[Biojava-l] Sequences as strings to RichSequence iterator

[Richard Holland]

PS. Spot the deliberate mistake in the hasNext() function... that should be <, not <=!

PPS. In your original email you stated you wanted to read your sequences as Fasta. In Biojava, all sequences are RichSequences - they have no format other than the object model of RichSequence itself. Fasta only gets involved when you're reading from a Fasta file, or writing to one. If you need to show the sequences as Fasta in your user interface, you should consider using the FastaWriter writeSequence() method with the PrintStream parameter and wiring in a StringWriter to the PrintStream so that you can get a String representation of a Fasta record.

On 6 Dec 2009, at 15:41, Richard Holland wrote:

> I'm not sure what you're trying to do here - are you trying to represent your string array of sequences as a RichSequenceIterator, or are you trying to convert them into FASTA? I'll answer both anyway...:
> 
> To convert your String[] of sequences into a RichSequenceIterator you need to create a new class that implements the RichSequenceIterator interface. You would probably write something like this (which I have not checked or compiled - so if it has bugs, sorry!):
> 
>   public class MyDNASeqIterator implements RichSequenceIterator {
>      private final String[] sequences;
>      private final int counter;
> 
>      public MyDNASeqIterator(String[] sequences) { this.sequences = sequences; this.counter = 0; }
> 
>      public hasNext() {  
>         return this.counter <= this.sequences.length;
>      }
> 
>      public Sequence nextSequence() { return nextRichSequence(); }
> 
>      public BioEntry nextBioEntry() { return nextRichSequence(); }
> 
>      public RichSequence nextRichSequence() {
>         String seqName = "MySeq"+this.counter;
>         return RichSequence.Tools.createRichSequence(seqName, this.sequences[this.counter++], DNATools.getDNA());
>      }
>   }
> 
> You can then instantiate an object using MyDNASeqIterator's constructor to give it your string array, and iterate over it to get corresponding RichSequence instances.
> 
> To convert your sequences to FASTA, use the above iterator to generate sequences to pass to FastaFormat in the same way that you would write a normal FASTA file.
> 
> cheers,
> Richard
> 
> On 6 Dec 2009, at 14:04, Oliver Stolpe wrote:
> 
>> Hello *,
>> 
>> I have a set of sequences as strings in an array. I now want to turn them into an iterator over RichSequences in fasta-format. I read in the cookbook, but I dont get it. And looked up the examples in biojavax-doc. I tried much but I have no good starting point. No starting point at all. How do the RichSequenceBuilder work? What about the FastaFormat-thing?
>> I thought about putting the sequences in a fast-file and then read the file. But there must be a much more straight-forward way!
>> 
>> Thanks in advance for any hints,
>> Oliver
>> 
>> 
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> 
> --
> Richard Holland, BSc MBCS
> Operations and Delivery Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
> http://www.eaglegenomics.com/
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/