Mon Dec 15 18:05:52 PST 2003

kaben		Mon Dec 15 10:05:52 2003 EDT

  Added files:                 (Branch: kaben)
    /avida/current	.cvsignore 
    /avida/current/source/qt-viewer/exp	CMakeLists.txt 
    /avida/current/source/qt-viewer/exp/exp_cleanup	CMakeLists.txt 
                                                   	Makefile.am 
                                                   	exp_cleanup.pro 
                                                   	main.cc modules.pri 
                                                   	notes 
                                                   	template2_t.cc 
                                                   	template2_t.hh 
                                                   	template_t.cc 
                                                   	template_t.hh 
                                                   	xqt_test_case.cc 
                                                   	xqt_test_case.hh 
    /avida/current/source/qt-viewer/exp/exp_cleanup/analyzer	
                                                            	analyzer.pri 
                                                            	avd_n_analyzer_batchlist_item.hh 
                                                            	avd_n_analyzer_batchlist_item_proto.hh 
                                                            	avd_n_analyzer_ctrl.cc 
                                                            	avd_n_analyzer_ctrl.hh 
                                                            	avd_n_analyzer_data_entry.hh 
                                                            	avd_n_analyzer_data_entry_command_list_item.cc 
                                                            	avd_n_analyzer_data_entry_command_list_item.hh 
                                                            	avd_n_analyzer_data_entry_command_list_item_proto.hh 
                                                            	avd_n_analyzer_data_entry_proto.hh 
                                                            	avd_n_analyzer_dbg_msgs.hh 
                                                            	avd_n_analyzer_dbg_msgs_proto.hh 
                                                            	avd_n_analyzer_genotype_list_item.hh 
                                                            	avd_n_analyzer_genotype_list_item_proto.hh 
                                                            	avd_n_analyzer_genotype_sel_ctrl.hh 
                                                            	avd_n_analyzer_genotype_sel_view.cc 
                                                            	avd_n_analyzer_genotype_sel_view.hh 
                                                            	avd_n_analyzer_gui.cc 
                                                            	avd_n_analyzer_listview.cc 
                                                            	avd_n_analyzer_listview.hh 
                                                            	avd_n_analyzer_mdl.cc 
                                                            	avd_n_analyzer_mdl.hh 
                                                            	avd_n_analyzer_mdl_proto.hh 
                                                            	avd_n_analyzer_menubar_handler.cc 
                                                            	avd_n_analyzer_menubar_handler.hh 
                                                            	avd_n_analyzer_out_fmt_sel.cc 
                                                            	avd_n_analyzer_out_fmt_sel.hh 
                                                            	avd_n_analyzer_view.cc 
                                                            	avd_n_analyzer_view.hh 
    /avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o	
                                                              	analyzer_o.pri 
                                                              	avd_analyzer_batchlist_item.hh 
                                                              	avd_analyzer_batchlist_item_proto.hh 
                                                              	avd_analyzer_controller.cc 
                                                              	avd_analyzer_controller.hh 
                                                              	avd_analyzer_controller_data.cc 
                                                              	avd_analyzer_controller_data.hh 
                                                              	avd_analyzer_creator.cc 
                                                              	avd_analyzer_creator.hh 
                                                              	avd_analyzer_data_entry.hh 
                                                              	avd_analyzer_data_entry_command_list_item.cc 
                                                              	avd_analyzer_data_entry_command_list_item.hh 
                                                              	avd_analyzer_data_entry_command_list_item_proto.hh 
                                                              	avd_analyzer_data_entry_proto.hh 
                                                              	avd_analyzer_dbg_msgs.cc 
                                                              	avd_analyzer_dbg_msgs.hh 
                                                              	avd_analyzer_dbg_msgs_proto.hh 
                                                              	avd_analyzer_genotype_list_item.hh 
                                                              	avd_analyzer_genotype_list_item_proto.hh 
                                                              	avd_analyzer_listview.cc 
                                                              	avd_analyzer_listview.hh 
                                                              	avd_analyzer_listview_proto.hh 
                                                              	avd_analyzer_menubar_handler.cc 
                                                              	avd_analyzer_menubar_handler.hh 
                                                              	avd_analyzer_model.cc 
                                                              	avd_analyzer_model.hh 
                                                              	avd_analyzer_model_proto.hh 
                                                              	avd_analyzer_output_fmt_selector.cc 
                                                              	avd_analyzer_output_fmt_selector.hh 
                                                              	avd_analyzer_utils.hh 
                                                              	avd_analyzer_view.cc 
                                                              	avd_analyzer_view.hh 
    /avida/current/source/qt-viewer/exp/exp_cleanup/containers	
                                                              	containers.pri 
                                                              	tRList.hh 
                                                              	tRList_proto.hh 
                                                              	tRetainable_list.hh 
                                                              	tRetainable_list_proto.hh 
    /avida/current/source/qt-viewer/exp/exp_cleanup/dumb_gui	
                                                            	avd_dumb_ctrl.cc 
                                                            	avd_dumb_ctrl.hh 
                                                            	avd_dumb_gui.cc 
                                                            	avd_dumb_gui_dbg.hh 
                                                            	avd_dumb_gui_dbg_proto.hh 
                                                            	avd_dumb_view.cc 
                                                            	avd_dumb_view.hh 
                                                            	dumb_gui.pri 
    /avida/current/source/qt-viewer/exp/exp_cleanup/exp_gui	
                                                           	avd_exp_ctrl.cc 
                                                           	avd_exp_ctrl.hh 
                                                           	avd_exp_gui.cc 
                                                           	avd_exp_gui_dbg.hh 
                                                           	avd_exp_gui_dbg_proto.hh 
                                                           	avd_exp_view.cc 
                                                           	avd_exp_view.hh 
                                                           	exp_gui.pri 
                                                           	test_thing.cc 
                                                           	test_thing.hh 
                                                           	test_thing_proto.hh 
                                                           	testing_interface.hh 
    /avida/current/source/qt-viewer/exp/exp_cleanup/gui_factory	
                                                               	avd_abstract_gui.hh 
                                                               	avd_abstract_gui_proto.hh 
                                                               	avd_gui_factory.cc 
                                                               	avd_gui_factory.hh 
                                                               	avd_gui_factory_error_policy.hh 
                                                               	avd_gui_factory_proto.hh 
                                                               	gui_factory.pri 
                                                               	tGUI.hh 
                                                               	tGUI_proto.hh 
    /avida/current/source/qt-viewer/exp/exp_cleanup/map_gui	
                                                           	avd_map_canvas.cc 
                                                           	avd_map_canvas.hh 
                                                           	avd_map_canvas_rectangle.cc 
                                                           	avd_map_canvas_rectangle.hh 
                                                           	avd_map_canvas_rectangle_proto.hh 
                                                           	avd_map_canvas_view.cc 
                                                           	avd_map_canvas_view.hh 
                                                           	avd_map_ctrl.cc 
                                                           	avd_map_ctrl.hh 
                                                           	avd_map_gui.cc 
                                                           	avd_map_gui_dbg.hh 
                                                           	avd_map_gui_dbg_proto.hh 
                                                           	avd_map_layer.cc 
                                                           	avd_map_layer.hh 
                                                           	avd_map_layer_proto.hh 
                                                           	avd_map_view.cc 
                                                           	avd_map_view.hh 
                                                           	map_gui.pri 
    /avida/current/source/qt-viewer/exp/exp_cleanup/mc	
                                                      	avd_avida_state_mediator.hh 
                                                      	avd_connections.cc 
                                                      	avd_connections.hh 
                                                      	avd_gui_factory_mediator.hh 
                                                      	avd_mc_dbg.cc 
                                                      	avd_mc_dbg.hh 
                                                      	avd_mc_dbg_proto.hh 
                                                      	avd_mc_mediator.cc 
                                                      	avd_mc_mediator.hh 
                                                      	avd_menubar_mediator.hh 
                                                      	avd_mission_control.cc 
                                                      	avd_mission_control.hh 
                                                      	avd_settings_mediator.hh 
                                                      	avd_windows_mediator.hh 
                                                      	mc.pri 
                                                      	setup_avida.cc 
                                                      	setup_avida.hh 
    /avida/current/source/qt-viewer/exp/exp_cleanup/mc/attributes	
                                                                 	requests_argv.hh 
    /avida/current/source/qt-viewer/exp/exp_cleanup/memory_mgt	
                                                              	ScopeGuard.h 
                                                              	activate_watcher.hh 
                                                              	activate_watcher_proto.hh 
                                                              	memory_mgt.pri 
                                                              	retainable.cc 
                                                              	retainable.hh 
                                                              	retainable_dbg.hh 
                                                              	retainable_dbg_proto.hh 
                                                              	retainable_proto.hh 
                                                              	watch_retains.cc 
                                                              	watch_retains.hh 
                                                              	watch_retains_proto.hh 
    /avida/current/source/qt-viewer/exp/exp_cleanup/menubar	
                                                           	avd_menubar_handler.cc 
                                                           	avd_menubar_handler.hh 
                                                           	avd_menubar_hdlr_creator.cc 
                                                           	menubar.pri 
    /avida/current/source/qt-viewer/exp/exp_cleanup/preferences	
                                                               	avd_prefs_ctrl.cc 
                                                               	avd_prefs_ctrl.hh 
                                                               	avd_prefs_dbg.cc 
                                                               	avd_prefs_dbg.hh 
                                                               	avd_prefs_dbg_proto.hh 
                                                               	avd_prefs_gui.cc 
                                                               	avd_prefs_item.cc 
                                                               	avd_prefs_item.hh 
                                                               	avd_prefs_item_proto.hh 
                                                               	avd_prefs_item_view.hh 
                                                               	avd_prefs_item_view_proto.hh 
                                                               	avd_prefs_view.cc 
                                                               	avd_prefs_view.hh 
                                                               	preferences.pri 
    /avida/current/source/qt-viewer/exp/exp_cleanup/prefs_gui_factory	
                                                                     	avd_abstract_prefs_gui.hh 
                                                                     	avd_abstract_prefs_gui_proto.hh 
                                                                     	avd_prefs_gui_factory.cc 
                                                                     	avd_prefs_gui_factory.hh 
                                                                     	avd_prefs_gui_factory_error_policy.hh 
                                                                     	avd_prefs_gui_factory_proto.hh 
                                                                     	prefs_gui_factory.pri 
                                                                     	tPrefsGUI.hh 
                                                                     	tPrefsGUI_proto.hh 
    /avida/current/source/qt-viewer/exp/exp_cleanup/threaded_driver	
                                                                   	avd_avida_driver.cc 
                                                                   	avd_avida_driver.hh 
                                                                   	avd_avida_thread_drvr_dbg.hh 
                                                                   	avd_avida_thread_drvr_dbg_proto.hh 
                                                                   	avd_driver_creator.cc 
                                                                   	avd_gui_msg_event.hh 
                                                                   	avd_orig_driver_controller.cc 
                                                                   	avd_orig_driver_controller.hh 
                                                                   	threaded_driver.pri 
    /avida/current/source/qt-viewer/exp/exp_cleanup/user_msg	
                                                            	avd_message_display.cc 
                                                            	avd_message_display.hh 
                                                            	avd_message_display_proto.hh 
                                                            	avd_message_display_typetrack.hh 
                                                            	avd_message_display_typetrack_proto.hh 
                                                            	avd_qstr_message_display.cc 
                                                            	avd_user_msg_ctrl.cc 
                                                            	avd_user_msg_ctrl.hh 
                                                            	avd_user_msg_ctrl_funct.hh 
                                                            	avd_user_msg_ctrl_funct_proto.hh 
                                                            	avd_user_msg_gui.cc 
                                                            	avd_user_msg_gui_dbg.hh 
                                                            	avd_user_msg_gui_dbg_proto.hh 
                                                            	avd_user_msg_prefs_ctrl.cc 
                                                            	avd_user_msg_prefs_ctrl.hh 
                                                            	avd_user_msg_prefs_gui.cc 
                                                            	avd_user_msg_prefs_view.cc 
                                                            	avd_user_msg_prefs_view.hh 
                                                            	avd_user_msg_view.cc 
                                                            	avd_user_msg_view.hh 
                                                            	gui_message_display.cc 
                                                            	user_msg.pri 
    /avida/current/source/qt-viewer/exp/exp_cleanup2	CMakeLists.txt 
                                                    	avd_dbg_msgs.hh 
                                                    	avd_message_closure.cc 
                                                    	avd_message_closure.hh 
                                                    	avd_message_closure_t.cc 
                                                    	avd_message_display.cc 
                                                    	avd_message_display.hh 
                                                    	avd_message_display_t.cc 
                                                    	avd_message_set_tracker.cc 
                                                    	avd_message_set_tracker.hh 
                                                    	avd_message_type_set.hh 
                                                    	demo_base_t.cc 
                                                    	main.cc 
                                                    	template2_t.cc 
                                                    	template2_t.hh 
                                                    	template_t.cc 
                                                    	template_t.hh 
                                                    	xqt_test_case.cc 
                                                    	xqt_test_case.hh 
    /avida/current/source/testsuites/qt_viewer_unit_testsuites	
                                                              	CMakeLists.txt 
                                                              	qt_test_case.cc 
                                                              	qt_test_case.hh 
                                                              	template.t.cc 
                                                              	template.t.hh 
    /avida/current/source/third-party/mockpp	CMakeLists.txt 

