owltools.gaf.parser
Class GpadParser

java.lang.Object
  extended by owltools.gaf.parser.GpadParser
All Implemented Interfaces:
Closeable

public class GpadParser
extends Object


Field Summary
protected  String[] currentCols
           
protected  String currentRow
           
protected  int lineNumber
           
protected  double version
           
 
Constructor Summary
GpadParser()
           
 
Method Summary
 void addCommentListener(CommentListener listener)
           
 void addParserListener(ParserListener listener)
           
protected  void addViolation(Object violation)
           
 void close()
           
 void createReader(InputStream inputStream)
           
protected  void fireParsingError(String message)
           
protected  void fireParsingWarning(String message)
           
 String getAnnotation_Extension()
           
 String getAnnotation_Properties()
           
 String getAssigned_by()
           
 String getColumn(owltools.gaf.parser.GpadParser.GpadColumns col)
           
 String getCurrentRow()
           
 String getDate()
           
 String getDB_Object_ID()
           
 String getDB_Reference()
           
 String getDB()
           
 String getEvidence_Code()
           
protected  int getExpectedColumnCount()
           
 String getGO_ID()
           
 String getInteracting_Taxon_ID()
           
 int getLineNumber()
           
 String getQualifier()
           
 List<Object> getViolations()
           
 String getWith()
           
protected  void handleComment(String line)
           
protected  boolean isFormatDeclaration(String line)
           
 boolean next()
          Try to parse a next line, may skip lines until a line is parsed successfully or the file ends.
protected  double parseVersion(String line)
           
 void remoteParserListener(ParserListener listener)
           
 void removeCommentListener(CommentListener listener)
           
 void setReader(BufferedReader reader)
           
protected  owltools.gaf.parser.AbstractAnnotationFileParser.ReadState validateLine(String[] currentCols)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

version

protected double version

currentRow

protected String currentRow

currentCols

protected String[] currentCols

lineNumber

protected int lineNumber
Constructor Detail

GpadParser

public GpadParser()
Method Detail

getColumn

public String getColumn(owltools.gaf.parser.GpadParser.GpadColumns col)

getDB

public String getDB()

getDB_Object_ID

public String getDB_Object_ID()

getQualifier

public String getQualifier()

getGO_ID

public String getGO_ID()

getDB_Reference

public String getDB_Reference()

getEvidence_Code

public String getEvidence_Code()

getWith

public String getWith()

getInteracting_Taxon_ID

public String getInteracting_Taxon_ID()

getDate

public String getDate()

getAssigned_by

public String getAssigned_by()

getAnnotation_Extension

public String getAnnotation_Extension()

getAnnotation_Properties

public String getAnnotation_Properties()

isFormatDeclaration

protected boolean isFormatDeclaration(String line)

parseVersion

protected double parseVersion(String line)

getExpectedColumnCount

protected int getExpectedColumnCount()

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

validateLine

protected owltools.gaf.parser.AbstractAnnotationFileParser.ReadState validateLine(String[] currentCols)
Parameters:
currentCols -
Returns:
readstate

handleComment

protected void handleComment(String line)
Parameters:
line -

fireParsingError

protected void fireParsingError(String message)

fireParsingWarning

protected void fireParsingWarning(String message)

createReader

public void createReader(InputStream inputStream)

setReader

public void setReader(BufferedReader reader)

getCurrentRow

public String getCurrentRow()

getLineNumber

public int getLineNumber()

addParserListener

public void addParserListener(ParserListener listener)

remoteParserListener

public void remoteParserListener(ParserListener listener)

addCommentListener

public void addCommentListener(CommentListener listener)

removeCommentListener

public void removeCommentListener(CommentListener listener)

addViolation

protected void addViolation(Object violation)

getViolations

public List<Object> getViolations()

close

public void close()
           throws IOException
Specified by:
close in interface Closeable
Throws:
IOException


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