[Biojava-dev] Tests failing

[Francois Pepin]

Sorry about that one. I was sure that I had run the tests before
commiting (and the hasChild bug was about as dumb as they come).

TerminatedSymbolList in itself isn't really needed, but I need to be
able to terminate the SymbolList. First because of the current code
structure assumes it. Secondly (and more importantly), we need to
terminate the sequences if we want to add more than 1 sequence and
expect every suffix to end at a leaf.

It could be possible to have some code in the tree construction that
puts an implicit termination symbol at the end. I like to have an actual
termination symbol in there, because it makes the code a lot simpler.

Francois

On Mon, 2003-08-25 at 10:15, Thomas Down wrote:
> There have been a few tests failing in the last couple of days:
> 
>   * org.biojava.bio.symbol.UkkonenSuffixTreeTest
> 
>    There were a couple of problems with this class:
> 
>    - The alphabet-copying code in TerminatedSymbolList was
>      badly wrong, and was trying to create a new alphabet
>      with non-atomic symbols in.  Probably another sign that
>      we need more documentation on alphabet-creation.  This
>      is fixed now (but not very beautifully).  Is
>      TerminatedSymbolList actually needed?
> 
>    - SuffixNode.hasChild was broken.
> 
>   * org.biojava.bio.symbol.AlphabetSerializationTest
> 
>      This was just a problem in the test case, fixed now.
> 
> 
> Thomas.
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