As CPG Map uses a three-tier componentary architecture, it can get it's data from a variety of sources as long as the data is assembled in to the correct format. A class has been written that acts as a default data-packer in the event that a programmer does not want to use their own data access classes and just wants to parse some CPG Maps out of a few flat files. This class is in the CPGMap package and is called FileParser. A file to be parsed by this class should have the following format:
//DOUBLE TRUE
//UNITS units1 units2
//***MAP map_title
//LOCUS locus_name position_1 error_1 position_2 error_2
//HOMOGROUP homology_group_name
//OWNS who_it_owns
//LOCUS ...
//HOMOGROUP ...
//OWNS ...
//LOCUS ...
//HOMOGROUP ...
//OWNS ...
//***END
//***MAP ...
//LOCUS ...
//HOMOGROUP ...
//OWNS ...
//***END
 | If you are creating a set of double maps you should have //DOUBLE tab TRUE on the first line of the file. If you have anything else but TRUE, the program will think it's making single maps. So if you want to make single maps, have something like FALSE here! | ||||||
| The next line tells the program what units to use on the left and right hand side of the CPG Maps. The units are separated by a tab so the line might look like //UNITS tab MB tab cM. The units can be any string. Note, as the units are defined here for all the maps, you have to have all the physical (or linkage) maps on the same side of all the double maps. If you want to make single maps, don't tab after the first units. | ||||||
| Next comes the data for the individual maps. Both a single or double map starts with
//***MAP and ends with //***END. In between those tags should be all the loci that are to
be placed in that map. There are three components to each locus:
|
