view
Class GRunTab

java.lang.Object
  view.GRunTab

public class GRunTab
extends java.lang.Object

Title: Bioinformatics Project

Description: Genomes Comparacent

Copyright: Copyright (c) 2005-2006

GRunTab- Running Genome preprocessing/showing result tab. contains the information on building the GUI of a tab that handles running preprocessing, or viewing results.

Version:

1.0

Author:

Shadi Ibrahem.

Field Summary

private org.eclipse.swt.widgets.Button	CancelButton For canceling the operation, and closing the tab.
private org.eclipse.swt.widgets.Group	ChartGroup Group that holds the canvas when it is visible.
private org.eclipse.swt.widgets.Label	computingLabel A label indicating a process is beeing done.
private IDataHandler	controller_ Magic controller.
(package private) static org.eclipse.swt.widgets.Display	display Data View display.
protected java.lang.String	DrawFileName String holding the file name of the output that the user wants to present it results.
private java.lang.String	gen1 First genome short name.
private java.lang.String	gen2 Second genome short name.
private org.eclipse.swt.widgets.Group	GenomeGroup Group containg the label, go button and cancel button, it also holds the progress bar when visible.
private org.eclipse.swt.widgets.Label	genomeNames A label clarifying the genomes names which it will run mapping/preprocessing phase on.
private org.eclipse.swt.widgets.Button	goButton Runs the actual mapping/preprocssing phase.
private java.lang.String	inputDir The preprocessing/mapping input directory.
protected boolean	isParaVisible A boolean value indicating if the parameters tab is visible.
private org.eclipse.swt.events.SelectionListener	MapListener A listener for the go button that runs the mapping phase.
private org.eclipse.swt.widgets.Composite	MapPComp The mapping parameters tab control.
private static java.util.ResourceBundle	messages Resource bundle, internationalization.
private org.eclipse.swt.widgets.Button	OnlyPreButton Check box, an advanced option so that the user can run preprocessing phase only.
private java.lang.String	outDir The preprocessing/mapping output directory.
private org.eclipse.swt.widgets.TabItem	ParaMapitem Parameters tab mapping item.
private org.eclipse.swt.widgets.TabItem	ParaPreitem Parameters tab preprocessing item.
private org.eclipse.swt.widgets.TabFolder	ParaTab Tab holding the preprocessing parameters.
org.eclipse.swt.widgets.ProgressBar	PB The progress bar, visible only when running a process.
private org.eclipse.swt.events.SelectionListener	PreListener A listener for the go button that runs the preprocessing phase.
private org.eclipse.swt.widgets.Composite	PrePComp The preprocessing parameters tab control.
long	runMapPid Pid for termentation, to enable the user to terminate process, process termination is NOT implemented, see "Developer GuideLine".
long	runPrePid Pid for termentation, to enable the user to terminate process, process termination is NOT implemented, see "Developer GuideLine".
private org.eclipse.swt.custom.CTabItem	RunTab The tab that will hold the view of the required form.
java.lang.Runnable	setProgress A runnable that runs in parallel to a process to indicate it state at each part, it updates the progress bar accordingly.
private static org.eclipse.swt.widgets.Shell	shell Data View shell.
private org.eclipse.swt.widgets.Button	ShowPButton Sets the parameters to be visible so the user can change them.
private java.lang.String	state A string that holds the state of process (0-100).
private org.eclipse.swt.widgets.Group	StatisGroup Group that holds the statistics when visible.
private SWTTable[]	table An array of tables holding tables of the parameters, first 3 of them are pre-processing tables, last 3 are for mapping.

Constructor Summary

GRunTab(org.eclipse.swt.custom.CTabFolder MainTab, java.lang.String Gen1, java.lang.String Gen2, IDataHandler cont)
C'tor, creates the basic view of running pre-processing/mapping phase tab.

Method Summary

private void	ClearTables() Impties tables, so it can be refilled with new values.
protected void	dispose() Disposing a Run tab when exiting or canceling.
void	DrawChart(java.lang.String file, long g1Len, long g2Len, boolean isHeadline) Shows the progress bar while drawing process is beeing done, show also the canvas afterwards.
static void	PrintMessageToScreen(int i, boolean complex) Opens an error message for the user in case mapping process fails , it also specifies the faliure reason.
private void	setMapTable(boolean editable) Sets the parameters table according to default values.
private void	setPreTable(boolean editable) Sets the parameters table according to default values.
void	setProgressLabel(java.lang.String msg) Sets the message during the a process to be "msg".
void	setResultsPage(java.lang.String OutputDir, boolean MapFlag) Sets the tab with the adequate view (pre/map/result).
void	setSelected(org.eclipse.swt.custom.CTabFolder mainTab) Sets the tab to be selected in the main tab of magic.

Methods inherited from class java.lang.Object

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

Field Detail

controller_

private IDataHandler controller_

Magic controller.

isParaVisible

protected boolean isParaVisible

A boolean value indicating if the parameters tab is visible.

table

private SWTTable[] table

An array of tables holding tables of the parameters, first 3 of them are pre-processing tables, last 3 are for mapping.

PrePComp

private org.eclipse.swt.widgets.Composite PrePComp

The preprocessing parameters tab control.

