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:[EMAIL PROTECTED]] Sent: Tuesday, 19 February 2002 11:34 a.m. To: [EMAIL PROTECTED] 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 _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
