ChangeLog

2013-03-20  Gary Polhill  <gary.polhill@hutton.ac.uk>

	* src/State.java
	(getBreedAxioms): Replace all non-word characters with underscores to avoid
	naming errors. ### possible bug if there are variables that end up over-writing
	each other's URIs -- e.g. var? and var_
	(perform): Throw an exception if the physical URI exists

2013-01-11  Gary Polhill  <gary.polhill@hutton.ac.uk>

	* src/OWLExtension.java
	(setDomain): Converted link argument to lower case.
	(setRange): Converted link argument to lower case.
	(getDomain): Converted link argument to lower case.
	(getRange): Converted link argument to lower case.
	(hasDomainSpecified): Converted link argument to lower case.
	(hasRangeSpecified): Converted link argument to lower case.
	* src/State.java
	(getGlobalAxioms): Ensured globals are accessed in order so that the correct
	values are associated with each variable
	(getPatchAxioms): Added an assertion that the patch individual is a member of
	the Patch class
	(getPatchAxioms): Do the processing if the no-patches option is NOT specified!
	(getPatchAxioms): Correct for the patch 'own' variables including NetLogo
	defaults. ### Possible bugs with Link and Turtle if they do the same. ###
	* src/Structure.java
	(getLinkAxioms): Added check of string length before comparing substrings with
	UNDIR_LINK_BR and DIR_LINK_BR when reading code
	(getPatchAxioms): Ignored first State.NETLOGO_PATCH_OWN_ARRAY_START in patches
	own
	(addLink): Make a comment if the link does not have any members and hence
	directedness cannot be assessed
	(getLinkAxioms): Compute the directedness of a link breed by checking its
	members
	* src/Options.java
	(perform): Added offending arg to error message when option not recognised
	(perform): Used arg.getString instead of arg.toString to obtain the arguments

2013-01-11  Gary Polhill  <gary.polhill@hutton.ac.uk>

	* All: code and comment tidy