Temp

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

@@ -79,6 +79,14 @@ private <T> void setConfigEntry(ConfigOption option, T value) throws ConfigExcep
     @Override
     public abstract String toString();
 
+    public String readableConfig() {
+        StringBuilder sb = new StringBuilder();
+        for  (ConfigEntry<?> entry : config) {
+            sb.append("Option: ").append(entry.option()).append("\tValue: ").append(entry.value()).append("\n");
+        }
+        return sb.toString();
+    }
+
     public abstract Mode mode();
 
     public LoggerHelper LOGGER() { return LOGGER; }

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

@@ -78,6 +78,7 @@ public EmptyInputSheetConfig(Arguments args, LoggerHelper logger) {
 
     @Override
     public String toString() { return "Empty Input Sheet Configuration"; }
+
     @Override
     public Mode mode() { return MODE; };
 }

src/main/java/org/awdevelopment/smithlab/data/Condition.java

@@ -1,18 +1,22 @@
 package org.awdevelopment.smithlab.data;
 
-import java.util.HashSet;
+import java.util.LinkedHashSet;
 import java.util.Set;
 
 public class Condition {
 
-    private final String name;
+    private String name;
     private final Set<Strain> strains;
     private final Set<Sample> samples;
 
     public Condition(String name) {
         this.name = name;
-        this.strains = new HashSet<>();
-        this.samples = new HashSet<>();
+        this.strains = new LinkedHashSet<>();
+        this.samples = new LinkedHashSet<>();
+    }
+
+    public void setName(String name) {
+        this.name = name;
     }
 
     public void addStrain(Strain strain) {
@@ -37,4 +41,6 @@ public Set<Sample> getSamples() {
     public String toString() {
         return name;
     }
+
+
 }

src/main/java/org/awdevelopment/smithlab/data/Strain.java

@@ -7,14 +7,15 @@
 public class Strain {
 
     private Condition condition;
-    private final String name;
+    private String name;
     private final Set<Sample> samples;
 
     public Strain(String name) {
         this.name = name;
         samples = new HashSet<>();
     }
 
+    public void setName(String name) { this.name = name; }
     public String getName() {
         return name;
     }
@@ -40,11 +41,18 @@ public boolean equals(Object obj) {
             return false;
         }
         Strain strain = (Strain) obj;
-        return name.equals(strain.name) && condition.equals(strain.condition);
+        if (condition == null) {
+            if (strain.condition != null) {
+                return false;
+            }
+        } else if (!condition.equals(strain.condition)) {
+            return false;
+        }
+        return name.equals(strain.name);
     }
 
     @Override
     public int hashCode() {
-        return name.hashCode() + condition.hashCode();
+        return name.hashCode() + (condition != null ? condition.hashCode() : 0);
     }
 }

src/main/java/org/awdevelopment/smithlab/data/experiment/EmptyExperiment.java

@@ -2,7 +2,6 @@
 
 import org.awdevelopment.smithlab.data.Condition;
 import org.awdevelopment.smithlab.data.Strain;
-import org.awdevelopment.smithlab.io.exceptions.NoDaysException;
 
 import java.util.Set;
 
@@ -17,85 +16,20 @@ public class EmptyExperiment extends AbstractExperiment {
     private final byte numDays;
     private final boolean usingNumDays;
 
-    public EmptyExperiment(Set<Strain> strains, Set<Condition> conditions, byte numReplicates, byte[] days, byte numDays) throws NoDaysException {
+    public EmptyExperiment(Set<Condition> conditions, Set<Strain> strains, byte numReplicates, byte numConditions,
+                           byte numStrains, boolean usingNumConditions, boolean usingNumStrains, byte[] days,
+                           byte numDays, boolean usingNumDays) {
         super(conditions, strains);
-        this.usingNumConditions = false;
-        this.usingNumStrains = false;
-        this.numConditions = (byte) conditions.size();
-        this.numStrains = (byte) strains.size();
         this.numReplicates = numReplicates;
-        if (numDays <= 0 && days.length == 0) throw new NoDaysException();
-        else {
-            usingNumDays = numDays > 0;
-            if (usingNumDays) {
-                this.days = new byte[numDays];
-                this.numDays = numDays;
-            } else {
-                this.days = days;
-                this.numDays = (byte) days.length;
-            }
-        }
-    }
-
-    public EmptyExperiment(byte numStrains, byte numConditions, byte numReplicates, byte[] days, byte numDays) throws NoDaysException {
-        super(null, null);
-        this.usingNumConditions = true;
-        this.usingNumStrains = true;
         this.numConditions = numConditions;
         this.numStrains = numStrains;
-        this.numReplicates = numReplicates;
-        if (numDays <= 0 && days.length == 0) throw new NoDaysException();
-        else {
-            usingNumDays = numDays > 0;
-            if (usingNumDays) {
-                this.days = new byte[numDays];
-                this.numDays = numDays;
-            } else {
-                this.days = days;
-                this.numDays = (byte) days.length;
-            }
-        }
-    }
-
-    public EmptyExperiment(Set<Strain> strains, byte numConditions, byte numReplicates, byte[] days, byte numDays) throws NoDaysException {
-        super(null, strains);
-        this.usingNumConditions = false;
-        this.usingNumStrains = true;
-        this.numConditions = numConditions;
-        this.numStrains = (byte) strains.size();
-        this.numReplicates = numReplicates;
-        if (numDays <= 0 && days.length == 0) throw new NoDaysException();
-        else {
-            usingNumDays = numDays > 0;
-            if (usingNumDays) {
-                this.days = new byte[numDays];
-                this.numDays = numDays;
-            } else {
-                this.days = days;
-                this.numDays = (byte) days.length;
-            }
-        }
+        this.usingNumConditions = usingNumConditions;
+        this.usingNumStrains = usingNumStrains;
+        this.days = days;
+        this.numDays = numDays;
+        this.usingNumDays = usingNumDays;
     }
 
