As long as the set of selected markers is unchanged, all the maps
produced and examined by CARTHAGENE in all the mapping process are
tentatively stored in a central map storage called ``the
heap''^{2.1}. The heap remembers all the best (w.r.t. the
loglikelihood) maps found since the last time the marker selection was
changed. The parameter is user configurable using the
`heapsize` command.

To actually visualize the maps stored in the heap, you can use either
a standard or detailed impression of the contents of the heap. This is
done using respectively the `heaprint` and `heaprintd`
commands. The whole content of the heap can be fetch and stored in a
list (for further analysis using the scripting language Tcl) with the
`heapget` command.

Actually, each map stored in the heap has a numerical
Id and this numerical id can be
used to print/fetch the maps stored in the heap. This is done using
repectively the `maprint` and `maprintd` commands or the
`mapget` command. Because the maps are always stored in the
heap in a ``standardized'' order, a `maprintdr` function is
also available to print a map using a reverse marker order. It is also
possible to compute the number of obligate chromosome breaks of a map
using the `mapocb` command. Finally, if you only want to access
the order of the markers used in a map, the command `mapordget`
will returns the marker ordering of the map indicated in a list.

The heap main use is to provide an approximation of all the markers
ordering around the optimal markers ordering. The heap can be directly
examined using the previous `heaprint` commands but a specific
command is available to perform the analysis of alternative maps in
the heap. The `heaprinto` command dumps all orders in the heap,
one by line, from the best to the worst. For each such order, the way
the order differs from the order of the original map is made explicit
and the difference of loglikelihood with the best map is reported.

A graphical representation of maps and the heap is given by `maprintg`, `maprintv` (only on Linux computers) and `heaprintg` commands.

Thomas Schiex 2009-10-27