  Modified files:              
    /avida/current	CMakeLists.txt 
    /avida/current/CMakeModules	FixFindQt.cmake 
    /avida/current/doc	CMakeLists.txt 
    /avida/current/doc/glossary	CMakeLists.txt 
    /avida/current/source/cpu	CMakeLists.txt 
    /avida/current/source/event	CMakeLists.txt cPopulation.events 
    /avida/current/source/main	CMakeLists.txt analyze.cc analyze.hh 
                              	birth_chamber.cc config.cc config.hh 
                              	population.cc 
    /avida/current/source/qt-viewer	CMakeLists.txt 
    /avida/current/source/support	CMakeLists.txt genesis 
    /avida/current/source/support/preset_organisms	CMakeLists.txt 
    /avida/current/source/testsuites	CMakeLists.txt 
    /avida/current/source/testsuites/unit_testsuites	CMakeLists.txt 
    /avida/current/source/testsuites/unit_testsuites/level_0	
                                                            	CMakeLists.txt 
    /avida/current/source/testsuites/unit_testsuites/level_1	
                                                            	CMakeLists.txt 
    /avida/current/source/third-party	CMakeLists.txt 
    /avida/current/source/third-party/trio	CMakeLists.txt 
    /avida/current/source/third-party/yaktest	CMakeLists.txt 
                                             	test_case.cpp test_case.h 
                                             	test_problem.cpp 
                                             	test_problem.h 
                                             	text_test_interpreter.cpp 
    /avida/current/source/tools	CMakeLists.txt tList.hh 
    /avida/current/source/viewers	CMakeLists.txt 
  Log:
  
  Synching my private cvs branch to my gnu-arch archive.
  
  
  
-------------- next part --------------
Index: avida/current/CMakeLists.txt
diff -u avida/current/CMakeLists.txt:1.1 avida/current/CMakeLists.txt:1.1.2.1

--- avida/current/CMakeLists.txt:1.1	Sat Dec  6 10:00:52 2003
+++ avida/current/CMakeLists.txt	Mon Dec 15 10:05:43 2003
@@ -1,11 +1,5 @@
 
-# CMake doesn't have a 'distclean' build target.  This provides a
-# makeshift distclean, but it doesn't recurse into subdirectories.
-
-INCLUDE(${PROJECT_SOURCE_DIR}/CMakeModules/TargetDistclean.cmake)
-
-
-# This section defines default configure options.
+# This section defines default builtin configure options.
 
 IF(UNIX)
 
@@ -15,7 +9,7 @@
   # - release (Release)
   # - release with debug info (RelWithDebInfo)
   SET(CMAKE_CXX_FLAGS_DEBUG
-    "-g -Wall -pedantic -DDEBUG"
+    "-g -Wall -Wno-long-double -Wno-long-long -pedantic -DDEBUG"
     CACHE STRING
     "Flags used by the compiler during debug builds."
   )
@@ -30,7 +24,7 @@
     "Flags used by the compiler during release builds."
   )
   SET(CMAKE_CXX_FLAGS_RELWITHDEBINFO
-    "-O2 -ffast-math -g -Wall -DDEBUG"
+    "-O2 -ffast-math -g -Wall -Wno-long-double -Wno-long-long -DDEBUG"
     CACHE STRING
     "Flags used by the compiler during release builds."
   )
@@ -41,7 +35,7 @@
   # - release (Release)
   # - release with debug info (RelWithDebInfo)
   SET(CMAKE_C_FLAGS_DEBUG
-    "-g -Wall -pedantic -DDEBUG"
+    "-g -Wall -Wno-long-double -Wno-long-long -pedantic -DDEBUG"
     CACHE STRING
     "Flags used by the compiler during debug builds."
   )
@@ -56,7 +50,7 @@
     "Flags used by the compiler during release builds."
   )
   SET(CMAKE_C_FLAGS_RELWITHDEBINFO
-    "-O2 -ffast-math -g -Wall -pedantic -DDEBUG"
+    "-O2 -ffast-math -g -Wall -Wno-long-double -Wno-long-long -pedantic -DDEBUG"
     CACHE STRING
     "Flags used by the compiler during release builds."
   )
@@ -65,7 +59,7 @@
   SET(CMAKE_VERBOSE_MAKEFILE
     TRUE
     CACHE BOOL
-    "If this value is on, makefiles will be generated without the .SILENT directive, and all commands will be echoed to the consoleduring the make.  This is useful for debugging only."
+    "If this value is on, makefiles will be generated without the .SILENT directive, and all commands will be echoed to the console during the make.  This is useful for debugging only."
   )
 ENDIF(UNIX)
 
@@ -92,24 +86,159 @@
   "Single output directory for building all executables."
 )
 
-# By default, compile all unit testing software.  Tests are run via
-# 'make test' under unix.
-OPTION(_UNIT_TESTS
-  "Enable building of unit test suites."
-  ON
-)
-IF(_UNIT_TESTS)
-  ENABLE_TESTING()
-ENDIF(_UNIT_TESTS)
-
 
-# This section introduces the Avida project to CMake.
+# This section introduces the Avida project to CMake.  In this file, it
+# must be between the configuration options above (otherwise it
+# overrides their defaults) and the configuration options, cmake module
+# includes, and convenience variables below (otherwise some variables
+# can't be properly defined because PROJECT_SOURCE_DIR and
+# PROJECT_BUILD_DIR aren't yet defined).
 
 PROJECT(AVIDA)
-
 SUBDIRS(source doc)
 
 
+# CMake doesn't have a 'distclean' build target.  This provides a
+# makeshift distclean, but it doesn't recurse into subdirectories.
+INCLUDE(${PROJECT_SOURCE_DIR}/CMakeModules/TargetDistclean.cmake)
+# Locate the ncurses screen handling package (for Avida's console
+# interface) and the Qt graphics API (for Avida's graphic interface).
+INCLUDE(${PROJECT_SOURCE_DIR}/CMakeModules/FindNcurses.cmake)
+INCLUDE(${PROJECT_SOURCE_DIR}/CMakeModules/FixFindQt.cmake)
+
+
+# By default, build the console interface to Avida.
+OPTION(_NCURSES_CONSOLE_INTERFACE
+  "Enable building Avida console interface."
+  ON
+)
+# Make sure requisites are present for build of console interface.  Give
+# user feedback if they're missing.
+IF(_NCURSES_CONSOLE_INTERFACE)
+  IF(NOT NCURSES_INCLUDE_PATH)
+    MESSAGE(
+      "Building Avida's console interface requires header files for the ncurses CRT screen handling package.  I can't find those header files.  If you know that the headers are installed, set the advanced variable NCURSES_INCLUDE_PATH to their include directory."
+    )
+  ENDIF(NOT NCURSES_INCLUDE_PATH)
+  IF(NOT NCURSES_LIBRARY)
+    MESSAGE(
+      "Building Avida's console interface requires the ncurses library 'libncurses', which I can't find.  If you know that the library is installed, set the advanced variable NCURSES_LIBRARY to its location."
+    )
+  ENDIF(NOT NCURSES_LIBRARY)
+ENDIF(_NCURSES_CONSOLE_INTERFACE)
+
+# By default, build the primitive version of Avida.
+OPTION(_PRIMITIVE_INTERFACE
+  "Enable building interfaceless Avida (fastest version)."
+  ON
+)
+
+# By default, build the graphic interface to Avida.
+OPTION(_QT_GRAPHIC_INTERFACE
+  "Enable building Avida graphic interface."
+  ON
+)
+# By default, don't build the experimental interface to Avida.
+OPTION(_QT_EXPERIMENTAL_GRAPHIC_INTERFACE
+  "Enable building experimental Avida graphic interface."
+  OFF
+)
+# Make sure requisites are present for build of graphic interface.  Give
+# user feedback if they're missing.
+IF(QT_FOUND)
+  IF(QT_QT_LIBRARY MATCHES "qt-mt")
+    SET(QT_IS_THREAD_CAPABLE TRUE)
+  ENDIF(QT_QT_LIBRARY MATCHES "qt-mt")
+ENDIF(QT_FOUND)
+VARIABLE_REQUIRES(_QT_GRAPHIC_INTERFACE QT_GRAPHIC_INTERFACE_REQUISITES
+  QT_FOUND
+  QT_IS_THREAD_CAPABLE
+  QT_WRAP_UI
+  QT_WRAP_CPP
+)
+VARIABLE_REQUIRES(_QT_EXPERIMENTAL_GRAPHIC_INTERFACE QT_EXP_GRAPHIC_INTERFACE_REQUISITES
+  QT_FOUND
+  QT_IS_THREAD_CAPABLE
+  QT_WRAP_UI
+  QT_WRAP_CPP
+)
+IF(_QT_GRAPHIC_INTERFACE OR _QT_EXPERIMENTAL_GRAPHIC_INTERFACE)
+  IF(NOT QT_FOUND)
+    MESSAGE(
+      "Building Avida's graphic interface requires the complete Qt graphics API.  Qt can be obtained from www.trolltech.com.  If you know that the complete Qt API is present, try setting the environment variable QTDIR to the subdirectory containing Qt."
+    )
+  ENDIF(NOT QT_FOUND)
+  IF(NOT QT_IS_THREAD_CAPABLE)
+    MESSAGE(
+      "Building Avida's graphic interface requires a version of Qt that supports multiple threads, i.e., that provides the library 'libqt-mt', which I can't find.  If you know that the library is present, set the advanced variable QT_QT_LIBRARY to its location."
+    )
+  ENDIF(NOT QT_IS_THREAD_CAPABLE)
+  IF(NOT QT_INCLUDE_DIR)
+    MESSAGE(
+      "Building Avida's graphic interface requires Qt header files, which I can't find.  If you know that the headers are installed, set the advanced variable QT_INCLUDE_DIR to their include directory."
+    )
+  ENDIF(NOT QT_INCLUDE_DIR)
+  IF(NOT QT_WRAP_CPP)
+    MESSAGE(
+      "Building Avida's graphic interface requires Qt's meta-object compiler (moc), which I can't find.  If you know that the moc executable is present, set the advanced variable QT_MOC_EXECUTABLE accordingly."
+    )
+  ENDIF(NOT QT_WRAP_CPP)
+  IF(NOT QT_WRAP_UI)
+    MESSAGE(
+      "Building Avida's graphic interface requires Qt's user-interface compiler (uic), which I can't find.  If you know that the uic executable is present, set the advanced variable QT_UIC_EXECUTABLE accordingly."
+    )
+  ENDIF(NOT QT_WRAP_UI)
+ENDIF(_QT_GRAPHIC_INTERFACE OR _QT_EXPERIMENTAL_GRAPHIC_INTERFACE)
+
+# By default, compile all unit tests of primitive Avida classes.  Tests
+# are run via 'make test' under unix.
+OPTION(_UNIT_TEST_PRIMITIVE
+  "Enable building primitive unit test suites."
+  ON
+)
+IF(_UNIT_TEST_PRIMITIVE)
+  SET(UNIT_TESTS TRUE)
+  ENABLE_TESTING()
+ENDIF(_UNIT_TEST_PRIMITIVE)
+
+# By default, compile all of the unit tests of avida's gui.  Tests are
+# run via 'make test' under unix.
+OPTION(_UNIT_TEST_QT_GUI
+  "Enable building Qt gui unit test suites."
+  ON
+)
+# Only test gui classes if gui is being built.
+IF(_UNIT_TEST_QT_GUI)
+  IF(_QT_GRAPHIC_INTERFACE)
+    SET(UNIT_TESTS TRUE)
+    ENABLE_TESTING()
+  ELSE(_QT_GRAPHIC_INTERFACE)
+    MESSAGE(
+      "The option _UNIT_TEST_QT_GUI is on, but the option _QT_GRAPHIC_INTERFACE is off.  Qt gui unit test suites have been disabled since the gui won't be built."
+    )
+  ENDIF(_QT_GRAPHIC_INTERFACE)
+ENDIF(_UNIT_TEST_QT_GUI)
+
+
+# By default, don't compile unit tests of avida's experimental gui.  Tests are
+# run via 'make test' under unix.
+OPTION(_UNIT_TEST_QT_EXP_GUI
+  "Enable building Qt experimental gui unit test suites."
+  OFF
+)
+# Only test gui classes if gui is being built.
+IF(_UNIT_TEST_QT_EXP_GUI)
+  IF(_QT_EXPERIMENTAL_GRAPHIC_INTERFACE)
+    SET(UNIT_TESTS TRUE)
+    ENABLE_TESTING()
+  ELSE(_QT_EXPERIMENTAL_GRAPHIC_INTERFACE)
+    MESSAGE(
+      "The option _UNIT_TEST_QT_EXP_GUI is on, but the option _QT_EXPERIMENTAL_GRAPHIC_INTERFACE is off.  Qt gui unit test suites have been disabled since the gui won't be built."
+    )
+  ENDIF(_QT_EXPERIMENTAL_GRAPHIC_INTERFACE)
+ENDIF(_UNIT_TEST_QT_EXP_GUI)
+
+
 # This section defines convenience variables.  They're available to
 # CMakeList.txt files in all subdirectories beneath the directory
 # containing this file..
@@ -120,6 +249,24 @@
 SET(CPU_SRC_DIR ${PROJECT_SOURCE_DIR}/source/cpu)
 SET(EVENT_SRC_DIR ${PROJECT_SOURCE_DIR}/source/event)
 SET(MAIN_SRC_DIR ${PROJECT_SOURCE_DIR}/source/main)
+SET(GUI_SRC_DIR ${PROJECT_SOURCE_DIR}/source/qt-viewer)
+
+SET(EXP_GUI_SRC_DIR
+  ${PROJECT_SOURCE_DIR}/source/qt-viewer/exp/exp_cleanup
+  ${PROJECT_SOURCE_DIR}/source/qt-viewer/exp/exp_cleanup/analyzer
+  ${PROJECT_SOURCE_DIR}/source/qt-viewer/exp/exp_cleanup/analyzer_o
+  ${PROJECT_SOURCE_DIR}/source/qt-viewer/exp/exp_cleanup/containers
+  ${PROJECT_SOURCE_DIR}/source/qt-viewer/exp/exp_cleanup/dumb_bui
+  ${PROJECT_SOURCE_DIR}/source/qt-viewer/exp/exp_cleanup/exp_gui
+  ${PROJECT_SOURCE_DIR}/source/qt-viewer/exp/exp_cleanup/map_gui
+  ${PROJECT_SOURCE_DIR}/source/qt-viewer/exp/exp_cleanup/mc
+  ${PROJECT_SOURCE_DIR}/source/qt-viewer/exp/exp_cleanup/memory_mgt
+  ${PROJECT_SOURCE_DIR}/source/qt-viewer/exp/exp_cleanup/menubar
+  ${PROJECT_SOURCE_DIR}/source/qt-viewer/exp/exp_cleanup/preferences
+  ${PROJECT_SOURCE_DIR}/source/qt-viewer/exp/exp_cleanup/prefs_gui_factory
+  ${PROJECT_SOURCE_DIR}/source/qt-viewer/exp/exp_cleanup/threaded_driver
+  ${PROJECT_SOURCE_DIR}/source/qt-viewer/exp/exp_cleanup/user_msg
+)
 
