Colony counting

.gitignore

@@ -2545,3 +2545,4 @@ bin/
 /javafx/src/javafx.web/javafx/scene/web/WebView.java
 /javafx/src/javafx.web/module-info.java
 /javafx/src.zip
+/test_output/ynb.xlsx

src/main/java/module-info.java

@@ -19,4 +19,11 @@
     opens org.awdevelopment.smithlab.gui to javafx.fxml, javafx.graphics, javafx.controls;
     opens org.awdevelopment.smithlab.gui.controllers to javafx.fxml, javafx.graphics, javafx.controls;
     opens org.awdevelopment.smithlab to javafx.fxml, javafx.graphics, javafx.controls;
+    exports org.awdevelopment.smithlab.config.exceptions;
+    opens org.awdevelopment.smithlab.config to javafx.controls, javafx.fxml, javafx.graphics;
+    exports org.awdevelopment.smithlab.gui.controllers.main;
+    opens org.awdevelopment.smithlab.gui.controllers.main to javafx.controls, javafx.fxml, javafx.graphics;
+    exports org.awdevelopment.smithlab.gui.controllers.main.validatable_field;
+    opens org.awdevelopment.smithlab.gui.controllers.main.validatable_field to javafx.controls, javafx.fxml, javafx.graphics;
+    opens org.awdevelopment.smithlab.logging to javafx.controls, javafx.fxml, javafx.graphics;
 }

src/main/java/org/awdevelopment/smithlab/MainApplication.java

@@ -3,8 +3,9 @@
 import javafx.stage.Stage;
 import org.apache.logging.log4j.LogManager;
 import org.awdevelopment.smithlab.args.Arguments;
-import org.awdevelopment.smithlab.config.Config;
+import org.awdevelopment.smithlab.config.EmptyInputSheetConfig;
 import org.awdevelopment.smithlab.config.Mode;
+import org.awdevelopment.smithlab.config.OutputSheetsConfig;
 import org.awdevelopment.smithlab.data.experiment.Experiment;
 import org.awdevelopment.smithlab.gui.FXMLResourceType;
 import org.awdevelopment.smithlab.gui.SceneLoader;
@@ -21,15 +22,16 @@ public static void main(String[] args) {
         if (args.length == 0) launch();
         else {
             Arguments arguments = new Arguments(args, LOGGER);
-            Config config = new Config(arguments);
             try {
-                if (config.mode() == Mode.GENERATE_EMPTY_INPUT_SHEET) {
-                    OutputGenerator outputGenerator = new OutputGenerator(config, LOGGER);
+                if (arguments.getMode() == Mode.GENERATE_EMPTY_INPUT_SHEET) {
+                    EmptyInputSheetConfig config = new EmptyInputSheetConfig(arguments, LOGGER);
+                    OutputGenerator outputGenerator = new OutputGenerator(config);
                     outputGenerator.generateEmptyInputSheet();
-                } else if (config.mode() == Mode.GENERATE_OUTPUT_SHEETS) {
+                } else if (arguments.getMode() == Mode.GENERATE_OUTPUT_SHEETS) {
+                    OutputSheetsConfig config = new OutputSheetsConfig(arguments, LOGGER);
+                    OutputGenerator outputGenerator = new OutputGenerator(config);
                     InputReader reader = new InputReader(config, LOGGER);
                     Experiment experiment = reader.readExperimentData();
-                    OutputGenerator outputGenerator = new OutputGenerator(config, LOGGER);
                     outputGenerator.generateOutput(experiment);
                 }
             } catch (Exception ignored) {

src/main/java/org/awdevelopment/smithlab/args/Arguments.java

@@ -1,7 +1,7 @@
 package org.awdevelopment.smithlab.args;
 
 import org.awdevelopment.smithlab.args.exceptions.*;
-import org.awdevelopment.smithlab.config.ConfigDefault;
+import org.awdevelopment.smithlab.config.ConfigDefaults;
 import org.awdevelopment.smithlab.config.Mode;
 import org.awdevelopment.smithlab.config.SampleLabelingType;
 import org.awdevelopment.smithlab.config.SortOption;
@@ -21,25 +21,25 @@ public class Arguments {
 
     private final LoggerHelper LOGGER;
 
