>The simple and dirty solution here, is to just have your Sequence class
>have a constructor that takes an object of type Sequence.
>The constructor just copies the data from the Sequence class ( that you get
>from SeqIOTools.readEMBL(br) ) into your own
>class. It will be about 20 lines of code or so ( from a quick look at my
>own code that does just this ).
>
I have made my own OrderedSequence Object
constructed thus
Sequence sequenceLoaded = null;
SequenceIterator stream = SeqIOTools.readEmbl(br);
stream = SeqIOTools
while (stream.hasNext())
sequenceLoaded = stream.nextSequence();
Sequence orderedSequence = new
OrderedSequence(sequenceLoaded.subList(1,sequenceLoaded.length()),
sequenceLoaded.getURN(), sequenceLoaded.getName(),
sequenceLoaded.getAnnotation());
that is all fine but I now can not see how to add features to it
I would like to do somthing like this:
Iterator featureIterator = sequenceLoaded.features();
while(featureIterator.hasNext()){
orderedSequence.add(featureIterator.next());
}
but there is no add in the Sequence interface
so I am going to have to use
orderedSequence.createFeature(Feature.Template ft);
the problem with this is that I would have to create the Templates and there
are several different types (eg StrandedFeature and RNAFeature) so I would
have to check which it is then construct that type - seems nasty?
ps
how do I find/join/logon biojava on irc.openprojects.net
_________________________________________________________________
Chat with friends online, try MSN Messenger: http://messenger.msn.com
_______________________________________________
Biojava-l mailing list - [EMAIL PROTECTED]
http://biojava.org/mailman/listinfo/biojava-l
