Changes between Version 2 and Version 3 of BioJavaRoundTripThirdPass

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Timestamp:
2008/02/14 12:50:33 (7 years ago)
Author:
holland
Comment:

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  • BioJavaRoundTripThirdPass

    v2 v3  
    11= !BioJava = 
    2 Working with BioJava-live SVN version 4723. 
     2 * Working with BioJava-live SVN version 4723. 
    33== Fasta Format == 
    44=== Major Issues === 
    5 None 
     5 * None 
    66=== Minor Issues === 
    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). 
     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). 
    99===Read-Write-Read=== 
    10 Succeeds! 
     10 * Succeeds! 
    1111 
    1212 
    1313== Genbank format == 
    1414=== Major Issues === 
    15 None. 
     15 * None. 
    1616=== Minor Issues === 
    17 Feature qualifier order is not preserved. 
    18 Because NCBI Taxonomy is referenced from memory or database if the version used 
     17 * Feature qualifier order is not preserved. --it is, but xrefs and organism are moved to end of list as they are not stored internally as qualifiers. 
     18 * Because NCBI Taxonomy is referenced from memory or database if the version used 
    1919doesn't match the version that was used to construct the record then minor  
    2020differences appear. For example the common name of Arabidopsis changed from thale cress 
    2121to mouse ear cress. 
    2222===Read-Write-Read=== 
    23 Success! 
     23 * Success! 
    2424 
    2525== GenbankXML format == 
    2626== Major Issues == 
    27 Not supported (INSD is). 
     27 * Not supported (INSD is). 
    2828 
    2929== INSD Format == 
    3030== Major Issues == 
    31 None. 
     31 * None. 
    3232== Minor Issues == 
    33 * BioJava inlcudes the Reference_position tag. NCBI doesn't unless it is not 1..1 
     33 * BioJava inlcudes the Reference_position tag. NCBI doesn't unless it is not 1..1 
    3434{{{ 
    3535<INSDReference_position>1..1</INSDReference_position> 
    3636}}} 
    37 * There are other examples of this redundancy. I think if this doesn't break the 
     37 * There are other examples of this redundancy. I think if this doesn't break the 
    3838dtd then it doesn't matter. 
    39 * Qualifiers order is not preserved. I don't think this matters. 
     39 * Qualifiers order is not preserved. I don't think this matters. --see Genbank 
    4040===Read-Write-Read=== 
    41 Success! 
     41 * Success! 
    4242 
    4343== EMBL Format == 
    4444=== Major Issues === 
    45 No major issues 
     45 * No major issues 
    4646=== Minor Issues === 
    4747 * Version in date is not correct on output. --fixed 
    4848 * Two XX lines after references. -- fixed 
    49  * Feature qualifiers out of order. 
     49 * Feature qualifiers out of order. --see Genbank 
    5050===Read-Write-Read=== 
    51 Succeeds! 
     51 * Succeeds! 
    5252 
    5353== SwissProt/ Uniprot == 
     
    5959 * We loose the copyright statement. -- fixed 
    6060===Read-Write-Read=== 
    61 Cannot read back in: -- fixed 
     61 * Cannot read back in: -- fixed 
    6262 
    6363<code> 
     
    9494== EMBLxml == 
    9595=== Major Issues === 
    96 none 
     96 * none 
    9797=== Minor Issues === 
    9898===Read-Write-Read=== 
    99 Success! 
     99 *  Success!