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GenBankWriter does not use information in the original header #942 - #1042
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name and not processing joins correctly
and hence much faster to test
from dbxref -> db_xref as the second form is most commonly used and appears in reference material for GenBank files
this differently because they don't have a value. Rather we need to use the database and ID values to create the output
josemduarte
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Very nice, thank you! A few minor comments
| * | ||
| * @param sequence | ||
| */ | ||
| private String _write_original_first_line(S sequence) { |
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Nitpick: could you keep the method name as per usual camel case convention?
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Sure happy to change, I would normally but I was just following the convention already used in the class
e.g. _write_single_line, _write_multi_line etc
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Oh I didn't realise that was the style already for that file. Well I guess we can live with that a bit longer...
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It was initially ported from biopython in a very rudimentary fashion, so
the function names pretty much match the equivalent biopython ones....
…On Wed, Oct 19, 2022, 6:01 PM Jose Manuel Duarte ***@***.***> wrote:
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------------------------------
In
biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderFormat.java
<#1042 (comment)>:
> @@ -222,6 +228,22 @@ private String _write_the_first_line(S sequence) {
*/
}
+ /**
+ * Write the original LOCUS line.
+ *
+ * @PARAM sequence
+ */
+ private String _write_original_first_line(S sequence) {
Oh I didn't realise that was the style already for that file. Well I guess
we can live with that a bit longer...
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@jamesmorris could I also ask you to update the CHANGELOG.md file describing what's changed here? After that, we should try to finally push the first java 11 release, see #1035 |
Updated changelog with a new release and details from pull request biojava#1042
Hello,
I have been working on the issue that a GenBank file read in through the parser and then written back out will result in loss of information from the original file. While looking into this I have also fixed a few other issues with the parser and writer for Genbank files. The highlights of this work includes: