org.emboss.jemboss.gui.sequenceChooser
Class InputSequenceAttributes

java.lang.Object
  org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes

public class InputSequenceAttributes

extends java.lang.Object

Creates the input sequence attibutes window

Field Summary

private javax.swing.JComboBox	dbs available databases
private java.lang.String[]	ff input format types
private javax.swing.JComboBox	fileFormats combobox for file formats
private javax.swing.JRadioButton	lower select to specify lower case
private javax.swing.JRadioButton	nucleotide select to specify a nucleotide sequence
private javax.swing.JRadioButton	protein select to specify a protein sequence
private javax.swing.JRadioButton	rev select to reverse sequence
private javax.swing.JScrollPane	rscroll scroll panel for attibute panel
private TextFieldInt	sbeg -sbegin flag
private TextFieldInt	send -send flag
private javax.swing.JTextField	UFO uniform feature object
private javax.swing.JRadioButton	upper select to specify upper case

Constructor Summary

InputSequenceAttributes(java.lang.String[] db, FileChooser fc)

Method Summary

java.lang.String	getBegSeq() Get the -sbegin flag
java.lang.String	getEndSeq() Get the -send flag
java.lang.String	getFormatChoosen() Get the file format selected
java.lang.String	getInputSeqAttr(int seq) Get the EMBOSS command line for the values selected for the input sequence attributes
javax.swing.JScrollPane	getJScrollPane() Get the scroll panel
boolean	isBeginSeqDefault() Determine if there is a default -sbeg value
boolean	isEndSeqDefault() Determine if there is a default -send value
boolean	isUFODefault() Determine if there is a default -sufo value
void	setBegSeq(int iseq) Set the -sbegin flag
void	setBegSeq(java.lang.String s) Set the -sbegin flag
void	setEndSeq(int iseq) Set the -send flag
void	setEndSeq(java.lang.String s) Set the -send flag

Methods inherited from class java.lang.Object

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

Field Detail

sbeg

private TextFieldInt sbeg

-sbegin flag

send

private TextFieldInt send

-send flag

UFO

private javax.swing.JTextField UFO

uniform feature object

dbs

private javax.swing.JComboBox dbs

available databases

fileFormats

private javax.swing.JComboBox fileFormats

combobox for file formats

rev

private javax.swing.JRadioButton rev

select to reverse sequence

nucleotide

private javax.swing.JRadioButton nucleotide

select to specify a nucleotide sequence

protein

private javax.swing.JRadioButton protein

select to specify a protein sequence

lower

private javax.swing.JRadioButton lower

select to specify lower case

upper

private javax.swing.JRadioButton upper

select to specify upper case

rscroll

private javax.swing.JScrollPane rscroll

scroll panel for attibute panel

ff

private java.lang.String[] ff

input format types

Constructor Detail

InputSequenceAttributes

public InputSequenceAttributes(java.lang.String[] db,
                               FileChooser fc)

Parameters:

db - available databases

fc - file chooser

Method Detail

getJScrollPane

public javax.swing.JScrollPane getJScrollPane()

Get the scroll panel

Returns:

scroll panel

setBegSeq

public void setBegSeq(int iseq)

Set the -sbegin flag

Parameters:

iseq - value for -sbeg

setEndSeq

public void setEndSeq(int iseq)

Set the -send flag

Parameters:

iseq - value for -send

setBegSeq

public void setBegSeq(java.lang.String s)

Set the -sbegin flag

Parameters:

s - value for -sbeg

setEndSeq

public void setEndSeq(java.lang.String s)

Set the -send flag

Parameters:

s - value for -send

getBegSeq

public java.lang.String getBegSeq()

Get the -sbegin flag

Returns:

value for -sbeg

getEndSeq

public java.lang.String getEndSeq()

Get the -send flag

Returns:

value for -send

isBeginSeqDefault

public boolean isBeginSeqDefault()

Determine if there is a default -sbeg value

Returns:

true if -sbeg is set

isEndSeqDefault

public boolean isEndSeqDefault()

Determine if there is a default -send value

Returns:

true if -send is set

isUFODefault

public boolean isUFODefault()

Determine if there is a default -sufo value

Returns:

true if -sufo is set

getFormatChoosen

public java.lang.String getFormatChoosen()

Get the file format selected

Returns:

file format

getInputSeqAttr

public java.lang.String getInputSeqAttr(int seq)

Get the EMBOSS command line for the values selected for the input sequence attributes

Parameters:

seq - sequence number

Returns:

command line input sequence options