[Biojava-l] How to pull out the detailed information in Genbankfeature table

[Gang Wu]

Sorry for the naive question. Just found out by adding several rows in the
printGenes() to dig out the gene annotation information.

	public static void printGenes(Iterator features) {
        	while(features.hasNext()) {
            	Feature f = (Feature) features.next();
	            if (f.getType().equalsIgnoreCase("gene")) {
      	      	System.out.print(f.getType() + " at "
				+ f.getLocation().toString());
				Annotation geneAnnotation = f.getAnnotation();
                		java.util.Set theKeys = geneAnnotation.keys();
                		java.util.Iterator keyIterator = theKeys.iterator();
                		while (keyIterator.hasNext()) {
                  		String key = (String) keyIterator.next();
	                    	System.out.println("\t" + key + " = "
					+ geneAnnotation.getProperty(key).toString());
            	    	}
                		printGenes(f.features());
      	     	}
        	}
    	}



-----Original Message-----
From: biojava-l-bounces at portal.open-bio.org
[mailto:biojava-l-bounces at portal.open-bio.org]On Behalf Of Gang Wu
Sent: Monday, April 12, 2004 1:43 PM
To: Bio-Java
Subject: [Biojava-l] How to pull out the detailed information in
Genbankfeature table


Following is a piece of code I used to retrieve the gene information in the
feature table of GeneBank flat file. Seems "location" is the only
inforamtion stored in Feature class. Is there a way to retrieve other
detailed informaiton like "/note", "/locus_tag" etc?

Thanks


	public static void main (String [] args) {
		BufferedReader br = new BufferedReader(new FileReader("GenBankFilePath"));
		SequenceIterator stream = SeqIOTools.readGenbank(br);
		Sequence seq = stream.nextSequence();
		printGenes(seq.features());
	}

	public static void printGenes(Iterator features) {
        	while(features.hasNext()) {
            	Feature f = (Feature) features.next();
	            if (f.getType().equalsIgnoreCase("gene")) {
      	      	System.out.print(f.getType() + " at " +
f.getLocation().toString());
                		printGenes(f.features());
      	      }
        	}
    	}

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