multichromosome revisions

CMakeLists.txt

@@ -137,7 +137,7 @@ if(WIN32)
     set(CMAKE_CXX_STANDARD_LIBRARIES "-static-libgcc -static-libstdc++ -lwsock32 -lws2_32 ${CMAKE_CXX_STANDARD_LIBRARIES}")
     set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Wl,-Bstatic,--whole-archive -lwinpthread -Wl,--no-whole-archive")
     set(GNULIB_NAMESPACE_SOURCES "${PROJECT_SOURCE_DIR}/core/chromosome.cpp" 
-        "${PROJECT_SOURCE_DIR}/core/genome.cpp" 
+        "${PROJECT_SOURCE_DIR}/core/haplosome.cpp" 
         "${PROJECT_SOURCE_DIR}/core/population.cpp"
         "${PROJECT_SOURCE_DIR}/core/slim_globals.cpp"
         "${PROJECT_SOURCE_DIR}/core/slim_sim_eidos.cpp"

EidosScribe/EidosHelpFunctions.rtf

@@ -5255,7 +5255,6 @@ If
 \f3\b0   In SLiM 3.5 and later, use 
 \f1\fs18 colors(n, "cm")
 \f3\fs20  instead.\
-\pard\pardeftab397\li547\ri720\sb60\sa60\partightenfactor0
 \cf5 Generate colors in a \'93cyan-magenta\'94 color palette.\
 \pard\pardeftab397\li720\fi-446\ri720\sb180\sa60\partightenfactor0
 
@@ -5369,7 +5368,6 @@ This function can also be called with a non-singleton vector of color strings in
 \f3\b0   In SLiM 3.5 and later, use 
 \f1\fs18 colors(n, "heat")
 \f3\fs20  instead.\
-\pard\pardeftab397\li547\ri720\sb60\sa60\partightenfactor0
 \cf5 Generate colors in a \'93heat map\'94 color palette.\
 \pard\pardeftab397\li720\fi-446\ri720\sb180\sa60\partightenfactor0
 
@@ -5492,7 +5490,6 @@ This function can also be called with a matrix of RGB values, with three columns
 \f3\b0   In SLiM 3.5 and later, use 
 \f1\fs18 colors(n, "terrain")
 \f3\fs20  instead.\
-\pard\pardeftab397\li547\ri720\sb60\sa60\partightenfactor0
 \cf5 Generate colors in a \'93terrain\'94 color palette.\
 \pard\pardeftab397\ri720\sb360\sa60\partightenfactor0
 
@@ -6146,7 +6143,7 @@ The task keys recognized, and the tasks they govern, are:\
 \f7\i N
 \f3\i0  points, 3D case
 \f1\fs18 \uc0\u8232 "SPATIAL_MAP_VALUE"	spatialMapValue()\
-"CONTAINS_MARKER_MUT"	containsMarkerMutation(returnMutation = F)\uc0\u8232 "I_COUNT_OF_MUTS_OF_TYPE"	countOfMutationsOfType() (Individual)\u8232 "G_COUNT_OF_MUTS_OF_TYPE"	countOfMutationsOfType() (Genome)\u8232 "INDS_W_PEDIGREE_IDS"	individualsWithPedigreeIDs()\u8232 "RELATEDNESS"	relatedness()\u8232 "SAMPLE_INDIVIDUALS_1"	sampleIndividuals()
+"CONTAINS_MARKER_MUT"	containsMarkerMutation(returnMutation = F)\uc0\u8232 "I_COUNT_OF_MUTS_OF_TYPE"	countOfMutationsOfType() (Individual)\u8232 "H_COUNT_OF_MUTS_OF_TYPE"	countOfMutationsOfType() (Haplosome)\u8232 "INDS_W_PEDIGREE_IDS"	individualsWithPedigreeIDs()\u8232 "RELATEDNESS"	relatedness()\u8232 "SAMPLE_INDIVIDUALS_1"	sampleIndividuals()
 \f3\fs20  simple case with replace=T
 \f1\fs18 \uc0\u8232 "SAMPLE_INDIVIDUALS_2"	sampleIndividuals()
 \f3\fs20  base case with replace=T
@@ -6195,7 +6192,7 @@ The task keys recognized, and the tasks they govern, are:\
 \f1\fs18 \uc0\u8232 "SIMPLIFY_SORT_POST"	
 \f3\fs20 cleanup after simplification sorting (internal)
 \f1\fs18 \uc0\u8232 "PARENTS_CLEAR"	
-\f3\fs20 clearing parental genomes at tick end in WF models
+\f3\fs20 clearing parental haplosomes at tick end in WF models
 \f1\fs18 \uc0\u8232 "UNIQUE_MUTRUNS"	
 \f3\fs20 uniquing mutation runs (internal bookkeeping)
 \f1\fs18 \uc0\u8232 "SURVIVAL"	

