Code Refactor - Disentangle domain setup and run configuration

src/main/java/nl/uu/cs/ape/APE.java

@@ -25,19 +25,19 @@
 import nl.uu.cs.ape.configuration.APERunConfig;
 import nl.uu.cs.ape.configuration.tags.validation.ValidationResults;
 import nl.uu.cs.ape.constraints.ConstraintTemplate;
-import nl.uu.cs.ape.domain.APEDimensionsException;
-import nl.uu.cs.ape.domain.APEDomainSetup;
-import nl.uu.cs.ape.domain.OWLReader;
 import nl.uu.cs.ape.models.MappingsException;
 import nl.uu.cs.ape.models.enums.SynthesisFlag;
 import nl.uu.cs.ape.models.logic.constructs.TaxonomyPredicate;
 import nl.uu.cs.ape.solver.SynthesisEngine;
+import nl.uu.cs.ape.solver.domainconfiguration.APEDimensionsException;
+import nl.uu.cs.ape.solver.domainconfiguration.Domain;
 import nl.uu.cs.ape.solver.minisat.SATSynthesisEngine;
 import nl.uu.cs.ape.solver.solutionStructure.SolutionWorkflow;
 import nl.uu.cs.ape.solver.solutionStructure.SolutionsList;
 import nl.uu.cs.ape.solver.solutionStructure.cwl.DefaultCWLCreator;
 import nl.uu.cs.ape.utils.APEFiles;
 import nl.uu.cs.ape.utils.APEUtils;
+import nl.uu.cs.ape.utils.OWLReader;
 
 /**
  * The {@code APE} class is the main class of the library and is supposed to be
@@ -52,7 +52,7 @@ public class APE implements APEInterface {
 	private final APECoreConfig config;
 
 	/** Object containing general APE encoding. */
-	private APEDomainSetup apeDomainSetup;
+	private Domain apeDomainSetup;
 
 	/**
 	 * Create instance of the APE solver.
@@ -125,7 +125,7 @@ private boolean setupDomain() throws APEDimensionsException, IOException, OWLOnt
 		 * Encode the taxonomies as objects - generate the list of all types / modules
 		 * occurring in the taxonomies defining their submodules/subtypes
 		 */
-		apeDomainSetup = new APEDomainSetup(config);
+		apeDomainSetup = new Domain(config);
 
 		OWLReader owlReader = new OWLReader(apeDomainSetup, config.getOntologyFile());
 		boolean ontologyRead = owlReader.readOntology();
@@ -185,7 +185,7 @@ public APECoreConfig getConfig() {
 	 * @return The object that contains all crucial information about the domain
 	 *         (e.g. list of tools, data types, constraint factory, etc.)
 	 */
-	public APEDomainSetup getDomainSetup() {
+	public Domain getDomainSetup() {
 		return apeDomainSetup;
 	}
 
@@ -284,7 +284,7 @@ public SolutionsList runSynthesis(APERunConfig runConfig) throws IOException, JS
 	 *                       file.
 	 * @throws JSONException Error in configuration object.
 	 */
-	private SolutionsList runSynthesis(JSONObject runConfigJson, APEDomainSetup apeDomainSetup)
+	private SolutionsList runSynthesis(JSONObject runConfigJson, Domain apeDomainSetup)
 			throws IOException, JSONException, APEConfigException {
 		apeDomainSetup.clearConstraints();
 		APERunConfig runConfig = new APERunConfig(runConfigJson, apeDomainSetup);

src/main/java/nl/uu/cs/ape/APEInterface.java

@@ -11,8 +11,8 @@
 import nl.uu.cs.ape.configuration.APECoreConfig;
 import nl.uu.cs.ape.configuration.APERunConfig;
 import nl.uu.cs.ape.constraints.ConstraintTemplate;
-import nl.uu.cs.ape.domain.APEDomainSetup;
 import nl.uu.cs.ape.models.logic.constructs.TaxonomyPredicate;
+import nl.uu.cs.ape.solver.domainconfiguration.Domain;
 import nl.uu.cs.ape.solver.solutionStructure.SolutionsList;
 