-    private OutputType outputType = ConfigDefault.OUTPUT_TYPE;
-    private Mode mode = ConfigDefault.MODE;
-    private boolean writeToDifferentFile = ConfigDefault.WRITE_TO_DIFFERENT_FILE;
-    private String outputFileName = ConfigDefault.OUTPUT_FILENAME;
-    private File inputFile = ConfigDefault.INPUT_FILE;
-    private SortOption outputSorting = ConfigDefault.SORT_OPTION;
-    private byte replicateNumber = ConfigDefault.NUMBER_OF_REPLICATES;
-    private String emptyInputSheetName = ConfigDefault.EMPTY_INPUT_SHEET_NAME;
-    private Set<Condition> conditions = ConfigDefault.CONDITIONS;
-    private Set<Strain> strains = ConfigDefault.STRAINS;
-    private Set<Byte> days = ConfigDefault.DAYS;
-    private byte numDays = ConfigDefault.NUM_DAYS;
-    private boolean includeBaselineColumn = ConfigDefault.INCLUDE_BASELINE_COLUMN;
-    private SampleLabelingType sampleLabelingType = ConfigDefault.SAMPLE_LABELING_TYPE;
-    private byte numConditions = ConfigDefault.NUM_CONDITIONS;
-    private byte numStrains = ConfigDefault.NUM_STRAINS;
-    private boolean usingNumDays = ConfigDefault.USING_NUM_DAYS;
-    private boolean usingNumConditions = ConfigDefault.USING_NUM_CONDITIONS;
-    private boolean usingNumStrains = ConfigDefault.USING_NUM_STRAINS;
+    private OutputType outputType = ConfigDefaults.OUTPUT_TYPE;
+    private Mode mode = ConfigDefaults.MODE;
+    private boolean writeToDifferentFile = ConfigDefaults.WRITE_TO_DIFFERENT_FILE;
+    private String outputFileName = ConfigDefaults.OUTPUT_FILENAME;
+    private File inputFile = ConfigDefaults.INPUT_FILE;
+    private SortOption outputSorting = ConfigDefaults.SORT_OPTION;
+    private byte replicateNumber = ConfigDefaults.NUMBER_OF_REPLICATES;
+    private String emptyInputSheetName = ConfigDefaults.EMPTY_INPUT_SHEET_NAME;
+    private Set<Condition> conditions = ConfigDefaults.CONDITIONS;
+    private Set<Strain> strains = ConfigDefaults.STRAINS;
+    private Set<Byte> days = ConfigDefaults.DAYS;
+    private byte numDays = ConfigDefaults.NUM_DAYS;
+    private boolean includeBaselineColumn = ConfigDefaults.INCLUDE_BASELINE_COLUMN;
+    private SampleLabelingType sampleLabelingType = ConfigDefaults.SAMPLE_LABELING_TYPE;
+    private byte numConditions = ConfigDefaults.NUM_CONDITIONS;
+    private byte numStrains = ConfigDefaults.NUM_STRAINS;
+    private boolean usingNumDays = ConfigDefaults.USING_NUM_DAYS;
+    private boolean usingNumConditions = ConfigDefaults.USING_NUM_CONDITIONS;
+    private boolean usingNumStrains = ConfigDefaults.USING_NUM_STRAINS;
 
     public Arguments(String[] args, LoggerHelper logger) {
         this.LOGGER = logger;
@@ -160,7 +160,7 @@ else if (outputFileName.equals(inputFile.getPath())) {
             }
         }
         if (replicateNumber == -1) {
-            if (outputType == OutputType.BOTH || outputType == OutputType.STATISTICAL_TESTS) {
+            if (outputType == OutputType.BOTH || outputType == OutputType.OASIS) {
                 throw new NoReplicatesProvidedException(outputType);
             } else {
                 LOGGER.atWarn("No replicate number provided. " +

