Changeset 78

Timestamp:

01/09/13 00:09:10 (12 years ago)

Author:

psniegowski

Message:

Add f0 parsing and f0->Model transformation.

Location:

java/main

Files:

• pom.xml (modified) (2 diffs)
• src/main/java/com/framsticks/core/Entity.java (modified) (3 diffs)
• src/main/java/com/framsticks/core/EntityListener.java (deleted)
• src/main/java/com/framsticks/core/EntityOwner.java (added)
• src/main/java/com/framsticks/core/Instance.java (modified) (9 diffs)
• src/main/java/com/framsticks/core/LocalInstance.java (modified) (2 diffs)
• src/main/java/com/framsticks/core/Parameters.java (modified) (2 diffs)
• src/main/java/com/framsticks/core/Program.java (modified) (6 diffs)
• src/main/java/com/framsticks/diagnostics/Diagnostics.java (modified) (1 diff)
• src/main/java/com/framsticks/dumping/FileInstance.java (modified) (1 diff)
• src/main/java/com/framsticks/dumping/SaveStream.java (modified) (4 diffs)
• src/main/java/com/framsticks/examples (added)
• src/main/java/com/framsticks/examples/GenotypeBrowser.java (added)
• src/main/java/com/framsticks/gui/Browser.java (modified) (1 diff)
• src/main/java/com/framsticks/gui/Frame.java (modified) (3 diffs)
• src/main/java/com/framsticks/gui/TreeNode.java (modified) (4 diffs)
• src/main/java/com/framsticks/hosting/ServerInstance.java (modified) (3 diffs)
• src/main/java/com/framsticks/model/BaseJoint.java (added)
• src/main/java/com/framsticks/model/BaseNeuro.java (added)
• src/main/java/com/framsticks/model/BasePart.java (added)
• src/main/java/com/framsticks/model/Creature.java (modified) (4 diffs)
• src/main/java/com/framsticks/model/F0Genotype.java (added)
• src/main/java/com/framsticks/model/F0Model.java (added)
• src/main/java/com/framsticks/model/Genotype.java (modified) (4 diffs)
• src/main/java/com/framsticks/model/Joint.java (modified) (1 diff)
• src/main/java/com/framsticks/model/MechJoint.java (modified) (1 diff)
• src/main/java/com/framsticks/model/MechPart.java (modified) (1 diff)
• src/main/java/com/framsticks/model/Neuro.java (modified) (2 diffs)
• src/main/java/com/framsticks/model/NeuroDef.java (modified) (3 diffs)
• src/main/java/com/framsticks/model/Package.java (added)
• src/main/java/com/framsticks/model/Part.java (modified) (3 diffs)
• src/main/java/com/framsticks/observers/Observer.java (modified) (2 diffs)
• src/main/java/com/framsticks/params/AccessInterface.java (modified) (2 diffs)
• src/main/java/com/framsticks/params/FramsClass.java (modified) (6 diffs)
• src/main/java/com/framsticks/params/ListAccess.java (modified) (1 diff)
• src/main/java/com/framsticks/params/Param.java (modified) (1 diff)
• src/main/java/com/framsticks/params/PropertiesAccess.java (modified) (2 diffs)
• src/main/java/com/framsticks/params/ReflectionAccess.java (modified) (7 diffs)
• src/main/java/com/framsticks/params/Registry.java (added)
• src/main/java/com/framsticks/params/SimpleAbstractAccess.java (modified) (3 diffs)
• src/main/java/com/framsticks/params/Util.java (modified) (2 diffs)
• src/main/java/com/framsticks/parsers/F0Parser.java (added)
• src/main/java/com/framsticks/parsers/FileSource.java (modified) (2 diffs)
• src/main/java/com/framsticks/parsers/Parser.java (deleted)
• src/main/java/com/framsticks/parsers/Schema.java (modified) (18 diffs)
• src/main/java/com/framsticks/portals/Portal.java (modified) (1 diff)
• src/main/java/com/framsticks/util/Exceptions.java (added)
• src/main/java/com/framsticks/util/Orientation.java (modified) (1 diff)
• src/main/java/com/framsticks/util/Point3d.java (modified) (3 diffs)
• src/main/java/com/framsticks/util/ProgramArguments.java (deleted)
• src/main/java/com/framsticks/viewer (added)
• src/main/java/com/framsticks/viewer/SimpleViewer.java (added)
• src/main/java/com/framsticks/visualization/Viewer.java (modified) (5 diffs)
• src/main/resources/configs/framsticks.properties (modified) (2 diffs)
• src/main/resources/configs/log4j.properties (modified) (2 diffs)
• src/main/resources/examples (added)
• src/main/resources/examples/f0_example.txt (added)
• src/main/resources/info (added)
• src/main/resources/info/Creature.info (added)
• src/main/resources/info/Genotype.info (added)
• src/main/resources/info/Joint.info (added)
• src/main/resources/info/MechJoint.info (added)
• src/main/resources/info/MechPart.info (added)
• src/main/resources/info/Neuro.info (added)
• src/main/resources/info/NeuroDef.info (added)
• src/main/resources/info/Part.info (added)
• src/main/resources/parsers (added)
• src/main/resources/parsers/f0def.xml (added)
• src/test/java (added)
• src/test/java/com (added)
• src/test/java/com/framsticks (added)
• src/test/java/com/framsticks/parsers (added)
• src/test/java/com/framsticks/parsers/F0ParserTest.java (added)
• src/test/resources (added)
• src/test/resources/log4j.properties (added)
• src/test/resources/parsers (added)
• src/test/resources/parsers/f0_example.txt (added)

java/main/pom.xml

@@ -15 +15 @@
                 </repository>
         </repositories>
-
+        <properties>
+                <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        </properties>
         <build>
                 <plugins>
@@ -58 +60 @@
                         <version>1.5.2</version>
                 </dependency>
+
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <version>4.8.1</version>
+            <scope>test</scope>
+        </dependency>
                 <!--dependency>
                 </dependency>

java/main/src/main/java/com/framsticks/core/Entity.java

@@ -4 +4 @@
 import com.framsticks.util.Thread;
 import org.apache.log4j.Logger;
-
-import java.util.HashSet;
-import java.util.Set;
 
