[Biojava-l] Need Help

[mark.schreiber at novartis.com]

I don't think we capture that property. Why do you want it? If it is the 
nucleotide sequence you are after then do something like


seq.sublist(from, to);
seq.seqString();
seq.symbolAt(index);

These are SymbolList methods but a Sequence is an instanceof a SymbolList.

See also the section on sequence manipulation on this webpage 
http://www.biojava.org/docs/bj_in_anger/index.htm

- Mark





"Goh khee Teck" <kheeteck at msn.com>
Sent by: biojava-l-bounces at portal.open-bio.org
10/07/2005 12:30 PM

 
        To:     Biojava-l at biojava.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Need Help


Hi..

Anybody know how to retrieve the annotation property
"ORIGIN"

My code look like this

while(sequences.hasNext()){
try {

seq = sequences.nextSequence();
//Annotation
Annotation anno = seq.getAnnotation();

//print each key value pair
for (Iterator i = anno.keys().iterator(); i.hasNext();
) {
Object key = i.next();

System.out.println(key +" : "+ anno.getProperty(key));
}//for
}//while

It print out the value for each annotation key but for
ORIGIN, there is nothing.

ORIGIN FOR A typical genbank file SCU49845
looks like
ORIGIN
        1 gatcctccat atacaacggt atctccacct caggtttaga tctcaacaac 
ggaaccattg
       61 ccgacatgag acagttaggt atcgtcgaga gttacaagct aaaacgagca 
gtagtcagct
      121 ctgcatctga agccgctgaa gttctactaa gggtggataa catcatccgt 
gcaagaccaa
      181 gaaccgccaa tagacaacat atgtaacata tttaggatat acctcgaaaa 
taataaaccg
      241 ccacactgtc attattataa ttagaaacag aacgcaaaaa ttatccacta 
tataattcaa
      301 agacgcgaaa aaaaaagaac aacgcgtcat agaacttttg gcaattcgcg 
tcacaaataa
      361 attttggcaa cttatgtttc ctcttcgagc agtactcgag ccctgtctca 
agaatgtaat
      421 aatacccatc gtaggtatgg ttaaagatag catctccaca acctcaaagc 
tccttgccga
      481 gagtcgccct cctttgtcga gtaattttca cttttcatat gagaacttat 
tttcttattc
      541 tttactctca catcctgtag tgattgacac tgcaacagcc accatcacta 
gaagaacaga
      601 acaattactt aatagaaaaa ttatatcttc ctcgaaacga tttcctgctt 
ccaacatcta
      661 cgtatatcaa gaagcattca cttaccatga cacagcttca gatttcatta 
ttgctgacag
      721 ctactatatc actactccat ctagtagtgg ccacgcccta tgaggcatat 
cctatcggaa


Regards
KheeTeck

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