First review

.gitignore

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+*.class
+
+.mtj.tmp/
+
+*.war
+*.ear
+
+hs_err_pid*
+log/
+target/
+

.project

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+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>Thermocycler</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+	</natures>
+</projectDescription>

.settings/org.eclipse.core.resources.prefs

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+eclipse.preferences.version=1
+encoding/<project>=UTF-8

.settings/org.eclipse.jdt.core.prefs

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+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
+org.eclipse.jdt.core.compiler.compliance=1.8
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.source=1.8

.settings/org.eclipse.jdt.ui.prefs

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+cleanup.add_default_serial_version_id=true
+cleanup.add_generated_serial_version_id=false
+cleanup.add_missing_annotations=true
+cleanup.add_missing_deprecated_annotations=true
+cleanup.add_missing_methods=false
+cleanup.add_missing_nls_tags=false
+cleanup.add_missing_override_annotations=true
+cleanup.add_missing_override_annotations_interface_methods=true
+cleanup.add_serial_version_id=false
+cleanup.always_use_blocks=true
+cleanup.always_use_parentheses_in_expressions=false
+cleanup.always_use_this_for_non_static_field_access=true
+cleanup.always_use_this_for_non_static_method_access=false
+cleanup.convert_functional_interfaces=false
+cleanup.convert_to_enhanced_for_loop=false
+cleanup.correct_indentation=true
+cleanup.format_source_code=true
+cleanup.format_source_code_changes_only=false
+cleanup.insert_inferred_type_arguments=false
+cleanup.make_local_variable_final=true
+cleanup.make_parameters_final=false
+cleanup.make_private_fields_final=true
+cleanup.make_type_abstract_if_missing_method=false
+cleanup.make_variable_declarations_final=false
+cleanup.never_use_blocks=false
+cleanup.never_use_parentheses_in_expressions=true
+cleanup.organize_imports=true
+cleanup.qualify_static_field_accesses_with_declaring_class=false
+cleanup.qualify_static_member_accesses_through_instances_with_declaring_class=true
+cleanup.qualify_static_member_accesses_through_subtypes_with_declaring_class=true
+cleanup.qualify_static_member_accesses_with_declaring_class=true
+cleanup.qualify_static_method_accesses_with_declaring_class=false
+cleanup.remove_private_constructors=true
+cleanup.remove_redundant_type_arguments=false
+cleanup.remove_trailing_whitespaces=true
+cleanup.remove_trailing_whitespaces_all=true
+cleanup.remove_trailing_whitespaces_ignore_empty=false
+cleanup.remove_unnecessary_casts=true
+cleanup.remove_unnecessary_nls_tags=true
+cleanup.remove_unused_imports=true
+cleanup.remove_unused_local_variables=false
+cleanup.remove_unused_private_fields=true
+cleanup.remove_unused_private_members=false
+cleanup.remove_unused_private_methods=true
+cleanup.remove_unused_private_types=true
+cleanup.sort_members=true
+cleanup.sort_members_all=false
+cleanup.use_anonymous_class_creation=false
+cleanup.use_blocks=false
+cleanup.use_blocks_only_for_return_and_throw=false
+cleanup.use_lambda=true
+cleanup.use_parentheses_in_expressions=false
+cleanup.use_this_for_non_static_field_access=true
+cleanup.use_this_for_non_static_field_access_only_if_necessary=false
+cleanup.use_this_for_non_static_method_access=false
+cleanup.use_this_for_non_static_method_access_only_if_necessary=true
+cleanup_profile=_DejanFullCleanup
+cleanup_settings_version=2
+eclipse.preferences.version=1

.settings/org.eclipse.m2e.core.prefs

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+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=true
+version=1

META-INF/MANIFEST.MF

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+Manifest-Version: 1.0
+Main-Class: com.codlex.thermocycler.view.ThermocyclerGUI
+

README.md

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+# raspberrypi-thermocycler
+After working for couple of months on arduino-thermocycler, we turned to Raspberry Pi to have more powerful machine and easier development in Java.

Thermocycler.iml

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+<?xml version="1.0" encoding="UTF-8"?>
+<module version="4">
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$">
+      <sourceFolder url="file://$MODULE_DIR$/src" isTestSource="false" />
+    </content>
+  </component>
+</module>

builds/1.0/ThermocyclerState.bin

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+55
+30
+5
+30
+24000
+15478

builds/1.0/deploy.sh

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+./killRemote.sh
+scp -r tc.jar pi@pi:~/tc/
+scp *.properties pi@pi:~/tc/
+scp *.sh pi@pi:~/tc/
+./startRemote.sh

builds/1.0/killRemote.sh

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+ssh pi@pi "sudo killall java"
+

