org.emboss.jemboss.gui.form
Class BuildJembossForm

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

All Implemented Interfaces:

java.awt.event.ActionListener, java.util.EventListener

public class BuildJembossForm

extends java.lang.Object

implements java.awt.event.ActionListener

Responsible for displaying the graphical representation of the ACD EMBOSS files. Generates & runs command lines and display results.

Author:

T. J. Carver

Field Summary

protected static javax.swing.JPanel	addSection
private javax.swing.Box	addSectionBox
protected static javax.swing.JPanel	advSection
private javax.swing.Box	advSectionBox
private AlignFormat	af
private java.lang.String	applName
private javax.swing.JButton	bresults
private java.awt.Cursor	cbusy
private java.awt.Cursor	cdone
private javax.swing.JCheckBox[]	checkBox
private java.lang.String	cwd
private java.lang.String[]	db
private java.lang.String	embossBin
private java.lang.String[]	envp
private javax.swing.JFrame	f
private JembossComboPopup[]	fieldOption
private ListFilePanel[]	filelist
private java.lang.String	helptext
protected static javax.swing.JPanel	inpSection
private SetInFileCard[]	inSeq
private InputSequenceAttributes[]	inSeqAttr
private javax.swing.JList[]	multiOption
private JembossParams	mysettings
private int	numofFields
private java.lang.String	outfileResult
protected static javax.swing.JPanel	outSection
protected static OutputSequenceAttributes	outSeqAttr
private ScrollPanel	p2
private ParseAcd	parseAcd
private javax.swing.JTextField[]	rangeField
protected static javax.swing.JPanel	reqdSection
private ReportFormat	rf
private java.lang.String	seqoutResult
private java.lang.String	stdout
private TextFieldSink[]	textf
private TextFieldFloat[]	textFloat
private TextFieldInt[]	textInt
private boolean	withSoap

Constructor Summary

BuildJembossForm(java.lang.String appDescription, java.lang.String[] db, java.lang.String applName, java.lang.String[] envp, java.lang.String cwd, java.lang.String acdText, boolean withSoap, ScrollPanel p2, JembossParams mysettings, javax.swing.JFrame f)

Method Summary

void	actionPerformed(java.awt.event.ActionEvent ae) Action events Exit, Help, GO, & Show results
void	attach(javax.swing.JPanel p3, javax.swing.Box fieldPane, java.lang.String appDescription)
private java.lang.String	checkParameters(ParseAcd parseAcd, int numofFields, java.util.Hashtable filesToMove)
private java.lang.String	filesForSoap(java.lang.String fn, java.lang.String options, java.lang.String val, java.util.Hashtable filesToMove)
void	finalize() Ensures garbaged collected when there are no more pointers to this.
private java.lang.String	getCommand() Get the command line for the Standalone version.
private java.lang.String	getCommand(java.util.Hashtable filesToMove) Get the command line for the SOAP version.
private byte[]	getLocalFile(java.io.File name)

Methods inherited from class java.lang.Object

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

Field Detail

rf

private ReportFormat rf

af

private AlignFormat af

textf

private TextFieldSink[] textf

textInt

private TextFieldInt[] textInt

textFloat

private TextFieldFloat[] textFloat

rangeField

private javax.swing.JTextField[] rangeField

checkBox

private javax.swing.JCheckBox[] checkBox

inSeqAttr

private InputSequenceAttributes[] inSeqAttr

filelist

private ListFilePanel[] filelist

outSeqAttr

protected static OutputSequenceAttributes outSeqAttr

advSectionBox

private javax.swing.Box advSectionBox

addSectionBox

private javax.swing.Box addSectionBox

advSection

protected static javax.swing.JPanel advSection

addSection

protected static javax.swing.JPanel addSection

reqdSection

protected static javax.swing.JPanel reqdSection

outSection

protected static javax.swing.JPanel outSection

inpSection

protected static javax.swing.JPanel inpSection

fieldOption

private JembossComboPopup[] fieldOption

multiOption

private javax.swing.JList[] multiOption

inSeq

private SetInFileCard[] inSeq

bresults

private javax.swing.JButton bresults

applName

private java.lang.String applName

db

private java.lang.String[] db

envp

private java.lang.String[] envp

cwd

private java.lang.String cwd

parseAcd

private ParseAcd parseAcd

cbusy

private java.awt.Cursor cbusy

cdone

private java.awt.Cursor cdone

seqoutResult

private java.lang.String seqoutResult

outfileResult

private java.lang.String outfileResult

stdout

private java.lang.String stdout

helptext

private java.lang.String helptext

withSoap

private boolean withSoap

f

private javax.swing.JFrame f

p2

private ScrollPanel p2

embossBin

private java.lang.String embossBin

numofFields

private int numofFields

mysettings

private JembossParams mysettings

Constructor Detail

BuildJembossForm

public BuildJembossForm(java.lang.String appDescription,
                        java.lang.String[] db,
                        java.lang.String applName,
                        java.lang.String[] envp,
                        java.lang.String cwd,
                        java.lang.String acdText,
                        boolean withSoap,
                        ScrollPanel p2,
                        JembossParams mysettings,
                        javax.swing.JFrame f)

Method Detail

attach

public void attach(javax.swing.JPanel p3,
                   javax.swing.Box fieldPane,
                   java.lang.String appDescription)

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent ae)

Action events Exit, Help, GO, & Show results

Specified by:

actionPerformed in interface java.awt.event.ActionListener

checkParameters

private java.lang.String checkParameters(ParseAcd parseAcd,
                                         int numofFields,
                                         java.util.Hashtable filesToMove)

filesForSoap

private java.lang.String filesForSoap(java.lang.String fn,
                                      java.lang.String options,
                                      java.lang.String val,
                                      java.util.Hashtable filesToMove)

getLocalFile

private byte[] getLocalFile(java.io.File name)

getCommand

private java.lang.String getCommand()

Get the command line for the Standalone version.

Returns:

String command line to use

getCommand

private java.lang.String getCommand(java.util.Hashtable filesToMove)

Get the command line for the SOAP version.

Returns:

String command line to use

finalize

public void finalize()
              throws java.lang.Throwable

Ensures garbaged collected when there are no more pointers to this.

Throws:

java.lang.Throwable