owltools.gaf.parser
Class GpiParser

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

public class GpiParser
extends Object


Field Summary
protected  String[] currentCols
           
protected  String currentRow
           
protected  int lineNumber
           
protected  double version
           
 
Constructor Summary
GpiParser()
           
 
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 getColumn(owltools.gaf.parser.GpiParser.GpiColumns col)
           
 String getCurrentRow()
           
 String getDB_Object_ID()
           
 String getDB_Object_Name()
           
 String getDB_Object_Symbol()
           
 String getDB_Object_Synonym()
           
 String getDB_Object_Type()
           
 String getDB_Xref()
           
protected  int getExpectedColumnCount()
           
 String getGene_Product_Properties()
           
 int getLineNumber()
           
 String getNamespace()
           
 String getParent_Object_ID()
           
 String getTaxon()
           
 List<Object> getViolations()
           
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

GpiParser

public GpiParser()
Method Detail

getColumn

public String getColumn(owltools.gaf.parser.GpiParser.GpiColumns col)

getDB_Object_ID

public String getDB_Object_ID()

getDB_Object_Symbol

public String getDB_Object_Symbol()

getDB_Object_Name

public String getDB_Object_Name()

getDB_Object_Synonym

public String getDB_Object_Synonym()

getDB_Object_Type

public String getDB_Object_Type()

getTaxon

public String getTaxon()

getParent_Object_ID

public String getParent_Object_ID()

getDB_Xref

public String getDB_Xref()

getGene_Product_Properties

public String getGene_Product_Properties()

getNamespace

public String getNamespace()

handleComment

protected void handleComment(String line)

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

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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