public class GAFParser extends Object
Modifier and Type | Field and Description |
---|---|
static int |
ANNOTATION_XP |
static int |
ASPECT |
static int |
ASSIGNED_BY |
static int |
DATE |
static int |
DB |
static int |
DB_OBJECT_ID |
static int |
DB_OBJECT_NAME |
static int |
DB_OBJECT_SYMBOL |
static int |
DB_OBJECT_SYNONYM |
static int |
DB_OBJECT_TYPE |
static int |
EVIDENCE |
static int |
GENE_PRODUCT_ISOFORM |
static int |
GOID |
protected static org.apache.log4j.Logger |
LOG |
static int |
QUALIFIER |
static int |
REFERENCE |
static int |
TAXON |
static int |
WITH |
Constructor and Description |
---|
GAFParser() |
protected static org.apache.log4j.Logger LOG
public static final int DB
public static final int DB_OBJECT_ID
public static final int DB_OBJECT_SYMBOL
public static final int QUALIFIER
public static final int GOID
public static final int REFERENCE
public static final int EVIDENCE
public static final int WITH
public static final int ASPECT
public static final int DB_OBJECT_NAME
public static final int DB_OBJECT_SYNONYM
public static final int DB_OBJECT_TYPE
public static final int TAXON
public static final int DATE
public static final int ASSIGNED_BY
public static final int ANNOTATION_XP
public static final int GENE_PRODUCT_ISOFORM
public boolean next() throws IOException
IOException
public void fireParsingError(String message)
public void fireParsingWarning(String message)
public String getCurrentRow()
public void init()
public void addParserListener(ParserListener listener)
public void remoteParserListener(ParserListener listener)
public void addCommentListener(CommentListener listener)
public void removeCommentListener(CommentListener listener)
public void parse(Reader reader)
public void parse(String file) throws IOException, URISyntaxException
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).IOException
URISyntaxException
public void parse(File gaf_file) throws IOException
IOException
public String getDb()
public String getDbObjectId()
public String getDbObjectSymbol()
public String getQualifier()
public String getGOId()
public String getReference()
public String getEvidence()
public String getWith()
public String getAspect()
public String getDbObjectName()
public String getDbObjectSynonym()
public String getDBObjectType()
public String getTaxon()
public String getDate()
public String getAssignedBy()
public String getAnnotationExtension()
public String getGeneProjectFormId()
public int getLineNumber()
public void dispose()
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