Changes between Version 1 and Version 2 of BioJavaRoundTripThirdPass

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Timestamp:
2008/02/14 12:23:23 (10 years ago)
Author:
holland
Comment:

--

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  • BioJavaRoundTripThirdPass

    v1 v2  
    55None 
    66=== Minor Issues === 
    7 Sequence case is not preserved. Line length varies (default is 80 cpl). 
     7Sequence case is not preserved. --not really a bug. It is preserved if you pass in a masked alphabet instead of the default DNA alphabet. 
     8Line length varies (default is 80 cpl). 
    89===Read-Write-Read=== 
    910Succeeds! 
     
    4445No major issues 
    4546=== 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 
    4849 * Feature qualifiers out of order. 
    4950===Read-Write-Read=== 
     
    5556 * BioSQL cannot store more than one database reference for a single publication, 
    5657eg 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 
    5960===Read-Write-Read=== 
    60 Cannot read back in: 
     61Cannot read back in: -- fixed 
    6162 
    6263<code> 
     
    8384== UniprotXML == 
    8485=== 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 
    8889 * 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 
    9091=== Minor Issues === 
    9192===Read-Write-Read===