builds/1.0/log4j.properties

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+log4j.rootLogger=DEBUG, ConsoleAppender, DebugFileAppender, ErrorFileAppender
+
+log4j.appender.ConsoleAppender=org.apache.log4j.ConsoleAppender
+log4j.appender.ConsoleAppender.layout=org.apache.log4j.PatternLayout
+log4j.appender.ConsoleAppender.layout.ConversionPattern=%-7p %d [%t] %c %x - %m%n
+
+log4j.appender.DebugFileAppender=org.apache.log4j.FileAppender
+log4j.appender.ErrorFileAppender.Threshold=DEBUG
+log4j.appender.DebugFileAppender.File=log/debug.log
+log4j.appender.DebugFileAppender.layout=org.apache.log4j.PatternLayout
+log4j.appender.DebugFileAppender.layout.ConversionPattern=%-7p %d [%t] %c %x - %m%n
+
+log4j.appender.ErrorFileAppender=org.apache.log4j.FileAppender
+log4j.appender.ErrorFileAppender.Threshold=ERROR
+log4j.appender.ErrorFileAppender.File=log/error.log
+log4j.appender.ErrorFileAppender.layout=org.apache.log4j.PatternLayout
+log4j.appender.ErrorFileAppender.layout.ConversionPattern=%-7p %d [%t] %c %x - %m%n

builds/1.0/settings.properties

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+Production = true
+FullScreen = false
+TranslationTimeMillis = 1500
+DistanceRefreshMillis = 1000
+TemperatureRefreshMillis = 1000
+
+# bath
+BathMinimumLevel = 60
+BathDepth = 20
+LevelEpsilon = 1
+TemperatureEpsilon = 1
+
+# hot bath
+HotBathLevelEchoPin = 4
+HotBathLevelTriggerPin = 3
+HotBathHeaterPin = 29
+HotBathWaterPump = 27
+HotBathCirculationWaterPump = 28
+
+# cold bath
+ColdBathLevelEchoPin = 1
+ColdBathLevelTriggerPin = 0
+ColdBathCoolerPin = 21
+ColdBathWaterPump = 25
+ColdBathEpsOn = 2
+ColdBathEpsOff = 5
+
+# translator 
+TranslatorPowerPin = 24
+ # indices for one wire
+TranslatorPulsePin = 22
+TranslatorToColdDirection = 26
+
+# validation
+ValidationCyclesRange = 1, 999999
+ValidationHotTemperatureRange = 20, 100
+ValidationColdTemperatureRange = -6, 20
+ValidationTimeRange = 1, 300
+
+# safety
+Safety = true
+SafetyHotBathTemperatureMax = 120
+SafetyLevelMin = 30
+SafetyLevelMax = 120

builds/1.0/start.sh

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+sudo service lightdm stop &
+# sudo java -jar -Dcom.sun.javafx.touch=true -Djavafx.platform=eglfb -Dcom.sun.javafx.isEmbedded=false Test.jar &
+sudo java -jar tc.jar &> log/startup.log &

builds/1.0/start2.sh

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+sudo service lightdm stop &
+# sudo java -jar -Dcom.sun.javafx.touch=true -Djavafx.platform=eglfb -Dcom.sun.javafx.isEmbedded=false Test.jar &
+sudo java -jar test.jar &> log/startup.log &

builds/1.0/startRemote.sh

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+ssh pi@pi "cd tc && ./start.sh"

builds/3.0/deploy.sh

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+./killRemote.sh
+scp *.jar pi@pi:~/tc3/
+scp *.properties pi@pi:~/tc3/
+scp *.sh pi@pi:~/tc3/
+./startRemote.sh

builds/3.0/killRemote.sh

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+ssh pi@pi "sudo killall java"
+

builds/3.0/log4j.properties

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+log4j.rootLogger=DEBUG, ConsoleAppender, DebugFileAppender, ErrorFileAppender
+
+log4j.appender.ConsoleAppender=org.apache.log4j.ConsoleAppender
+log4j.appender.ConsoleAppender.layout=org.apache.log4j.PatternLayout
+log4j.appender.ConsoleAppender.layout.ConversionPattern=%-7p %d [%t] %c %x - %m%n
+
+log4j.appender.DebugFileAppender=org.apache.log4j.FileAppender
+log4j.appender.ErrorFileAppender.Threshold=DEBUG
+log4j.appender.DebugFileAppender.File=log/debug.log
+log4j.appender.DebugFileAppender.layout=org.apache.log4j.PatternLayout
+log4j.appender.DebugFileAppender.layout.ConversionPattern=%-7p %d [%t] %c %x - %m%n
+
+log4j.appender.ErrorFileAppender=org.apache.log4j.FileAppender
+log4j.appender.ErrorFileAppender.Threshold=ERROR
+log4j.appender.ErrorFileAppender.File=log/error.log
+log4j.appender.ErrorFileAppender.layout=org.apache.log4j.PatternLayout
+log4j.appender.ErrorFileAppender.layout.ConversionPattern=%-7p %d [%t] %c %x - %m%n