Thanks Ron,
I've patched this in. Does something similar need to be done for Embl?
Matthew
Ron Kuhn wrote:
> I have another fix for an exception that I got when parsing GenBank
> sequences that have strands defined on the LOCUS line (e.g. AF343912).
> BioJava assumes that the strands and topology (when both given) are separate
> tokens. This is not true. Here is the fix for the processHeaderLine method
> in GenbankFormat.java:
>
> Substitute the following code for the code inside the if LOCUS:
>
> if (line.startsWith(GenbankFormat.LOCUS_TAG)
> {
> // the LOCUS line is a special case because it contains the
> // locus, size, molecule type, GenBank division, and the date
> // of last modification.
> if (line.length() < 73)
> throw new ParseException("LOCUS line too short [" + line + "]");
>
> saveSeqAnno2(GenbankFormat.LOCUS_TAG, line.substring(12, 22));
> saveSeqAnno2(GenbankFormat.SIZE_TAG, line.substring(22, 29));
> saveSeqAnno2(GenbankFormat.STRAND_NUMBER_TAG, line.substring(33, 35));
> saveSeqAnno2(GenbankFormat.TYPE_TAG, line.substring(36, 41));
> saveSeqAnno2(GenbankFormat.CIRCULAR_TAG, line.substring(42, 52));
> saveSeqAnno2(GenbankFormat.DIVISION_TAG, line.substring(52, 55));
> saveSeqAnno2(GenbankFormat.DATE_TAG, line.substring(62, 73));
> }
>
> And add the supporting method:
> /**
> * Private method to process a header tag and associated value.
> *
> * @param tag The tag to add
> * @param value The value of the associated tag
> * @throws ParseException Thrown when an error occurs parsing the file
> */
> private void saveSeqAnno2(String tag, String value)
> throws ParseException
> {
> value = value.trim(); // strip whitespace
> if (value.length() > 0) {
> this.saveSeqAnno();
> headerTag = tag;
> headerTagText = new StringBuffer(value);
> }
> }
>
> Ron Kuhn
> _______________________________________________
> Biojava-l mailing list - [EMAIL PROTECTED]
> http://biojava.org/mailman/listinfo/biojava-l
> .
>
>
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