 /**
@@ -37 +34 @@
     }
 
-    public final void configurePublic() {
+    public final void configurePublic() throws Exception {
         configure();
     }
 
-    protected void configure() {
+    protected void configure() throws Exception {
 
     }
@@ -58 +55 @@
     }
 
+        public final void done() {
+                LOGGER.info("stopping entity");
+                if (owner != null) {
+                        owner.onDone();
+                }
+        }
+
 
 }

java/main/src/main/java/com/framsticks/core/Instance.java

@@ -23 +23 @@
     protected Node root;
 
-        protected final Map<String, FramsClass> infoCache = new HashMap<String, FramsClass>();
     public Set<InstanceListener> listeners = new HashSet<InstanceListener>();
 
@@ -34 +33 @@
     protected void run() {
         super.run();
-        registerTypicalReflectedClasses();
+                com.framsticks.model.Package.register(registry);
     }
 
     @Override
-    protected void configure() {
+    protected void configure() throws Exception {
         super.configure();
     }
 
-    protected abstract void fetchInfo(Path path, Future<FramsClass> future);
-    public abstract void resolve(Path path, Future<Path> future);
-    public abstract void fetchValue(Path path, Param param, StateFunctor stateFunctor);
-    public abstract void fetchValues(Path path, StateFunctor stateFunctor);
-    protected abstract void tryRegisterOnChangeEvents(Path path);
+    protected void fetchInfo(Path path, Future<FramsClass> future) {
+                future.result(null, new UnsupportedOperationException());
+        }
+
+        public void resolve(Path path, Future<Path> future) {
+                assert isActive();
+                assert path.isOwner(this);
+                if (path.getTop().getObject() != null) {
+                        future.result(path, null);
+                        return;
+                }
+                AccessInterface access = bindAccess(path.getUnder());
+                Object object = access.get(path.getTop().getParam(), Object.class);
+                if (object == null) {
+                        future.result(path, null);
+                        return;
+                }
+                future.result(path.appendResolution(object), null);
+        }
+
+    public void fetchValue(Path path, Param param, StateFunctor stateFunctor) {
+                stateFunctor.call(null);
+        }
+
+    public void fetchValues(Path path, StateFunctor stateFunctor) {
+                stateFunctor.call(null);
+        }
+
+    protected void tryRegisterOnChangeEvents(Path path) {
+
+        }
 
         public void storeValue(Path path, Param param, Object value, final StateFunctor stateFunctor) {
@@ -98 +123 @@
         }
 
-        public void putInfoIntoCache(FramsClass framsClass) {
-        assert isActive();
-        if (infoCache.containsKey(framsClass.getId())) {
-            LOGGER.info("already cached " + framsClass);
-            return;
-        }
-        LOGGER.debug("caching info for " + framsClass);
-                infoCache.put(framsClass.getId(), framsClass);
-        }
 
     public final FramsClass getInfoFromCache(Path path) {
@@ -115 +131 @@
     public FramsClass getInfoFromCache(String id) {
         assert isActive();
-        if (id == null) {
-                        return null;
-                }
-        if (infoCache.containsKey(id)) {
-            return infoCache.get(id);
-        }
-                return null;
-        }
-
-        protected final Map<String, Class> reflectedClasses = new HashMap<String, Class>();
-
-    public final void registerReflectedClass(String name, String className) {
-        assert isActive();
-        try {
-            registerReflectedClass(name, Class.forName(className));
-        } catch (ClassNotFoundException e) {
-            LOGGER.fatal("class not found during registration: " + e);
-        }
-    }
-
-    public void registerReflectedClass(String name, Class reflectedClass) {
-        assert isActive();
-        reflectedClasses.put(name, reflectedClass);
-        }
+                return registry.getInfoFromCache(id);
+        }
+
+        protected Registry registry = new Registry();
 
         public AccessInterface createAccess(String name) {
@@ -150 +146 @@
                 }
 
-                if (reflectedClasses.containsKey(name)) {
-                        return new ReflectionAccess(reflectedClasses.get(name), framsClass);
-                }
-
-                return new PropertiesAccess(framsClass);
+                return registry.createAccess(name, framsClass);
         }
 
@@ -188 +180 @@
         AccessInterface access = prepareAccess(node.getParam());
         if (access == null) {
+                        LOGGER.error("missing access for: " + node.getParam());
             return null;
         }
@@ -287 +280 @@
             }
         }
-        putInfoIntoCache(framsClass);
+        registry.putInfoIntoCache(framsClass);
         return framsClass;
     }
@@ -338 +331 @@
     }
 
-    public void registerTypicalReflectedClasses() {
-        registerReflectedClass("MechPart", "com.framsticks.model.MechPart");
-        registerReflectedClass("Joint", "com.framsticks.model.Joint");
-        registerReflectedClass("MechJoint", "com.framsticks.model.MechJoint");
-        registerReflectedClass("Neuro", "com.framsticks.model.Neuro");
-        registerReflectedClass("NeuroDef", "com.framsticks.model.NeuroDef");
-        registerReflectedClass("Part", "com.framsticks.model.Part");
-        registerReflectedClass("Creature", "com.framsticks.model.Creature");
-        registerReflectedClass("Genotype", "com.framsticks.model.Genotype");
-    }
-
     public static Iterator<String> splitPath(String path) {
         List<String> list = new LinkedList<String>();
@@ -359 +341 @@
     }
 
+        public Registry getRegistry() {
+                return registry;
+        }
 }
+

java/main/src/main/java/com/framsticks/core/LocalInstance.java

@@ -45 +45 @@
 
     @Override
-    protected void configure() {
+    protected void configure() throws Exception {
         super.configure();
     }
@@ -97 +97 @@
     }
 
