model
Class Magic

java.lang.Object
  model.Magic

public class Magic
extends java.lang.Object

Title: Bioinformatics Project

Description: Genomes Comparacent

Copyright: Copyright (c) 2005-2006

Magic is a class that contain information about the project workspace and parameters(default or as set by the user).

Version:

1.0

Author:

Shadi Ibrahem.

Field Summary

(package private) java.lang.String	cleanISPerc Parameter: removing transposable elements.
(package private) java.lang.String	cleanMinLen Parameter: removing short entries.
(package private) java.lang.String	cleanProPerc Parameter: removing prophages.
(package private) java.lang.String	dupPerc Parameter: finding duplicates.
(package private) java.lang.String	eval
(package private) java.lang.String	gapExtractLength Parameter: gap extraction length.
(package private) java.lang.String	gapJoinLength Parameter: gap join length.
(package private) java.lang.String	inputDir Input directory.
private java.lang.String	Language The languge as set by the user.
(package private) java.lang.String	orthPerc Parameter: identifying orthologs.
(package private) java.lang.String	outputDir Output directory.
(package private) java.lang.String	stitchDifference Parameter: stitch difference.
(package private) java.lang.String	stitchDistance Parameter: stitch distance.
(package private) java.lang.String	stitchMinLength Parameter: stitch minimum length.

Constructor Summary

Magic(java.lang.String settings)
C'tor, imports data from the settings file.

Method Summary

java.lang.String	getcleanISPerc() Retruns the removing transposable elements parameter.
java.lang.String	getcleanMinLen() Retruns the removing short entries parameter.
java.lang.String	getcleanProPerc() Retruns the removing prophages parameter.
java.lang.String	getdupPerc() Retruns the finding duplicates parameter.
java.lang.String	geteval() Retruns eval.
java.lang.String	getgapExtractLength() Retruns the gap extract length.
java.lang.String	getgapJoinLength() Retruns the gap join length.
java.lang.String	getInputDirectory() Retruns the input directory.
java.lang.String	getLanguage() Returns the language as imported from the settings file.
java.lang.String	getorthPerc() Retruns the identifying orthologs parameter.
java.lang.String	getOutputDirectory() Retruns the output directory.
java.lang.String	getstitchDifference() Retruns the stitch difference.
java.lang.String	getstitchDistance() Retruns the stitch distance.
java.lang.String	getstitchMinLength() Retruns the stitch minimum length.
java.lang.String	ReadLine(java.io.FileReader fileR, char[] c) Reads a line from the given stream.

Methods inherited from class java.lang.Object

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

Field Detail

gapExtractLength

java.lang.String gapExtractLength

Parameter: gap extraction length.

gapJoinLength

java.lang.String gapJoinLength

Parameter: gap join length.

stitchDifference

java.lang.String stitchDifference

Parameter: stitch difference.

stitchMinLength

java.lang.String stitchMinLength

Parameter: stitch minimum length.

stitchDistance

java.lang.String stitchDistance

Parameter: stitch distance.

eval

java.lang.String eval

cleanISPerc

java.lang.String cleanISPerc

Parameter: removing transposable elements.

cleanProPerc

java.lang.String cleanProPerc

Parameter: removing prophages.

cleanMinLen

java.lang.String cleanMinLen

Parameter: removing short entries.

dupPerc

java.lang.String dupPerc

Parameter: finding duplicates.

orthPerc

java.lang.String orthPerc

Parameter: identifying orthologs.

inputDir

java.lang.String inputDir

Input directory.

outputDir

java.lang.String outputDir

Output directory.

Language

private java.lang.String Language

The languge as set by the user.

Constructor Detail

Magic

public Magic(java.lang.String settings)

C'tor, imports data from the settings file. this methods asummes that the file cotents are in correct form.

Parameters:

settings - String : path to the settings file.

Method Detail

ReadLine

public java.lang.String ReadLine(java.io.FileReader fileR,
                                 char[] c)

Reads a line from the given stream.

Parameters:

fileR - FileReader: opened file stream.

c - char[]: buffer.

Returns:

a read line.

getInputDirectory

public java.lang.String getInputDirectory()

Retruns the input directory.

Returns:

String :input directory.

getOutputDirectory

public java.lang.String getOutputDirectory()

Retruns the output directory.

Returns:

String :output directory.

getgapExtractLength

public java.lang.String getgapExtractLength()

Retruns the gap extract length.

Returns:

String :parameter as a String.

getgapJoinLength

public java.lang.String getgapJoinLength()

Retruns the gap join length.

Returns:

String :parameter as a String.

getstitchDifference

public java.lang.String getstitchDifference()

Retruns the stitch difference.

Returns:

String :parameter as a String.

getstitchMinLength

public java.lang.String getstitchMinLength()

Retruns the stitch minimum length.

Returns:

String :parameter as a String.

getstitchDistance

public java.lang.String getstitchDistance()

Retruns the stitch distance.

Returns:

String :parameter as a String.

geteval

public java.lang.String geteval()

Retruns eval.

Returns:

String :parameter as a String.

getcleanISPerc

public java.lang.String getcleanISPerc()

Retruns the removing transposable elements parameter.

Returns:

String :parameter as a String.

getcleanProPerc

public java.lang.String getcleanProPerc()

Retruns the removing prophages parameter.

Returns:

String :parameter as a String.

getcleanMinLen

public java.lang.String getcleanMinLen()

Retruns the removing short entries parameter.

Returns:

String :parameter as a String.

getdupPerc

public java.lang.String getdupPerc()

Retruns the finding duplicates parameter.

Returns:

String :parameter as a String.

getorthPerc

public java.lang.String getorthPerc()

Retruns the identifying orthologs parameter.

Returns:

String :parameter as a String.

getLanguage

public java.lang.String getLanguage()

Returns the language as imported from the settings file.

Returns:

String: the langauage index.