src/main/java/org/awdevelopment/smithlab/config/AbstractConfig.java

@@ -0,0 +1,85 @@
+package org.awdevelopment.smithlab.config;
+
+import org.awdevelopment.smithlab.config.exceptions.ConfigException;
+import org.awdevelopment.smithlab.config.exceptions.ConfigOptionNotFoundException;
+import org.awdevelopment.smithlab.config.exceptions.WrongObjectTypeException;
+import org.awdevelopment.smithlab.logging.LoggerHelper;
+
+import java.util.HashSet;
+import java.util.Optional;
+import java.util.Set;
+
+public abstract class AbstractConfig {
+
+    private final Set<ConfigEntry<?>> config;
+    private final LoggerHelper LOGGER;
+
+    protected AbstractConfig(LoggerHelper logger) {
+        this.config = new HashSet<>();
+        this.LOGGER = logger;
+        config.add(new ConfigEntry<>(ConfigOption.GUI, ConfigDefaults.GUI));
+    }
+
+    public <T> T get(ConfigOption option) {
+        try {
+            return getConfigEntryValue(option);
+        } catch (ConfigException e) {
+            LOGGER().atFatal(e.getMessage());
+            System.exit(1);
+        }
+        return null;
+    }
+
+    public <T> void set(ConfigOption option, T value) {
+        try {
+            setConfigEntry(option, value);
+        } catch (ConfigException e) {
+            LOGGER().atFatal(e.getMessage());
+            System.exit(1);
+        }
+    }
+
+    protected <T> void addConfigEntry(ConfigEntry<T> entry) {
+        config.add(entry);
+    }
+
+    private Optional<ConfigEntry<?>> getConfigEntry(ConfigOption option) {
+        return config.stream().filter(e -> e.option().equals(option)).findFirst();
+    }
+
+    private <T> T getConfigEntryValue(ConfigOption option) throws ConfigException {
+        Optional<ConfigEntry<?>> entryOptional = getConfigEntry(option);
+        if (entryOptional.isPresent()) {
+            ConfigEntry<T> typedEntry;
+            try {
+                typedEntry = (ConfigEntry<T>) entryOptional.get();
+            } catch (ClassCastException e) {
+                throw new WrongObjectTypeException(entryOptional.get(), this);
+            }
+            return typedEntry.value();
+        } else {
+            throw new ConfigOptionNotFoundException(option, this);
+        }
+    }
+
+
+    private <T> void setConfigEntry(ConfigOption option, T value) throws ConfigException {
+        Optional<ConfigEntry<?>> entryOptional = getConfigEntry(option);
+        if (entryOptional.isPresent()) {
+            ConfigEntry<T> typedEntry;
+            try { typedEntry = (ConfigEntry<T>) entryOptional.get(); }
+            catch (ClassCastException e) { throw new WrongObjectTypeException(entryOptional.get(), this); }
+            typedEntry.setValue(value);
+        } else throw new ConfigOptionNotFoundException(option, this);
+    }
+
+    public boolean GUI() { return get(ConfigOption.GUI); }
+    public void setGUI(boolean GUI) { set(ConfigOption.GUI, GUI); }
+
+    @Override
+    public abstract String toString();
+
+    public abstract Mode mode();
+
+    public LoggerHelper LOGGER() { return LOGGER; }
+}

src/main/java/org/awdevelopment/smithlab/config/ConfigDefault.java → src/main/java/org/awdevelopment/smithlab/config/ConfigDefaults.java

@@ -8,10 +8,12 @@
 import java.util.HashSet;
 import java.util.Set;
 
-public class ConfigDefault {
+public class ConfigDefaults {
 
     public static final byte NUM_DAYS = 0;
+    public static final Object GUI = Boolean.TRUE;
     private static final String DEFAULT_FILENAME = "Spreadsheet Formatter Output.xlsx";
+    public static final String EMPTY_INPUT_SHEET_FILENAME = "Empty Data Entry Sheet.xlsx";
     public static final OutputType OUTPUT_TYPE = OutputType.BOTH;
     public static final String OUTPUT_FILENAME = DEFAULT_FILENAME;
     public static final Mode MODE = Mode.GENERATE_OUTPUT_SHEETS;