model
Class ImportedTableFile

java.lang.Object
  model.ImportedTableFile

public class ImportedTableFile
extends java.lang.Object

Title: Bioinformatics Project

Description: Genomes Comparacent

Copyright: Copyright (c) 2005-2006

ImportedTableFile is the class that import a file into a vector of lines.

Version:

1.0

Author:

Shadi Ibrahem.

Field Summary

private java.io.BufferedReader	BufReader file descriptor.
private boolean	flag A flag that indicates that the file can be opened successfuly.
private long	LineCount Line number in the file.
private java.util.Vector	LineVector Vector containing the lines as imported from the file.
private boolean	VecIsImported Indicates the file lines has been imported successfuly.
private long	xScale Default settings, to be deleted in the future.
private long	yScale Default settings, to be deleted in the future.

Constructor Summary

ImportedTableFile(java.lang.String file)
Opens a file

Method Summary

Line	getLineAt(int indx) Returns a vector item(coordinates-line)
java.util.Vector	getLineVector() Returns the ImportedTable data base
private boolean	IsFileImported() Returns a flag that indicates whether the file has been imported into lines-vector
private void	setLineInVector(long x1, long y1, long x2, long y2, char sign) The genomes length(xScale/yScale) is set to be the range of canvas.
void	setLineVector(boolean HEADLINE) Sets the table lines into coordinates-Lines and then insert it into a the ImportedFileTable vector
void	setRegularTableFileConfiguration(long length, long length2, boolean HEADLINE) Sets the ImportedFileTable Default configurations.
private int	skipSpaces(java.lang.String str, int i) Return the updated index which is used to read a string after skipping spaces.

Methods inherited from class java.lang.Object

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

Field Detail

LineVector

private java.util.Vector LineVector

Vector containing the lines as imported from the file.

BufReader

private java.io.BufferedReader BufReader

file descriptor.

flag

private boolean flag

A flag that indicates that the file can be opened successfuly.

LineCount

private long LineCount

Line number in the file.

VecIsImported

private boolean VecIsImported

Indicates the file lines has been imported successfuly.

xScale

private long xScale

Default settings, to be deleted in the future.

yScale

private long yScale

Default settings, to be deleted in the future.

Constructor Detail

ImportedTableFile

public ImportedTableFile(java.lang.String file)

Opens a file

Parameters:

file - String : given file path.

Method Detail

IsFileImported

private boolean IsFileImported()

Returns a flag that indicates whether the file has been imported into lines-vector

Returns:

true if the file has been imported.

setLineVector

public void setLineVector(boolean HEADLINE)
                   throws java.io.IOException

Sets the table lines into coordinates-Lines and then insert it into a the ImportedFileTable vector

Throws:

java.io.IOException

skipSpaces

private int skipSpaces(java.lang.String str,
                       int i)

Return the updated index which is used to read a string after skipping spaces.

Parameters:

str - String given string.

i - int the index to begin with.

Returns:

int - the updated index.

getLineAt

public Line getLineAt(int indx)

Returns a vector item(coordinates-line)

Parameters:

indx - int the line index.

Returns:

Line a coordinates-line.

setRegularTableFileConfiguration

public void setRegularTableFileConfiguration(long length,
                                             long length2,
                                             boolean HEADLINE)

Sets the ImportedFileTable Default configurations.

Parameters:

length2 -

length -

HEADLINE -

getLineVector

public java.util.Vector getLineVector()

Returns the ImportedTable data base

Returns:

Vector - coordinates-line-vector.

setLineInVector

private void setLineInVector(long x1,
                             long y1,
                             long x2,
                             long y2,
                             char sign)

The genomes length(xScale/yScale) is set to be the range of canvas. This method checks if the line is out of the given range (circularity) and assigns new line accordingly; if all of the line is inside the range it insert it in the line vector as it gets it, otherwise it cuts it into 2 or three part and changes the coordinates of each part.

Parameters:

x1 - long: the sigment start point coordinates.

y1 - long: the sigment start point coordinates.

x2 - long: the sigment end point coordinates.

y2 - long: the sigment end point coordinates.

sign - char: the sigment sign.