Changes between Initial Version and Version 1 of BioJavaRoundTripFirstPass

Show
Ignore:
Timestamp:
2008/02/12 17:15:59 (16 years ago)
Author:
markjschreiber
Comment:

--

Legend:

Unmodified
Added
Removed
Modified
  • BioJavaRoundTripFirstPass

    v1 v1  
     1= !BioJava = 
     2Working with !BioJava-live SVN build 4716 
     3 
     4== Fasta Format == 
     5=== Major Issues === 
     6None 
     7=== Minor Issues === 
     8Sequence case is not preserved. Line length varies (default is 80 cpl). 
     9 
     10 
     11== Genbank format == 
     12=== Major Issues === 
     13None. 
     14=== Minor Issues === 
     15Feature qualifier order is not preserved. 
     16Because NCBI Taxonomy is referenced from memory or database if the version used 
     17doesn't match the version that was used to construct the record then minor  
     18differences appear. For example the common name of Arabidopsis changed from thale cress 
     19to mouse ear cress. 
     20 
     21== GenbankXML format == 
     22== Major Issues == 
     23Not supported (INSD is). 
     24 
     25== INSD Format == 
     26== Major Issues == 
     27 
     28== Minor Issues == 
     29Biojava doesn't add the XML header and INSDSet tags, starts with INSDSeq. 
     30{{{ 
     31<?xml version="1.0"?> 
     32<!DOCTYPE INSDSet PUBLIC "-//NCBI//INSD INSDSeq/EN" "http://www.ncbi.nlm.nih.gov/dtd/INSD_INSDSeq.dtd"> 
     33<INSDSet> 
     34<INSDSeq> 
     35... 
     36}}} 
     37 
     38* !BioJava inlcudes the Reference_position tag. NCBI doesn't unless it is not 1..1 
     39{{{ 
     40<INSDReference_position>1..1</INSDReference_position> 
     41}}} 
     42 
     43* There are other examples of this redundancy. I think if this doesn't break the 
     44dtd then it doesn't matter. 
     45 
     46* Qualifiers order is not preserved. I don't think this matters.