MapPComp

private org.eclipse.swt.widgets.Composite MapPComp

The mapping parameters tab control.

goButton

private org.eclipse.swt.widgets.Button goButton

Runs the actual mapping/preprocssing phase.

CancelButton

private org.eclipse.swt.widgets.Button CancelButton

For canceling the operation, and closing the tab.

genomeNames

private org.eclipse.swt.widgets.Label genomeNames

A label clarifying the genomes names which it will run mapping/preprocessing phase on.

gen1

private java.lang.String gen1

First genome short name.

gen2

private java.lang.String gen2

Second genome short name.

GenomeGroup

private org.eclipse.swt.widgets.Group GenomeGroup

Group containg the label, go button and cancel button, it also holds the progress bar when visible.

ShowPButton

private org.eclipse.swt.widgets.Button ShowPButton

Sets the parameters to be visible so the user can change them.

ParaTab

private org.eclipse.swt.widgets.TabFolder ParaTab

Tab holding the preprocessing parameters.

ChartGroup

private org.eclipse.swt.widgets.Group ChartGroup

Group that holds the canvas when it is visible.

OnlyPreButton

private org.eclipse.swt.widgets.Button OnlyPreButton

Check box, an advanced option so that the user can run preprocessing phase only.

RunTab

private org.eclipse.swt.custom.CTabItem RunTab

The tab that will hold the view of the required form.

computingLabel

private org.eclipse.swt.widgets.Label computingLabel

A label indicating a process is beeing done.

PB

public org.eclipse.swt.widgets.ProgressBar PB

The progress bar, visible only when running a process.

state

private java.lang.String state

A string that holds the state of process (0-100).

setProgress

public java.lang.Runnable setProgress

A runnable that runs in parallel to a process to indicate it state at each part, it updates the progress bar accordingly.

messages

private static java.util.ResourceBundle messages

Resource bundle, internationalization.

PreListener

private org.eclipse.swt.events.SelectionListener PreListener

A listener for the go button that runs the preprocessing phase.

MapListener

private org.eclipse.swt.events.SelectionListener MapListener

A listener for the go button that runs the mapping phase.

outDir

private java.lang.String outDir

The preprocessing/mapping output directory.

inputDir

private java.lang.String inputDir

The preprocessing/mapping input directory.

ParaPreitem

private org.eclipse.swt.widgets.TabItem ParaPreitem

Parameters tab preprocessing item.

ParaMapitem

private org.eclipse.swt.widgets.TabItem ParaMapitem

Parameters tab mapping item.

StatisGroup

private org.eclipse.swt.widgets.Group StatisGroup

Group that holds the statistics when visible.

DrawFileName

protected java.lang.String DrawFileName

String holding the file name of the output that the user wants to present it results.

runPrePid

public long runPrePid

Pid for termentation, to enable the user to terminate process, process termination is NOT implemented, see "Developer GuideLine".

runMapPid

public long runMapPid

Pid for termentation, to enable the user to terminate process, process termination is NOT implemented, see "Developer GuideLine".

shell

private static org.eclipse.swt.widgets.Shell shell

Data View shell.

display

static org.eclipse.swt.widgets.Display display

Data View display.

Constructor Detail

GRunTab

public GRunTab(org.eclipse.swt.custom.CTabFolder MainTab,
               java.lang.String Gen1,
               java.lang.String Gen2,
               IDataHandler cont)

C'tor, creates the basic view of running pre-processing/mapping phase tab.

Parameters:

MainTab - CTabFolder: that main tab from the data view.

Gen1 - String: 1st genome short name.

Gen2 - String: 2nd genome short name.

cont - IDataHandler: the controller of magic.

Method Detail

PrintMessageToScreen

public static void PrintMessageToScreen(int i,
                                        boolean complex)

Opens an error message for the user in case mapping process fails , it also specifies the faliure reason.

Parameters:

i - int: the mapping process returned status.

dispose

protected void dispose()

Disposing a Run tab when exiting or canceling.

setPreTable

private void setPreTable(boolean editable)

Sets the parameters table according to default values.

Parameters:

editable - boolean, true if the tab is ment to be used for running preprocessing.

setMapTable

private void setMapTable(boolean editable)

Sets the parameters table according to default values.

Parameters:

editable - true if the tab is for running preprocessing/mapping phase.

setResultsPage

public void setResultsPage(java.lang.String OutputDir,
                           boolean MapFlag)

Sets the tab with the adequate view (pre/map/result).

Parameters:

OutputDir - String: the output directory.

MapFlag - boolean: indicates if the tab is used for running the mapping phase.

DrawChart

public void DrawChart(java.lang.String file,
                      long g1Len,
                      long g2Len,
                      boolean isHeadline)

Shows the progress bar while drawing process is beeing done, show also the canvas afterwards.

Parameters:

file - String:the input file for the drawing.

g1Len - String:the 1st genome length.

g2Len - String:the 2nd genome length.

isHeadline -

ClearTables

private void ClearTables()

Impties tables, so it can be refilled with new values.

setSelected

public void setSelected(org.eclipse.swt.custom.CTabFolder mainTab)

Sets the tab to be selected in the main tab of magic.

Parameters:

mainTab - CTabFolder: the tab holding all the items of magic.

setProgressLabel

public void setProgressLabel(java.lang.String msg)

Sets the message during the a process to be "msg".

Parameters:

msg - String: given string.