[Biojava-l] How to get Sequence from a file other than ABI or SCF?

[abhinav]

Hello all,
I need some help once again.

My situation is that I have already generated the following files from
phred: .scf, .qual, .seq.  The goal is to create a Trace object for an

applet.

Now I want to get a Sequence file as my final output for displaying it onto a SequencePanel.

I want to use the files generated from the phred tool to create a Sequence. I have explored much of biojava but i could not find any suitable classes that could be used to encapsulate the data obtained from the phred output.


The approach that I want to use is somehow get a SymbolList from the data that I have.After that I want to Run the PhredSequence . After that I want to run the PhredTools.create()   method to generate the Sequence...

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File ft = new File("C:/Documents and Settings/Abhi/apptest/src/3422_A01.ab1");

// I am currently using the ab1 file but I want to use the .phd or the .seq file here.

SymbolList  seq_sym =  trace.getSequence();

PhredSequence temp = new PhredSequence(seq_sem , " " ," ", Annotation.EMPTY_ANNOTATION);

SymbolList seq_qual = temp.getQuality();

Sequence final_seq = PhredTools.create(seq_sym,seq_qual);

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When I run this particular code I get the exception that PhredSequence cannot DNA symbolList as input. So that basically is the problem.


I wanted to make sure if the method that I am following is the correct one and if not then what approach can be taken so that my Final output is a sequence that can be rendered.