Sometimes you'll come across a file that is not strictly in the correct format, or you may even uncover a bug in one of the parsers. We always appreciate feedback in these cases, including the input file in question and a full stack trace. However, sometimes you may want to find the problem yourself, or even attempt to fix it! So we have produced the DebuggingRichSeqIOListener for this purpose.

The DebuggingRichSeqIOListener is a class that acts both as a BufferedInputStream, so it can be passed to a RichSequenceFormat for reading data, and as a RichSeqIOListener, so that it can be passed to the same RichSequenceFormat to listen to the sequence generation events. It dumps all input out to STDOUT as it reads it, and notifies every sequence generation event to STDOUT as it is received. This way you can see exactly at which points in the file the events are being generated, the data the format was working on at the time the event was generated, and if an exception happens, it will appear immediately after the section of the file that was in error.

The idea is that you do something like this (the example debugs the parsing of a FASTA file):

<java>

Namespace ns = RichObjectFactory.getDefaultNamespace();

InputStream is = new FileInputStream("myFastaFile.fasta");

FASTAFormat format = new FASTAFormat();

DebuggingRichSeqIOListener debug = new DebuggingRichSeqIOListener(is);

BufferedReader br = new BufferedReader(new InputStreamReader(debug));

SymbolTokenization symParser = format.guessSymbolTokenization(debug);

format.readRichSequence(br, symParser, debug, ns);

</java>

Note that you will often get bits of file repeated in the output, as the format runs backwards and forwards through the file between markers it has set. This is perfectly normal although it may look a little strange.

When reporting problems with file parsing, it would be very useful if you could run the above code on your chosen input file and chosen RichSequenceFormat, and send us a copy of the output along with the stacktrace and input file.