#####################
#
# adegenet TODO list
#
#####################
#
# please list here all intended modifications
# and all detected bugs
#
# please add a "-- done" or "-- fixed" tag when
# you achieved something
#
# Inside a given section, priority goes decreasing.
#
# Delete fixed things each new release.
#
# T.J. 2008
#
######################



# FOR NEXT STABLE VERSION
=========================
=========================

# CODE ISSUES:
==============
* genepop2genind: bug when both newlines and commas are used
to separate loci in the header of the file -- fixed (TJ)
* package conversion to S4 -- done (TJ)
* !!! new("genind")$pop gives a really nasty thing - maybe a bug in methods -- was a bug in '$' operator -- fixed (TJ)
*

# DOCUMENTATION ISSUES:
=======================
* document df2genind -- done (TJ)
* split documentation of read.[...] functions -- done (TJ)
* document repool function -- done (TJ)
*

# NEW IMPLEMENTATIONS:
=====================
* provide the list of the points crossed by a Monmonier's boundary -- done (PS)
* read.structure code -- done (TJ)
* read.structure doc -- done (TJ)
* include new simulated datasets of sPCA -- done (TJ)
* document new simulated datasets of sPCA -- done (TJ)
* split read.genetix in: 
   - a "true" read.genetix, similar to other read... functions  -- done (TJ)
   - a "df2genind" which takes a matrix of char strings of lengths 2,4
   or 6  -- done (TJ)
* method to split a genind object, keeping only certain populations
   - seppop  -- done (TJ)
* implement a $[$ method for genind and genpop objects (and call it in
   seppop)  -- done (TJ)
* implement na.replace methods for genind and genpop objects (call it
   in df2genind)  -- done (TJ)
* repool function  -- done (TJ)
*

# TESTING:
==========
* test hybridize example -- done (TJ)
* 



# LOW PRIORITY / MINOR BUGS
===========================
===========================
* in spca, when nfposi=0, the returned object actually contains what corresponds to nfposi=1. Comes from multispati in ade4. To correct.
* use spcaIllus to illustrate global.rtest and local.rtest
*





# LONG TERM
==========================
==========================
* import from geneticsBase or so
* export to geneticsBase or so
*