public class OpenAnnotationRDFWriter extends Object
GeneAnnotation
objects.
TODOs:
- use subProperties of hasBody and hasTarget?
- use subClass of oa:Annotation
- use own vocabulary for evidence
- fix evidence
- decide on policy for isoforms
- vocabulary for GPAD relation
- decide on model for annotation extensions
- add all GPAD fields
- include option to have labels and other data from bioentities (tho expected to come from elsewhere)
- decide on URI policy for bioentities, entities in WITH column
- many more things...Constructor and Description |
---|
OpenAnnotationRDFWriter()
Creates a new writer, using the default output format (turtle)
|
OpenAnnotationRDFWriter(String outputFormat) |
Modifier and Type | Method and Description |
---|---|
void |
add(Bioentity bioentity)
Adds a single
Bioentity to a model |
void |
add(GeneAnnotation ann)
Adds a single
GeneAnnotation to a model |
void |
addHeaderInfo(GafDocument gdoc)
Adds header info from a GAF, use the comments from the
GafDocument . |
void |
createModel(GafDocument gdoc)
Generate an RDF model from a GAF Document
|
void |
setGafMode()
If set, calling {
write(GafDocument, File) generates bioentities plus annotations (as in a GAF file) |
void |
setGpadfMode()
If set, calling {
write(GafDocument, File) generates annotations only (as in a GPAD file)
This is the default |
void |
setGpifMode()
If set, calling {
write(GafDocument, File) generates bioentities only (as in a GPI file) |
void |
write(GafDocument gdoc,
File ttl) |
void |
write(GafDocument gdoc,
PrintStream out)
Writes associations from GAF document as RDF on out
|
void |
write(GafDocument gdoc,
String path) |
public OpenAnnotationRDFWriter()
public OpenAnnotationRDFWriter(String outputFormat)
outputFormat
- - any format accepted by Jenapublic void setGafMode()
write(GafDocument, File)
generates bioentities plus annotations (as in a GAF file)public void setGpadfMode()
write(GafDocument, File)
generates annotations only (as in a GPAD file)
This is the defaultpublic void setGpifMode()
write(GafDocument, File)
generates bioentities only (as in a GPI file)public void write(GafDocument gdoc, PrintStream out)
gdoc
- out
- public void write(GafDocument gdoc, File ttl) throws FileNotFoundException
FileNotFoundException
public void write(GafDocument gdoc, String path) throws FileNotFoundException
FileNotFoundException
public void createModel(GafDocument gdoc)
gdoc
- public void addHeaderInfo(GafDocument gdoc)
GafDocument
.gdoc
- public void add(GeneAnnotation ann)
GeneAnnotation
to a modelann
- Copyright © 2010-2015. All Rights Reserved.