-    public EmptyExperiment(byte numStrains, Set<Condition> conditions, byte numReplicates, byte[] days, byte numDays) throws NoDaysException {
-        super(conditions, null);
-        this.usingNumConditions = true;
-        this.usingNumStrains = false;
-        this.numConditions = (byte) conditions.size();
-        this.numStrains = numStrains;
-        this.numReplicates = numReplicates;
-        if (numDays <= 0 && days.length == 0) throw new NoDaysException();
-        else {
-            usingNumDays = numDays > 0;
-            if (usingNumDays) {
-                this.days = new byte[numDays];
-                this.numDays = numDays;
-            } else {
-                this.days = days;
-                this.numDays = (byte) days.length;
-            }
-        }
-    }
 
     public byte getNumReplicates() { return numReplicates; }
     public boolean hasNoDays() { return days.length == 0 && !usingNumDays; }
@@ -106,4 +40,37 @@ public EmptyExperiment(byte numStrains, Set<Condition> conditions, byte numRepli
     public boolean usingNumStrains() { return usingNumStrains; }
     public byte getNumConditions() { return numConditions; }
     public byte getNumStrains() { return numStrains; }
+
+    public String readableExperiment() {
+        StringBuilder sb = new StringBuilder();
+        sb.append("Experiment with ");
+        if (usingNumStrains) {
+            sb.append(numStrains).append(" strains, ");
+        } else {
+            StringBuilder strainsList = new StringBuilder();
+            for (Strain strain : strains()) { strainsList.append(strain.getName()).append(", "); }
+            strainsList.setLength(Math.max(strainsList.length() - 2, 0)); // Remove trailing comma and space, if any
+            sb.append(strains().size()).append(" strains (").append(strainsList).append("), ");
+        }
+        if (usingNumConditions) {
+            sb.append(numConditions).append(" conditions, ");
+        } else {
+            StringBuilder conditionsList = new StringBuilder();
+            for (Condition condition : conditions()) { conditionsList.append(condition.getName()).append(", "); }
+            conditionsList.setLength(Math.max(conditionsList.length() - 2, 0)); // Remove trailing comma and space, if any
+            sb.append(conditions().size()).append(" conditions (").append(conditionsList).append("), ");
+        }
+        sb.append(numReplicates).append(" replicates");
+        if (usingNumDays) {
+            sb.append(", ").append(numDays).append(" days.");
+        } else if (days.length > 0) {
+            sb.append(", days: ");
+            for (byte day : days) {
+                sb.append(day).append(" ");
+            }
+        } else {
+            sb.append(".");
+        }
+        return sb.toString();
+    }
 }

src/main/java/org/awdevelopment/smithlab/gui/SceneLoader.java

@@ -3,6 +3,7 @@
 import javafx.stage.Stage;
 import org.awdevelopment.smithlab.config.EmptyInputSheetConfig;
 import org.awdevelopment.smithlab.gui.controllers.AbstractLabelController;
+import org.awdevelopment.smithlab.gui.controllers.main.MainApplicationController;
 import org.awdevelopment.smithlab.logging.LoggerHelper;
 
 public class SceneLoader {
@@ -16,13 +17,17 @@ public static void loadScene(Stage stage, FXMLResourceType fxmlResourceType, Log
         stage.show();
     }
 
-    public static AbstractLabelController loadScene(Stage stage, FXMLResourceType fxmlResourceType, LoggerHelper logger, EmptyInputSheetConfig config) {
+    public static AbstractLabelController loadScene(Stage stage, FXMLResourceType fxmlResourceType, LoggerHelper logger,
+                                                    EmptyInputSheetConfig config,
+                                                    MainApplicationController mainController) {
         FXMLResource fxmlResource = FXMLResourceLoader.load(fxmlResourceType, logger);
         fxmlResource.controller().setLogger(logger);
         ((AbstractLabelController) fxmlResource.controller()).setConfig(config);
         fxmlResource.controller().setup();
         stage.setTitle(fxmlResourceType.getWindowTitle());
         stage.setScene(fxmlResource.scene());
+        AbstractLabelController controller = (AbstractLabelController) fxmlResource.controller();
+        controller.setMainController(mainController);
         stage.show();
         return (AbstractLabelController) fxmlResource.controller();
     }

src/main/java/org/awdevelopment/smithlab/gui/controllers/AbstractLabelController.java

@@ -1,18 +1,25 @@
 package org.awdevelopment.smithlab.gui.controllers;
 
 import org.awdevelopment.smithlab.config.EmptyInputSheetConfig;
+import org.awdevelopment.smithlab.gui.controllers.main.MainApplicationController;
 
 public abstract class AbstractLabelController extends AbstractController {
 
     private EmptyInputSheetConfig config;
+    private MainApplicationController mainController;
 
     public AbstractLabelController() { super(); }
 
     public void setConfig(EmptyInputSheetConfig config) {
         this.config = config;
     }
 
+    public void setMainController(MainApplicationController mainController) { this.mainController = mainController; }
+
     public EmptyInputSheetConfig config() {
         return config;
     }
+
+    public MainApplicationController getMainController() { return mainController; }
+
 }