 # Shortcuts to the build subdirectories.
 SET(THIRDPARTY_BLD_DIR ${PROJECT_BINARY_DIR}/source/third-party)
@@ -127,6 +274,24 @@
 SET(CPU_BLD_DIR ${PROJECT_BINARY_DIR}/source/cpu)
 SET(EVENT_BLD_DIR ${PROJECT_BINARY_DIR}/source/event)
 SET(MAIN_BLD_DIR ${PROJECT_BINARY_DIR}/source/main)
+SET(GUI_BLD_DIR ${PROJECT_BINARY_DIR}/source/qt-viewer)
+
+SET(EXP_GUI_BLD_DIR
+  ${PROJECT_BINARY_DIR}/source/qt-viewer/exp/exp_cleanup
+  ${PROJECT_BINARY_DIR}/source/qt-viewer/exp/exp_cleanup/analyzer
+  ${PROJECT_BINARY_DIR}/source/qt-viewer/exp/exp_cleanup/analyzer_o
+  ${PROJECT_BINARY_DIR}/source/qt-viewer/exp/exp_cleanup/containers
+  ${PROJECT_BINARY_DIR}/source/qt-viewer/exp/exp_cleanup/dumb_bui
+  ${PROJECT_BINARY_DIR}/source/qt-viewer/exp/exp_cleanup/exp_gui
+  ${PROJECT_BINARY_DIR}/source/qt-viewer/exp/exp_cleanup/map_gui
+  ${PROJECT_BINARY_DIR}/source/qt-viewer/exp/exp_cleanup/mc
+  ${PROJECT_BINARY_DIR}/source/qt-viewer/exp/exp_cleanup/memory_mgt
+  ${PROJECT_BINARY_DIR}/source/qt-viewer/exp/exp_cleanup/menubar
+  ${PROJECT_BINARY_DIR}/source/qt-viewer/exp/exp_cleanup/preferences
+  ${PROJECT_BINARY_DIR}/source/qt-viewer/exp/exp_cleanup/prefs_gui_factory
+  ${PROJECT_BINARY_DIR}/source/qt-viewer/exp/exp_cleanup/threaded_driver
+  ${PROJECT_BINARY_DIR}/source/qt-viewer/exp/exp_cleanup/user_msg
+)
 
 # A list of all source subdirectories (convenient for naming
 # include-directories).
Index: avida/current/CMakeModules/FixFindQt.cmake
diff -u avida/current/CMakeModules/FixFindQt.cmake:1.1 avida/current/CMakeModules/FixFindQt.cmake:1.1.2.1
--- avida/current/CMakeModules/FixFindQt.cmake:1.1	Sat Dec  6 10:00:54 2003
+++ avida/current/CMakeModules/FixFindQt.cmake	Mon Dec 15 10:05:43 2003
@@ -27,7 +27,7 @@
     SET(APPLE_EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR})
   ENDIF(EXECUTABLE_OUTPUT_PATH)
 
-  MACRO(CREATE_EXECUTABLE
+  MACRO(CREATE_QT_EXECUTABLE
     NAME
     SOURCES
     LIBRARIES
@@ -60,10 +60,10 @@
       ADD_DEPENDENCIES(distclean clean-${NAME}.app)
     ENDIF(DISTCLEAN_FILES)
 
-  ENDMACRO(CREATE_EXECUTABLE)
+  ENDMACRO(CREATE_QT_EXECUTABLE)
 
 ELSE(QT_MACX_INCLUDE_DIR)
-  MACRO(CREATE_EXECUTABLE
+  MACRO(CREATE_QT_EXECUTABLE
     NAME
     SOURCES
     LIBRARIES
@@ -71,7 +71,18 @@
     ADD_EXECUTABLE(${NAME} ${${SOURCES}})
     TARGET_LINK_LIBRARIES(${NAME} ${${LIBRARIES}})
     INSTALL_TARGETS(${INSTALL_PREFIX} ${NAME})
-  ENDMACRO(CREATE_EXECUTABLE)
+  ENDMACRO(CREATE_QT_EXECUTABLE)
 ENDIF(QT_MACX_INCLUDE_DIR)
 
+FIND_LIBRARY(QT_QT_LIBRARY 
+  NAMES qt-mt qt-mt230nc
+  PATHS
+  $ENV{QTDIR}/lib
+  /usr/local/qt/lib
+  /usr/local/lib
+  /usr/lib
+  /usr/share/qt3/lib
+  C:/Progra~1/qt/lib
+  )
 
+INCLUDE(${CMAKE_ROOT}/Modules/FindQt.cmake)
Index: avida/current/doc/CMakeLists.txt
diff -u avida/current/doc/CMakeLists.txt:1.1 avida/current/doc/CMakeLists.txt:1.1.2.1
--- avida/current/doc/CMakeLists.txt:1.1	Sat Dec  6 10:00:56 2003
+++ avida/current/doc/CMakeLists.txt	Mon Dec 15 10:05:43 2003
@@ -1,4 +1,3 @@
-
 SUBDIRS(glossary)
 
 INSTALL_FILES(/doc_html .*[.]html)
Index: avida/current/doc/glossary/CMakeLists.txt
diff -u avida/current/doc/glossary/CMakeLists.txt:1.1 avida/current/doc/glossary/CMakeLists.txt:1.1.2.1
--- avida/current/doc/glossary/CMakeLists.txt:1.1	Sat Dec  6 10:00:56 2003
+++ avida/current/doc/glossary/CMakeLists.txt	Mon Dec 15 10:05:43 2003
@@ -1,3 +1,2 @@
-
 INSTALL_FILES(/doc_html/glossary .*[.]html)
 INSTALL_FILES(/doc_html/glossary .*[.]help)
Index: avida/current/source/cpu/CMakeLists.txt
diff -u avida/current/source/cpu/CMakeLists.txt:1.1 avida/current/source/cpu/CMakeLists.txt:1.1.2.1
--- avida/current/source/cpu/CMakeLists.txt:1.1	Sat Dec  6 10:00:58 2003
+++ avida/current/source/cpu/CMakeLists.txt	Mon Dec 15 10:05:43 2003
@@ -1,4 +1,3 @@
-
 SET(libcpu_a_SOURCES
   4stack_head.cc
   code_label.cc
Index: avida/current/source/event/CMakeLists.txt
diff -u avida/current/source/event/CMakeLists.txt:1.1 avida/current/source/event/CMakeLists.txt:1.1.2.1
--- avida/current/source/event/CMakeLists.txt:1.1	Sat Dec  6 10:00:59 2003
+++ avida/current/source/event/CMakeLists.txt	Mon Dec 15 10:05:43 2003
@@ -1,7 +1,8 @@
-
 ADD_CUSTOM_COMMAND(
   OUTPUT
     cPopulation_construct_event_auto.ci
+    cPopulation_descr.ci
+    cPopulation_descr.hi
     cPopulation_enums_auto.ci
     cPopulation_name2enum_auto.ci
     cPopulation_process_auto.ci
Index: avida/current/source/event/cPopulation.events
diff -u avida/current/source/event/cPopulation.events:1.49 avida/current/source/event/cPopulation.events:1.49.2.1
--- avida/current/source/event/cPopulation.events:1.49	Wed Dec 10 13:56:56 2003
+++ avida/current/source/event/cPopulation.events	Mon Dec 15 10:05:43 2003
@@ -1586,7 +1586,7 @@
 /**
 * Remove the connections between cells along a column in an avida grid.
 * Arguments:
-*  col_id:  indicates the number of columns to the left of the cut.
+*  col_id:  indicats the number of columns to the left of the cut.
 *           default (or -1) = cut population in half
 *  min_row: First row to start cutting from
 *           default = 0
@@ -1625,152 +1625,6 @@
   cellB_list.Remove(&population->GetCell(idA));
   cellB_list.Remove(&population->GetCell(idA0));
   cellB_list.Remove(&population->GetCell(idA1));
-}
-
-sever_grid_row
-:descr:
-/**
-* Remove the connections between cells along a column in an avida grid.
-* Arguments:
-*  row_id:  indicates the number of rows abovef the cut.
-*           default (or -1) = cut population in half
-*  min_col: First row to start cutting from
-*           default = 0
-*  max_col: Last row to cut to
-*           default (or -1) = last row in population.
-**/
-:args:
-int row_id -1
-int min_col 0
-int max_col -1
-:body:
-const int world_x = population->GetWorldX();
-const int world_y = population->GetWorldY();
-if (row_id == -1) row_id = world_y / 2;
-if (max_col == -1) max_col = world_x;
-if (row_id < 0 || row_id >= world_y) {
-  cerr << "Event Error: Row ID " << row_id
-       << " out of range for sever_grid_row" << endl;
-  return;
-}
-// Loop through all of the cols and make the cut on each...
-for (int col_id = min_col; col_id < max_col; col_id++) {
-  int idA = row_id * world_x + col_id;
-  int idB  = Neighbor(idA, world_x, world_y,  0, -1);
-  int idA0 = Neighbor(idA, world_x, world_y, -1,  0);
-  int idA1 = Neighbor(idA, world_x, world_y,  1,  0);
-  int idB0 = Neighbor(idA, world_x, world_y, -1, -1);
-  int idB1 = Neighbor(idA, world_x, world_y,  1, -1);
-  cPopulationCell & cellA = population->GetCell(idA);
-  cPopulationCell & cellB = population->GetCell(idB);
-  tList<cPopulationCell> & cellA_list = cellA.ConnectionList();
-  tList<cPopulationCell> & cellB_list = cellB.ConnectionList();
-  cellA_list.Remove(&population->GetCell(idB));
-  cellA_list.Remove(&population->GetCell(idB0));
-  cellA_list.Remove(&population->GetCell(idB1));
-  cellB_list.Remove(&population->GetCell(idA));
-  cellB_list.Remove(&population->GetCell(idA0));
-  cellB_list.Remove(&population->GetCell(idA1));
-}
-
-join_grid_col
-:descr:
-/**
-* Join the connections between cells along a column in an avida grid.
-* Arguments:
-*  col_id:  indicates the number of columns to the left of the joining.
-*           default (or -1) = join population halves.
-*  min_row: First row to start joining from
-*           default = 0
-*  max_row: Last row to join to
-*           default (or -1) = last row in population.
-**/
-:args:
-int col_id -1
-int min_row 0
-int max_row -1
-:body:
-const int world_x = population->GetWorldX();
-const int world_y = population->GetWorldY();
-if (col_id == -1) col_id = world_x / 2;
-if (max_row == -1) max_row = world_y;
-if (col_id < 0 || col_id >= world_x) {
-  cerr << "Event Error: Column ID " << col_id
-       << " out of range for join_grid_col" << endl;
-  return;
-}
-// Loop through all of the rows and make the cut on each...
-for (int row_id = min_row; row_id < max_row; row_id++) {
-  int idA = row_id * world_x + col_id;
-  int idB  = Neighbor(idA, world_x, world_y, -1,  0);
-  cPopulationCell & cellA = population->GetCell(idA);
-  cPopulationCell & cellB = population->GetCell(idB);
-  cPopulationCell & cellA0 =
-	 population->GetCell(Neighbor(idA, world_x, world_y,  0, -1));
-  cPopulationCell & cellA1 =
-	 population->GetCell(Neighbor(idA, world_x, world_y,  0,  1));
-  cPopulationCell & cellB0 =
-	 population->GetCell(Neighbor(idA, world_x, world_y, -1, -1));
-  cPopulationCell & cellB1 =
-	 population->GetCell(Neighbor(idA, world_x, world_y, -1,  1));
-  tList<cPopulationCell> & cellA_list = cellA.ConnectionList();
-  tList<cPopulationCell> & cellB_list = cellB.ConnectionList();
-  if (cellA_list.FindPtr(&cellB)  == NULL) cellA_list.Push(&cellB);
-  if (cellA_list.FindPtr(&cellB0) == NULL) cellA_list.Push(&cellB0);
-  if (cellA_list.FindPtr(&cellB1) == NULL) cellA_list.Push(&cellB1);
-  if (cellB_list.FindPtr(&cellA)  == NULL) cellB_list.Push(&cellA);
-  if (cellB_list.FindPtr(&cellA0) == NULL) cellB_list.Push(&cellA0);
-  if (cellB_list.FindPtr(&cellA1) == NULL) cellB_list.Push(&cellA1);
-}
-
-join_grid_row
-:descr:
-/**
-* Remove the connections between cells along a column in an avida grid.
-* Arguments:
-*  row_id:  indicates the number of rows abovef the cut.
-*           default (or -1) = cut population in half
-*  min_col: First row to start cutting from
-*           default = 0
-*  max_col: Last row to cut to
-*           default (or -1) = last row in population.
-**/
-:args:
-int row_id -1
-int min_col 0
-int max_col -1
-:body:
-const int world_x = population->GetWorldX();
-const int world_y = population->GetWorldY();
-if (row_id == -1) row_id = world_y / 2;
-if (max_col == -1) max_col = world_x;
-if (row_id < 0 || row_id >= world_y) {
-  cerr << "Event Error: Row ID " << row_id
-       << " out of range for join_grid_row" << endl;
-  return;
-}
-// Loop through all of the cols and make the cut on each...
-for (int col_id = min_col; col_id < max_col; col_id++) {
-  int idA = row_id * world_x + col_id;
-  int idB  = Neighbor(idA, world_x, world_y,  0, -1);
-  cPopulationCell & cellA = population->GetCell(idA);
-  cPopulationCell & cellB = population->GetCell(idB);
-  cPopulationCell & cellA0 =
-	 population->GetCell(Neighbor(idA, world_x, world_y, -1,  0));
-  cPopulationCell & cellA1 =
-	 population->GetCell(Neighbor(idA, world_x, world_y,  1,  0));
-  cPopulationCell & cellB0 =
-	 population->GetCell(Neighbor(idA, world_x, world_y, -1, -1));
-  cPopulationCell & cellB1 =
-	 population->GetCell(Neighbor(idA, world_x, world_y,  1, -1));
-  tList<cPopulationCell> & cellA_list = cellA.ConnectionList();
-  tList<cPopulationCell> & cellB_list = cellB.ConnectionList();
-  if (cellA_list.FindPtr(&cellB)  == NULL) cellA_list.Push(&cellB);
-  if (cellA_list.FindPtr(&cellB0) == NULL) cellA_list.Push(&cellB0);
-  if (cellA_list.FindPtr(&cellB1) == NULL) cellA_list.Push(&cellB1);
-  if (cellB_list.FindPtr(&cellA)  == NULL) cellB_list.Push(&cellA);
-  if (cellB_list.FindPtr(&cellA0) == NULL) cellB_list.Push(&cellA0);
-  if (cellB_list.FindPtr(&cellA1) == NULL) cellB_list.Push(&cellA1);
 }
 
