owltools.gaf
Class GAFParser

java.lang.Object
  extended by owltools.gaf.GAFParser

public class GAFParser
extends Object

Author:
Shahid Manzoor

Field Summary
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 Summary
GAFParser()
           
 
Method Summary
 void addParserListener(GafParserListener listener)
           
 String getAnnotationExtension()
           
 List<Object> getAnnotationRuleViolations()
           
 String getAspect()
           
 String getAssignedBy()
           
 String getCurrentRow()
           
 String getDate()
           
 String getDb()
           
 String getDbObjectId()
           
 String getDbObjectName()
           
 String getDbObjectSymbol()
           
 String getDbObjectSynonym()
           
 String getDBObjectType()
           
 String getEvidence()
           
 String getGeneProjectFormId()
           
 String getGOId()
           
 int getLineNumber()
           
 String getQualifier()
           
 String getReference()
           
 String getTaxon()
           
 String getWith()
           
 void init()
           
 boolean next()
          Method declaration
 void parse(File gaf_file)
           
 void parse(Reader reader)
           
 void parse(String file)
           
 void remoteParserListener(GafParserListener listener)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

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
Constructor Detail

GAFParser

public GAFParser()
Method Detail

getAnnotationRuleViolations

public List<Object> getAnnotationRuleViolations()

next

public boolean next()
             throws IOException
Method declaration

Returns:
true, if next was successful
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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