The getNegated method returns whether the property or qualifier is negative (that is, something that you do not want to match).
getNegated()
(Boolean) A Boolean that specifies whether the property or qualifier is negated (true for negative properties and qualifiers, false otherwise).
For a LuaIncompleteFactProperty object:
local props = incomplete:getProperties()
for i=1,#props do
if props[i]:getNegated() then
-- do not return facts that match this property
...
For a LuaIncompleteFactQualifier object:
local quals = props[i]:getQualifiers()
for j=1,#quals do
if quals[i]:getNegated() then
-- do not return facts that match this qualifier
...
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