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 <[email protected]>:
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....
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