edu.iastate.metnet.aracyc
Class AttributeFileReaderEx

java.lang.Object
  edu.iastate.metnet.aracyc.AbstractAracycFileReader
      edu.iastate.metnet.aracyc.AttributeFileReaderEx

All Implemented Interfaces:

IAracycFileReader

public class AttributeFileReaderEx
extends AbstractAracycFileReader

same as AttributeFileReader except implementing the data structure by Map of MultiMap

Author:

Jie Li

Field Summary

(package private) static org.apache.log4j.Logger	logger log4j facility
(package private) int	PARSE file line scanner status
(package private) int	SEARCH file line scanner status for one unique-id record

Constructor Summary

AttributeFileReaderEx()

Method Summary

protected java.util.Map	parseFile(java.util.LinkedList lines) parse the file lines and turn into maps
java.util.Map	read(java.io.InputStream inputStream)
java.util.Map	read(java.lang.String filename) read in the file and turn into map data structure like ATP=> {UID=>[ATP], SYNONYM=>[ATPase, ADP]}

Methods inherited from class edu.iastate.metnet.aracyc.AbstractAracycFileReader

getFileLines, getFileLines, print

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

logger

static org.apache.log4j.Logger logger

log4j facility

SEARCH

final int SEARCH

file line scanner status for one unique-id record

See Also:

Constant Field Values

PARSE

final int PARSE

file line scanner status

See Also:

Constant Field Values

Constructor Detail

AttributeFileReaderEx

public AttributeFileReaderEx()

Method Detail

read

public java.util.Map read(java.lang.String filename)

read in the file and turn into map data structure like ATP=> {UID=>[ATP], SYNONYM=>[ATPase, ADP]}

 IAracycFileReader reader = new AttributeFileReaderEx();
 
 Map map = reader.read(filename);
 
 

Specified by:

read in interface IAracycFileReader

Overrides:

read in class AbstractAracycFileReader

Parameters:

filename - filename of the dump file,

Returns:

the data structure

read

public java.util.Map read(java.io.InputStream inputStream)

Specified by:

read in interface IAracycFileReader

Overrides:

read in class AbstractAracycFileReader

parseFile

protected java.util.Map parseFile(java.util.LinkedList lines)

parse the file lines and turn into maps

Parameters:

lines - the line read from the file

Returns:

the map of data