Karin Lagesen wrote:
On Wed, Jan 08, 2003 at 09:28:37AM +1300, Schreiber, Mark wrote:It seems the class you cant find, KnuthMorrisPrattSearch isnt included in the last
Hi -
If you already have the SimpleGene features constructed these will
contain a Location object. However, I think you are saying how can I
find a subsequence in my Genomic sequence and locate the gene that way?
To rapidly find exact matches you can use the biojava
KnuthMorrisPrattSearch object from the org.biojava.bio.search package.
It contains a main method that demonstrates it's use. This is a very
efficient algorithm for finding exact matches.
Thankyou for your help. However, I seem to have a different version of biojava than you, since I cannot find that class in that package (and not in none of the others either). The biojava I am using is version 1.22 downloaded from biojava.org. I did however discover a KnuthMorrisPrattSearch in a biojava API at http://rosetteer.icu.ac.kr/, however, I could not figure out how to get at the actual class....Am I missing something again? Karin
official release of Biojava. But its available in the CVS source tree.
So you will have to retrieve the biojava source from CVS, and compile biojava.
Instructions on how to retrieve the source code from cvs can be found at http://cvs.biojava.org/
In order to build biojava from source you will need to have Ant installed ( available
from http://jakarta.apache.org/ant/index.html ). And you build it by just going to the
top directory of the biojava source tree, and then run ant ( run "ant javadocs" to build
the javadoc documentation aswell )
Kalle
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