[Biojava-l] Saving back chromatogram?

[Ashika Umanga Umagiliya]

Greetings all,

Thank you for all your answers.
What I want to do is ,after modifying callbases, I need to use the 
sequences with 'phrad' foro DNA assembly.For 'phrad', I need to give 
Fasta files and Quality files.
I can modify callbases using my chromatogram editor , and save the new 
sequence in Fasta file.But my problem is , If I change the original 
callbases from AB1  file ,does it effect the Qualitiy files also? Or can 
I use the original Quality files generated by 'phred' with  the new 
callbases.


Here is a image demonstrating my scenario:

http://img3.imageshack.us/img3/3564/f92df0815fab523f3c72aa3qx7.png


Step (2) Ab1 files are passed into 'phred' and Fasta,Quality files are 
generated.
Step (3) If user want to edit callbases , he can use the chromatogram 
editor.Then the Fasta files generated by 'phred' are replaced with new 
onces generated by editor.

My problem is can I use the same Quality files ,with  the modified 
callbases ?


Sorry if this is off the topic.

Thanks in advance,
Umanga



Andy Yates wrote:
> Hi Umanga,
>
> Unfortunately there is no write feature available in the BioJava API. My
> advice would be to store these new basecalls in a separate file & look
> into using the Staden IO package which does support write functions (not
> sure if it will write into AB1 but it will do SCF & ZTR). Sadly this is
> written in C so you will have to write either some glue code with JNI to
> get it working or write a small C program to munge an AB1 trace & your
> new file together.
>
> Sorry I can't be of any more help,
>
> Andy
>
> Ashika Umanga Umagiliya wrote:
>   
>> Greetings all,
>>
>> I was able to display chromatogram using ABIFChromatogram class .
>> Now what I want to implement is a chromatogram Editor,where user can
>> edit base calls and save aback to AB1 files.
>> Is there a way to do this in BioJava?
>>
>> Best Regards,
>> umanga
>> _______________________________________________
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>>     
>
>