[biosilico][ants][anthill] work on biosilio, common & crypto

README.md

@@ -4,7 +4,7 @@ Some ideas about Artificial Life, Creatures (game series) and Neural Networks. R
 
 Probably out-of-date for some reasons (but many ideas inside), codes from 2008-2012 (and before then) ; ideas I didn't continue for times spent reasons and I wish to continue (year 2020). 
 
-Tests and learning on coding / programming (Java, Perl, I did some HyperTalk / HyperCard before that long ago) ; some studies on biochemistry and video games (Myst, Marathon, and the first Creature game) then bioinformatics. Find some old code here !
+Tests and learning on coding / programming (Java, Perl, I did some HyperTalk / HyperCard before that long ago) ; some studies on biochemistry and video games (Myst, Marathon, and the first Creature game) then bioinformatics. Find some old code here ! And reviewed so far. 
 
 Some parts where done in Java 1.4 (before the Generics of Java 1.5) ! Some review for generics and some other for stream (Java 8 !). Adding some unit tests and more review !
 
@@ -14,7 +14,19 @@ Units Tests ; review...
 
 For dev on BioSilico : 
 
-* genetic execution / genes use  age and cycle (to avoid multiple instantiation of Brain / BrainLobe ++ execution of InitConcGene) : make good usage of age_min and age_max (0, 0) for initiation at start / 'birth'. 
+* genetic execution / genes use  age and cycle (to avoid multiple instantiation of Brain / BrainLobe ++ execution of InitConcGene) : make good usage of ageMin and ageMax (0, 0) for initiation at start / 'birth'. 
 * Design Patterns 'Builder' to make better implements
 * ... 
 
+## Common resources
+
+Some utils. Data (File, Directory, Filter), Structures, View... 
+
+## Ant Hill Example
+
+First Aim was to do / retake an example with Ants, ans some plants and fruits. Not totally from scratch / from nothing : it gives some ideas about how the engine could works. 
+
+## Creatures (Game Series) ressources
+
+Some (original) ideas comes from here, some articles, documentations, ressources...
+

biosilico-biosilico/src/main/java/gabywald/biosilico/anthill/Ant.java

@@ -0,0 +1,42 @@
+package gabywald.biosilico.anthill;
+
+import gabywald.biosilico.model.Organism;
+
+/**
+ * 
+ * @author Gabriel Chandesris (2009, 2020)
+ */
+public class Ant extends Organism {
+
+	public enum AntStatus {
+		EGG_LARVA, 	// (0, 1), 
+		WORKER, 	// (2, 3, 4, 5, 6, 7), 
+		SOLDIER, 	// (8), 
+		QUEEN; 		// (9);
+	}
+	/**
+	 * Status of ant. 
+	 * <p></p>
+	 * <ul>
+	 * <li><b>0-1</b> : Egg / Larva</li>
+	 * <li><b>2-7</b> : Worker</li>
+	 * <li><b>8</b> : Soldier</li>
+	 * <li><b>9</b> : Queen</li>
+	 * </ul>
+	 */
+	private int status;
+
+	/** Default constructor of an Ant agent (alive). */
+	public Ant() { 
+		super();
+		this.setAlive( true );
+		this.setEatable( false );
+		this.setMovable( false );
+
+		this.setNameCommon("Ant");
+		this.setOrganismType(OrganismType.BIOSILICO_ANIMA);
+
+		this.status		= 0; /** start with an egg. */
+	}
+
+}