-
-
-    @Override
-    public void resolve(Path path, Future<Path> future) {
-        assert isActive();
-        assert path.isOwner(this);
-        if (path.getTop().getObject() != null) {
-            future.result(path, null);
-            return;
-        }
-        AccessInterface access = bindAccess(path.getUnder());
-        Object object = access.get(path.getTop().getParam(), Object.class);
-        if (object == null) {
-            future.result(path, null);
-            return;
-        }
-        future.result(path.appendResolution(object), null);
-    }
-
-
-    @Override
-    public void fetchValue(Path path, Param param, StateFunctor stateFunctor) {
-        stateFunctor.call(null);
-    }
-
-    @Override
-    public void fetchValues(Path path, StateFunctor stateFunctor) {
-        stateFunctor.call(null);
-    }
-
-
 }

java/main/src/main/java/com/framsticks/core/Parameters.java

@@ -12 +12 @@
     protected String name;
     protected Dispatcher dispatcher;
+        protected EntityOwner owner;
 
-    public Parameters(Configuration config, String name, Dispatcher dispatcher) {
+
+
+    public Parameters(Configuration config, String name, Dispatcher dispatcher, EntityOwner owner) {
         this.config = config;
         this.name = name;
         this.dispatcher = dispatcher;
+                this.owner = owner;
     }
 
@@ -23 +27 @@
         name = parameters.name;
         dispatcher = parameters.dispatcher;
+                owner = parameters.owner;
     }
 

java/main/src/main/java/com/framsticks/core/Program.java

@@ -6 +6 @@
 import org.apache.log4j.Logger;
 import org.apache.log4j.PropertyConfigurator;
-import sun.misc.Signal;
-import sun.misc.SignalHandler;
+//import sun.misc.Signal;
+//import sun.misc.SignalHandler;
 
 import java.lang.reflect.Constructor;
@@ -19 +19 @@
     private final static Logger LOGGER = Logger.getLogger(Program.class.getName());
 
+/*
     protected SignalHandler signalHandler = new SignalHandler() {
         @Override
@@ -26 +27 @@
         }
     };
+*/
 
     protected Entity entity;
@@ -34 +36 @@
     public Program(String name) {
         super(name, java.lang.Thread.currentThread());
-        Signal.handle(new Signal("INT"), signalHandler);
-        Signal.handle(new Signal("TERM"), signalHandler);
+//        Signal.handle(new Signal("INT"), signalHandler);
+//        Signal.handle(new Signal("TERM"), signalHandler);
     }
 
@@ -44 +46 @@
             Class type = Class.forName(typeName);
             Constructor constructor = type.getConstructor(Parameters.class);
-            Entity entity = (Entity) constructor.newInstance(parameters);
-            return entity;
+            return (Entity) constructor.newInstance(parameters);
         } catch (Exception e) {
             LOGGER.error("failed to instantiate: " + e);
@@ -96 +97 @@
         }
 
-        entity = configureEntity(new Parameters(config.subset("com.framsticks.entity"), "main", null));
-        entity.configurePublic();
+        entity = configureEntity(new Parameters(config.subset("com.framsticks.entity"), "main", null, new EntityOwner() {
+                        @Override
+                        public void onDone() {
+                                LOGGER.info("exiting");
+                                Runtime.getRuntime().exit(0);
+                        }
+                }));
+                try {
+                entity.configurePublic();
+                } catch (Exception e) {
+                        LOGGER.fatal("exception caught during configuration: " + e);
+                }
         LOGGER.info("all entities were configured");
         entity.start();

java/main/src/main/java/com/framsticks/diagnostics/Diagnostics.java

@@ -23 +23 @@
 
     @Override
-    protected void configure() {
+    protected void configure() throws Exception {
 
         super.configure();

java/main/src/main/java/com/framsticks/dumping/FileInstance.java

@@ -53 +53 @@
     }
 
-
-    @Override
-    protected void fetchInfo(Path path, Future<FramsClass> future) {
-        future.result(null, new UnsupportedOperationException());
-    }
-
-    @Override
-    protected void tryRegisterOnChangeEvents(Path path) {
-    }
-
-
     @Override
     public String toString() {

java/main/src/main/java/com/framsticks/dumping/SaveStream.java

@@ -37 +37 @@
         this.instance = instance;
         this.stateFunctor = stateFunctor;
-        dispatched = 1;
-        write(root);
+                dispatchWrite(root);
     }
+
+        protected void dispatchWrite(final Path path) {
+                ++dispatched;
+                instance.invokeLater(new Runnable() {
+                        @Override
+                        public void run() {
+                                write(path);
+                        }
+                });
+        }
 
     protected void finished() {
@@ -53 +62 @@
         } else {
             AccessInterface access = instance.bindAccess(path);
+                        assert access != null;
             FramsClass framsClass = access.getFramsClass();
             assert framsClass != null;
@@ -76 +86 @@
                     final Path childPath = path.appendNode(new Node(childParam, access.get(childParam, Object.class)));
                     if (childPath.isResolved() && instance.getInfoFromCache(childPath) != null) {
-                        ++dispatched;
-                        instance.invokeLater(new Runnable() {
-                            @Override
-                            public void run() {
-                                write(childPath);
-                            }
-                        });
+                                                dispatchWrite(childPath);
                     }
                 }
@@ -92 +96 @@
         }
     }
-
-
 }

java/main/src/main/java/com/framsticks/gui/Browser.java

@@ -45 +45 @@
 
     @Override
-    protected void configure() {
+    protected void configure() throws Exception {
         super.configure();
     }

java/main/src/main/java/com/framsticks/gui/Frame.java

@@ -1 +1 @@
 package com.framsticks.gui;
 
