owltools.idmap
Class AbstractMappingParser

java.lang.Object
  extended by owltools.idmap.AbstractMappingParser
Direct Known Subclasses:
IDMappingPIRParser, UniProtIDMapParser

public abstract class AbstractMappingParser
extends Object

Parses the IDMapping file available here: ftp://ftp.pir.georgetown.edu/databases/idmapping/idmapping.tb.gz

Author:
cjm

Field Summary
protected  String[] currentCols
           
protected  String currentRow
           
protected  int expectedNumCols
           
protected  int lineNumber
           
protected  BufferedReader reader
           
 
Constructor Summary
AbstractMappingParser()
           
 
Method Summary
 void parse(File file)
           
abstract  void parse(Reader reader)
           
 void parse(String file)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

reader

protected BufferedReader reader

currentRow

protected String currentRow

currentCols

protected String[] currentCols

expectedNumCols

protected int expectedNumCols

lineNumber

protected int lineNumber
Constructor Detail

AbstractMappingParser

public AbstractMappingParser()
Method Detail

parse

public void parse(String file)
           throws IOException,
                  URISyntaxException
Parameters:
file - is the location of the mapping file. The location could be http url, absolute path and uri.
Throws:
IOException
URISyntaxException

parse

public abstract void parse(Reader reader)
                    throws IOException
Throws:
IOException

parse

public void parse(File file)
           throws IOException
Throws:
IOException


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