[Biojava-dev] [Bug 2316] New: UniProtFormat fail on read RX record.

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2316

           Summary: UniProtFormat fail on read RX record.
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: seq.io
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: miyabe at port4.info


Isn't the delimiter not ";" but "; "?

I changed row #481 of UniProtFormat to below and it works.

String[] refs = val.split("; ");

--
Exception in thread "main" org.biojava.bio.BioException: Could not read
sequence
        at
org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113)
        at jp.co.maze.intact.RestructMain.exec(RestructMain.java:90)
        at jp.co.maze.intact.RestructMain.main(RestructMain.java:42)
Caused by: org.biojava.bio.seq.io.ParseException: 

A Exception Has Occurred During Parsing. 
Please submit the details that follow to biojava-l at biojava.org or post a bug
report to http://bugzilla.open-bio.org/ 

Format_object=org.biojavax.bio.seq.io.UniProtFormat
Accession=Q13362
Id=
Comments=
Parse_block=RN   [6]RP   IDENTIFICATION AS A RENAL CANCER ANTIGEN.RC  
TISSUE=Renal cell carcinoma;RX   MEDLINE=99438124; PubMed=10508479;
DOI=10.1002/(SICI)1097-0215(19991112)83:4<456::AID-IJC4>3.0.CO;2-5;RA   Scanlan
M.J., Gordan J.D., Williamson B., Stockert E., Bander N.H.,
Jongeneel C.V., Gure A.O., Jaeger D., Jaeger E., Knuth A., Chen Y.-T.,
Old L.J.;RT   "Antigens recognized by autologous antibody in patients with
renal-
cell carcinoma.";RL   Int. J. Cancer 83:456-464(1999).
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)
        ... 2 more
Caused by: java.lang.ArrayIndexOutOfBoundsException: 1
        at
org.biojavax.bio.seq.io.UniProtFormat.readRichSequence(UniProtFormat.java:486)
        ... 3 more


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