+import com.framsticks.core.Node;
 import com.framsticks.core.Path;
 import com.framsticks.gui.view.*;
@@ -12 +13 @@
 import javax.swing.tree.*;
 import java.awt.*;
+import java.awt.datatransfer.StringSelection;
 import java.awt.event.ActionEvent;
 import java.awt.event.MouseAdapter;
@@ -75 +77 @@
         treePopupMenu.add(new JMenuItem("Refresh"));
         treePopupMenu.add(new JMenuItem("Open in new frame as root"));
+                addNodeActionToTreePopupMenu("Copy path to clipboard", new NodeAction() {
+                        @Override
+                        public void actionPerformed(TreeNode treeNode) {
+                                Path path = treeNode.getInstancePath();
+                                StringSelection selection = new StringSelection(path.toString());
+                                getToolkit().getSystemClipboard().setContents(selection, selection);
+                        }
+                });
         //this.add(createMenuItem("Add to favourites", null));
         //this.add(createMenuItem("Remove from favourites", null));

java/main/src/main/java/com/framsticks/gui/TreeNode.java

@@ -124 +124 @@
         LOGGER.debug("updating children of " + this);
         AccessInterface access = p.getInstance().bindAccess(p.getTop());
+                if (access == null) {
+                        return;
+                }
         final List<Path> childrenPaths = new LinkedList<Path>();
         /**Prepare path for each child.*/
@@ -210 +213 @@
     }
 
-
         public final Panel getPanel() {
         assert frame.isActive();
@@ -222 +224 @@
         }
         AccessInterface access = p.getInstance().bindAccess(p);
-        assert access != null;
+                if (access == null) {
+                        return;
+                }
         StringBuilder t = new StringBuilder();
         /** html formatting is used here, since tooltips in swing do not support simple \n line breaks */
@@ -494 +498 @@
 
                 return true;
+        }
+
+        public Path getInstancePath() {
+                assert frame.isActive();
+                return path;
         }
 

java/main/src/main/java/com/framsticks/hosting/ServerInstance.java

@@ -30 +30 @@
 
     @Override
-    protected void configure() {
+    protected void configure() throws Exception {
         super.configure();
 
-        Parameters p = new Parameters(config.subset("hosted.entity"), "hosted", this);
+        Parameters p = new Parameters(config.subset("hosted.entity"), "hosted", this, null);
         hosted = Program.configureEntity(p);
         if (hosted == null) {
@@ -49 +49 @@
             return null;
         }
-        if (infoCache.containsKey(id)) {
-            return infoCache.get(id);
+                FramsClass cached = registry.getInfoFromCache(id);
+        if (cached != null) {
+                        return cached;
         }
         try {
@@ -56 +57 @@
             FramsClass framsClass = new FramsClass.Constructor(nativeClass, id).getResult();
 
-            registerReflectedClass(id, nativeClass);
-            putInfoIntoCache(framsClass);
+            registry.registerReflectedClass(null, id, nativeClass);
+            registry.putInfoIntoCache(framsClass);
             return framsClass;
         } catch (ClassNotFoundException ignored) {

java/main/src/main/java/com/framsticks/model/Creature.java

@@ -1 +1 @@
 package com.framsticks.model;
 
-import com.framsticks.model.MechPart;
-import com.framsticks.model.Joint;
+import com.framsticks.params.FramsClass;
+import com.framsticks.util.Orientation;
 import com.framsticks.util.Point3d;
 
@@ -8 +8 @@
 import java.util.List;
 
-public class Creature {
+public class Creature extends F0Model {
         public String name;
 
@@ -94 +94 @@
         public void setVertpos(Double c_vertpos) { averageVerticalPosition = c_vertpos; }
 
-        public Point3d position = new Point3d();
+        /** pos_x, pos_y, pos_z*/
+        public double pos_x, pos_y, pos_z;
 
-        public Double getPos_x() { return position.x; }
-        public void setPos_x(Double pos_x) { position.x = pos_x; }
+        public Point3d getPosition() { return new Point3d(pos_x, pos_y, pos_z) ; }
+        public void setPosition(Point3d pos) { pos_x = pos.x; pos_y = pos.y; pos_z = pos.z; }
 
-        public Double getPos_y() { return position.y; }
-        public void setPos_y(Double pos_y) { position.y = pos_y; }
+        public double size_x, size_y, size_z;
 
-        public Double getPos_z() { return position.z; }
-        public void setPos_z(Double pos_z) { position.z = pos_z; }
+        public Point3d getBoundingBox() { return new Point3d(size_x, size_y, size_z) ; }
+        public void setBoundingBox(Point3d size) { size_x = size.x; size_y = size.y; size_z = size.z; }
 
-        public Point3d boundingBox = new Point3d();
-        public Double getSize_x() { return boundingBox.x; }
-        public void setSize_x(Double size_x) { boundingBox.x = size_x; }
 
-        public Double getSize_y() { return boundingBox.y; }
-        public void setSize_y(Double size_y) { boundingBox.y = size_y; }
+        /** center_x, center_y, center_z*/
+        public double center_x, center_y, center_z;
 
-        public Double getSize_z() { return boundingBox.z; }
-        public void setSize_z(Double size_z) { boundingBox.z = size_z; }
-
-        public Point3d center = new Point3d();
-
-        public Double getCenter_x() { return center.x; }
-        public void setCenter_x(Double center_x) { center.x = center_x; }
-
-        public Double getCenter_y() { return center.y; }
-        public void setCenter_y(Double center_y) { center.y = center_y; }
-
-        public Double getCenter_z() { return center.z; }
-        public void setCenter_z(Double center_z) { center.z = center_z; }
+        public Point3d getCenter() { return new Point3d(center_x, center_y, center_z) ; }
+        public void setCenter(Point3d center) { center_x = center.x; center_y = center.y; center_z = center.z; }
 
         public Integer getNumparts() { return parts.size(); }
@@ -161 +147 @@
         public final List<NeuroDef> neurodefs = new ArrayList<NeuroDef>();
 
-        public final List<MechPart> mechparts = new ArrayList<MechPart>();
-        public final List<MechJoint> mechjoints = new ArrayList<MechJoint>();
-        public final List<Neuro> neurons = new ArrayList<Neuro>();
+
+
+        public final List<Part> getParts() { return parts; }
+        public final List<Joint> getJoints() { return joints; }
+        public final List<NeuroDef> getNeuroDefs() { return neurodefs; }
 
 
 
