[Biojava-l] SCF Chromatogram Read Error

[Andy Yates]

Hi Kikia,

Have you tried the latest version of the chromatogram parser code from 
CVS. It didn't make it into the 1.4 release of biojava which is why you 
may be having a problem. If not then I guess it is a proper bug. The src 
can be accessed @

http://code.open-bio.org/cgi/viewcvs.cgi/biojava-live/src/org/biojava/bio/program/scf/SCF.java?cvsroot=biojava

Cheers,

Andy Yates

Kikia Carter wrote:
> I am having the following problem when trying to create a chromatogram 
> from an SCF file:
> java.lang.IndexOutOfBoundsException
>     at java.io.FileInputStream.readBytes(Native Method)
>     at java.io.FileInputStream.read(FileInputStream.java:194)
>     at java.io.DataInputStream.read(DataInputStream.java:224)
>     at org.biojava.bio.program.scf.SCF$Parser.parsePrivate(SCF.java:348)
>     at org.biojava.bio.program.scf.SCF$Parser.parse(SCF.java:313)
>     at org.biojava.bio.program.scf.SCF$ParserFactory.parse(SCF.java:176)
>     at org.biojava.bio.program.scf.SCF.load(SCF.java:122)
>     at org.biojava.bio.program.scf.SCF.load(SCF.java:117)
>     at org.biojava.bio.program.scf.SCF.create(SCF.java:104)
>     at 
> org.biojava.bio.chromatogram.ChromatogramFactory.create(ChromatogramFactory.java:75) 
> 
> 
> Can anyone offer advice on this problem? Thanks in advance!
> 
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