[Biojava-l] RichSequenceIterator.hasNext from empty file return true!!!

[George Waldon]

Hi Khali,

In my hands I found "java.io.FileNotFoundException: emptyFile.txt (The  
system cannot find the file specified)", which is not exactly the same  
thing as an empty file. Anyway, I think you are right and  
RichStreamReader should switch the moreSequenceAvailable flag before  
throwing the exception. In your case just get out of the loop and you  
should be safe. Thanks for reporting.

George

Quoting Khalil El Mazouari <khalil.elmazouari at gmail.com>:

> Hi,
>
> RichSequenceIterator.hasNext from empty file return true!!! and  
> throws an infinite BioException loop!!!
> Any explanation?? Thanks
>
> khalil
>
> test using the following code
>
>     public static void main(String[] args) {
>        String path = "emptyFile.txt";
>
>          BufferedReader br = null;
>       try {
>          br = new BufferedReader(new FileReader(path));
>       } catch (FileNotFoundException ex) {
>          ex.printStackTrace();
>       }
>       RichSequenceIterator seqs =  
> RichSequence.IOTools.readFastaProtein(br, null);
>         while (seqs.hasNext()) {
>          try {
>             RichSequence seq = seqs.nextRichSequence();
>          } catch (NoSuchElementException ex) {
>             ex.printStackTrace();
>          } catch (BioException ex) {
>             ex.printStackTrace();
>          }
>         }
>
> ====
>
> org.biojava.bio.BioException: Could not read sequence
>         at  
> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113)
>         at com.kem.ae.core.Empty.main(Empty.java:51)
> Caused by: java.io.IOException: Premature stream end
>         at  
> org.biojavax.bio.seq.io.FastaFormat.readRichSequence(FastaFormat.java:178)
>         at  
> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
>         ... 1 more
> org.biojava.bio.BioException: Could not read sequence
>         at  
> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113)
>         at com.kem.ae.core.Empty.main(Empty.java:51)
> Caused by: java.io.IOException: Premature stream end
>         at  
> org.biojavax.bio.seq.io.FastaFormat.readRichSequence(FastaFormat.java:178)
>         at  
> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
>
> infinite loop....
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>