model
Class Genome

java.lang.Object
  model.Genome

public class Genome
extends java.lang.Object

Title: Bioinformatics Project

Description: Genomes Comparacent

Copyright: Copyright (c) 2005-2006

Genome is a class that contains single genome details; name,length,files,..etc.

Version:

1.0

Author:

Shadi Ibrahem.

Field Summary

private java.lang.String	anchor Genome anchor file path.
private java.lang.String	Chromosome_num Genome chromosome number.
private java.lang.String	ent Genome ent file path.
private java.lang.String	genome Genome genome file path.
private boolean	isCircular Genome circularity.
private long	length Genome length.
private java.lang.String	name Genome full name.
private java.lang.String	Plasmid_num Genome plasmid number.
private java.lang.String	prop Genome prop file path.
private java.lang.String	protein_gene_num Genome protein gene number.
private java.lang.String	RNA_gene_num Genome RNA gene number.
private java.lang.String	SymbolicName Genome symbolic(short) name.
private java.lang.String	te Genome te file path.
private java.lang.String	ve Genome ve file path.
private java.lang.String	virus Genome virus file path.

Constructor Summary

Genome(java.lang.String path, java.lang.String GSymbol)
C'tor, imports data from prop file and saves genome files paths.

Method Summary

protected long	checkField(java.lang.String str) Returns the extracted number, in case it is not a number returns -1.
java.lang.String	getAnchor() returns the genome anchor file path.
java.lang.String	getChromosome_num() returns the genome chromosome gene num.
java.lang.String	getEnt() returns the genome ent file path.
private java.lang.String	getFile(java.lang.String[] str, java.lang.String ext) Locates the file with the extention ext in the directory list str.
java.lang.String	getGenome() returns the genome ".Genome" file path.
java.lang.String	getGenomeName() returns the genome full name.
long	getLength() returns the genome length(as imported from the prop).
java.lang.String	getPlasmid_num() returns the genome plasmid gene num.
java.lang.String	getProp() returns the genome prop file path.
java.lang.String	getProtein_gene_num() returns the genome Protein gene num.
java.lang.String	getRNA_gene_num() returns the genome RNA gene num.
java.lang.String	getSymbolName() returns the genome symbolic(short) name.
java.lang.String	getTE() returns the genome te file path.
java.lang.String	getVe() returns the genome ve file path.
java.lang.String	getVIRUS() returns the genome virus file path.
boolean	isCircular() returns wether if the genome is circular or not.
private void	setGenomeProp(java.lang.String prop) Imports porp files into local variables.

Methods inherited from class java.lang.Object

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

Field Detail

anchor

private java.lang.String anchor

Genome anchor file path.

genome

private java.lang.String genome

Genome genome file path.

ent

private java.lang.String ent

Genome ent file path.

te

private java.lang.String te

Genome te file path.

virus

private java.lang.String virus

Genome virus file path.

prop

private java.lang.String prop

Genome prop file path.

ve

private java.lang.String ve

Genome ve file path.

name

private java.lang.String name

Genome full name.

length

private long length

Genome length.

isCircular

private boolean isCircular

Genome circularity.

protein_gene_num

private java.lang.String protein_gene_num

Genome protein gene number.

RNA_gene_num

private java.lang.String RNA_gene_num

Genome RNA gene number.

Chromosome_num

private java.lang.String Chromosome_num

Genome chromosome number.

Plasmid_num

private java.lang.String Plasmid_num

Genome plasmid number.

SymbolicName

private java.lang.String SymbolicName

Genome symbolic(short) name.

Constructor Detail

Genome

public Genome(java.lang.String path,
              java.lang.String GSymbol)

C'tor, imports data from prop file and saves genome files paths.

Parameters:

path - String: genome directory path.

GSymbol - String: genome symbolic (short) name, it is also the name of the directory.

Method Detail

setGenomeProp

private void setGenomeProp(java.lang.String prop)

Imports porp files into local variables.

Parameters:

prop - String: genome prop file path.

checkField

protected long checkField(java.lang.String str)

Returns the extracted number, in case it is not a number returns -1.

Parameters:

str - String: given string.

Returns:

long: the given string if a number or -1 if not.

getFile

private java.lang.String getFile(java.lang.String[] str,
                                 java.lang.String ext)

Locates the file with the extention ext in the directory list str.

Parameters:

str - String[]:directory list.

ext - String: the file suffex.

Returns:

String:the file path.

getGenomeName

public java.lang.String getGenomeName()

returns the genome full name.

Returns:

String: the genome full name.

getSymbolName

public java.lang.String getSymbolName()

returns the genome symbolic(short) name.

Returns:

String: the genome symbolic(short) name.

getAnchor

public java.lang.String getAnchor()

returns the genome anchor file path.

Returns:

String: the genome anchor file path.

getGenome

public java.lang.String getGenome()

returns the genome ".Genome" file path.

Returns:

String: the genome ".Genome" file path.

getEnt

public java.lang.String getEnt()

returns the genome ent file path.

Returns:

String: the genome ent file path.

getVe

public java.lang.String getVe()

returns the genome ve file path.

Returns:

String: the genome ve file path.

getTE

public java.lang.String getTE()

returns the genome te file path.

Returns:

String: the genome te file path.

getVIRUS

public java.lang.String getVIRUS()

returns the genome virus file path.

Returns:

String: the genome virus file path.

getLength

public long getLength()

returns the genome length(as imported from the prop).

Returns:

long: the genome length.

isCircular

public boolean isCircular()

returns wether if the genome is circular or not.

Returns:

true: if the genome is circular.

getProtein_gene_num

public java.lang.String getProtein_gene_num()

returns the genome Protein gene num.

Returns:

String: the genome Protein gene num.

getRNA_gene_num

public java.lang.String getRNA_gene_num()

returns the genome RNA gene num.

Returns:

String: the genome RNA gene num.

getChromosome_num

public java.lang.String getChromosome_num()

returns the genome chromosome gene num.

Returns:

String: the genome chromosome gene num.

getPlasmid_num

public java.lang.String getPlasmid_num()

returns the genome plasmid gene num.

Returns:

String: the genome plasmid gene num.

getProp

public java.lang.String getProp()

returns the genome prop file path.

Returns:

String: the genome prop file path.