[Biojava-dev] [Bug 2260] New: Bug in UkkonenSuffixTree

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2260

           Summary: Bug in UkkonenSuffixTree
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: minor
          Priority: P2
         Component: symbol
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: mark.schreiber at novartis.com


There is a bug in the UkkonenSuffixTree when one tries to add concatenated
Strings which are delimited with a $. This doesn't seem to be a problem when
Strings are added individually. A simple work around is to add Strings
individually. The following code causes the bug:

public class Main {

    /** Creates a new instance of Main */
    public Main() {
    }

    /**
     * @param args the command line arguments
     */
    public static void main(String[] args) {
        String seqs = "atcgcgcgcgctcggcctgggggctcgcgct$acgggtggtggt";

        UkkonenSuffixTree suff = new UkkonenSuffixTree(seqs);

    }   
}

Someone with a better knowledge of suffix trees than I have would need to look
at this...

Additionally there are several places in code where variables are declared and
never used or declared globally when they need not be or are not declared final
when they are never modified. There is also System.out.println() statements
that should be messages in exceptions or errors. The code could do with a good
clean up.

I am marking this as minor because there is a work around. The simplest thing
might be to disable the advertised feature of being able to deal with
concatenated strings as it seems it cannot and probably never has been able to.


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