cytoscape.data.servers
Class BioDataServer
java.lang.Object
cytoscape.data.servers.BioDataServer
- public class BioDataServer
- extends Object
Constructor Summary |
BioDataServer()
|
BioDataServer(String serverName)
serverName is either an RMI URI, or a manifest file which says what files
to load into an in-process server; the manifest, the annotations, and the
ontologies, may be files on a filesystem, files in a jar, or files
retrieved by HTTP
Mod. by Kei (9/10/2005): 1. |
Method Summary |
void |
addAnnotation(cytoscape.data.annotation.Annotation annotation)
|
void |
addThesaurus(String species,
cytoscape.data.synonyms.Thesaurus thesaurus)
|
void |
clear()
|
String |
describe()
|
String[][] |
getAllAnnotations(cytoscape.data.annotation.AnnotationDescription description,
String entity)
|
String[] |
getAllCommonNames(String species,
String commonName)
|
cytoscape.data.annotation.Annotation |
getAnnotation(cytoscape.data.annotation.AnnotationDescription description)
|
cytoscape.data.annotation.Annotation |
getAnnotation(String species,
String curator,
String type)
|
int |
getAnnotationCount()
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cytoscape.data.annotation.AnnotationDescription[] |
getAnnotationDescriptions()
|
String |
getCanonicalName(String species,
String commonName)
|
int[] |
getClassifications(cytoscape.data.annotation.AnnotationDescription description,
String entity)
|
int[] |
getClassifications(String species,
String curator,
String type,
String entity)
|
String |
getCommonName(String species,
String canonicalName)
|
void |
loadAnnotationFiles(String[] annotationFilenames,
String[] ontologyFilenames)
|
void |
loadObo(String[] annotationFilenames,
String[] ontologyFilenames)
|
void |
loadThesaurusFiles(String[] thesaurusFilenames)
|
void |
loadThesaurusFiles2(String[] thesaurusFilenames)
|
cytoscape.data.annotation.Ontology[] |
readOntologyFlatFiles(String[] ontologyFilenames)
|
cytoscape.data.annotation.Ontology[] |
readOntologyFlatFiles2(String[] ontologyFilenames)
|
BioDataServer
public BioDataServer(String serverName)
throws Exception
- serverName is either an RMI URI, or a manifest file which says what files
to load into an in-process server; the manifest, the annotations, and the
ontologies, may be files on a filesystem, files in a jar, or files
retrieved by HTTP
Mod. by Kei (9/10/2005): 1. Read new obo file and gene_association file
format. 2. Wrote a taxon number <-> taxon name converter. This function
is based on the list in the file, users need to put the file in the dir.
Bio Data Server manages ontologies mapped onto
CyAttributes This can be managed through GO Mapper GUI. kono(4/12/2006)
BioDataServer
public BioDataServer()
throws Exception
readOntologyFlatFiles
public cytoscape.data.annotation.Ontology[] readOntologyFlatFiles(String[] ontologyFilenames)
throws Exception
- Throws:
Exception
readOntologyFlatFiles2
public cytoscape.data.annotation.Ontology[] readOntologyFlatFiles2(String[] ontologyFilenames)
throws Exception
- Throws:
Exception
loadObo
public void loadObo(String[] annotationFilenames,
String[] ontologyFilenames)
throws Exception
- Throws:
Exception
loadAnnotationFiles
public void loadAnnotationFiles(String[] annotationFilenames,
String[] ontologyFilenames)
throws Exception
- Throws:
Exception
loadThesaurusFiles
public void loadThesaurusFiles(String[] thesaurusFilenames)
throws Exception
- Throws:
Exception
loadThesaurusFiles2
public void loadThesaurusFiles2(String[] thesaurusFilenames)
throws Exception
- Throws:
Exception
clear
public void clear()
addAnnotation
public void addAnnotation(cytoscape.data.annotation.Annotation annotation)
getAnnotationCount
public int getAnnotationCount()
getAnnotationDescriptions
public cytoscape.data.annotation.AnnotationDescription[] getAnnotationDescriptions()
getAnnotation
public cytoscape.data.annotation.Annotation getAnnotation(String species,
String curator,
String type)
getAnnotation
public cytoscape.data.annotation.Annotation getAnnotation(cytoscape.data.annotation.AnnotationDescription description)
getClassifications
public int[] getClassifications(String species,
String curator,
String type,
String entity)
getClassifications
public int[] getClassifications(cytoscape.data.annotation.AnnotationDescription description,
String entity)
getAllAnnotations
public String[][] getAllAnnotations(cytoscape.data.annotation.AnnotationDescription description,
String entity)
describe
public String describe()
addThesaurus
public void addThesaurus(String species,
cytoscape.data.synonyms.Thesaurus thesaurus)
getCanonicalName
public String getCanonicalName(String species,
String commonName)
getAllCommonNames
public String[] getAllCommonNames(String species,
String commonName)
getCommonName
public String getCommonName(String species,
String canonicalName)