Do you know any Open Source GIS that supports MGRS Coordinate System ?
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If you can find out the relevant parameters, you can probably create a projection definition. Then make up a high number and add it into your EPSG projection definitions file (somewhere in /usr/share probably). MGRS is basically UTM with some different naming.
I doubt you'll support the varying length references though. You may have to make a script that accepts a valid MGRS reference of any length, creates the polygon, and puts it on the map.
Doing MGRS for a single 'zone' shouldn't be too hard. Doing it for multiple zones may be trickier - you'll probably have to define the relevant Transverse Mercator for each zone.
I searched on google and found a discussion going on w.r.t a MGRS plugin patch for Kde Marble. I have mailed to their mailing list and I am waiting for the response. Quantum Gis doesn't have a MGRS plugin.
And if no patch is found anywhere probably we'll follow your valuable suggessions of converting a MGRS coordinate to latitude/longitude !
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