In the Est plugin, if EST are incompatible,  for the same number of gaps select first the smallest covered region.

If the parameter spliceNonCan is true, allow noncanonical splice sites (defined in EuGene.NonCanDon and EuGene.NonCanAcc)

Order, upstream and downstream context length, site are read directly in the wam file name.
$EUGENEDIR/models/WAM/species/acceptor/WAM.o4.uc60.dc60.AG.TP.001


in the WAM directory ($EUGENEDIR/models/WAM) the available wam models.

Raise a warning if the site read on the sequence (for instance GC) is different to the site given in parameter (ex GT).

Name of created wam files looks like: EUGENEDIR/models/wam/species/acceptor/WAM.o01.uc60.dc60.AG.TP.*
Check that the training sequences contain the site (GT|AG).

Improve speed in optimization mode: search the signals in the builder method instead of GiveInfo method. (Launch only one time)

Il n'y  a plus de contrainte sur la taille des motifs lus. (les suffixes des fichiers wam sont crees en fonction de la taille lue)

Ajout d un message pour signaler que plugin a ne pas utiliser. Non teste depuis les modification faites dans WAM
Utiliser SignalWAM a la place

Add some debugging msg

Dans  compte2probas, cas particulier ou a l'ordre 0, pas assez d'info pour calculer une proba=> VAL[i] = 0
Ajout de commentaires + reindentation de quelques blocs

motiffile (multifasta file),
pat (the signal pattern, for instance GC or AT),
uc (upstream context lg),
dc (downstream context lg),
markovOrder,
outfileprefix

Add MarkovIMM.CodingPot parameter. Value between 1 and 100. Allow to reduce coding potential (No effect if value=100)

Release 4.1d: add MarkovIMM.CodingPot parameter. Value between 1 and 100. Allow to reduce coding potential (No effect if value=100)