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 final String

ALT_ID

static final String

BROAD_SYNONYM

static final String

COMMENT

static final String

DEF

static final String

DISJOINT_FROM

static final String

EXACT_SYNONYM

static final String

ID_KEY

static final String

INTERSECTION_OF

static final String

IS_A

static final String

IS_OBSOLETE

static final String

NAME

static final String

NARROW_SYNONYM

static final String

ONTOLOGY

static final String

REL_SYNONYM

static final String

RELATIONSHIP

static final String

SUBSET

static final String

SYNONYM

static final String

TERM

static final String

TYPEDEF

static final String

XREF_ANALOG
Constructor Summary

Constructors

Constructor

Description

OboFileHandler(Ontology ontology)
Method Summary

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 Details
- 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
- ALT_ID
  
  public static final String ALT_ID
  See Also:
  
  Constant Field Values
Constructor Details
- OboFileHandler
  
  public OboFileHandler(Ontology ontology)
Method Details
- 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 Details

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

ALT_ID

Constructor Details

OboFileHandler

Method Details

documentEnd

documentStart

newOboFileHeader

newStanza

newKey

newSynonym