Package org.biojava.ontology.obo
Class OboFileHandler
- java.lang.Object
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- org.biojava.ontology.obo.OboFileHandler
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- All Implemented Interfaces:
OboFileEventListener
public class OboFileHandler extends java.lang.Object implements OboFileEventListener
A file handler for .obo files- Author:
- Andreas Prlic
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
ALT_ID
static java.lang.String
BROAD_SYNONYM
static java.lang.String
COMMENT
static java.lang.String
DEF
static java.lang.String
DISJOINT_FROM
static java.lang.String
EXACT_SYNONYM
static java.lang.String
ID_KEY
static java.lang.String
INTERSECTION_OF
static java.lang.String
IS_A
static java.lang.String
IS_OBSOLETE
static java.lang.String
NAME
static java.lang.String
NARROW_SYNONYM
static java.lang.String
ONTOLOGY
static java.lang.String
REL_SYNONYM
static java.lang.String
RELATIONSHIP
static java.lang.String
SUBSET
static java.lang.String
SYNONYM
static java.lang.String
TERM
static java.lang.String
TYPEDEF
static java.lang.String
XREF_ANALOG
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Constructor Summary
Constructors Constructor Description OboFileHandler(Ontology ontology)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
documentEnd()
end of parsing a new OBO filevoid
documentStart()
starting to parse a new OBO filevoid
newKey(java.lang.String key, java.lang.String value)
found a new key in the filevoid
newOboFileHeader()
parsed a new OBO file headervoid
newStanza(java.lang.String stanza)
parsed a new stanza in the filevoid
newSynonym(Synonym synonym)
a new synonym has been found
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Field Detail
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TERM
public static final java.lang.String TERM
- See Also:
- Constant Field Values
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TYPEDEF
public static final java.lang.String TYPEDEF
- See Also:
- Constant Field Values
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ONTOLOGY
public static final java.lang.String ONTOLOGY
- See Also:
- Constant Field Values
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ID_KEY
public static final java.lang.String ID_KEY
- See Also:
- Constant Field Values
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SYNONYM
public static final java.lang.String SYNONYM
- See Also:
- Constant Field Values
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EXACT_SYNONYM
public static final java.lang.String EXACT_SYNONYM
- See Also:
- Constant Field Values
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BROAD_SYNONYM
public static final java.lang.String BROAD_SYNONYM
- See Also:
- Constant Field Values
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NARROW_SYNONYM
public static final java.lang.String NARROW_SYNONYM
- See Also:
- Constant Field Values
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REL_SYNONYM
public static final java.lang.String REL_SYNONYM
- See Also:
- Constant Field Values
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NAME
public static final java.lang.String NAME
- See Also:
- Constant Field Values
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DEF
public static final java.lang.String DEF
- See Also:
- Constant Field Values
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XREF_ANALOG
public static final java.lang.String XREF_ANALOG
- See Also:
- Constant Field Values
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COMMENT
public static final java.lang.String COMMENT
- See Also:
- Constant Field Values
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IS_A
public static final java.lang.String IS_A
- See Also:
- Constant Field Values
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IS_OBSOLETE
public static final java.lang.String IS_OBSOLETE
- See Also:
- Constant Field Values
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RELATIONSHIP
public static final java.lang.String RELATIONSHIP
- See Also:
- Constant Field Values
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DISJOINT_FROM
public static final java.lang.String DISJOINT_FROM
- See Also:
- Constant Field Values
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SUBSET
public static final java.lang.String SUBSET
- See Also:
- Constant Field Values
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INTERSECTION_OF
public static final java.lang.String INTERSECTION_OF
- See Also:
- Constant Field Values
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ALT_ID
public static final java.lang.String ALT_ID
- See Also:
- Constant Field Values
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Constructor Detail
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OboFileHandler
public OboFileHandler(Ontology ontology)
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Method Detail
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documentEnd
public void documentEnd()
Description copied from interface:OboFileEventListener
end of parsing a new OBO file- Specified by:
documentEnd
in interfaceOboFileEventListener
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documentStart
public void documentStart()
Description copied from interface:OboFileEventListener
starting to parse a new OBO file- Specified by:
documentStart
in interfaceOboFileEventListener
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newOboFileHeader
public void newOboFileHeader()
Description copied from interface:OboFileEventListener
parsed a new OBO file header- Specified by:
newOboFileHeader
in interfaceOboFileEventListener
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newStanza
public void newStanza(java.lang.String stanza)
Description copied from interface:OboFileEventListener
parsed a new stanza in the file- Specified by:
newStanza
in interfaceOboFileEventListener
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newKey
public void newKey(java.lang.String key, java.lang.String value)
Description copied from interface:OboFileEventListener
found a new key in the file- Specified by:
newKey
in interfaceOboFileEventListener
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newSynonym
public void newSynonym(Synonym synonym)
Description copied from interface:OboFileEventListener
a new synonym has been found- Specified by:
newSynonym
in interfaceOboFileEventListener
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