biosilico-biosilico/src/main/java/gabywald/biosilico/anthill/AntBuilder.java

@@ -0,0 +1,85 @@
+package gabywald.biosilico.anthill;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import gabywald.biosilico.genetics.Gene;
+import gabywald.biosilico.genetics.builders.BiochemicalReactionBuilder;
+
+/**
+ * 
+ * @author Gabriel Chandesris (2020)
+ */
+public class AntBuilder {
+
+	public AntBuilder() {
+		;
+	}
+
+	public List<Gene> generateBasicGenome() {
+		List<Gene> toReturn = new ArrayList<Gene>();
+
+		// NOTEs :: 
+		// // // need some initial concentration !!
+		// // // need some biochemical reaction
+		// // // receptor for some variables from environment
+		// // // emitter for some variables from environment
+		// // // Decision to take fruits !
+		// // // Decision to drop fruits ! (in the AntHill)
+		// // // Decision to eat fruits !
+		// // // Decision to display pheromones !
+
+		// // // detection of pheromones !
+		// // // choice of destination :: movement !!
+
+
+		BiochemicalReactionBuilder brb = new BiochemicalReactionBuilder();
+		toReturn.add(brb.achem( 20 ).acoef( 1 )
+				.bchem( 21 ).bcoef( 1 )
+				.cchem( 22 ).ccoef( 1 )
+				.dchem( 23 ).dcoef( 1 )
+				.kmvm( 5 ).agemax(999).mutation(25).build());
+		toReturn.add(brb.achem( 22 ).acoef( 1 )
+				.bchem( 23 ).bcoef( 1 )
+				.cchem( 24 ).ccoef( 1 )
+				.dchem( 25 ).dcoef( 1 )
+				.kmvm( 5 ).agemax(999).mutation(25).build());
+		toReturn.add(brb.achem( 24 ).acoef( 1 )
+				.bchem( 25 ).bcoef( 1 )
+				.cchem( 26 ).ccoef( 1 )
+				.dchem( 27 ).dcoef( 1 )
+				.kmvm( 5 ).agemax(999).mutation(25).build());
+		toReturn.add(brb.achem( 26 ).acoef( 1 )
+				.bchem( 27 ).bcoef( 1 )
+				.cchem( 28 ).ccoef( 1 )
+				.dchem( 29 ).dcoef( 1 )
+				.kmvm( 5 ).agemax(999).mutation(25).build());
+		toReturn.add(brb.achem( 28 ).acoef( 1 )
+				.bchem( 29 ).bcoef( 1 )
+				.cchem( 30 ).ccoef( 1 )
+				.dchem( 31 ).dcoef( 1 )
+				.kmvm( 5 ).agemax(999).mutation(25).build());
+		toReturn.add(brb.achem( 30 ).acoef( 1 )
+				.bchem( 31 ).bcoef( 1 )
+				.cchem( 32 ).ccoef( 1 )
+				.dchem( 33 ).dcoef( 1 )
+				.kmvm( 5 ).agemax(999).mutation(25).build());
+		toReturn.add(brb.achem( 32 ).acoef( 1 )
+				.bchem( 33 ).bcoef( 1 )
+				.cchem( 34 ).ccoef( 1 )
+				.dchem( 35 ).dcoef( 1 )
+				.kmvm( 5 ).agemax(999).mutation(25).build());
+		toReturn.add(brb.achem( 34 ).acoef( 1 )
+				.bchem( 35 ).bcoef( 1 )
+				.cchem( 36 ).ccoef( 1 )
+				.dchem( 37 ).dcoef( 1 )
+				.kmvm( 5 ).agemax(999).mutation(25).build());
+		return toReturn;
+	}
+
+	public Ant build() {
+
+		return null;
+	}
+
+}

biosilico-biosilico/src/main/java/gabywald/biosilico/anthill/Fruit.java

@@ -0,0 +1,46 @@
+package gabywald.biosilico.anthill;
+
+import gabywald.biosilico.model.Chemicals;
+import gabywald.biosilico.model.Organism;
+
+/**
+ * This class defines a specific element which is not alive but can be move and eat by agents in the system. 
+ * <br />Produced by plants, do not do anything either. 
+ * @author Gabriel Chandesris (2009, 2020)
+ */
+public class Fruit extends Organism {
+
+	/**
+	 * Default constructor for Fruit.
+	 */
+	public Fruit() { 
+		super();
+		this.setAlive( false );
+		this.setEatable( true );
+		this.setMovable( true );
+
+		this.setNameCommon("Fruit");
+		this.setOrganismType(OrganismType.BIOSILICO_VIRIDITA);
+	}
+
+	/**
+	 * Constructor of a Fruit which have only one variable to feed.  
+	 * @param var (int)
+	 * @param val (int)
+	 * @see Chemicals#setVarPlus(int, int)
+	 */
+	public Fruit(int var, int val) { 
+		this();
+		this.variables.setVarPlus(var, val);
+	}
+
+	/** 
+	 * Constructor with pre-established Variables set. 
+	 * @param toFeed (Chemicals)
+	 */
+	public Fruit(Chemicals toFeed) {
+		this();
+		this.variables = toFeed;
+	}
+
+}