 /**
@@ -45,7 +45,7 @@ public interface APEInterface {
 	 * @return The object that contains all crucial information about the domain
 	 *         (e.g. list of tools, data types, constraint factory, etc.)
 	 */
-	public APEDomainSetup getDomainSetup();
+	public Domain getDomainSetup();
 
 	/**
 	 * Returns all the taxonomy elements that are subclasses of the given element.

src/main/java/nl/uu/cs/ape/Main.java

@@ -27,8 +27,15 @@ public class Main {
      * The entry point of application when the library is used in a Command Line
      * Interface (CLI).
      *
-     * @param args APE expects at most one (1) argument: The absolute or relative
-     *             path to the configuration file.
+     * @param args APE expects at most two (2) arguments: <br/>
+     *             <br/>
+     *             (1) the absolute or relative path to the configuration file.<br/>
+     *             <br/>
+     *             (2) the maximum number of solutions to be returned.
+     * 
+     *             Note: If no arguments are provided, the default configuration
+     *             file on location ./config.json is used.
+     * 
      */
     public static void main(String[] args) {
         String path;

src/main/java/nl/uu/cs/ape/automaton/Block.java

@@ -14,7 +14,7 @@ public class Block {
      * States that comprise this block. Number of stater correspond to the max
      * number of inputs or outputs.
      */
-    private List<State> typeStates;
+    private final List<State> typeStates;
 
     /**
      * Order number of the block in the solution.
@@ -27,7 +27,7 @@ public class Block {
      * @param blockNumber The block number.
      */
     public Block(int blockNumber) {
-        typeStates = new ArrayList<State>();
+        typeStates = new ArrayList<>();
         this.blockNumber = blockNumber;
     }
 

src/main/java/nl/uu/cs/ape/automaton/ModuleAutomaton.java

@@ -19,7 +19,7 @@
  */
 public class ModuleAutomaton implements Automaton {
 
-    private List<State> moduleStates;
+    private final List<State> moduleStates = new ArrayList<>();
 
     /**
      * Generate the Module State automatons based on the defined length.
@@ -31,7 +31,6 @@ public class ModuleAutomaton implements Automaton {
      *                        modules).
      */
     public ModuleAutomaton(int automataBound, int inputBranching, int outputBranching) {
-        moduleStates = new ArrayList<State>();
         automataBound = Math.max(automataBound, 1);
 
         for (int i = 1; i <= automataBound; i++) {

src/main/java/nl/uu/cs/ape/automaton/State.java

@@ -1,7 +1,7 @@
 package nl.uu.cs.ape.automaton;
 
 import nl.uu.cs.ape.models.enums.AtomType;
-import nl.uu.cs.ape.models.logic.constructs.PredicateLabel;
+import nl.uu.cs.ape.models.logic.constructs.Predicate;
 
 /***
  * The {@code State} class is used to represent the states in module and type
@@ -15,7 +15,7 @@
  *
  * @author Vedran Kasalica
  */
-public class State implements PredicateLabel, StateInterface {
+public class State implements Predicate, StateInterface {
 
     /** Unique name of the state */
     private final String stateName;
@@ -98,7 +98,7 @@ public boolean equals(Object obj) {
      *         before than, equal to, or after than the specified State.
      */
     @Override
-    public int compareTo(PredicateLabel other) {
+    public int compareTo(Predicate other) {
         if (!(other instanceof State)) {
             return this.getPredicateID().compareTo(other.getPredicateID());
         }

src/main/java/nl/uu/cs/ape/automaton/TypeAutomaton.java

@@ -27,13 +27,13 @@ public class TypeAutomaton implements Automaton {
      * Blocks of data types that are being added to the memory (usually outputs from
      * the tools, apart from the initial workflow input).
      */
-    private List<Block> memoryTypesAutomaton;
+    private final List<Block> memoryTypesAutomaton = new ArrayList<>();
 
