[Bug] in def findNode

[conscho]

I believe there is a small bug in def findNode. It can be found in line 168 in lib/Newick.rb.

The line is currently: if (@name =~/#{name}/)
and should be: if @name == name

Why?
If there are nodes with the names 111, 11 and 1 in the tree and you are looking for node 1. It will find either of them and stop at the first one found.

Cheers and thanks!

[jhbadger]

Hi Constantin,

The way I use the routines myself is that I often work with multiple trees
of orthologous genes, where the nodes are named with species and gene -- I
want to be able to find the E.coli node regardless of what gene it is. So a
regular expression works for that and an exact match wouldn't.

However, I have added a second optional argument to findNode that sets the
matching to exact -- findNode("E. coli", true) will only find nodes just
named "E. coli", but findNode("E. coli") will still find "E. coli recA",
"E. coli dnaK", etc.

Jonathan

On Tue, May 26, 2015 at 10:33 AM Constantin Scholl notifications@github.com
wrote:

I believe there is a small bug in def findNode. It can be found in line
168 in lib/Newick.rb.

The line is currently: if (@name https://github.com/name =~/#{name}/)
and should be: if @name https://github.com/name == name

Why?
If there are nodes with the names 111, 11 and 1 in the tree and you are
looking for node 1. It will find either of them and stop at the first one
found.

Cheers and thanks!

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