[Biojava-l] Propsed change for fastaFormat

[Schreiber, Mark]

Hi -

I'm pretty sure the phredFormat should be immune to such a change.

Mark

 Mark Schreiber
 Bioinformatics
 AgResearch Invermay
 PO Box 50034
 Mosgiel
 New Zealand
 
 PH: +64 3 489 9175
 

-----Original Message-----
From: Cox, Greg [mailto:gcox@netgenics.com] 
Sent: Tuesday, 19 February 2002 11:34 a.m.
To: biojava-l@biojava.org
Subject: [Biojava-l] Propsed change for fastaFormat


What I'd like to do is write the name + description of a sequence out in
fasta format.  Right now, it prints the name for a non-phred file, and
the description of a phred file (greped the code for the key used; it's
only in phredFormat).  I don't work with phred files, so I don't want to
bull in and break things.  Could someone who uses phred look at this
proposed change and
tell me if it would cause problems for you?	

	public static String PROPERTY_DESCRIPTIONLINE =
"description_line";

	public void setPropertyDescriptionLine(String theLine) // New
method
	{
		PROPERTY_DESCRIPTIONLINE = theLine;
	}

	public String getPropertyDescriptionLine() // New method
	{
		return PROPERTY_DESCRIPTIONLINE;
	}

	protected String describeSequence(Sequence seq) // Rewritten
method
	{
	StringBuffer description = new StringBuffer(seq.getName());
	try 
	{
	description.append(" " +
seq.getAnnotation().getProperty(this.getPropertyDescriptionLine()).toStr
ing(
));
	} 
	catch (NoSuchElementException ex) 
	{
		// Intentionally blank
	}
	return description.toString();
	}

Thanks,
Greg Cox
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