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