartqinfo qinfo,
      const AjPStr name,
      ajuint idx
);

TypeNameRead/WriteDescription
AjPMartqinfoqinfoModifySeqin object
const AjPStrnameInputName
ajuintidxInputDataset number (0->n-1)
void RETURN

Input
name:(Input)Name
idx:(Input)Dataset number (0->n-1)
Input & Output
qinfo:(Modify)Seqin object
Returns
void:No return value

Description

Set a Qinfo dataset name field

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartSetQueryDatasetInterfaceC

Set a Qinfo dataset interface field

Synopsis

Prototype
void ajMartSetQueryDatasetInterfaceC (
      AjPMartqinfo qinfo,
      const char* iface,
      ajuint idx
);

TypeNameRead/WriteDescription
AjPMartqinfoqinfoModifySeqin object
const char*ifaceInputInterface
ajuintidxInputDataset number (0->n-1)
void RETURN

Input
iface:(Input)Interface
idx:(Input)Dataset number (0->n-1)
Input & Output
qinfo:(Modify)Seqin object
Returns
void:No return value

Description

Set a Qinfo dataset interface field

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartCheckQinfo

Try to fill in missing fields and check user attributes/filters

Synopsis

Prototype
AjBool ajMartCheckQinfo (
      AjPSeqin seqin,
      AjPMartqinfo qinfo
);

TypeNameRead/WriteDescription
AjPSeqinseqinModifySeqin object
AjPMartqinfoqinfoModifyMart qinfo object
AjBool RETURNTrue if valid

Input & Output
seqin:(Modify)Seqin object
qinfo:(Modify)Mart qinfo object
Returns
AjBool:True if valid

Description

Try to fill in missing fields and check user attributes/filters

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartGetConfiguration

Return config info given a mart dataset and a mart host/path/port

Synopsis

Prototype
AjBool ajMartGetConfiguration (
      AjPSeqin seqin,
      const AjPStr dataset
);

TypeNameRead/WriteDescription
AjPSeqinseqinModify"Sequence" input object
const AjPStrdatasetInput"Sequence" mart dataset name
AjBool RETURNtrue on success

Input
dataset:(Input)"Sequence" mart dataset name
Input & Output
seqin:(Modify)"Sequence" input object
Returns
AjBool:true on success

Description

Return config info given a mart dataset and a mart host/path/port

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartconfigurationParse

Parse a mart configuration buffer

Synopsis

Prototype
AjBool ajMartconfigurationParse (
      AjPSeqin seqin
);

TypeNameRead/WriteDescription
AjPSeqinseqinModifySeqin object holding mart info
AjBool RETURNTrue on success

Input & Output
seqin:(Modify)Seqin object holding mart info
Returns
AjBool:True on success

Description

Parse a mart configuration buffer

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartattributesPageSort

Sort attributes based on page name

Synopsis

Prototype
AjBool ajMartattributesPageSort (
      AjPSeqin seqin
);

TypeNameRead/WriteDescription
AjPSeqinseqinModifySeqin object holding attribute info
AjBool RETURNTrue on success

Input & Output
seqin:(Modify)Seqin object holding attribute info
Returns
AjBool:True on success

Description

Sort attributes based on page name

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartNameIsNucC

Test whether name matches any of the set of known nucleic acid biomart terms

Synopsis

Prototype
AjBool ajMartNameIsNucC (
      const char* name
);

TypeNameRead/WriteDescription
const char*nameInputName
AjBool RETURNTrue if nucleic acid name match

Input
name:(Input)Name
Returns
AjBool:True if nucleic acid name match

Description

Test whether name matches any of the set of known nucleic acid biomart terms

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartNameIsProtC

Test whether name matches any of the set of known protein biomart terms

Synopsis

Prototype
AjBool ajMartNameIsProtC (
      const char* name
);

TypeNameRead/WriteDescription
const char*nameInputName
AjBool RETURNTrue if nucleic acid name match

Input
name:(Input)Name
Returns
AjBool:True if nucleic acid name match

Description

Test whether name matches any of the set of known protein biomart terms

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartTableNameIsNuc

Test whether table 'name' value matches any of the set of known nucleic acid biomart terms

Synopsis

Prototype
AjBool ajMartTableNameIsNuc (
      const AjPTable t
);

TypeNameRead/WriteDescription
const AjPTabletInputTable
AjBool RETURNTrue if nucleic acid name match

Input
t:(Input)Table
Returns
AjBool:True if nucleic acid name match

Description

Test whether table 'name' value matches any of the set of known nucleic acid biomart terms

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartTableNameIsProt

Test whether table 'name' value matches any of the set of known protein biomart terms

Synopsis

Prototype
AjBool ajMartTableNameIsProt (
      const AjPTable t
);

TypeNameRead/WriteDescription
const AjPTabletInputTable
AjBool RETURNTrue if protein name match

Input
t:(Input)Table
Returns
AjBool:True if protein name match

Description

Test whether table 'name' value matches any of the set of known protein biomart terms

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartCheckHeader

Return an array of attribute names in the order in which they are returned by the biomart server. Requires that the header flag was set and that an attribute query has previously loaded to MartAttribute field.

Synopsis

Prototype
AjPStr* ajMartCheckHeader (
      AjPSeqin seqin,
      AjPMartqinfo qinfo
);

TypeNameRead/WriteDescription
AjPSeqinseqinModifySeqin object
AjPMartqinfoqinfoModifyMart qinfo object
AjPStr* RETURNArray of attribute names terminated by a NULL entry. or NULL if mapping cannot be done

Input & Output
seqin:(Modify)Seqin object
qinfo:(Modify)Mart qinfo object
Returns
AjPStr*:Array of attribute names terminated by a NULL entry. or NULL if mapping cannot be done

Description

Return an array of attribute names in the order in which they are returned by the biomart server. Requires that the header flag was set and that an attribute query has previously loaded to MartAttribute field.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajMartDecodeHname

Decode directory name into host/path/port

Synopsis

Prototype
void ajMartDecodeHname (
      const AjPStr dir,
      AjPStr* host,
      AjPStr* path,
      ajuint* port
);

TypeNameRead/WriteDescription
const AjPStrdirInputEncoded directory name
AjPStr*hostOutputHost
AjPStr*pathOutputPath
ajuint*portOutputPort
void RETURN

Input
dir:(Input)Encoded directory name
Output
host:(Output)Host
path:(Output)Path
port:(Output)Port
Returns
void:No return value

Description

Decode directory name into host/path/port

See Also

See other functions in this section

Availability

In release 6.4.0