+        public static void constructFramsClass(FramsClass.Constructor constructor) {
+                constructor.field("name");
+                constructor.field("parts");
+                constructor.field("joints");
+                constructor.field("neurodefs");
+        }
+
 }

java/main/src/main/java/com/framsticks/model/Genotype.java

@@ -2 +2 @@
 
 
-import com.framsticks.util.Containers;
+import org.apache.log4j.Logger;
 
-import java.util.ArrayList;
-import java.util.List;
+public class Genotype extends F0Genotype {
+        private final static Logger LOGGER = Logger.getLogger(Genotype.class);
 
-public class Genotype {
         public String name;
         public String genotype;
@@ -15 +14 @@
         public Double getSimi() { return similarity; }
         public void setSimi(Double simi) { similarity = simi; }
-
-        public Double startingEnergy;
-        public Double getEnerg0() { return startingEnergy; }
-        public void setEnerg0(Double energ0) { startingEnergy = energ0; }
 
         public Double brainConnections;
@@ -40 +35 @@
         public Double velocity;
         public Double distance;
-
 
         public Double verticalVelocity;
@@ -78 +72 @@
         public String uid;
 
-        public final List<Part> parts = new ArrayList<Part>();
-        public final List<Joint> joints = new ArrayList<Joint>();
-        public final List<NeuroDef> neurodefs = new ArrayList<NeuroDef>();
+}
 
-
-    public Double getNumparts() { return (double)parts.size(); }
-        public Double getNumjoints() { return (double)joints.size(); }
-        public Double getNumneurons() { return (double)neurodefs.size(); }
-
-    //this is impossible to use, because numparts field is marked as readonly
-    public void setNumparts(Double numparts) { Containers.resizeList(parts, (int)(double)numparts); }
-    public void setNumjoints(Double numjoints) { Containers.resizeList(joints, (int)(double)numjoints); }
-    public void setNumneurons(Double numneurons) { Containers.resizeList(neurodefs, (int)(double)numneurons); }
-}

java/main/src/main/java/com/framsticks/model/Joint.java

@@ -8 +8 @@
  * All accessors are used by ReflectionAccess.
  */
-public class Joint {
+public class Joint extends BaseJoint {
 
+        /** i */
+        public String info;
+        public String getI() { return info; }
+        public void setI(String i) { info = i; }
+
+        /** p1 */
+        public Integer part1;
         public void setP1(Integer p1) { part1 = p1; }
         public Integer getP1() { return part1; }
+
+        /** p2 */
+        public Integer part2;
         public void setP2(Integer p2) { part2 = p2; }
         public Integer getP2() { return part2; }
 
-        public void setDx(Double dx) { delta.x = dx; }
-        public void setDy(Double dy) { delta.y = dy; }
-        public void setDz(Double dz) { delta.z = dz; }
 
-        public Double getDx() { return delta.x; }
-        public Double getDy() { return delta.y; }
-        public Double getDz() { return delta.z; }
-
-        public void setRx(Double rx) { rotation.x = rx; }
-        public void setRy(Double ry) { rotation.y = ry; }
-        public void setRz(Double rz) { rotation.z = rz; }
-
-        public Double getRx() { return rotation.x; }
-        public Double getRy() { return rotation.y; }
-        public Double getRz() { return rotation.z; }    
-
+        /** stam */
+        public Double stamina;
         public Double getStam() { return stamina; }
         public void setStam(Double stam) { stamina = stam; }
 
-        public Double getStif() { return stiffness; }
-        public void setStif(Double stif) { stiffness = stif; }
-
-        public Double getRotstif() { return rotationStiffness; }
-        public void setRotstif(Double rotstif) { rotationStiffness = rotstif; }
-
-        public String getI() { return info; }
-        public void setI(String i) { info = i; }
-
-        public String getVstyle() { return visualizationStyle; }
-        public void setVstyle(String Vstyle) { visualizationStyle = Vstyle; }
-
-        /** p1 */
-        public Integer part1;
-
-        /** p2 */
-        public Integer part2;
-
-        /** dx, dy, dz*/
-        public final Point3d delta = new Point3d();
-
-        /** rx, ry, rz*/
-        public final Point3d rotation = new Point3d();
-
-        /** stam */
-        public Double stamina;
-
-        /** stif */
-        public Double stiffness;
-
-        /** rotstif */
-        public Double rotationStiffness;
-
-        /** i */
-        public String info;
 
         /** Vstyle */
         public String visualizationStyle;
-
-
+        public String getVstyle() { return visualizationStyle; }
+        public void setVstyle(String Vstyle) { visualizationStyle = Vstyle; }
 }

java/main/src/main/java/com/framsticks/model/MechJoint.java

@@ -6 +6 @@
  * @author Piotr Sniegowski
  */
-public class MechJoint {
-        /** rx, ry, rz*/
-        public final Point3d rotation = new Point3d();
-
-        /** dx, dy, dz*/
-        public final Point3d delta = new Point3d();
-
-        /** stif */
-        public Double stiffness;
-
-        /** rotstif */
-        public Double rotationStiffness;
+public class MechJoint extends BaseJoint {
 
         /** stress */
         public Double stress;
+        public Double getStress() { return stress; }
+        public void setStress(Double stress) { this.stress = stress; }
 
         /** rotstress */
         public Double rotationStress;
-
-        public Double getRx() { return rotation.x; }
-        public void setRx(Double rx) { rotation.x = rx; }
-
-        public Double getRy() { return rotation.y; }
-        public void setRy(Double ry) { rotation.y = ry; }
-
-        public Double getRz() { return rotation.z; }
-        public void setRz(Double rz) { rotation.z = rz; }
-
-        public Double getDx() { return delta.x; }
-        public void setDx(Double dx) { delta.x = dx; }
-
-        public Double getDy() { return delta.y; }
-        public void setDy(Double dy) { delta.y = dy; }
-
-        public Double getDz() { return delta.z; }
-        public void setDz(Double dz) { delta.z = dz; }
-
-        public Double getStif() { return stiffness; }
-        public void setStif(Double stif) { stiffness = stif; }
-
-        public Double getRotstif() { return rotationStiffness; }
-        public void setRotstif(Double rotstif) { rotationStiffness = rotstif; }
-
-        public Double getStress() { return stress; }
-        public void setStress(Double stress) { this.stress = stress; }
-
         public Double getRotstress() { return rotationStress; }
         public void setRotstress(Double rotstress) { rotationStress = rotstress; }
-
 }

java/main/src/main/java/com/framsticks/model/MechPart.java

@@ -6 +6 @@
 /*
  */
-public class MechPart {
-
-        /** x, y, z */
-        public final Point3d position = new Point3d();
-
-        /** m */
-        public Double mass = 0.0;
-
-        /** s */
-        public Double size = 0.0;
+public class MechPart extends BasePart {
 
