owltools.gaf
Class GAFParser
java.lang.Object
owltools.gaf.GAFParser
public class GAFParser
- extends Object
- Author:
- Shahid Manzoor
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
LOG
protected static org.apache.log4j.Logger LOG
DB
public static final int DB
- See Also:
- Constant Field Values
DB_OBJECT_ID
public static final int DB_OBJECT_ID
- See Also:
- Constant Field Values
DB_OBJECT_SYMBOL
public static final int DB_OBJECT_SYMBOL
- See Also:
- Constant Field Values
QUALIFIER
public static final int QUALIFIER
- See Also:
- Constant Field Values
GOID
public static final int GOID
- See Also:
- Constant Field Values
REFERENCE
public static final int REFERENCE
- See Also:
- Constant Field Values
EVIDENCE
public static final int EVIDENCE
- See Also:
- Constant Field Values
WITH
public static final int WITH
- See Also:
- Constant Field Values
ASPECT
public static final int ASPECT
- See Also:
- Constant Field Values
DB_OBJECT_NAME
public static final int DB_OBJECT_NAME
- See Also:
- Constant Field Values
DB_OBJECT_SYNONYM
public static final int DB_OBJECT_SYNONYM
- See Also:
- Constant Field Values
DB_OBJECT_TYPE
public static final int DB_OBJECT_TYPE
- See Also:
- Constant Field Values
TAXON
public static final int TAXON
- See Also:
- Constant Field Values
DATE
public static final int DATE
- See Also:
- Constant Field Values
ASSIGNED_BY
public static final int ASSIGNED_BY
- See Also:
- Constant Field Values
ANNOTATION_XP
public static final int ANNOTATION_XP
- See Also:
- Constant Field Values
GENE_PRODUCT_ISOFORM
public static final int GENE_PRODUCT_ISOFORM
- See Also:
- Constant Field Values
GAFParser
public GAFParser()
getAnnotationRuleViolations
public List<Object> getAnnotationRuleViolations()
next
public boolean next()
throws IOException
- Try to parse a next line, may skip lines until a line is parsed successfully or the file ends.
- Returns:
- true, if there is a next line.
- Throws:
IOException
getCurrentRow
public String getCurrentRow()
init
public void init()
addParserListener
public void addParserListener(GafParserListener listener)
remoteParserListener
public void remoteParserListener(GafParserListener listener)
parse
public void parse(Reader reader)
parse
public void parse(String file)
throws IOException,
URISyntaxException
- Parameters:
file
- is the location of the gaf file. The location
could be http url, absolute path and uri. The could refer to a gaf file or compressed gaf (gzip fle).
- Throws:
IOException
URISyntaxException
parse
public void parse(File gaf_file)
throws IOException
- Throws:
IOException
getDb
public String getDb()
getDbObjectId
public String getDbObjectId()
getDbObjectSymbol
public String getDbObjectSymbol()
getQualifier
public String getQualifier()
getGOId
public String getGOId()
getReference
public String getReference()
getEvidence
public String getEvidence()
getWith
public String getWith()
getAspect
public String getAspect()
getDbObjectName
public String getDbObjectName()
getDbObjectSynonym
public String getDbObjectSynonym()
getDBObjectType
public String getDBObjectType()
getTaxon
public String getTaxon()
getDate
public String getDate()
getAssignedBy
public String getAssignedBy()
getAnnotationExtension
public String getAnnotationExtension()
getGeneProjectFormId
public String getGeneProjectFormId()
getLineNumber
public int getLineNumber()
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