 connect_cells
Index: avida/current/source/main/CMakeLists.txt
diff -u avida/current/source/main/CMakeLists.txt:1.1 avida/current/source/main/CMakeLists.txt:1.1.2.1
--- avida/current/source/main/CMakeLists.txt:1.1	Sat Dec  6 10:00:59 2003
+++ avida/current/source/main/CMakeLists.txt	Mon Dec 15 10:05:43 2003
@@ -1,4 +1,3 @@
-
 INCLUDE_DIRECTORIES(${ALL_INC_DIRS})
 
 SET(libmain_a_SOURCES
@@ -63,10 +62,6 @@
 
 ADD_LIBRARY(main ${libmain_a_SOURCES})
 
-OPTION(_PRIMITIVE_INTERFACE
-  "Enable building interfaceless Avida (fastest version)."
-  ON
-)
 IF(_PRIMITIVE_INTERFACE)
   ADD_EXECUTABLE(primitive primitive.cc)
   TARGET_LINK_LIBRARIES(primitive main cpu event main tools)
Index: avida/current/source/main/analyze.cc
diff -u avida/current/source/main/analyze.cc:1.89 avida/current/source/main/analyze.cc:1.89.2.1
--- avida/current/source/main/analyze.cc:1.89	Wed Dec 10 13:56:57 2003
+++ avida/current/source/main/analyze.cc	Mon Dec 15 10:05:43 2003
@@ -2843,7 +2843,7 @@
 void cAnalyze::WriteInjectEvents(cString cur_string)
 {
   // Load in the variables...
-  cString filename("events_inj.cfg");
+  cString filename("clone.dat");
   int start_cell = 0;
   int lineage = 0;
   if (cur_string.GetSize() != 0) filename = cur_string.PopWord();
@@ -2872,109 +2872,6 @@
 }
 
 
-void cAnalyze::WriteCompetition(cString cur_string)
-{
-  cout << "Writing Competition events..." << endl;
-
-  // Load in the variables...
-  int join_UD = 0;
-  double start_merit = 50000;
-  cString filename("events_comp.cfg");
-  int batch_A = cur_batch - 1;
-  int batch_B = cur_batch;
-  int grid_side = -1;
-  int lineage = 0;
-
-  // Make sure we have reasonable default batches.
-  if (cur_batch == 0) { batch_A = 0; batch_B = 1; }
-
-  if (cur_string.GetSize() != 0) join_UD = cur_string.PopWord().AsInt();
-  if (cur_string.GetSize() != 0) start_merit = cur_string.PopWord().AsDouble();
-  if (cur_string.GetSize() != 0) filename = cur_string.PopWord();
-  if (cur_string.GetSize() != 0) batch_A = cur_string.PopWord().AsInt();
-  if (cur_string.GetSize() != 0) batch_B = cur_string.PopWord().AsInt();
-  if (cur_string.GetSize() != 0) grid_side = cur_string.PopWord().AsInt();
-  if (cur_string.GetSize() != 0) lineage = cur_string.PopWord().AsInt();
-
-  // Check inputs...
-  if (join_UD < 0) join_UD = 0;
-  if (batch_A < 0 || batch_B < 0) {
-    cerr << "Error: Batch IDs must be positive!" << endl;
-    return;
-  }
-  
-  ofstream & fp = data_file_manager.GetOFStream(filename);
-
-  // Count the number of organisms in each batch...
-  cAnalyzeGenotype * genotype = NULL;
-
-  int org_count_A = 0;
-  tListIterator<cAnalyzeGenotype> batchA_it(batch[batch_A].List());
-  while ((genotype = batchA_it.Next()) != NULL) {
-    org_count_A += genotype->GetNumCPUs();
-  }
-
-  int org_count_B = 0;
-  tListIterator<cAnalyzeGenotype> batchB_it(batch[batch_B].List());
-  while ((genotype = batchB_it.Next()) != NULL) {
-    org_count_B += genotype->GetNumCPUs();
-  }
-
-  int max_count = Max(org_count_A, org_count_B);
-  if (max_count > 10000) {
-    cout << "Warning: more than 10,000 organisms in sub-population!" << endl;
-  }
-
-  if (grid_side <= 0) {
-    for (grid_side = 5; grid_side < 100; grid_side += 5) {
-      if (grid_side * grid_side >= max_count) break;
-    }
-    if (verbose == true) {
-      cout << "...assuming population size "
-	   << grid_side << "x" << grid_side << "." << endl;
-    }
-  }
-
-
-  int pop_size = grid_side * grid_side;
-
-  int inject_pos = 0;
-  while ((genotype = batchA_it.Next()) != NULL) {
-    const int cur_count = genotype->GetNumCPUs();
-    const cGenome & genome = genotype->GetGenome();
-    double cur_merit = start_merit;
-    if (cur_merit < 0) cur_merit = genotype->GetMerit();
-    fp << "u 0 inject_sequence "
-       << genome.AsString() << " "
-       << inject_pos << " "
-       << inject_pos + cur_count << " "
-       << cur_merit << " "
-       << lineage << " "
-       << endl;
-    inject_pos += cur_count;
-  }
-
-  inject_pos = pop_size;
-  while ((genotype = batchB_it.Next()) != NULL) {
-    const int cur_count = genotype->GetNumCPUs();
-    const cGenome & genome = genotype->GetGenome();
-    double cur_merit = start_merit;
-    if (cur_merit < 0) cur_merit = genotype->GetMerit();
-    fp << "u 0 inject_sequence "
-       << genome.AsString() << " "
-       << inject_pos << " "
-       << inject_pos + cur_count << " "
-       << cur_merit << " "
-       << lineage+1 << " "
-       << endl;
-    inject_pos += cur_count;
-  }
-
-  fp << "u 0 sever_grid_row" << grid_side << endl;
-  fp << "u " << join_UD << " join_grid_row " << grid_side << endl;
-}
-
-
 void cAnalyze::AnalyzeMuts(cString cur_string)
 {
   cout << "Analyzing Mutations" << endl;
@@ -4510,7 +4407,6 @@
   // Build input files for avida...
   AddLibraryDef("WRITE_CLONE", &cAnalyze::WriteClone);
   AddLibraryDef("WRITE_INJECT_EVENTS", &cAnalyze::WriteInjectEvents);
-  AddLibraryDef("WRITE_COMPETITION", &cAnalyze::WriteCompetition);
 
   // Automated analysis
   AddLibraryDef("ANALYZE_MUTS", &cAnalyze::AnalyzeMuts);
Index: avida/current/source/main/analyze.hh
diff -u avida/current/source/main/analyze.hh:1.52 avida/current/source/main/analyze.hh:1.52.2.1
--- avida/current/source/main/analyze.hh:1.52	Wed Dec 10 13:56:57 2003
+++ avida/current/source/main/analyze.hh	Mon Dec 15 10:05:44 2003
@@ -152,7 +152,6 @@
   // Build Input Files for Avida
   void WriteClone(cString cur_string);
   void WriteInjectEvents(cString cur_string);
-  void WriteCompetition(cString cur_string);
 
   // Automated analysis...
   void AnalyzeMuts(cString cur_string);
Index: avida/current/source/main/birth_chamber.cc
diff -u avida/current/source/main/birth_chamber.cc:1.10 avida/current/source/main/birth_chamber.cc:1.10.2.1
--- avida/current/source/main/birth_chamber.cc:1.10	Thu Dec 11 14:13:04 2003
+++ avida/current/source/main/birth_chamber.cc	Mon Dec 15 10:05:44 2003
@@ -24,9 +24,6 @@
 #ifndef TOOLS_HH
 #include "tools.hh"
 #endif
-#ifndef CONFIG_HH
-#include "config.hh"
-#endif
 
 using namespace std;
 
@@ -75,10 +72,7 @@
   genome_waiting = false;
 
   // How many crossovers should be do? For now, 0 or 1
-  // Also check the probability of recombination in case
-  // it is less then 1 
-  if (parent.GetPhenotype().CrossNum() ==0 || 
-	cConfig::GetRecombProb() < g_random.GetDouble()) {
+  if (parent.GetPhenotype().CrossNum() ==0) {
     child_array.Resize(2);
     child_array[0] = new cOrganism(wait_entry.genome, pop_interface,
 				   environment);
@@ -89,7 +83,6 @@
     return true;
   }
   else {
-
     cCPUMemory genome0 = wait_entry.genome;
     cCPUMemory genome1 = child_genome;
 