     /**
      * Blocks of data types that are being used by tools from the memory (inputs to
      * the tools).
      */
-    private List<Block> usedTypesAutomaton;
+    private final List<Block> usedTypesAutomaton = new ArrayList<>();
 
     /**
      * State is used in order to represent no state.
@@ -54,8 +54,6 @@ public class TypeAutomaton implements Automaton {
      *                        modules)
      */
     public TypeAutomaton(int automataBound, int inputBranching, int outputBranching) {
-        memoryTypesAutomaton = new ArrayList<Block>();
-        usedTypesAutomaton = new ArrayList<Block>();
         nullState = new State(null, null, -1, inputBranching, outputBranching);
 
         automataBound = automataBound < 1 ? 1 : automataBound;
@@ -224,7 +222,7 @@ public Block getMemoryTypesBlock(int i) {
      * @return List of memory States.
      */
     public List<State> getMemoryStatesUntilBlockNo(int maxBlockNo) {
-        List<State> untilStates = new ArrayList<State>();
+        List<State> untilStates = new ArrayList<>();
         for (int i = 0; i <= maxBlockNo && i < this.usedTypesAutomaton.size(); i++) {
             Block currBlock = this.getMemoryTypesBlock(i);
             for (State currState : currBlock.getStates()) {
@@ -244,7 +242,7 @@ public List<State> getMemoryStatesUntilBlockNo(int maxBlockNo) {
      * @return List of Type States.
      */
     public List<State> getAllStatesUntilBlockNo(int maxBlockNo) {
-        List<State> untilStates = new ArrayList<State>();
+        List<State> untilStates = new ArrayList<>();
         for (int i = 0; i <= maxBlockNo && i < this.usedTypesAutomaton.size(); i++) {
             Block currBlock = this.usedTypesAutomaton.get(i);
             for (State currState : currBlock.getStates()) {
@@ -268,7 +266,7 @@ public List<State> getAllStatesUntilBlockNo(int maxBlockNo) {
      * @return List of Memory Type States.
      */
     public List<State> getAllMemoryStatesUntilBlockNo(int maxBlockNo) {
-        List<State> untilStates = new ArrayList<State>();
+        List<State> untilStates = new ArrayList<>();
         for (int i = 0; i <= maxBlockNo && i < this.usedTypesAutomaton.size(); i++) {
             Block currBlock = this.memoryTypesAutomaton.get(i);
             for (State currState : currBlock.getStates()) {
@@ -287,7 +285,7 @@ public List<State> getAllMemoryStatesUntilBlockNo(int maxBlockNo) {
      * @return List of memory States.
      */
     public List<State> getMemoryStatesAfterBlockNo(int minBlockNo) {
-        List<State> afterStates = new ArrayList<State>();
+        List<State> afterStates = new ArrayList<>();
         for (int i = minBlockNo + 1; i < this.memoryTypesAutomaton.size(); i++) {
             Block currBlock = this.getMemoryTypesBlock(i);
             for (State currState : currBlock.getStates()) {
@@ -307,7 +305,7 @@ public List<State> getMemoryStatesAfterBlockNo(int minBlockNo) {
      * @return List of Used States.
      */
     public List<State> getUsedStatesAfterBlockNo(int minBlockNo) {
-        List<State> afterStates = new ArrayList<State>();
+        List<State> afterStates = new ArrayList<>();
         for (int i = minBlockNo + 1; i < this.usedTypesAutomaton.size(); i++) {
             Block currBlock = this.usedTypesAutomaton.get(i);
             for (State currState : currBlock.getStates()) {
@@ -324,7 +322,7 @@ public List<State> getUsedStatesAfterBlockNo(int minBlockNo) {
      */
     @Override
     public List<State> getAllStates() {
-        List<State> allStates = new ArrayList<State>();
+        List<State> allStates = new ArrayList<>();
         for (Block currBlock : getAllBlocks()) {
             for (State currState : currBlock.getStates()) {
                 allStates.add(currState);
@@ -339,7 +337,7 @@ public List<State> getAllStates() {
      * @return List of memory type states.
      */
     public List<State> getAllMemoryTypesStates() {
-        List<State> allMemoryStates = new ArrayList<State>();
+        List<State> allMemoryStates = new ArrayList<>();
         for (Block currBlock : getMemoryTypesBlocks()) {
             for (State currState : currBlock.getStates()) {
                 allMemoryStates.add(currState);
@@ -354,7 +352,7 @@ public List<State> getAllMemoryTypesStates() {
      * @return List of used type states.
      */
     public List<State> getAllUsedTypesStates() {
-        List<State> allUsedStates = new ArrayList<State>();
+        List<State> allUsedStates = new ArrayList<>();
         for (Block currBlock : getUsedTypesBlocks()) {
             for (State currState : currBlock.getStates()) {
                 allUsedStates.add(currState);