         /** vol */
         public Double volume = 0.0;
-
-        /** fr */
-        public Double friction = 0.0;
-
-        /** vx, vy, vz */
-        public final Point3d velocity = new Point3d();
-
-    /** oxx, oxy, oxz, oyx, oyy, oyz, ozx, ozy, ozz*/
-    public final Orientation orientation = new Orientation();
-
-        public Double getX() { return position.x; }
-        public void setX(Double x) { position.x = x; }
-
-        public Double getY() { return position.y; }
-        public void setY(Double y) { position.y = y; }
-
-        public Double getZ() { return position.z; }
-        public void setZ(Double z) { position.z = z; }
-
-        public Double getM() { return mass; }
-        public void setM(Double m) { mass = m; }
-
-        public Double getS() { return size; }
-        public void setS(Double s) { size = s; }
-
         public Double getVol() { return volume; }
         public void setVol(Double vol) { volume = vol; }
 
-        public Double getFr() { return friction; }
-        public void setFr(Double fr) { friction = fr; }
+        /** vx, vy, vz*/
+        public double vx, vy, vz;
 
-        public Double getVx() { return velocity.x; }
-        public void setVx(Double vx) { velocity.x = vx; }
+        public Point3d getVelocity() { return new Point3d(vx, vy, vz); }
+        public void setVelocity(Point3d v) { vx = v.x; vy = v.y; vz = v.z; }
 
-        public Double getVy() { return velocity.y; }
-        public void setVy(Double vy) { velocity.y = vy; }
+    public double oxx, oxy, oxz, oyx, oyy, oyz, ozx, ozy, ozz;
 
-        public Double getVz() { return velocity.z; }
-        public void setVz(Double vz) { velocity.z = vz; }
+        public Orientation getOrientation() { return new Orientation(new Point3d(oxx, oxy, oxz), new Point3d(oyx, oyy, oyz), new Point3d(ozx, ozy, ozz)); }
 
-        public Double getOxx() { return orientation.x.x; }
-        public void setOxx(Double oxx) { orientation.x.x = oxx; }
-
-        public Double getOxy() { return orientation.x.y; }
-        public void setOxy(Double oxy) { orientation.x.y = oxy; }
-
-        public Double getOxz() { return orientation.x.z; }
-        public void setOxz(Double oxz) { orientation.x.z = oxz; }
-
-        public Double getOyx() { return orientation.y.x; }
-        public void setOyx(Double oyx) { orientation.y.x = oyx; }
-
-        public Double getOyy() { return orientation.y.y; }
-        public void setOyy(Double oyy) { orientation.y.y = oyy; }
-
-        public Double getOyz() { return orientation.y.z; }
-        public void setOyz(Double oyz) { orientation.y.z = oyz; }
-
-        public Double getOzx() { return orientation.z.x; }
-        public void setOzx(Double ozx) { orientation.z.x = ozx; }
-
-        public Double getOzy() { return orientation.z.y; }
-        public void setOzy(Double ozy) { orientation.z.y = ozy; }
-
-        public Double getOzz() { return orientation.z.z; }
-        public void setOzz(Double ozz) { orientation.z.z = ozz; }
+        public void setOrientation(Orientation o) {
+                oxx = o.x.x;
+                oxy = o.x.y;
+                oxz = o.x.z;
+                oyx = o.y.x;
+                oyy = o.y.y;
+                oyz = o.y.z;
+                ozx = o.z.x;
+                ozy = o.z.y;
+                ozz = o.z.z;
+        }
 
 }

java/main/src/main/java/com/framsticks/model/Neuro.java

@@ -6 +6 @@
  * @author Piotr Sniegowski
  */
-public class Neuro {
+public class Neuro extends BaseNeuro {
 
         public Integer channelCount;
-
-        public Integer inputCount;
-        public Integer getGetInputCount() { return inputCount; }
-        public void setGetInputCount(Integer getInputCount) { inputCount = getInputCount; }
 
         public Double inputSum;
@@ -26 +22 @@
         public Boolean hold;
 
+        public double position_x, position_y, position_z;
 
-        /** position_x, position_y, position_z*/
-        public final Point3d position = new Point3d();
-
-        public Double getPosition_x() { return position.x; }
-        public void setPosition_x(Double position_x) { position.x = position_x; }
-
-        public Double getPosition_y() { return position.y; }
-        public void setPosition_y(Double position_y) { position.y = position_y; }
-
-        public Double getPosition_z() { return position.z; }
-        public void setPosition_z(Double position_z) { position.z = position_z; }
+        public Point3d getPosition() { return new Point3d(position_x, position_y, position_z); }
+        public void setPosition(Point3d p) { position_x = p.x; position_y = p.y; position_z = p.z; }
 
 }

java/main/src/main/java/com/framsticks/model/NeuroDef.java

@@ -4 +4 @@
  * @author Piotr Sniegowski
  */
-public class NeuroDef {
+public class NeuroDef extends BaseNeuro {
 
         /** p */
@@ -21 +21 @@
         public String visualizationStyle;
 
-        /** getInputCount */
-        public Integer inputCount;
-
         public Integer getP() { return part; }
         public void setP(Integer p) { part = p; }
@@ -39 +36 @@
         public void setVstyle(String Vstyle) { visualizationStyle = Vstyle; }
 