Index: avida/current/source/main/config.cc
diff -u avida/current/source/main/config.cc:1.68 avida/current/source/main/config.cc:1.68.2.1
--- avida/current/source/main/config.cc:1.68	Thu Dec 11 14:13:04 2003
+++ avida/current/source/main/config.cc	Mon Dec 15 10:05:44 2003
@@ -58,7 +58,6 @@
 double cConfig::divide_del_prob;
 double cConfig::parent_mut_prob;
 int cConfig::special_mut_line;
-double cConfig::recomb_prob;
 int cConfig::num_instructions;
 int cConfig::hardware_type;
 int cConfig::max_cpu_threads;
@@ -73,7 +72,6 @@
 int cConfig::num_resources;
 int cConfig::slicing_method;
 int cConfig::birth_method;
-int cConfig::prefer_empty;
 int cConfig::death_method;
 int cConfig::alloc_method;
 int cConfig::divide_method;
@@ -164,8 +162,6 @@
   
   repro_group->Add(birth_method, "4", "BIRTH_METHOD",
 		   "0 = Replace random organism in neighborhood\n1 = Replace oldest organism in neighborhood\n2 = Replace largest Age/Merit in neighborhood\n3 = Place only in empty cells in neighborhood\n4 = Replace random from population (Mass Action)\n5 = Replace oldest in entire population (like Tierra)");
-  repro_group->Add(prefer_empty, "1", "PREFER_EMPTY",
-		   "Are empty cells given preference in offsping placement?");
   repro_group->Add(death_method, "0", "DEATH_METHOD",
 		   "0 = Never die of old age.\n1 = Die when inst executed = AGE_LIMIT (+deviation)\n2 = Die when inst executed = length*AGE_LIMIT (+dev)");
   repro_group->Add(age_limit, "5000", "AGE_LIMIT",
@@ -178,8 +174,6 @@
 		   "0 = Divide leaves state of mother untouched.\n1 = Divide resets state of mother (after the divide, we have 2 children)\n2 = Divide resets state of current thread only(does not touch possible parasite threads)");
   repro_group->Add(generation_inc_method, "1", "GENERATION_INC_METHOD",
 		   "0 = Only the generation of the child is\n    increased on divide.\n1 = Both the generation of the mother and child are\n    increased on divide (good with DIVIDE_METHOD 1).");
-  repro_group->Add(recomb_prob, "1", "RECOMBINATION_PROB",
-		   "probability that recombination will happen when div-sex is used");
 
 
   // Divide Restrictions Group.
@@ -221,9 +215,9 @@
   muts_group->Add(parent_mut_prob, "0.0", "PARENT_MUT_PROB",
 		  "Per-site, in parent, on divide");
   muts_group->Add(special_mut_line, "-1", "SPECIAL_MUT_LINE",
-                  "If this is >= 0, ONLY this line is mutated");
-
+		  "If this is >= 0, ONLY this line is mutated");
 
+  
   // Mutation reversions group
   cConfigGroup * rev_group = new cConfigGroup("Mutation Reversion");
   rev_group->SetComment("These slow down avida a lot, and should be set to 0.0 normally.");
Index: avida/current/source/main/config.hh
diff -u avida/current/source/main/config.hh:1.61 avida/current/source/main/config.hh:1.61.2.1
--- avida/current/source/main/config.hh:1.61	Thu Dec 11 14:13:04 2003
+++ avida/current/source/main/config.hh	Mon Dec 15 10:05:44 2003
@@ -219,11 +219,9 @@
   // Methodology
   static int slicing_method;
   static int birth_method;
-  static int prefer_empty;
   static int death_method;
   static int alloc_method;
   static int divide_method;
-  static double recomb_prob;
   static int required_task;
   static int lineage_creation_method;
   static int generation_inc_method;
@@ -342,11 +340,9 @@
 
   static int GetSlicingMethod() { return slicing_method; }
   static int GetBirthMethod() { return birth_method; }
-  static int GetPreferEmpty() { return prefer_empty; }
   static int GetDeathMethod() { return death_method; }
   static int GetAllocMethod() { return alloc_method; }
   static int GetDivideMethod() { return divide_method; }
-  static double GetRecombProb() { return recomb_prob; }
   static int GetRequiredTask() { return required_task; }
   static int GetLineageCreationMethod() { return lineage_creation_method; }
   static int GetGenerationIncMethod() { return generation_inc_method; }
@@ -438,8 +434,6 @@
 
   static void SetBirthMethod(int in_birth_method)
     { birth_method = in_birth_method; }
-  static void SetPreferEmpty(int in_prefer_empty)
-    { prefer_empty = in_prefer_empty; }
   static void SetDeathMethod(int in_death_method)
     { death_method = in_death_method; }
   static void SetAllocMethod(int in_alloc_method)
Index: avida/current/source/main/population.cc
diff -u avida/current/source/main/population.cc:1.124 avida/current/source/main/population.cc:1.124.2.1
--- avida/current/source/main/population.cc:1.124	Wed Dec 10 14:18:43 2003
+++ avida/current/source/main/population.cc	Mon Dec 15 10:05:44 2003
@@ -703,14 +703,7 @@
 
   // First, check if there is an empty organism to work with (always preferred)
   tList<cPopulationCell> & conn_list = parent_cell.ConnectionList();
-
-  if (cConfig::GetPreferEmpty() == false &&
-      cConfig::GetBirthMethod == POSITION_CHILD_RANDOM) {
-    found_list.Append(conn_list);
-    if (parent_ok == true) found_list.Push(&parent_cell);
-  } else {
-    FindEmptyCell(conn_list, found_list);
-  }
+  FindEmptyCell(conn_list, found_list);
 
   // If we have not found an empty organism, we must use the specified function
   // to determine how to choose among the filled organisms.
@@ -732,7 +725,7 @@
     }
   }
 
-  // If there are no possibilities, return parent.
+  // If there are no possibilities, return NULL.
   if (found_list.GetSize() == 0) return parent_cell;
 
   // Choose the organism randomly from those in the list, and return it.
Index: avida/current/source/qt-viewer/CMakeLists.txt
diff -u avida/current/source/qt-viewer/CMakeLists.txt:1.1 avida/current/source/qt-viewer/CMakeLists.txt:1.1.2.1
--- avida/current/source/qt-viewer/CMakeLists.txt:1.1	Sat Dec  6 10:01:00 2003
+++ avida/current/source/qt-viewer/CMakeLists.txt	Mon Dec 15 10:05:44 2003
@@ -1,25 +1,9 @@
+SUBDIRS(exp)
 
 INCLUDE(${PROJECT_SOURCE_DIR}/CMakeModules/TargetDistclean.cmake)
 INCLUDE(${PROJECT_SOURCE_DIR}/CMakeModules/FixFindQt.cmake)
-INCLUDE(${CMAKE_ROOT}/Modules/FindQt.cmake)
-
-IF(QT_FOUND)
-  IF(QT_QT_LIBRARY MATCHES "qt-mt")
-    SET(QT_IS_THREAD_CAPABLE TRUE)
-  ENDIF(QT_QT_LIBRARY MATCHES "qt-mt")
-ENDIF(QT_FOUND)
-
-OPTION(_QT_GRAPHIC_INTERFACE
-  "Enable building Avida graphic interface."
-  ON
-)
-VARIABLE_REQUIRES(_QT_GRAPHIC_INTERFACE QT_GRAPHIC_INTERFACE_REQUISITES
-  QT_FOUND
-  QT_WRAP_UI
-  QT_WRAP_CPP
-  QT_IS_THREAD_CAPABLE
-)
 
+ADD_DEFINITIONS(-DQT_THREAD_SUPPORT)
 IF(_QT_GRAPHIC_INTERFACE)
   INCLUDE_DIRECTORIES(
     ${ALL_INC_DIRS}
@@ -28,7 +12,6 @@
     ${QT_INCLUDE_PATH}
     .
   )
-  ADD_DEFINITIONS(-DQT_THREAD_SUPPORT)
   
   SET(libqtviewer_a_SOURCES
     avd_mission_control.cc
@@ -187,5 +170,5 @@
     ${THIRDPARTY_BLD_DIR}/trio
     .
   )
-  CREATE_EXECUTABLE(Avida Avida_SOURCES Avida_LIBRARIES /)
+  CREATE_QT_EXECUTABLE(Avida Avida_SOURCES Avida_LIBRARIES /)
 ENDIF(_QT_GRAPHIC_INTERFACE)
Index: avida/current/source/support/CMakeLists.txt
diff -u avida/current/source/support/CMakeLists.txt:1.1 avida/current/source/support/CMakeLists.txt:1.1.2.1
--- avida/current/source/support/CMakeLists.txt:1.1	Sat Dec  6 10:01:01 2003
+++ avida/current/source/support/CMakeLists.txt	Mon Dec 15 10:05:48 2003
@@ -1,4 +1,3 @@
-
 SUBDIRS(preset_organisms)
 
 INSTALL_FILES(/ FILES
Index: avida/current/source/support/genesis
diff -u avida/current/source/support/genesis:1.45 avida/current/source/support/genesis:1.45.2.1
--- avida/current/source/support/genesis:1.45	Wed Dec 10 13:56:57 2003
+++ avida/current/source/support/genesis	Mon Dec 15 10:05:48 2003
@@ -35,7 +35,6 @@
 		  # 3 = Place only in empty cells in neighborhood
 		  # 4 = Replace random from entire population (Mass Action)
 		  # 5 = Replace oldest in entire population (like Tierra)
-PREFER_EMPTY 1    # Are empty cells given preference in offspring placement?
 DEATH_METHOD 0    # 0 = Never die of old age.
 		  # 1 = Die when inst executed = AGE_LIMIT (with deviation)
 		  # 2 = Die when inst executed = length * AGE_LIMIT (+ dev.)
Index: avida/current/source/support/preset_organisms/CMakeLists.txt
diff -u avida/current/source/support/preset_organisms/CMakeLists.txt:1.1 avida/current/source/support/preset_organisms/CMakeLists.txt:1.1.2.1
--- avida/current/source/support/preset_organisms/CMakeLists.txt:1.1	Sat Dec  6 10:01:02 2003
+++ avida/current/source/support/preset_organisms/CMakeLists.txt	Mon Dec 15 10:05:48 2003
@@ -1,4 +1,3 @@
-
 INSTALL_FILES(/preset_organisms FILES
   dummy
   organism.4stack
Index: avida/current/source/testsuites/CMakeLists.txt
diff -u avida/current/source/testsuites/CMakeLists.txt:1.1 avida/current/source/testsuites/CMakeLists.txt:1.1.2.1
--- avida/current/source/testsuites/CMakeLists.txt:1.1	Sat Dec  6 10:01:02 2003
+++ avida/current/source/testsuites/CMakeLists.txt	Mon Dec 15 10:05:48 2003
@@ -1,4 +1 @@
-
-SET(EXECUTABLE_OUTPUT_PATH "")
-
-SUBDIRS(unit_testsuites)
+SUBDIRS(unit_testsuites qt_viewer_unit_testsuites)
Index: avida/current/source/testsuites/unit_testsuites/CMakeLists.txt
diff -u avida/current/source/testsuites/unit_testsuites/CMakeLists.txt:1.1 avida/current/source/testsuites/unit_testsuites/CMakeLists.txt:1.1.2.1
--- avida/current/source/testsuites/unit_testsuites/CMakeLists.txt:1.1	Sat Dec  6 10:01:03 2003
+++ avida/current/source/testsuites/unit_testsuites/CMakeLists.txt	Mon Dec 15 10:05:48 2003
@@ -1,6 +1,8 @@
+SET(EXECUTABLE_OUTPUT_PATH "")
+
 SUBDIRS(level_0 level_1)
 
