[Biojava-l] ABIFParser question

Heather Kent heatkent at gmail.com
Wed May 2 17:58:14 UTC 2007

I'm currently working on an ABI file parser (i'm working with an extension
of the biojava parser for various reasons) and file writer and running into
some problems.   The biojava ABIParser class creates a Map of
TaggedDataRecords but you can only get one record at a time and i want to
iterate through all the records.  I can't access the Map because it is a
private variable.  Does it have to be a private variable?
So far i am working around it by making large arrays of the tagnames to send
to the getDataRecord method in the ABIFParser to retrieve records and
creating my own map but this seems really inefficient.....is there a better

Also i think i found an error in the toString method of the
TaggedDataRecord....in all the if statements i use numberOfElements instead
of elementLength when reading the DATA_TYPE_ASCII_ARRAY..the elementLength
refers only to the number of bytes in one element and the numberoOfElements
refers to the number of elements in the item....i dont actually use that
method but when i'm reading other records of type
ASCII_ARRAY, or PSTRING or CSTRING that is how i set it up


Duct tape is like the force. It has a light side, a dark side, and it holds
the universe together....
    Carl Zwanzig

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