biosilico-biosilico/src/main/java/gabywald/biosilico/anthill/Plant.java

@@ -0,0 +1,26 @@
+package gabywald.biosilico.anthill;
+
+import gabywald.biosilico.model.Organism;
+
+/**
+ * This class describes plants which produce fruits. 
+ * @author Gabriel Chandesris (2009, 2020)
+ * @see Fruit
+ */
+public class Plant extends Organism {
+
+	/** Default Constructor. */
+	public Plant() { 
+		super();
+		this.setAlive( true );
+		this.setEatable( false );
+		this.setMovable( false );
+
+		this.setNameCommon("Plant");
+		this.setOrganismType(OrganismType.BIOSILICO_VIRIDITA);
+
+		// ***** Here creation of 'egg' => create fruits !
+
+	}
+
+}

biosilico-biosilico/src/main/java/gabywald/biosilico/anthill/PlantBuilder.java

@@ -0,0 +1,131 @@
+package gabywald.biosilico.anthill;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import gabywald.biosilico.genetics.Gene;
+import gabywald.biosilico.genetics.builders.BiochemicalReactionBuilder;
+import gabywald.biosilico.genetics.builders.InitialConcentrationBuilder;
+
+/**
+ * 
+ * @author Gabriel Chandesris (2020)
+ */
+public class PlantBuilder {
+
+	public PlantBuilder() {
+		;
+	}
+
+	public List<Gene> generateBasicGenome() {
+		List<Gene> toReturn = new ArrayList<Gene>();
+
+		// NOTEs :: 
+		// // // need some initial concentration !!
+		// // // need some biochemical reaction
+		// // // receptor for some variables from environment
+		// // // emitter for some variables from environment
+		// // // Decision to make fruits !
+
+		InitialConcentrationBuilder icb	= new InitialConcentrationBuilder();
+		toReturn.add( icb.varia( 0 ).value( 100 ).agemin( 0 ).agemax( 0 ).mutation(25).build() );
+
+		BiochemicalReactionBuilder brb = new BiochemicalReactionBuilder();
+		toReturn.add(brb.achem( 0 ).acoef( 1 )
+				.bchem( 1 ).bcoef( 1 )
+				.cchem( 2 ).ccoef( 1 )
+				.dchem( 3 ).dcoef( 1 )
+				.kmvm( 5 ).agemax(999).mutation(25).build());
+		toReturn.add(brb.achem( 2 ).acoef( 1 )
+				.bchem( 3 ).bcoef( 1 )
+				.cchem( 4 ).ccoef( 1 )
+				.dchem( 5 ).dcoef( 1 )
+				.kmvm( 5 ).agemax(999).mutation(25).build());
+		toReturn.add(brb.achem( 4 ).acoef( 1 )
+				.bchem( 5 ).bcoef( 1 )
+				.cchem( 6 ).ccoef( 1 )
+				.dchem( 7 ).dcoef( 1 )
+				.kmvm( 5 ).agemax(999).mutation(25).build());
+		toReturn.add(brb.achem( 6 ).acoef( 1 )
+				.bchem( 7 ).bcoef( 1 )
+				.cchem( 8 ).ccoef( 1 )
+				.dchem( 9 ).dcoef( 1 )
+				.kmvm( 5 ).agemax(999).mutation(25).build());
+		toReturn.add(brb.achem( 8 ).acoef( 1 )
+				.bchem( 9 ).bcoef( 1 )
+				.cchem( 10 ).ccoef( 1 )
+				.dchem( 11 ).dcoef( 1 )
+				.kmvm( 5 ).agemax(999).mutation(25).build());
+		toReturn.add(brb.achem( 10 ).acoef( 1 )
+				.bchem( 11 ).bcoef( 1 )
+				.cchem( 12 ).ccoef( 1 )
+				.dchem( 13 ).dcoef( 1 )
