org.emboss.jemboss.gui.form
Class SectionPanel

java.lang.Object
  org.emboss.jemboss.gui.form.SectionPanel

public class SectionPanel

extends java.lang.Object

Responsible for displaying the Jemboss application form generated from the ACD file. This also handles events related to dependent parameters.

Field Summary

private AlignFormat	af alignment format
static int	ajaxLength sequence length
static boolean	ajaxProtein sequence type
static float	ajaxWeight sequence weight
private java.lang.String	appName application name
private javax.swing.JCheckBox[]	checkBox boolean fields
private java.lang.String[]	db available databases
private javax.swing.JFrame	f Jemboss frame
private JembossComboPopup[]	fieldOption checkbox popup field for list and select
private ListFilePanel[]	filelist list file panel
private SetInFileCard[]	inSeq input sequence field
private InputSequenceAttributes[]	inSeqAttr input sequence attributes
private boolean	isAdd true if the additional section
private boolean	isAdv true if the advanced section
private boolean	isInp true if the input section
private boolean	isOut true if the output section
private boolean	isReq true if the required section
private boolean	isShadedGUI true if shading disabled fields, otherwise they are removed from the form
private javax.swing.Box[]	lab field label container
static java.awt.Color	labelColor label colour
static java.awt.Font	labfont label font
static java.awt.Font	labfont2 small label font
private int	maxSectionWidth maximum width of the form
private javax.swing.JList[]	multiOption multiple option field for list and select
private JembossParams	mysettings jemboss properties
private int	nf field number to start from
private int	numofFields number of fields in the ACD
private javax.swing.JPanel	p3 Jemboss form panel
private ParseAcd	parseAcd ACD parser for the application selected
private javax.swing.JTextField[]	rangeField range field
private ReportFormat	rf report format
private javax.swing.Box	sectionBox container for this ACD section
private javax.swing.JPanel	sectionPane container for this ACD section
private TextFieldSink[]	textf text field sink
private TextFieldFloat[]	textFloat float field sink
private TextFieldInt[]	textInt integer field sink
private boolean	withSoap true if in client-server mode

Constructor Summary

protected

SectionPanel(javax.swing.JFrame f, javax.swing.JPanel p3, javax.swing.Box fieldPane, ParseAcd parseAcd, int nff, TextFieldSink[] textf, TextFieldInt[] textInt, TextFieldFloat[] textFloat, javax.swing.JTextField[] rangeField, javax.swing.JCheckBox[] checkBox, InputSequenceAttributes[] inSeqAttr, JembossComboPopup[] fieldOption, javax.swing.JList[] multiOption, SetInFileCard[] inSeq, ListFilePanel[] filelist, java.lang.String[] db, java.lang.String des, javax.swing.Box[] lab, int numofFields, JembossParams mysettings, boolean withSoap, java.lang.String[] envp)

Method Summary

private void	checkDependents(javax.swing.Box section, java.lang.String[] envp) Checks for dependent variables and adds in action listeners
private boolean	cygwinSeqAttr(java.lang.String fc, java.lang.String[] envp, java.lang.String att) Cygwin uses infoseq to get sequence length and type and uses infoalign to get the sequence weight.
protected AlignFormat	getAlignFormat() Get the alignment format
protected int	getFieldNum() Get the current field
private java.lang.String	getMinMaxDefault(java.lang.String min, java.lang.String max, java.lang.String def, int nfield) Get the min, max and default values for a field in the ACD as a string representation in the form (min: max: default:)
protected ReportFormat	getReportFormat() Get the report format
protected javax.swing.Box	getSectionBox() get the box or this section
protected javax.swing.JPanel	getSectionPanel() get the panel for this section
protected boolean	isAdditionalSection()
protected boolean	isAdvancedSection()
protected boolean	isAlignFormat() Determine if alignment formats are used in the EMBOSS program
protected boolean	isInputSection()
protected boolean	isOutputSection()
protected boolean	isReportFormat() Determine if report formats are used in the EMBOSS program
protected boolean	isRequiredSection()
private void	resolveDependents(int nod, Dependent[] dep, java.lang.String textVal, java.lang.String varName) Given an ACD variable and the value it takes, resolve any dependent attribute values.
private void	sectionResize(javax.swing.JPanel p) Resize the section panel
private void	setAppTitle(java.lang.String des, javax.swing.JPanel p3) Set the application title panel
private void	setShadingAndVisibility(java.awt.Component c, boolean useThis, int field) Set the shading or visibility of a component
private boolean	updateBeginEnd(java.lang.String s, java.lang.String e) Check sbeg and send values before updating in the panel to avoid overriding user selection