-        public Integer getGetInputCount() { return inputCount; }
-        public void setGetInputCount(Integer getInputCount) { inputCount = getInputCount; }
 
 

java/main/src/main/java/com/framsticks/model/Part.java

@@ -7 +7 @@
  * The Class Part.
  */
-public class Part {
-
-        /** x, y, z*/
-        public final Point3d position = new Point3d();
+public class Part extends BasePart {
 
         /** rx, ry, rz*/
-        public final Point3d rotation = new Point3d();
+        public double rx, ry, rz;
 
-        /** m */
-        public Double mass;
-
-        /** s */
-        public Double size;
+        public Point3d getRotation() { return new Point3d(rx, ry, rz); }
+        public void setRotation(Point3d r) { rx = r.x; ry = r.y; rz = r.z; }
 
         /** dn */
         public Double density;
-
-        /** fr */
-        public Double friction;
 
         /** ing */
@@ -39 +30 @@
         public String visualizationStyle;
 
-        public Double getX() { return position.x; }
-        public void setX(Double x) { position.x = x; }
-
-        public Double getY() { return position.y; }
-        public void setY(Double y) { position.y = y; }
-
-        public Double getZ() { return position.z; }
-        public void setZ(Double z) { position.z = z; }
-
-        public Double getM() { return mass; }
-        public void setM(Double m) { mass = m; }
-
-        public Double getS() { return size; }
-        public void setS(Double s) { size = s; }
-
         public Double getDn() { return density; }
         public void setDn(Double dn) { density = dn; }
 
-        public Double getFr() { return friction; }
-        public void setFr(Double fr) { friction = fr; }
 
         public Double getIng() { return ingestion; }
@@ -65 +39 @@
         public Double getAs() { return assimilation; }
         public void setAs(Double as) { assimilation = as; }
-
-        public Double getRx() { return rotation.x; }
-        public void setRx(Double rx) { rotation.x = rx; }
-
-        public Double getRy() { return rotation.y; }
-        public void setRy(Double ry) { rotation.y = ry; }
-
-        public Double getRz() { return rotation.z; }
-        public void setRz(Double rz) { rotation.z = rz; }
 
         public String getI() { return info; }

java/main/src/main/java/com/framsticks/observers/Observer.java

@@ -30 +30 @@
 
     @Override
-    protected void configure() {
+    protected void configure() throws Exception {
         super.configure();
         for (String name : config.getStringArray("endpoints")) {
@@ -38 +38 @@
             }
             Configuration c = config.subset("endpoints." + name);
-            Parameters p = new Parameters(c.subset("entity"), name, null);
+            Parameters p = new Parameters(c.subset("entity"), name, null, null);
             Entity e = Program.configureEntity(p);
             Instance i = Casting.tryCast(Instance.class, e);

java/main/src/main/java/com/framsticks/params/AccessInterface.java

@@ -80 +80 @@
 
         /**
-         * Load values from single line String.
-         * 
-         * @param line
-         *            the line with values
-         * @return the list of not severe exceptions which occurred while loading
-         * @throws Exception
-         *             the severe exception occurred while loading
-         */
-        List<Exception> load2(String line) throws Exception;
-
-        /**
          * Removes all the properties values.
          */
@@ -107 +96 @@
     FramsClass getFramsClass();
 
+
 }

java/main/src/main/java/com/framsticks/params/FramsClass.java

@@ -5 +5 @@
 import com.framsticks.params.types.FloatParam;
 import com.framsticks.params.types.StringParam;
+import com.framsticks.parsers.FileSource;
+import com.framsticks.parsers.Loaders;
 import com.framsticks.util.Casting;
 import org.apache.log4j.Logger;
 
 import javax.lang.model.element.TypeElement;
+import java.io.InputStream;
 import java.lang.reflect.*;
 import java.util.*;
@@ -58 +61 @@
 
         public Collection<Param> getParamEntries() {
-                return paramEntryMap.values();
+                return paramList;
         }
 
@@ -214 +217 @@
                 }
             }
+                        if (rawType.equals(List.class)) {
+                                Type containedType = p.getActualTypeArguments()[0];
+                                if (containedType instanceof Class) {
+                                        return "l " + ((Class) containedType).getCanonicalName();
+                                }
+                        }
             return null;
         }
@@ -234 +243 @@
     public static final String GENERATE_HELP_PREFIX = "automatically generated from: ";
 
-
-
-    public static class Constructor {
+        public static FramsClass readFromStream(InputStream stream) {
+                return Loaders.loadFramsClass(new FileSource(stream));
+        }
+
+        public static class Constructor {
         protected final FramsClass result;
         protected Class currentClass;
@@ -249 +260 @@
                 currentClass = currentClass.getSuperclass();
             }
+                        currentClass = src;
         }
 
@@ -254 +266 @@
             return result;
         }
+
+                public Constructor allFields() {
+                        for (Field f : currentClass.getFields()) {
+                                field(f.getName());
+                        }
+                        return this;
+                }
 
         public Constructor method(String name, Class<?> ... arguments) {

java/main/src/main/java/com/framsticks/params/ListAccess.java

@@ -73 +73 @@
         }
 
-        @Override
-        public List<Exception> load2(String line) throws Exception {
-                return null;
-        }
-
         public AccessInterface getElementAccess() {
                 return elementAccess;

java/main/src/main/java/com/framsticks/params/Param.java

@@ -109 +109 @@
         } catch (ClassCastException e) {
             throw new ClassCastException("property \"" + name
-                    + "\" getType is \"" + value.getClass().getName()
+                    + "\" type is \"" + value.getClass().getName()
                     + "\", not \"" + type.getName() + "\"");
         }

java/main/src/main/java/com/framsticks/params/PropertiesAccess.java

@@ -20 +20 @@
     @Override
         public Map<String, Object> createAccessee() {
+                return PropertiesAccess.createPropertiesMap();
+        }
+
+        public static Map<String, Object> createPropertiesMap() {
                 return new HashMap<String, Object>();
         }
-
 
         public PropertiesAccess(FramsClass framsClass) {
@@ -83 +86 @@
 
 
-
-
 }

java/main/src/main/java/com/framsticks/params/ReflectionAccess.java

@@ -3 +3 @@
 import java.lang.reflect.Field;
 import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Modifier;
+import java.lang.reflect.Type;
 import java.util.List;
 
