java.lang.Object
- org.biojava.nbio.ontology.obo.OboFileHandler

All Implemented Interfaces:

OboFileEventListener
```
public class OboFileHandler
extends Object
implements OboFileEventListener
```
A file handler for .obo files

Author:

Andreas Prlic

Field Summary

Fields
Modifier and Type	Field	Description
`static String`	`ALT_ID`
`static String`	`BROAD_SYNONYM`
`static String`	`COMMENT`
`static String`	`DEF`
`static String`	`DISJOINT_FROM`
`static String`	`EXACT_SYNONYM`
`static String`	`ID_KEY`
`static String`	`INTERSECTION_OF`
`static String`	`IS_A`
`static String`	`IS_OBSOLETE`
`static String`	`NAME`
`static String`	`NAMESPACE`
`static String`	`NARROW_SYNONYM`
`static String`	`ONTOLOGY`
`static String`	`REL_SYNONYM`
`static String`	`RELATIONSHIP`
`static String`	`REPLACED_BY`
`static String`	`SUBSET`
`static String`	`SYNONYM`
`static String`	`TERM`
`static String`	`TYPEDEF`
`static String`	`XREF_ANALOG`

Constructor Summary

Constructors
Constructor Description

OboFileHandler(Ontology ontology)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`documentEnd()`	end of parsing a new OBO file
`void`	`documentStart()`	starting to parse a new OBO file
`void`	`newKey(String key, String value)`	found a new key in the file
`void`	`newOboFileHeader()`	parsed a new OBO file header
`void`	`newStanza(String stanza)`	parsed a new stanza in the file
`void`	`newSynonym(Synonym synonym)`	a new synonym has been found

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - TERM
```
public static final String TERM
```
    See Also:
    
    Constant Field Values
  - TYPEDEF
```
public static final String TYPEDEF
```
    See Also:
    
    Constant Field Values
  - ONTOLOGY
```
public static final String ONTOLOGY
```
    See Also:
    
    Constant Field Values
  - ID_KEY
```
public static final String ID_KEY
```
    See Also:
    
    Constant Field Values
  - SYNONYM
```
public static final String SYNONYM
```
    See Also:
    
    Constant Field Values
  - EXACT_SYNONYM
```
public static final String EXACT_SYNONYM
```
    See Also:
    
    Constant Field Values
  - BROAD_SYNONYM
```
public static final String BROAD_SYNONYM
```
    See Also:
    
    Constant Field Values
  - NARROW_SYNONYM
```
public static final String NARROW_SYNONYM
```
    See Also:
    
    Constant Field Values
  - REL_SYNONYM
```
public static final String REL_SYNONYM
```
    See Also:
    
    Constant Field Values
  - NAME
```
public static final String NAME
```
    See Also:
    
    Constant Field Values
  - DEF
```
public static final String DEF
```
    See Also:
    
    Constant Field Values
  - XREF_ANALOG
```
public static final String XREF_ANALOG
```
    See Also:
    
    Constant Field Values
  - COMMENT
```
public static final String COMMENT
```
    See Also:
    
    Constant Field Values
  - IS_A
```
public static final String IS_A
```
    See Also:
    
    Constant Field Values
  - IS_OBSOLETE
```
public static final String IS_OBSOLETE
```
    See Also:
    
    Constant Field Values
  - RELATIONSHIP
```
public static final String RELATIONSHIP
```
    See Also:
    
    Constant Field Values
  - DISJOINT_FROM
```
public static final String DISJOINT_FROM
```
    See Also:
    
    Constant Field Values
  - SUBSET
```
public static final String SUBSET
```
    See Also:
    
    Constant Field Values
  - INTERSECTION_OF
```
public static final String INTERSECTION_OF
```
    See Also:
    
    Constant Field Values
  - NAMESPACE
```
public static final String NAMESPACE
```
    See Also:
    
    Constant Field Values
  - REPLACED_BY
```
public static final String REPLACED_BY
```
    See Also:
    
    Constant Field Values
  - ALT_ID
```
public static final String ALT_ID
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - OboFileHandler
```
public OboFileHandler(Ontology ontology)
```
- Method Detail
  - documentEnd
```
public void documentEnd()
```
    Description copied from interface: OboFileEventListener
    
    end of parsing a new OBO file
    
    Specified by:
    
    documentEnd in interface OboFileEventListener
  - documentStart
```
public void documentStart()
```
    Description copied from interface: OboFileEventListener
    
    starting to parse a new OBO file
    
    Specified by:
    
    documentStart in interface OboFileEventListener
  - newOboFileHeader
```
public void newOboFileHeader()
```
    Description copied from interface: OboFileEventListener
    
    parsed a new OBO file header
    
    Specified by:
    
    newOboFileHeader in interface OboFileEventListener
  - newStanza
```
public void newStanza(String stanza)
```
    Description copied from interface: OboFileEventListener
    
    parsed a new stanza in the file
    
    Specified by:
    
    newStanza in interface OboFileEventListener
  - newKey
```
public void newKey(String key,
                   String value)
```
    Description copied from interface: OboFileEventListener
    
    found a new key in the file
    
    Specified by:
    
    newKey in interface OboFileEventListener
  - newSynonym
```
public void newSynonym(Synonym synonym)
```
    Description copied from interface: OboFileEventListener
    
    a new synonym has been found
    
    Specified by:
    
    newSynonym in interface OboFileEventListener

Class OboFileHandler

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

TERM

TYPEDEF

ONTOLOGY

ID_KEY

SYNONYM

EXACT_SYNONYM

BROAD_SYNONYM

NARROW_SYNONYM

REL_SYNONYM

NAME

DEF

XREF_ANALOG

COMMENT

IS_A

IS_OBSOLETE

RELATIONSHIP

DISJOINT_FROM

SUBSET

INTERSECTION_OF

NAMESPACE

REPLACED_BY

ALT_ID

Constructor Detail

OboFileHandler

Method Detail

documentEnd

documentStart

newOboFileHeader

newStanza

newKey

newSynonym