src/main/java/nl/uu/cs/ape/configuration/APECoreConfig.java

@@ -11,10 +11,10 @@
 import nl.uu.cs.ape.configuration.tags.APEConfigTags;
 import nl.uu.cs.ape.configuration.tags.APEConfigTagFactory.TAGS.*;
 import nl.uu.cs.ape.configuration.tags.validation.ValidationResults;
-import nl.uu.cs.ape.domain.APEDimensionsException;
+import nl.uu.cs.ape.solver.domainconfiguration.APEDimensionsException;
 import nl.uu.cs.ape.utils.APEFiles;
 import nl.uu.cs.ape.utils.APEUtils;
-import nl.uu.cs.ape.domain.OWLReader;
+import nl.uu.cs.ape.utils.OWLReader;
 
 import java.io.File;
 import java.io.IOException;

src/main/java/nl/uu/cs/ape/configuration/APERunConfig.java

@@ -11,11 +11,11 @@
 import nl.uu.cs.ape.configuration.tags.APEConfigTags;
 import nl.uu.cs.ape.configuration.tags.APEConfigTagFactory.TAGS.*;
 import nl.uu.cs.ape.configuration.tags.validation.ValidationResults;
-import nl.uu.cs.ape.domain.APEDomainSetup;
 import nl.uu.cs.ape.models.Range;
 import nl.uu.cs.ape.models.Type;
 import nl.uu.cs.ape.models.enums.ConfigEnum;
 import nl.uu.cs.ape.models.enums.SolverType;
+import nl.uu.cs.ape.solver.domainconfiguration.Domain;
 
 import java.io.IOException;
 import java.nio.file.Path;
@@ -99,12 +99,12 @@ public class APERunConfig {
     /**
      * Input types of the workflow.
      */
-    private final APEConfigDependentTag.One<List<Type>, APEDomainSetup> PROGRAM_INPUTS = new APEConfigTagFactory.TAGS.PROGRAM_INPUTS(
+    private final APEConfigDependentTag.One<List<Type>, Domain> PROGRAM_INPUTS = new APEConfigTagFactory.TAGS.PROGRAM_INPUTS(
             this::getApeDomainSetup);
     /**
      * Output types of the workflow.
      */
-    private final APEConfigDependentTag.One<List<Type>, APEDomainSetup> PROGRAM_OUTPUTS = new APEConfigTagFactory.TAGS.PROGRAM_OUTPUTS(
+    private final APEConfigDependentTag.One<List<Type>, Domain> PROGRAM_OUTPUTS = new APEConfigTagFactory.TAGS.PROGRAM_OUTPUTS(
             this::getApeDomainSetup);
     /**
      * All the Tags specified in this class. Should be in correct order of
@@ -153,10 +153,7 @@ public class APERunConfig {
      * Object containing domain information needed for the execution.
      */
     @Getter
-    private APEDomainSetup apeDomainSetup;
-
-    /** Solver type that should be used (SAT). */
-    private SolverType solverType = SolverType.SAT;
+    private Domain apeDomainSetup;
 
