= !BioJava =
Working with BioJava-live SVN version 4723.
== Fasta Format ==
=== Major Issues ===
None
=== Minor Issues ===
Sequence case is not preserved. Line length varies (default is 80 cpl).
===Read-Write-Read===
Succeeds!


== Genbank format ==
=== Major Issues ===
None.
=== Minor Issues ===
Feature qualifier order is not preserved.
Because NCBI Taxonomy is referenced from memory or database if the version used
doesn't match the version that was used to construct the record then minor 
differences appear. For example the common name of Arabidopsis changed from thale cress
to mouse ear cress.
===Read-Write-Read===
Success!

== GenbankXML format ==
== Major Issues ==
Not supported (INSD is).

== INSD Format ==
== Major Issues ==
None.
== Minor Issues ==
* BioJava inlcudes the Reference_position tag. NCBI doesn't unless it is not 1..1
{{{
<INSDReference_position>1..1</INSDReference_position>
}}}
* There are other examples of this redundancy. I think if this doesn't break the
dtd then it doesn't matter.
* Qualifiers order is not preserved. I don't think this matters.
===Read-Write-Read===
Success!

== EMBL Format ==
=== Major Issues ===
No major issues
=== Minor Issues ===
 * Version in date is not correct on output.
 * Two XX lines after references.
 * Feature qualifiers out of order.
===Read-Write-Read===
Succeeds!

== SwissProt/ Uniprot ==
=== Major Issues ===
=== Minor Issues ===
 * BioSQL cannot store more than one database reference for a single publication,
eg Pubmed and medline Id and DOI.
 * We are putting 'and' before the last author.
 * We loose the copyright statement. 
===Read-Write-Read===
Cannot read back in:

<code>
Format_object=org.biojavax.bio.seq.io.UniProtFormat
Accession=Q43385
Id=
Comments=
Parse_block=OS   Arabidopsis thaliana (Mouse-ear cress) (Arabidopsis thaliana (L.) Heynh.).OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;OS   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
eurosids II; Brassicales; Brassicaceae; Arabidopsis.OX   NCBI_TaxID=3702;
Stack trace follows ....


        at org.biojavax.bio.seq.io.UniProtFormat.readRichSequence(UniProtFormat.java:615)
        at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
        ... 3 more
Caused by: java.lang.IllegalArgumentException: NCBI taxonomy names cannot embed new lines - at:74, in name: <Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
eurosids II; Brassicales; Brassicaceae; Arabidopsis>
        at org.biojavax.bio.taxa.SimpleNCBITaxonName.<init>(SimpleNCBITaxonName.java:47)
        at org.biojavax.bio.taxa.SimpleNCBITaxon.addName(SimpleNCBITaxon.java:148)
        at org.biojavax.bio.seq.io.UniProtFormat.readRichSequence(UniProtFormat.java:339)
        ... 4 more
</code>

== UniprotXML ==
=== Major Issues ===
 * Missing the namespace and the version from entry tag
 * Don't write editor list if there are no editors
 * Reference tag not correctly constructed.
 * When writing Uniprot XML it would be illegal to use anything other than
    Swiss-Prot or TrEMBL as the Namespace
=== Minor Issues ===
===Read-Write-Read===

== EMBLxml ==
=== Major Issues ===
none
=== Minor Issues ===
===Read-Write-Read===
Success!