+				.kmvm( 5 ).agemax(999).mutation(25).build());
+		toReturn.add(brb.achem( 12 ).acoef( 1 )
+				.bchem( 13 ).bcoef( 1 )
+				.cchem( 14 ).ccoef( 1 )
+				.dchem( 15 ).dcoef( 1 )
+				.kmvm( 5 ).agemax(999).mutation(25).build());
+		toReturn.add(brb.achem( 14 ).acoef( 1 )
+				.bchem( 15 ).bcoef( 1 )
+				.cchem( 16 ).ccoef( 1 )
+				.dchem( 17 ).dcoef( 1 )
+				.kmvm( 5 ).agemax(999).mutation(25).build());
+		toReturn.add(brb.achem( 16 ).acoef( 1 )
+				.bchem( 17 ).bcoef( 1 )
+				.cchem( 18 ).ccoef( 1 )
+				.dchem( 19 ).dcoef( 1 )
+				.kmvm( 5 ).agemax(999).mutation(25).build());
+		toReturn.add(brb.achem( 18 ).acoef( 1 )
+				.bchem( 19 ).bcoef( 1 )
+				.cchem( 20 ).ccoef( 1 )
+				.dchem( 21 ).dcoef( 1 )
+				.kmvm( 5 ).agemax(999).mutation(25).build());
+		toReturn.add(brb.achem( 20 ).acoef( 1 )
+				.bchem( 21 ).bcoef( 1 )
+				.cchem( 22 ).ccoef( 1 )
+				.dchem( 23 ).dcoef( 1 )
+				.kmvm( 5 ).agemax(999).mutation(25).build());
+		toReturn.add(brb.achem( 22 ).acoef( 1 )
+				.bchem( 23 ).bcoef( 1 )
+				.cchem( 24 ).ccoef( 1 )
+				.dchem( 25 ).dcoef( 1 )
+				.kmvm( 5 ).agemax(999).mutation(25).build());
+		toReturn.add(brb.achem( 24 ).acoef( 1 )
+				.bchem( 25 ).bcoef( 1 )
+				.cchem( 26 ).ccoef( 1 )
+				.dchem( 27 ).dcoef( 1 )
+				.kmvm( 5 ).agemax(999).mutation(25).build());
+		toReturn.add(brb.achem( 26 ).acoef( 1 )
+				.bchem( 27 ).bcoef( 1 )
+				.cchem( 28 ).ccoef( 1 )
+				.dchem( 29 ).dcoef( 1 )
+				.kmvm( 5 ).agemax(999).mutation(25).build());
+		toReturn.add(brb.achem( 28 ).acoef( 1 )
+				.bchem( 29 ).bcoef( 1 )
+				.cchem( 30 ).ccoef( 1 )
+				.dchem( 31 ).dcoef( 1 )
+				.kmvm( 5 ).agemax(999).mutation(25).build());
+		toReturn.add(brb.achem( 30 ).acoef( 1 )
+				.bchem( 31 ).bcoef( 1 )
+				.cchem( 32 ).ccoef( 1 )
+				.dchem( 33 ).dcoef( 1 )
+				.kmvm( 5 ).agemax(999).mutation(25).build());
+		toReturn.add(brb.achem( 32 ).acoef( 1 )
+				.bchem( 33 ).bcoef( 1 )
+				.cchem( 34 ).ccoef( 1 )
+				.dchem( 35 ).dcoef( 1 )
+				.kmvm( 5 ).agemax(999).mutation(25).build());
+		toReturn.add(brb.achem( 34 ).acoef( 1 )
+				.bchem( 35 ).bcoef( 1 )
+				.cchem( 36 ).ccoef( 1 )
+				.dchem( 37 ).dcoef( 1 )
+				.kmvm( 5 ).agemax(999).mutation(25).build());
+		return toReturn;
+	}
+
+	public Plant build() {
+
+		return null;
+	}
+}

biosilico-biosilico/src/main/java/gabywald/biosilico/data/FilterBioSilico.java

@@ -18,7 +18,7 @@ public class FilterBioSilico extends FilterUtils {
 
 	/** Default Constructor. */
 	public FilterBioSilico() {
-		super(FilterType.NONE, "BioSilico Files");
+		super(FilterGroupType.NONE, "BioSilico Files");
 		/** super();this.emptyListe(); */
 		this.addExtension(FilterBioSilico.ph2);
 		this.addExtension(FilterBioSilico.gatorg);