PARALLEL

@@ -57,19 +57,19 @@ PARALLEL changes (now in the master branch, but disabled):
 	parallelize match(), tabulate(), sample (int/float/object, replace=T, weights=NULL), mean(l/i/f)
 	parallelize Individual -relatedness(), -countOfMutationsOfType(), -setSpatialPosition(); Species -individualsWithPedigreeIDs()
 	parallelize Subpopulation -pointInBounds(), -pointReflected(), -pointStopped(), pointPeriodic(), pointUniform()
-	parallelize Genome -containsMarkerMutation()
+	parallelize Haplosome -containsMarkerMutation()
 	change how RNG seeding works, for single-threaded and multi-threaded runs: use /dev/random to generate initial seeds, and for multi-threaded runs, use /dev/random for seeds for all threads beyond thread 0
-	parallelize Genome -countOfMutationsOfType(), Subpopulation -spatialMapValue() and -sampleIndividuals()
+	parallelize Haplosome -countOfMutationsOfType(), Subpopulation -spatialMapValue() and -sampleIndividuals()
 	add unit tests for various SLiM methods that have been parallelized
 	parallelize InteractionType nearestNeighbors(), nearestInteractingNeighbors(), drawByStrength() by adding a returnDict parameter that lets the user get a Dictionary as a result, with one entry per receiver
 		their "receiver" parameter is no longer required to be singleton (when returnDict == T), and their return value is now just "object" since it can be Individual or Dictionary
 	overhaul the internal MutationRun design to allow it to be used multithreaded - get rid of refcounting, switch to usage tallying
 	parallelize offspring generation in WF models, when no callbacks (mateChoice(), modifyChild(), recombination(), mutation()) are active; no tree-seq, no cloning
 	parallelize offspring generation in WF model: add support for cloning
-	parallelize tallying of mutation runs, clearing of parental genomes at the end of WF model ticks, and mutation run uniquing
+	parallelize tallying of mutation runs, clearing of parental haplosomes at the end of WF model ticks, and mutation run uniquing
 	add support for parallel reproduction when a non-default stacking policy is in use
 	add support for parallel reproduction with tree-sequence recording
-	add parallel reproduction in nonWF models, with no callbacks (recombination(), mutation()) active - modifyChild() callbacks are legal but cannot access child genomes since they are deferred
+	add parallel reproduction in nonWF models, with no callbacks (recombination(), mutation()) active - modifyChild() callbacks are legal but cannot access child haplosomes since they are deferred
 		this is achieved by passing defer=T to addCrossed(), addCloned(), addSelfed(), or addRecombinant()
 	thread-safety work - break in backward reproducibility for scripts that use a type 's' DFE, because the code path for that shifted
 	algorithm change for nearestNeighbors() and nearestNeighborsOfPoint(), when count is >1 and <N; the old algorithm was not thread-safe, and was inefficient; breaks backward reproducibility for the relevant case