     /**
      * Constructor used to implement the Builder Pattern.
@@ -189,10 +186,10 @@ private APERunConfig(Builder builder) {
 
     /**
      * Private constructor used by
-     * {@link APERunConfig#validate(JSONObject config, APEDomainSetup setup)}
+     * {@link APERunConfig#validate(JSONObject config, Domain setup)}
      * to create an empty instance.
      */
-    private APERunConfig(APEDomainSetup setup) {
+    private APERunConfig(Domain setup) {
         this.apeDomainSetup = setup;
     }
 
@@ -206,7 +203,7 @@ private APERunConfig(APEDomainSetup setup) {
      * @param setup the domain setup
      * @return the validation results
      */
-    public static ValidationResults validate(JSONObject json, APEDomainSetup setup) {
+    public static ValidationResults validate(JSONObject json, Domain setup) {
         APERunConfig dummy = new APERunConfig(setup);
         ValidationResults results = new ValidationResults();
         for (APEConfigTag<?> tag : dummy.all_tags) {
@@ -229,7 +226,7 @@ public static ValidationResults validate(JSONObject json, APEDomainSetup setup)
      * @throws JSONException      Error in parsing the configuration file.
      * @throws APEConfigException Error in setting up the the configuration.
      */
-    public APERunConfig(JSONObject runConfiguration, APEDomainSetup apeDomainSetup)
+    public APERunConfig(JSONObject runConfiguration, Domain apeDomainSetup)
             throws IOException, JSONException, APEConfigException {
 
         /* JSONObject must have been parsed correctly. */
@@ -577,22 +574,6 @@ public void setSolutionLength(int solutionMinLength, int solutionMaxLength) {
         this.SOLUTION_LENGTH_RANGE.setValue(Range.of(solutionMinLength, solutionMaxLength));
     }
 
-    /**
-     * Gets the Solver type that should be used for solving.
-     * 
-     * @return {@link SolverType} that corresponds to the solver type
-     */
-    public SolverType getSolverType() {
-        return this.solverType;
-    }
-
-    /**
-     * @param solverType the solverType to set
-     */
-    public void setSolverType(SolverType solverType) {
-        this.solverType = solverType;
-    }
-
     /**
      * Creates interface for the min length of {@link APERunConfig}.
      */
@@ -624,7 +605,7 @@ public interface IMaxNoSolutionsStage {
      * Creates interface to setup the domain of {@link APERunConfig}.
      */
     public interface IApeDomainSetupStage {
-        IBuildStage withApeDomainSetup(APEDomainSetup apeDomainSetup);
+        IBuildStage withApeDomainSetup(Domain apeDomainSetup);
     }
 
     /**
@@ -671,7 +652,7 @@ public static final class Builder implements ISolutionMinLengthStage, ISolutionM
         private int solutionMinLength;
         private int solutionMaxLength;
         private int maxNoSolutions;
-        private APEDomainSetup apeDomainSetup;
+        private Domain apeDomainSetup;
         private JSONArray constraintsJSON;
         private boolean toolSeqRepeat;
         private String solutionDirPath;
@@ -708,7 +689,7 @@ public IApeDomainSetupStage withMaxNoSolutions(int maxNoSolutions) {
         }
 
         @Override
-        public IBuildStage withApeDomainSetup(APEDomainSetup apeDomainSetup) {
+        public IBuildStage withApeDomainSetup(Domain apeDomainSetup) {
             this.apeDomainSetup = apeDomainSetup;
             return this;
         }