Methods inherited from class java.lang.Object

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

Field Detail

textf

private TextFieldSink[] textf

text field sink

textInt

private TextFieldInt[] textInt

integer field sink

textFloat

private TextFieldFloat[] textFloat

float field sink

rangeField

private javax.swing.JTextField[] rangeField

range field

checkBox

private javax.swing.JCheckBox[] checkBox

boolean fields

inSeqAttr

private InputSequenceAttributes[] inSeqAttr

input sequence attributes

filelist

private ListFilePanel[] filelist

list file panel

fieldOption

private JembossComboPopup[] fieldOption

checkbox popup field for list and select

multiOption

private javax.swing.JList[] multiOption

multiple option field for list and select

inSeq

private SetInFileCard[] inSeq

input sequence field

lab

private javax.swing.Box[] lab

field label container

db

private java.lang.String[] db

available databases

parseAcd

private ParseAcd parseAcd

ACD parser for the application selected

numofFields

private int numofFields

number of fields in the ACD

nf

private int nf

field number to start from

ajaxLength

public static int ajaxLength

sequence length

ajaxWeight

public static float ajaxWeight

sequence weight

ajaxProtein

public static boolean ajaxProtein

sequence type

withSoap

private boolean withSoap

true if in client-server mode

appName

private java.lang.String appName

application name

p3

private javax.swing.JPanel p3

Jemboss form panel

sectionPane

private javax.swing.JPanel sectionPane

container for this ACD section

sectionBox

private javax.swing.Box sectionBox

container for this ACD section

mysettings

private JembossParams mysettings

jemboss properties

isInp

private boolean isInp

true if the input section

isReq

private boolean isReq

true if the required section

isAdv

private boolean isAdv

true if the advanced section

isAdd

private boolean isAdd

true if the additional section

isOut

private boolean isOut

true if the output section

isShadedGUI

private boolean isShadedGUI

true if shading disabled fields, otherwise they are removed from the form

labelColor

public static java.awt.Color labelColor

label colour

labfont

public static java.awt.Font labfont

label font

labfont2

public static java.awt.Font labfont2

small label font

maxSectionWidth

private final int maxSectionWidth

maximum width of the form

See Also:

Constant Field Values

f

private javax.swing.JFrame f

Jemboss frame

rf

private ReportFormat rf

report format

af

private AlignFormat af

alignment format

Constructor Detail

SectionPanel

protected SectionPanel(javax.swing.JFrame f,
                       javax.swing.JPanel p3,
                       javax.swing.Box fieldPane,
                       ParseAcd parseAcd,
                       int nff,
                       TextFieldSink[] textf,
                       TextFieldInt[] textInt,
                       TextFieldFloat[] textFloat,
                       javax.swing.JTextField[] rangeField,
                       javax.swing.JCheckBox[] checkBox,
                       InputSequenceAttributes[] inSeqAttr,
                       JembossComboPopup[] fieldOption,
                       javax.swing.JList[] multiOption,
                       SetInFileCard[] inSeq,
                       ListFilePanel[] filelist,
                       java.lang.String[] db,
                       java.lang.String des,
                       javax.swing.Box[] lab,
                       int numofFields,
                       JembossParams mysettings,
                       boolean withSoap,
                       java.lang.String[] envp)