-IF(_UNIT_TESTS)
+IF(_UNIT_TEST_PRIMITIVE)
   INCLUDE_DIRECTORIES(
     ${ALL_INC_DIRS}
     ${THIRDPARTY_SRC_DIR}/yaktest
@@ -160,4 +162,4 @@
     )
     ADD_TEST(${TESTSUITE} ${TESTSUITE})
   ENDFOREACH(TESTSUITE)
-ENDIF(_UNIT_TESTS)
+ENDIF(_UNIT_TEST_PRIMITIVE)
Index: avida/current/source/testsuites/unit_testsuites/level_0/CMakeLists.txt
diff -u avida/current/source/testsuites/unit_testsuites/level_0/CMakeLists.txt:1.1 avida/current/source/testsuites/unit_testsuites/level_0/CMakeLists.txt:1.1.2.1
--- avida/current/source/testsuites/unit_testsuites/level_0/CMakeLists.txt:1.1	Sat Dec  6 10:01:03 2003
+++ avida/current/source/testsuites/unit_testsuites/level_0/CMakeLists.txt	Mon Dec 15 10:05:49 2003
@@ -1,5 +1,4 @@
-
-IF(_UNIT_TESTS)
+IF(_UNIT_TEST_PRIMITIVE)
   INCLUDE_DIRECTORIES(
     ${ALL_INC_DIRS}
     ${THIRDPARTY_SRC_DIR}/yaktest
@@ -32,4 +31,4 @@
     )
     ADD_TEST(${TESTSUITE} ${TESTSUITE})
   ENDFOREACH(TESTSUITE)
-ENDIF(_UNIT_TESTS)
+ENDIF(_UNIT_TEST_PRIMITIVE)
Index: avida/current/source/testsuites/unit_testsuites/level_1/CMakeLists.txt
diff -u avida/current/source/testsuites/unit_testsuites/level_1/CMakeLists.txt:1.1 avida/current/source/testsuites/unit_testsuites/level_1/CMakeLists.txt:1.1.2.1
--- avida/current/source/testsuites/unit_testsuites/level_1/CMakeLists.txt:1.1	Sat Dec  6 10:01:04 2003
+++ avida/current/source/testsuites/unit_testsuites/level_1/CMakeLists.txt	Mon Dec 15 10:05:49 2003
@@ -1,5 +1,4 @@
-
-IF(_UNIT_TESTS)
+IF(_UNIT_TEST_PRIMITIVE)
   INCLUDE_DIRECTORIES(
     ${ALL_INC_DIRS}
     ${THIRDPARTY_SRC_DIR}/yaktest
@@ -24,4 +23,4 @@
     )
     ADD_TEST(${TESTSUITE} ${TESTSUITE})
   ENDFOREACH(TESTSUITE)
-ENDIF(_UNIT_TESTS)
+ENDIF(_UNIT_TEST_PRIMITIVE)
Index: avida/current/source/third-party/CMakeLists.txt
diff -u avida/current/source/third-party/CMakeLists.txt:1.1 avida/current/source/third-party/CMakeLists.txt:1.1.2.1
--- avida/current/source/third-party/CMakeLists.txt:1.1	Sat Dec  6 10:01:05 2003
+++ avida/current/source/third-party/CMakeLists.txt	Mon Dec 15 10:05:49 2003
@@ -1,2 +1,2 @@
-SUBDIRS(trio yaktest)
+SUBDIRS(trio yaktest mockpp)
 
Index: avida/current/source/third-party/trio/CMakeLists.txt
diff -u avida/current/source/third-party/trio/CMakeLists.txt:1.1 avida/current/source/third-party/trio/CMakeLists.txt:1.1.2.1
--- avida/current/source/third-party/trio/CMakeLists.txt:1.1	Sat Dec  6 10:01:06 2003
+++ avida/current/source/third-party/trio/CMakeLists.txt	Mon Dec 15 10:05:49 2003
@@ -1,4 +1,3 @@
-
 SET(libtrio_a_SOURCES
   trio.c
   triostr.c
Index: avida/current/source/third-party/yaktest/CMakeLists.txt
diff -u avida/current/source/third-party/yaktest/CMakeLists.txt:1.1 avida/current/source/third-party/yaktest/CMakeLists.txt:1.1.2.1
--- avida/current/source/third-party/yaktest/CMakeLists.txt:1.1	Sat Dec  6 10:01:06 2003
+++ avida/current/source/third-party/yaktest/CMakeLists.txt	Mon Dec 15 10:05:49 2003
@@ -1,5 +1,4 @@
-
-IF(_UNIT_TESTS)
+IF(UNIT_TESTS)
   SET(libyaktest_a_SOURCES
     test_problem.cpp
     test_result.cpp
@@ -7,4 +6,4 @@
     text_test_interpreter.cpp
   )
   ADD_LIBRARY(yaktest ${libyaktest_a_SOURCES})
-ENDIF(_UNIT_TESTS)
+ENDIF(UNIT_TESTS)
Index: avida/current/source/third-party/yaktest/test_case.cpp
diff -u avida/current/source/third-party/yaktest/test_case.cpp:1.1 avida/current/source/third-party/yaktest/test_case.cpp:1.1.2.1
--- avida/current/source/third-party/yaktest/test_case.cpp:1.1	Tue Nov 25 10:50:08 2003
+++ avida/current/source/third-party/yaktest/test_case.cpp	Mon Dec 15 10:05:49 2003
@@ -56,6 +56,7 @@
 test_case::test_non_error_stub( bool condition,
 			        const std::string& condition_name,
 			        const std::string& filename,
+			        const std::string& functionname,
 			        long line_number )
 {
   if ( !condition )
@@ -64,6 +65,7 @@
       message.append( condition_name );
       message.append( std::string( "\" evaluated to false." ) );
       m_last_result.add_error( test_problem( filename,
+					       functionname,
 					       line_number,
 					       message ));
     }
@@ -76,6 +78,7 @@
 test_case::test_is_true_stub( bool condition,
 			      const std::string& condition_name,
 			      const std::string& filename,
+			      const std::string& functionname,
 			      long line_number )
 {
   if ( condition )
@@ -88,6 +91,7 @@
       message.append( condition_name );
       message.append( std::string( "\" evaluated to false." ) );
       m_last_result.add_failure( test_problem( filename,
+					       functionname,
 					       line_number,
 					       message ));
     }
@@ -99,13 +103,14 @@
 test_case::create_equality_problem_report( const std::string& actual_message,
 					   const std::string& expected_message,
 					   const std::string& filename,
+					   const std::string& functionname,
 					   long line_number )
 {
   std::string message = "Equality failed.  Got ";
   message.append( actual_message );
   message.append( ", expected " );
   message.append( expected_message );
-  return test_problem( filename, line_number, message );
+  return test_problem( filename, functionname, line_number, message );
 }
 
 
@@ -115,6 +120,7 @@
 test_case::test_int_is_equal_stub( long actual,
 			       long expected,
 			       const std::string& filename,
+			       const std::string& functionname,
 			       long line_number )
 {
   if ( actual == expected ) 
@@ -131,6 +137,7 @@
       m_last_result.add_failure( create_equality_problem_report( actual_message,
 								 expected_message,
 								 filename,
+								 functionname,
 								 line_number ) );
     }
 }
@@ -139,6 +146,7 @@
 test_case::test_double_is_equal_stub( double actual,
 				      double expected,
 				      const std::string& filename,
+				      const std::string& functionname,
 				      long line_number,
 // msvc didn't like the redeclaration of default parameter RS 2/14/2001
 //				      double tolerance = 0.005 )
@@ -158,6 +166,7 @@
       m_last_result.add_failure( create_equality_problem_report( actual_message,
 								 expected_message,
 								 filename,
+								 functionname,
 								 line_number ));
     }
 }
@@ -168,6 +177,7 @@
 test_case::test_string_is_equal_stub( const std::string& actual,
 			   const std::string& expected,
 			   const std::string& filename,
+			   const std::string& functionname,
 			   long line_number )
 {
   if ( actual == expected ) 
@@ -185,6 +195,7 @@
       m_last_result.add_failure( create_equality_problem_report( actual_message,
 								 expected_message,
 								 filename,
+								 functionname,
 								 line_number ));
     }
 }
Index: avida/current/source/third-party/yaktest/test_case.h
diff -u avida/current/source/third-party/yaktest/test_case.h:1.1 avida/current/source/third-party/yaktest/test_case.h:1.1.2.1
--- avida/current/source/third-party/yaktest/test_case.h:1.1	Tue Nov 25 10:50:08 2003
+++ avida/current/source/third-party/yaktest/test_case.h	Mon Dec 15 10:05:49 2003
@@ -14,7 +14,7 @@
 using std::ostringstream;
 #endif //WIN32
 
-// $Id: test_case.h,v 1.1 2003/11/25 18:50:08 kaben Exp $
+// $Id: test_case.h,v 1.1.2.1 2003/12/15 18:05:49 kaben Exp $
 /*! A composite test case 
  * its atomic test can be redefined by overriding
  * test(); it can also serve as a suite of tests by adding test_cases
@@ -53,38 +53,45 @@
   void test_non_error_stub( bool condition, 
 			    const std::string& condition_name,
 			    const std::string& filename,
+			    const std::string& functionname,
 			    long line_number );
   //! tests to see if the supplied condition is true; called by the test_is_true macro
   void test_is_true_stub( bool condition, 
 			  const std::string& condition_name,
 			  const std::string& filename,
+			  const std::string& functionname,
 			  long line_number );
   //! tests to see if two longs are equal
   void test_int_is_equal_stub( long actual,
 			   long expected,
 			   const std::string& filename,
+			   const std::string& functionname,
 			   long line_number );
   //! tests to see if two doubles are within limits
   void test_double_is_equal_stub( double actual,
 				  double expected,
 				  const std::string& filename,
+			          const std::string& functionname,
 				  long line_number,
 				  double tolerance = 0.005 );
   //! tests to see if two strings are equal
   void test_string_is_equal_stub( const std::string& actual,
 				  const std::string& expected,
 				  const std::string& filename,
+			          const std::string& functionname,
 				  long line_number );
   //! creates an "equality test failed" problem report
   test_problem create_equality_problem_report( const std::string& actual_message,
 					       const std::string& expected_message,
 					       const std::string& filename,
+			                       const std::string& functionname,
 					       long line_number );
   
 				 
   template< class T >void test_is_equal_stub( const T& actual,
 					      const T& expected,
 					      const std::string& filename,
+			                      const std::string& functionname,
 					      long line_number )
     {
       if ( actual == expected ) 
@@ -105,7 +112,8 @@
 	    ( expected_ptr == NULL ) ? "" : expected_ptr->to_string();
 	  m_last_result.add_failure( create_equality_problem_report( actual_message,
 								     expected_message,
-							     filename,
+							             filename,
+							             functionname,
 								     line_number ) );
 #endif // LINUX
         //will use strstreams to get generic i/o working
@@ -118,7 +126,8 @@
     expected_message << expected;
 	  m_last_result.add_failure( create_equality_problem_report( actual_message.str(),
 								     expected_message.str(),
-							     filename,
+							             filename,
+							             functionname,
 								     line_number ) );
 
 #endif // WIN32
@@ -142,13 +151,23 @@
 
 //these macros are used instead of the code stubs in test_case
 //in order to use preprocessor features to get filename/line number
-#define test_non_error( condition ) (this->test_non_error_stub( (condition), (#condition), __FILE__, __LINE__ ))
-#define test_is_true( condition ) (this->test_is_true_stub( (condition), (#condition), __FILE__, __LINE__ ))
-#define test_int_is_equal( actual_value, expected_value ) (this->test_int_is_equal_stub( actual_value, expected_value, __FILE__, __LINE__ ))
-#define test_double_is_equal( actual_value, expected_value ) (this->test_double_is_equal_stub( actual_value, expected_value, __FILE__, __LINE__ ))
-#define double_is_within_tolerance( actual_value, expected_value, tolerance ) ( this->test_double_is_equal_stub( actual_value, expected_value, __FILE__, __LINE__, tolerance ))
-#define test_string_is_equal( actual_value, expected_value ) (this->test_string_is_equal_stub( actual_value, expected_value, __FILE__, __LINE__ ))
-#define test_is_equal( actual_value, expected_value ) (this->test_is_equal_stub( actual_value, expected_value, __FILE__, __LINE__ ))
+#ifdef WIN32
+  #define test_non_error( condition ) (this->test_non_error_stub( (condition), (#condition), __FILE__, __LINE__ ))
+  #define test_is_true( condition ) (this->test_is_true_stub( (condition), (#condition), __FILE__, __LINE__ ))
+  #define test_int_is_equal( actual_value, expected_value ) (this->test_int_is_equal_stub( actual_value, expected_value, __FILE__, __LINE__ ))
+  #define test_double_is_equal( actual_value, expected_value ) (this->test_double_is_equal_stub( actual_value, expected_value, __FILE__, __LINE__ ))
+  #define double_is_within_tolerance( actual_value, expected_value, tolerance ) ( this->test_double_is_equal_stub( actual_value, expected_value, __FILE__, __LINE__, tolerance ))
+  #define test_string_is_equal( actual_value, expected_value ) (this->test_string_is_equal_stub( actual_value, expected_value, __FILE__, __LINE__ ))
+  #define test_is_equal( actual_value, expected_value ) (this->test_is_equal_stub( actual_value, expected_value, __FILE__, __LINE__ ))
+#else // WIN32
+  #define test_non_error( condition ) (this->test_non_error_stub( (condition), (#condition), __FILE__, __PRETTY_FUNCTION__, __LINE__ ))
+  #define test_is_true( condition ) (this->test_is_true_stub( (condition), (#condition), __FILE__, __PRETTY_FUNCTION__, __LINE__ ))
+  #define test_int_is_equal( actual_value, expected_value ) (this->test_int_is_equal_stub( actual_value, expected_value, __FILE__, __PRETTY_FUNCTION__, __LINE__ ))
+  #define test_double_is_equal( actual_value, expected_value ) (this->test_double_is_equal_stub( actual_value, expected_value, __FILE__, __PRETTY_FUNCTION__, __LINE__ ))
+  #define double_is_within_tolerance( actual_value, expected_value, tolerance ) ( this->test_double_is_equal_stub( actual_value, expected_value, __FILE__, __PRETTY_FUNCTION__, __LINE__, tolerance ))
+  #define test_string_is_equal( actual_value, expected_value ) (this->test_string_is_equal_stub( actual_value, expected_value, __FILE__, __PRETTY_FUNCTION__, __LINE__ ))
+  #define test_is_equal( actual_value, expected_value ) (this->test_is_equal_stub( actual_value, expected_value, __FILE__, __PRETTY_FUNCTION__, __LINE__ ))
+#endif // WIN32
 
