org.emboss.jemboss.gui.form
Class AlignFormat

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

public class AlignFormat

extends java.lang.Object

Handles emboss alignment formats http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Themes/AlignFormats.html

Field Summary

private static java.lang.String[]	align_msf EMBOSS alignment formats
private static java.lang.String[]	align_pairwise EMBOSS pairwise alignment formats
private JembossComboPopup	cp component to display formats
private java.lang.String	def default format
private boolean	lpair true if pairwise alignment format

Constructor Summary

AlignFormat(ParseAcd parseAcd, int nf)

AlignFormat(java.lang.String def, boolean lpair)

Method Summary

java.lang.String	getAlignFormat() Get the alignment format to add to the EMBOSS command line
private java.lang.String[]	getAlignFormats(boolean lpair) Get the alignment formats as a string array
JembossComboPopup	getComboPopup() Get the combo-popup component for alignment formats
java.lang.String	getDefaultFormat()
java.lang.String	getToolTip()
private boolean	isPairWise(ParseAcd parseAcd, int nf) Method to determine whether this is a pairwise (returning true) or multiple sequence alignment format.

Methods inherited from class java.lang.Object

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

Field Detail

align_msf

private static java.lang.String[] align_msf

EMBOSS alignment formats

align_pairwise

private static java.lang.String[] align_pairwise

EMBOSS pairwise alignment formats

cp

private JembossComboPopup cp

component to display formats

def

private java.lang.String def

default format

lpair

private boolean lpair

true if pairwise alignment format

Constructor Detail

AlignFormat

public AlignFormat(ParseAcd parseAcd,
                   int nf)

Parameters:

parseAcd - ACD parser for the application

nf - field number in ACD

AlignFormat

public AlignFormat(java.lang.String def,
                   boolean lpair)

Parameters:

def - default format

lpair - true if pairwise alignment format

Method Detail

getComboPopup

public JembossComboPopup getComboPopup()

Get the combo-popup component for alignment formats

Returns:

combo-popup component for alignment formats

getDefaultFormat

public java.lang.String getDefaultFormat()

Returns:

def default alignment format

getAlignFormats

private java.lang.String[] getAlignFormats(boolean lpair)

Get the alignment formats as a string array

Parameters:

lpair - true if pairwise alignment

Returns:

alignment formats as a string array

getAlignFormat

public java.lang.String getAlignFormat()

Get the alignment format to add to the EMBOSS command line

Returns:

alignment format for EMBOSS command line

isPairWise

private boolean isPairWise(ParseAcd parseAcd,
                           int nf)

Method to determine whether this is a pairwise (returning true) or multiple sequence alignment format.

Parameters:

parseAcd - ACD parser for the application

nf - field number in ACD

Returns:

true if a pairwise alignment

getToolTip

public java.lang.String getToolTip()

Returns:

String report of the available report formats