[Biojava-l] ABIFParser question

Mark Schreiber markjschreiber at gmail.com
Wed May 9 06:56:34 UTC 2007

Hi -

Because you have the source code available it might be easier to copy
and paste the code into your class and then modify as needed.

It may be a bit extreme for it to be private. It is probably safe
enough for it to be protected. Alternatively having public or
protected methods to get it's internal members without allowing
modification may be another good approach. If you have a nice solution
we can check it in to CVS.

If you believe the getString() method is incorrect please poste a bug
report with example code to demonstrate the problem. If you know how
to solve it even better. we can then use the bug report as the basis
for a fix and a regression test.

- Mark

On 5/3/07, Heather Kent <heatkent at gmail.com> wrote:
> 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
> way?
> 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
> heather
> --
> 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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