 #endif
 
Index: avida/current/source/third-party/yaktest/test_problem.cpp
diff -u avida/current/source/third-party/yaktest/test_problem.cpp:1.1 avida/current/source/third-party/yaktest/test_problem.cpp:1.1.2.1
--- avida/current/source/third-party/yaktest/test_problem.cpp:1.1	Tue Nov 25 10:50:08 2003
+++ avida/current/source/third-party/yaktest/test_problem.cpp	Mon Dec 15 10:05:49 2003
@@ -2,9 +2,22 @@
 
 //constructor (dumb initializer) for test_problem
 test_problem::test_problem(  const std::string& filename, 
+			     const std::string& functionname,
 			     long line_number, 
 			     const std::string& message ) :
 m_line_number( line_number ),
+m_functionname( functionname ),
+m_filename( filename ),
+m_message( message )
+{
+}
+
+//constructor (dumb initializer) for test_problem, sans functionname
+test_problem::test_problem(  const std::string& filename, 
+			     long line_number, 
+			     const std::string& message ) :
+m_line_number( line_number ),
+m_functionname( "" ),
 m_filename( filename ),
 m_message( message )
 {
@@ -13,6 +26,7 @@
 //copy constructor
 test_problem::test_problem( const test_problem& rhs ) :
 m_line_number( rhs.m_line_number ),
+m_functionname( rhs.m_functionname ),
 m_filename( rhs.m_filename ),
 m_message( rhs.m_message )
 {
@@ -23,6 +37,7 @@
 test_problem::operator=( const test_problem& rhs )
 {
   m_line_number = rhs.m_line_number;
+  m_functionname = rhs.m_functionname;
   m_filename = rhs.m_filename;
   m_message = rhs.m_message;
   return *this;
@@ -35,6 +50,13 @@
   return m_line_number;
 }
 
+
+//data access
+const std::string&
+test_problem::functionname( void ) const
+{
+  return m_functionname;
+}
 
 //data access
 const std::string&
Index: avida/current/source/third-party/yaktest/test_problem.h
diff -u avida/current/source/third-party/yaktest/test_problem.h:1.1 avida/current/source/third-party/yaktest/test_problem.h:1.1.2.1
--- avida/current/source/third-party/yaktest/test_problem.h:1.1	Tue Nov 25 10:50:08 2003
+++ avida/current/source/third-party/yaktest/test_problem.h	Mon Dec 15 10:05:49 2003
@@ -11,6 +11,8 @@
   //protected data members
   //line number of the error, if appropriate
   long m_line_number;
+  //functionname of the error, if appropriate
+  std::string m_functionname;
   //filename of the error, if appropriate
   std::string m_filename;
   //additional message as appropriate
@@ -18,11 +20,13 @@
 
  public:
   //construction
+  test_problem( const std::string& filename, const std::string& functionname, long line_number, const std::string& message );
   test_problem( const std::string& filename, long line_number, const std::string& message );
   test_problem( const test_problem& rhs );
   test_problem& operator= (const test_problem& rhs);
   //data access
   long line_number( void ) const;
+  const std::string& functionname( void ) const;
   const std::string& filename( void ) const;
   const std::string& message( void ) const;
 
Index: avida/current/source/third-party/yaktest/text_test_interpreter.cpp
diff -u avida/current/source/third-party/yaktest/text_test_interpreter.cpp:1.1 avida/current/source/third-party/yaktest/text_test_interpreter.cpp:1.1.2.1
--- avida/current/source/third-party/yaktest/text_test_interpreter.cpp:1.1	Tue Nov 25 10:50:08 2003
+++ avida/current/source/third-party/yaktest/text_test_interpreter.cpp	Mon Dec 15 10:05:49 2003
@@ -79,7 +79,9 @@
   Result.append( problem.filename() );
   Result.append( ":" );
   Result.append( _yak_itoa( problem.line_number() ) );
-  Result.append( ":" );
+  Result.append( ":<" );
+  Result.append( problem.functionname() );
+  Result.append( "> " );
   Result.append( problem.message() );
   Result.append( "\n" );
   return Result;
Index: avida/current/source/tools/CMakeLists.txt
diff -u avida/current/source/tools/CMakeLists.txt:1.1 avida/current/source/tools/CMakeLists.txt:1.1.2.1
--- avida/current/source/tools/CMakeLists.txt:1.1	Sat Dec  6 10:01:07 2003
+++ avida/current/source/tools/CMakeLists.txt	Mon Dec 15 10:05:49 2003
@@ -1,4 +1,3 @@
-
 SET(libtools_a_SOURCES
   block_struct.cc
   const_schedule.cc
Index: avida/current/source/tools/tList.hh
diff -u avida/current/source/tools/tList.hh:1.12 avida/current/source/tools/tList.hh:1.12.2.1
--- avida/current/source/tools/tList.hh:1.12	Wed Dec 10 13:56:57 2003
+++ avida/current/source/tools/tList.hh	Mon Dec 15 10:05:49 2003
@@ -238,21 +238,10 @@
     while (other_it.Next() != NULL) PushRear(other_it.Get());
   }
 
-  // Find by value
   T * Find(T * _in) const {
     tListNode<T> * test = root.next;
     while (test != &root) {
       if ( *(test->data) == *(_in) ) return test->data;
-      test = test->next;
-    }
-    return NULL;
-  }
-
-  // Find by Pointer
-  T * FindPtr(T * _in) const {
-    tListNode<T> * test = root.next;
-    while (test != &root) {
-      if ( test->data == _in ) return test->data;
       test = test->next;
     }
     return NULL;
Index: avida/current/source/viewers/CMakeLists.txt
diff -u avida/current/source/viewers/CMakeLists.txt:1.1 avida/current/source/viewers/CMakeLists.txt:1.1.2.1
--- avida/current/source/viewers/CMakeLists.txt:1.1	Sat Dec  6 10:01:07 2003
+++ avida/current/source/viewers/CMakeLists.txt	Mon Dec 15 10:05:50 2003
@@ -1,15 +1,4 @@
-
-INCLUDE(${PROJECT_SOURCE_DIR}/CMakeModules/TargetDistclean.cmake)
 INCLUDE(${PROJECT_SOURCE_DIR}/CMakeModules/FindNcurses.cmake)
-
-OPTION(_NCURSES_CONSOLE_INTERFACE
-  "Enable building Avida console interface."
-  ON
-)
-# )
-#VARIABLE_REQUIRES(_NCURSES_CONSOLE_INTERFACE NCURSES_REQUISITES
-#  NCURSES_INCLUDE_PATH
-#)
 
 IF(_NCURSES_CONSOLE_INTERFACE)
   INCLUDE_DIRECTORIES(

Index: avida/current/.cvsignore
+++ avida/current/.cvsignore

Index: avida/current/source/qt-viewer/exp/CMakeLists.txt
+++ avida/current/source/qt-viewer/exp/CMakeLists.txt

Index: avida/current/source/qt-viewer/exp/exp_cleanup/CMakeLists.txt
+++ avida/current/source/qt-viewer/exp/exp_cleanup/CMakeLists.txt

Index: avida/current/source/qt-viewer/exp/exp_cleanup/Makefile.am
+++ avida/current/source/qt-viewer/exp/exp_cleanup/Makefile.am

Index: avida/current/source/qt-viewer/exp/exp_cleanup/exp_cleanup.pro
+++ avida/current/source/qt-viewer/exp/exp_cleanup/exp_cleanup.pro

Index: avida/current/source/qt-viewer/exp/exp_cleanup/main.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/main.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/modules.pri
+++ avida/current/source/qt-viewer/exp/exp_cleanup/modules.pri

Index: avida/current/source/qt-viewer/exp/exp_cleanup/template2_t.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/template2_t.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/template2_t.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/template2_t.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/template_t.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/template_t.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/template_t.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/template_t.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/xqt_test_case.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/xqt_test_case.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/xqt_test_case.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/xqt_test_case.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/analyzer.pri
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/analyzer.pri

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_batchlist_item.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_batchlist_item.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_batchlist_item_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_batchlist_item_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_ctrl.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_ctrl.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_ctrl.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_ctrl.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_data_entry.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_data_entry.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_data_entry_command_list_item.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_data_entry_command_list_item.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_data_entry_command_list_item.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_data_entry_command_list_item.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_data_entry_command_list_item_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_data_entry_command_list_item_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_data_entry_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_data_entry_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_dbg_msgs.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_dbg_msgs.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_dbg_msgs_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_dbg_msgs_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_genotype_list_item.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_genotype_list_item.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_genotype_list_item_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_genotype_list_item_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_genotype_sel_ctrl.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_genotype_sel_ctrl.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_genotype_sel_view.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_genotype_sel_view.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_genotype_sel_view.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_genotype_sel_view.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_gui.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_gui.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_listview.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_listview.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_listview.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_listview.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_mdl.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_mdl.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_mdl.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_mdl.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_mdl_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_mdl_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_menubar_handler.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_menubar_handler.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_menubar_handler.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_menubar_handler.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_out_fmt_sel.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_out_fmt_sel.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_out_fmt_sel.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_out_fmt_sel.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_view.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_view.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_view.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer/avd_n_analyzer_view.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/analyzer_o.pri
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/analyzer_o.pri

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_batchlist_item.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_batchlist_item.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_batchlist_item_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_batchlist_item_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_controller.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_controller.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_controller.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_controller.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_controller_data.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_controller_data.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_controller_data.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_controller_data.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_creator.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_creator.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_creator.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_creator.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_data_entry.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_data_entry.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_data_entry_command_list_item.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_data_entry_command_list_item.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_data_entry_command_list_item.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_data_entry_command_list_item.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_data_entry_command_list_item_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_data_entry_command_list_item_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_data_entry_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_data_entry_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_dbg_msgs.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_dbg_msgs.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_dbg_msgs.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_dbg_msgs.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_dbg_msgs_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_dbg_msgs_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_genotype_list_item.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_genotype_list_item.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_genotype_list_item_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_genotype_list_item_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_listview.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_listview.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_listview.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_listview.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_listview_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_listview_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_menubar_handler.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_menubar_handler.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_menubar_handler.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_menubar_handler.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_model.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_model.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_model.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_model.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_model_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_model_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_output_fmt_selector.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_output_fmt_selector.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_output_fmt_selector.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_output_fmt_selector.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_utils.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_utils.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_view.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_view.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_view.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/analyzer_o/avd_analyzer_view.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/containers/containers.pri
+++ avida/current/source/qt-viewer/exp/exp_cleanup/containers/containers.pri

Index: avida/current/source/qt-viewer/exp/exp_cleanup/containers/tRList.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/containers/tRList.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/containers/tRList_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/containers/tRList_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/containers/tRetainable_list.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/containers/tRetainable_list.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/containers/tRetainable_list_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/containers/tRetainable_list_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/dumb_gui/avd_dumb_ctrl.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/dumb_gui/avd_dumb_ctrl.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/dumb_gui/avd_dumb_ctrl.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/dumb_gui/avd_dumb_ctrl.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/dumb_gui/avd_dumb_gui.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/dumb_gui/avd_dumb_gui.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/dumb_gui/avd_dumb_gui_dbg.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/dumb_gui/avd_dumb_gui_dbg.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/dumb_gui/avd_dumb_gui_dbg_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/dumb_gui/avd_dumb_gui_dbg_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/dumb_gui/avd_dumb_view.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/dumb_gui/avd_dumb_view.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/dumb_gui/avd_dumb_view.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/dumb_gui/avd_dumb_view.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/dumb_gui/dumb_gui.pri
+++ avida/current/source/qt-viewer/exp/exp_cleanup/dumb_gui/dumb_gui.pri

