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java.lang.Objectuk.ac.sanger.cgp.standalonecsa.jabawat.Jabawat
public class Jabawat
Originally part of CGP's internal geneutil package JaBaWAT basically stands for Java Basic Word Alignment Tool. It aligns a string with a larger string and finds the coordinates of the hit within the larger string.
Constructor Summary | |
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Jabawat()
Creates a new instance of Jabawat |
Method Summary | |
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static JabawatResults |
runJabawat(java.lang.String target,
java.lang.String query,
JabawatResults jr,
int mismatches)
Runs the core of the JaBaWAT alignment program using two strings representing the sequences. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public Jabawat()
Method Detail |
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public static JabawatResults runJabawat(java.lang.String target, java.lang.String query, JabawatResults jr, int mismatches)
target
- Target sequencequery
- Query sequencejr
- results objectmismatches
- number of mismatches allowed
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