edu.iastate.biocyc.io
Class AttributeFileReaderEx

java.lang.Object
  edu.iastate.biocyc.io.AttributeFileReaderEx

public class AttributeFileReaderEx
extends java.lang.Object

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

void	print(java.util.Map file) the map structure should contain the unique as the key, then another map as the value.
java.util.Map	read(java.io.InputStream inputStream) read data from the input stream
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]}
static java.lang.String	trim(java.lang.String original, char header, char tail) cut the header and the tail of the string, do not consider if it is already a trimmed one

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);
 
 

read

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

read data from the input stream

Parameters:

inputStream - the input stream

Returns:

the map data

trim

public static java.lang.String trim(java.lang.String original,
                                    char header,
                                    char tail)

cut the header and the tail of the string, do not consider if it is already a trimmed one

Parameters:

original - the original string

header - the header char to be removed

tail - the tail char to be removed

Returns:

the trimmed string

print

public void print(java.util.Map file)

the map structure should contain the unique as the key, then another map as the value. the secondary map contain the string as the key and a set of value for the key

Parameters:

file - the data structure