Parameters:

f - Jemboss frame

p3 - JPanel ACD form panel

fieldPane - containing all the fields

parseAcd - representing the ACD file to display as a form

nff - field number

textf - text fields in the form

textInt - integer fields in the form

textFloat - float fields in the form

rangeField - ranges in the form

checkBox - for the boolean switches

inSeqAttr - the input sequence(s) attributes

fieldOption - for the list/selection data types

multiOption - for multiple selection lists

inSeq - the input sequence(s)

filelist - list file panel

db - String array containing the databases

des - String containing the one line description for the application

lab - Box for all the component labels

numofFields - total number of fields

mysettings - jemboss properties

withSoap - true if using a soap server

Method Detail

getReportFormat

protected ReportFormat getReportFormat()

Get the report format

isReportFormat

protected boolean isReportFormat()

Determine if report formats are used in the EMBOSS program

Returns:

true if a report format is used

getAlignFormat

protected AlignFormat getAlignFormat()

Get the alignment format

isAlignFormat

protected boolean isAlignFormat()

Determine if alignment formats are used in the EMBOSS program

Returns:

true if a alignment format is used

getSectionPanel

protected javax.swing.JPanel getSectionPanel()

get the panel for this section

getSectionBox

protected javax.swing.Box getSectionBox()

get the box or this section

isInputSection

protected boolean isInputSection()

Returns:

true if the input section

isOutputSection

protected boolean isOutputSection()

Returns:

true if the output section

isRequiredSection

protected boolean isRequiredSection()

Returns:

true if the required section

isAdvancedSection

protected boolean isAdvancedSection()

Returns:

true if the advanced section

isAdditionalSection

protected boolean isAdditionalSection()

Returns:

true if the additional section

getFieldNum

protected int getFieldNum()

Get the current field

Returns:

current field number

setAppTitle

private void setAppTitle(java.lang.String des,
                         javax.swing.JPanel p3)

Set the application title panel

Parameters:

des - short description of the program

p3 - JPanel for the ACD form

getMinMaxDefault

private java.lang.String getMinMaxDefault(java.lang.String min,
                                          java.lang.String max,
                                          java.lang.String def,
                                          int nfield)

Get the min, max and default values for a field in the ACD as a string representation in the form (min: max: default:)

Parameters:

min - minimum value for parameter

max - maximum value for parameter

def - default value for parameter

nfield - field number in ACD

Returns:

string of (min: max: default:) if specified

checkDependents

private void checkDependents(javax.swing.Box section,
                             java.lang.String[] envp)

Checks for dependent variables and adds in action listeners

Parameters:

section - form container for parameters

cygwinSeqAttr

private boolean cygwinSeqAttr(java.lang.String fc,
                              java.lang.String[] envp,
                              java.lang.String att)

Cygwin uses infoseq to get sequence length and type and uses infoalign to get the sequence weight.

updateBeginEnd

private boolean updateBeginEnd(java.lang.String s,
                               java.lang.String e)

Check sbeg and send values before updating in the panel to avoid overriding user selection

Parameters:

s - start

e - end

Returns:

true to automatically update

resolveDependents

private void resolveDependents(int nod,
                               Dependent[] dep,
                               java.lang.String textVal,
                               java.lang.String varName)

Given an ACD variable and the value it takes, resolve any dependent attribute values.

Parameters:

nod - number of dependent values

textVal - value of variable

varName - variable name

setShadingAndVisibility

private void setShadingAndVisibility(java.awt.Component c,
                                     boolean useThis,
                                     int field)

Set the shading or visibility of a component

Parameters:

c - component

useThis - true if enabled/visible

field - field number in the ACD

sectionResize

private void sectionResize(javax.swing.JPanel p)

Resize the section panel

Parameters:

p - section panel