Index: avida/current/source/qt-viewer/exp/exp_cleanup/exp_gui/avd_exp_ctrl.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/exp_gui/avd_exp_ctrl.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/exp_gui/avd_exp_ctrl.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/exp_gui/avd_exp_ctrl.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/exp_gui/avd_exp_gui.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/exp_gui/avd_exp_gui.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/exp_gui/avd_exp_gui_dbg.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/exp_gui/avd_exp_gui_dbg.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/exp_gui/avd_exp_gui_dbg_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/exp_gui/avd_exp_gui_dbg_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/exp_gui/avd_exp_view.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/exp_gui/avd_exp_view.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/exp_gui/avd_exp_view.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/exp_gui/avd_exp_view.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/exp_gui/exp_gui.pri
+++ avida/current/source/qt-viewer/exp/exp_cleanup/exp_gui/exp_gui.pri

Index: avida/current/source/qt-viewer/exp/exp_cleanup/exp_gui/test_thing.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/exp_gui/test_thing.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/exp_gui/test_thing.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/exp_gui/test_thing.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/exp_gui/test_thing_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/exp_gui/test_thing_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/exp_gui/testing_interface.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/exp_gui/testing_interface.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/gui_factory/avd_abstract_gui.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/gui_factory/avd_abstract_gui.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/gui_factory/avd_abstract_gui_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/gui_factory/avd_abstract_gui_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/gui_factory/avd_gui_factory.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/gui_factory/avd_gui_factory.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/gui_factory/avd_gui_factory.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/gui_factory/avd_gui_factory.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/gui_factory/avd_gui_factory_error_policy.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/gui_factory/avd_gui_factory_error_policy.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/gui_factory/avd_gui_factory_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/gui_factory/avd_gui_factory_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/gui_factory/gui_factory.pri
+++ avida/current/source/qt-viewer/exp/exp_cleanup/gui_factory/gui_factory.pri

Index: avida/current/source/qt-viewer/exp/exp_cleanup/gui_factory/tGUI.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/gui_factory/tGUI.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/gui_factory/tGUI_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/gui_factory/tGUI_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_canvas.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_canvas.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_canvas.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_canvas.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_canvas_rectangle.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_canvas_rectangle.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_canvas_rectangle.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_canvas_rectangle.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_canvas_rectangle_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_canvas_rectangle_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_canvas_view.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_canvas_view.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_canvas_view.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_canvas_view.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_ctrl.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_ctrl.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_ctrl.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_ctrl.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_gui.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_gui.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_gui_dbg.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_gui_dbg.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_gui_dbg_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_gui_dbg_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_layer.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_layer.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_layer.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_layer.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_layer_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_layer_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_view.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_view.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_view.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/avd_map_view.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/map_gui.pri
+++ avida/current/source/qt-viewer/exp/exp_cleanup/map_gui/map_gui.pri

Index: avida/current/source/qt-viewer/exp/exp_cleanup/mc/avd_avida_state_mediator.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/mc/avd_avida_state_mediator.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/mc/avd_connections.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/mc/avd_connections.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/mc/avd_connections.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/mc/avd_connections.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/mc/avd_gui_factory_mediator.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/mc/avd_gui_factory_mediator.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/mc/avd_mc_dbg.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/mc/avd_mc_dbg.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/mc/avd_mc_dbg.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/mc/avd_mc_dbg.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/mc/avd_mc_dbg_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/mc/avd_mc_dbg_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/mc/avd_mc_mediator.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/mc/avd_mc_mediator.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/mc/avd_mc_mediator.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/mc/avd_mc_mediator.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/mc/avd_menubar_mediator.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/mc/avd_menubar_mediator.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/mc/avd_mission_control.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/mc/avd_mission_control.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/mc/avd_mission_control.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/mc/avd_mission_control.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/mc/avd_settings_mediator.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/mc/avd_settings_mediator.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/mc/avd_windows_mediator.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/mc/avd_windows_mediator.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/mc/mc.pri
+++ avida/current/source/qt-viewer/exp/exp_cleanup/mc/mc.pri

Index: avida/current/source/qt-viewer/exp/exp_cleanup/mc/setup_avida.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/mc/setup_avida.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/mc/setup_avida.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/mc/setup_avida.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/mc/attributes/requests_argv.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/mc/attributes/requests_argv.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/memory_mgt/ScopeGuard.h
+++ avida/current/source/qt-viewer/exp/exp_cleanup/memory_mgt/ScopeGuard.h

Index: avida/current/source/qt-viewer/exp/exp_cleanup/memory_mgt/activate_watcher.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/memory_mgt/activate_watcher.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/memory_mgt/activate_watcher_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/memory_mgt/activate_watcher_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/memory_mgt/memory_mgt.pri
+++ avida/current/source/qt-viewer/exp/exp_cleanup/memory_mgt/memory_mgt.pri

Index: avida/current/source/qt-viewer/exp/exp_cleanup/memory_mgt/retainable.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/memory_mgt/retainable.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/memory_mgt/retainable.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/memory_mgt/retainable.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/memory_mgt/retainable_dbg.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/memory_mgt/retainable_dbg.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/memory_mgt/retainable_dbg_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/memory_mgt/retainable_dbg_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/memory_mgt/retainable_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/memory_mgt/retainable_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/memory_mgt/watch_retains.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/memory_mgt/watch_retains.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/memory_mgt/watch_retains.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/memory_mgt/watch_retains.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/memory_mgt/watch_retains_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/memory_mgt/watch_retains_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/menubar/avd_menubar_handler.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/menubar/avd_menubar_handler.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/menubar/avd_menubar_handler.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/menubar/avd_menubar_handler.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/menubar/avd_menubar_hdlr_creator.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/menubar/avd_menubar_hdlr_creator.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/menubar/menubar.pri
+++ avida/current/source/qt-viewer/exp/exp_cleanup/menubar/menubar.pri

Index: avida/current/source/qt-viewer/exp/exp_cleanup/preferences/avd_prefs_ctrl.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/preferences/avd_prefs_ctrl.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/preferences/avd_prefs_ctrl.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/preferences/avd_prefs_ctrl.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/preferences/avd_prefs_dbg.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/preferences/avd_prefs_dbg.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/preferences/avd_prefs_dbg.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/preferences/avd_prefs_dbg.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/preferences/avd_prefs_dbg_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/preferences/avd_prefs_dbg_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/preferences/avd_prefs_gui.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/preferences/avd_prefs_gui.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/preferences/avd_prefs_item.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/preferences/avd_prefs_item.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/preferences/avd_prefs_item.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/preferences/avd_prefs_item.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/preferences/avd_prefs_item_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/preferences/avd_prefs_item_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/preferences/avd_prefs_item_view.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/preferences/avd_prefs_item_view.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/preferences/avd_prefs_item_view_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/preferences/avd_prefs_item_view_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/preferences/avd_prefs_view.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/preferences/avd_prefs_view.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/preferences/avd_prefs_view.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/preferences/avd_prefs_view.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/preferences/preferences.pri
+++ avida/current/source/qt-viewer/exp/exp_cleanup/preferences/preferences.pri

Index: avida/current/source/qt-viewer/exp/exp_cleanup/prefs_gui_factory/avd_abstract_prefs_gui.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/prefs_gui_factory/avd_abstract_prefs_gui.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/prefs_gui_factory/avd_abstract_prefs_gui_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/prefs_gui_factory/avd_abstract_prefs_gui_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/prefs_gui_factory/avd_prefs_gui_factory.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/prefs_gui_factory/avd_prefs_gui_factory.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/prefs_gui_factory/avd_prefs_gui_factory.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/prefs_gui_factory/avd_prefs_gui_factory.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/prefs_gui_factory/avd_prefs_gui_factory_error_policy.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/prefs_gui_factory/avd_prefs_gui_factory_error_policy.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/prefs_gui_factory/avd_prefs_gui_factory_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/prefs_gui_factory/avd_prefs_gui_factory_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/prefs_gui_factory/prefs_gui_factory.pri
+++ avida/current/source/qt-viewer/exp/exp_cleanup/prefs_gui_factory/prefs_gui_factory.pri

Index: avida/current/source/qt-viewer/exp/exp_cleanup/prefs_gui_factory/tPrefsGUI.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/prefs_gui_factory/tPrefsGUI.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/prefs_gui_factory/tPrefsGUI_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/prefs_gui_factory/tPrefsGUI_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/threaded_driver/avd_avida_driver.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/threaded_driver/avd_avida_driver.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/threaded_driver/avd_avida_driver.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/threaded_driver/avd_avida_driver.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/threaded_driver/avd_avida_thread_drvr_dbg.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/threaded_driver/avd_avida_thread_drvr_dbg.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/threaded_driver/avd_avida_thread_drvr_dbg_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/threaded_driver/avd_avida_thread_drvr_dbg_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/threaded_driver/avd_driver_creator.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/threaded_driver/avd_driver_creator.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/threaded_driver/avd_gui_msg_event.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/threaded_driver/avd_gui_msg_event.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/threaded_driver/avd_orig_driver_controller.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/threaded_driver/avd_orig_driver_controller.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/threaded_driver/avd_orig_driver_controller.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/threaded_driver/avd_orig_driver_controller.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/threaded_driver/threaded_driver.pri
+++ avida/current/source/qt-viewer/exp/exp_cleanup/threaded_driver/threaded_driver.pri

Index: avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_message_display.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_message_display.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_message_display.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_message_display.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_message_display_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_message_display_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_message_display_typetrack.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_message_display_typetrack.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_message_display_typetrack_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_message_display_typetrack_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_qstr_message_display.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_qstr_message_display.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_user_msg_ctrl.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_user_msg_ctrl.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_user_msg_ctrl.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_user_msg_ctrl.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_user_msg_ctrl_funct.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_user_msg_ctrl_funct.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_user_msg_ctrl_funct_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_user_msg_ctrl_funct_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_user_msg_gui.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_user_msg_gui.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_user_msg_gui_dbg.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_user_msg_gui_dbg.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_user_msg_gui_dbg_proto.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_user_msg_gui_dbg_proto.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_user_msg_prefs_ctrl.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_user_msg_prefs_ctrl.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_user_msg_prefs_ctrl.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_user_msg_prefs_ctrl.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_user_msg_prefs_gui.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_user_msg_prefs_gui.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_user_msg_prefs_view.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_user_msg_prefs_view.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_user_msg_prefs_view.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_user_msg_prefs_view.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_user_msg_view.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_user_msg_view.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_user_msg_view.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/avd_user_msg_view.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/gui_message_display.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/gui_message_display.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/user_msg.pri
+++ avida/current/source/qt-viewer/exp/exp_cleanup/user_msg/user_msg.pri

Index: avida/current/source/qt-viewer/exp/exp_cleanup2/CMakeLists.txt
+++ avida/current/source/qt-viewer/exp/exp_cleanup2/CMakeLists.txt

Index: avida/current/source/qt-viewer/exp/exp_cleanup2/avd_dbg_msgs.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup2/avd_dbg_msgs.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup2/avd_message_closure.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup2/avd_message_closure.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup2/avd_message_closure.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup2/avd_message_closure.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup2/avd_message_closure_t.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup2/avd_message_closure_t.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup2/avd_message_display.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup2/avd_message_display.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup2/avd_message_display.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup2/avd_message_display.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup2/avd_message_display_t.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup2/avd_message_display_t.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup2/avd_message_set_tracker.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup2/avd_message_set_tracker.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup2/avd_message_set_tracker.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup2/avd_message_set_tracker.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup2/avd_message_type_set.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup2/avd_message_type_set.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup2/demo_base_t.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup2/demo_base_t.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup2/main.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup2/main.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup2/template2_t.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup2/template2_t.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup2/template2_t.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup2/template2_t.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup2/template_t.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup2/template_t.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup2/template_t.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup2/template_t.hh

Index: avida/current/source/qt-viewer/exp/exp_cleanup2/xqt_test_case.cc
+++ avida/current/source/qt-viewer/exp/exp_cleanup2/xqt_test_case.cc

Index: avida/current/source/qt-viewer/exp/exp_cleanup2/xqt_test_case.hh
+++ avida/current/source/qt-viewer/exp/exp_cleanup2/xqt_test_case.hh

Index: avida/current/source/testsuites/qt_viewer_unit_testsuites/CMakeLists.txt
+++ avida/current/source/testsuites/qt_viewer_unit_testsuites/CMakeLists.txt

Index: avida/current/source/testsuites/qt_viewer_unit_testsuites/qt_test_case.cc
+++ avida/current/source/testsuites/qt_viewer_unit_testsuites/qt_test_case.cc

Index: avida/current/source/testsuites/qt_viewer_unit_testsuites/qt_test_case.hh
+++ avida/current/source/testsuites/qt_viewer_unit_testsuites/qt_test_case.hh

Index: avida/current/source/testsuites/qt_viewer_unit_testsuites/template.t.cc
+++ avida/current/source/testsuites/qt_viewer_unit_testsuites/template.t.cc

Index: avida/current/source/testsuites/qt_viewer_unit_testsuites/template.t.hh
+++ avida/current/source/testsuites/qt_viewer_unit_testsuites/template.t.hh

Index: avida/current/source/third-party/mockpp/CMakeLists.txt
+++ avida/current/source/third-party/mockpp/CMakeLists.txt
