Changes between Version 1 and Version 2 of BioJavaRoundTripThirdPass
- Timestamp:
- 2008/02/14 12:23:23 (17 years ago)
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BioJavaRoundTripThirdPass
v1 v2 5 5 None 6 6 === Minor Issues === 7 Sequence case is not preserved. Line length varies (default is 80 cpl). 7 Sequence case is not preserved. --not really a bug. It is preserved if you pass in a masked alphabet instead of the default DNA alphabet. 8 Line length varies (default is 80 cpl). 8 9 ===Read-Write-Read=== 9 10 Succeeds! … … 44 45 No major issues 45 46 === Minor Issues === 46 * Version in date is not correct on output. 47 * Two XX lines after references. 47 * Version in date is not correct on output. --fixed 48 * Two XX lines after references. -- fixed 48 49 * Feature qualifiers out of order. 49 50 ===Read-Write-Read=== … … 55 56 * BioSQL cannot store more than one database reference for a single publication, 56 57 eg Pubmed and medline Id and DOI. 57 * We are putting 'and' before the last author. 58 * We loose the copyright statement. 58 * We are putting 'and' before the last author. --fixed 59 * We loose the copyright statement. -- fixed 59 60 ===Read-Write-Read=== 60 Cannot read back in: 61 Cannot read back in: -- fixed 61 62 62 63 <code> … … 83 84 == UniprotXML == 84 85 === Major Issues === 85 * Missing the namespace and the version from entry tag 86 * Don't write editor list if there are no editors 87 * Reference tag not correctly constructed. 86 * Missing the namespace and the version from entry tag -- fixed 87 * Don't write editor list if there are no editors -- fixed 88 * Reference tag not correctly constructed. -- fixed 88 89 * When writing Uniprot XML it would be illegal to use anything other than 89 Swiss-Prot or TrEMBL as the Namespace 90 Swiss-Prot or TrEMBL as the Namespace -- fixed but only if record originally had correct NS 90 91 === Minor Issues === 91 92 ===Read-Write-Read===
