===========================================================================
SMap problems/enhancements etc.



sMapLocalMap()
--------------

sMapLocalMap() is broken in that it takes not notice of the input coords for the purposes of
clipping the local alignment block coords. It just returns an array of gaps regardless of whether
they are outside of the specified coordinate range.

I discovered this when working on a bug which caused blixem to crash. The cause turned out to be
that there was an EST alignment in the database, one block of which extended beyond the end of its
parent object. Unfortunately sMapLocalMap() returns all the blocks which then a call to sMapMap()
attempts to map, the code orginally ingnored the return status from sMapMap and passed on random
coords to blixem.

Really there is little point in sMapLocalMap() returning coords for blocks that are outside their
parent, this is A WASTE OF TIME.

The fix is to add range checking to sMapLocalMap() and change its function signature so that it
returns a status like other mapping calls and returns the gaps array as an "in/out" call
parameter:

SMapStatus sMapLocalMap(OBJ obj,    /* in parent located at #SmapInfo */
		        int pStart, /* start coord in parent */
		        int pEnd,   /* end coord in parent */
		        STORE_HANDLE h,   /* return array on this. */
                        Array *gaps) ;  /* gaps array */

The way to test this is to create a parent smapped object with a homology child but make sure at
least one of the blocks of the child is off the end of the parent.

Here endeth the lesson......



sMapMap()
---------

This call and what it calls,  sMapMapEx(), return values even when the thing to be mapped is
outside the area. This is really STUPID as it encourages ignoring the status returned by these
calls. I don't know who thought this was a good idea but it isn't. I don't have time to fix this
just now but one day I will.