org.biojava.ontology.obo
Class OboFileHandler

java.lang.Object
  extended by org.biojava.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
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 NARROW_SYNONYM
           
static String ONTOLOGY
           
static String REL_SYNONYM
           
static String RELATIONSHIP
           
static String SUBSET
           
static String SYNONYM
           
static String TERM
           
static String TYPEDEF
           
static String XREF_ANALOG
           
 
Constructor Summary
OboFileHandler(Ontology ontology)
           
 
Method Summary
 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

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