@@ -43 +45 @@
                         String id = param.getId();
                         try {
-                                return type.cast(object.getClass().getField(id).get(object));
+                                return type.cast(reflectedClass.getField(id).get(object));
                         } catch (NoSuchFieldException ignored) {
                         }
                         try {
-                                return type.cast(object.getClass().getMethod(accessorName(true, id)).invoke(object));
+                                return type.cast(reflectedClass.getMethod(accessorName(true, id)).invoke(object));
                         } catch (NoSuchMethodException ex) {
                                 //ex.printStackTrace();
@@ -68 +70 @@
         }
 
-        private <T> void setValue(Param param, T val) {
+        private <T> void setValue(Param param, T value) {
                 if (object == null) {
                         return;
@@ -75 +77 @@
                         String id = param.getId();
                         try {
-                                object.getClass().getField(id).set(object, val);
+                                Field f = reflectedClass.getField(id);
+                                Class t = f.getType();
+                                if (Modifier.isFinal(f.getModifiers())) {
+                                        return;
+                                }
+                                if (value != null || (!t.isPrimitive())) {
+                                        f.set(object, value);
+                                }
                                 return;
                         } catch (NoSuchFieldException ignored) {
                         }
                         try {
-                                object.getClass().getMethod(accessorName(false, id), new Class[]{val.getClass()}).invoke(object, val);
-                        } catch (InvocationTargetException e) {
-                                //e.printStackTrace();
+                                reflectedClass.getMethod(accessorName(false, id), new Class[]{param.getStorageType()}).invoke(object, value);
+                        } catch (InvocationTargetException ignored) {
                         } catch (NoSuchMethodException ignored) {
                         }
-                } catch (IllegalAccessException ex) {
-                        LOGGER.warn("illegal access error occurred while trying to access returnedObject");
+                } catch (Exception ex) {
                         ex.printStackTrace();
                 }
@@ -103 +110 @@
                 resetErrors();
 
-                Field[] fields;
                 try {
-                        // TODO: conceptually invalid - should clean only fields that are specified in FramsClass
-                        fields = object.getClass().getFields();
-
-                        for (Field field : fields) {
-                                field.set(object, null);
+                        for (Param p : framsClass.getParamEntries()) {
+                                setValue(p, p.getDef(Object.class));
                         }
-                } catch (IllegalAccessException ex) {
-                        LOGGER.warn("IllegalAccessException thrown while trying to reset object values");
+                } catch (IllegalArgumentException ex) {
                         ex.printStackTrace();
                 }
@@ -125 +127 @@
         @Override
         public void select(Object object) {
+                assert object == null || reflectedClass.isInstance(object);
                 this.object = object;
         }
@@ -166 +169 @@
         }
         LOGGER.fatal("failed to create reflected object of class " + reflectedClass.getCanonicalName() + " for frams type " + framsClass.getId());
-
         return null;
     }

java/main/src/main/java/com/framsticks/params/SimpleAbstractAccess.java

@@ -38 +38 @@
                 this.framsClass = framsClass;
         }
-
-
-
-
     /**
          * Simple String key, value class.
          */
-        private static class Entry {
-
-                String key;
-                String value;
-
-                Entry(String key, String value) {
+        public static class Entry {
+
+                public final String key;
+                public final String value;
+
+                public Entry(String key, String value) {
                         this.key = key;
                         this.value = value;
@@ -331 +327 @@
 
         Entry entry;
-
         while ((entry = readEntry(source)) != null) {
             Param param = getParam(entry.key);
@@ -351 +346 @@
     }
 
-    @Override
-        public List<Exception> load2(String line) throws Exception {
-                this.clearValues();
-
-                // list of not terminable exceptions that occured
-                List<Exception> exceptions = new ArrayList<Exception>();
-
-                int indexOfColon = line.indexOf(':');
-                if (indexOfColon < 0)
-                        indexOfColon = line.length();
-                String classId = line.substring(0, indexOfColon).trim();
-                if (!getId().equals(classId))
-                        throw new Exception(
-                                        "Inappropriate getId of param interface (class), specified \""
-                                                        + classId + "\" while should be \"" + getId()
-                                                        + "\"");
-                String parameters;
-                if (indexOfColon == line.length())
-                        parameters = "";
-                else
-                        parameters = line.substring(indexOfColon + 1);
-
-                // tokenize
-                boolean doubleQuotes = false;
-                char previousChar = ',';
-                List<Entry> result = new ArrayList<Entry>();
-                StringBuilder stringBuilder = new StringBuilder();
-                String key = "";
-                if (parameters.trim().length() > 0) {
-                        for (char currentChar : parameters.toCharArray()) {
-                                if (!doubleQuotes && currentChar == '=' && "".equals(key)) {
-                                        key = stringBuilder.toString();
-                                        stringBuilder = new StringBuilder();
-                                } else if (!doubleQuotes && currentChar == ',') {
-                                        if (previousChar == ',') {
-                                                result.add(new Entry(key.trim(), null));
-                                        } else {
-                                                result.add(new Entry(key.trim(), stringBuilder
-                                                                .toString().trim()));
-                                        }
-                                        stringBuilder = new StringBuilder();
-                                        key = "";
-                                } else if (currentChar == '"') {
-                                        if (previousChar == '\\') {
-                                                stringBuilder.deleteCharAt(stringBuilder.length() - 1);
-                                                stringBuilder.append(currentChar);
-                                        } else
-                                                doubleQuotes = !doubleQuotes;
-                                } else {
-                                        stringBuilder.append(currentChar);
-                                }
-
-                                previousChar = currentChar;
-                        }
-
-                        String last = stringBuilder.toString().trim();
-                        // if (last.length() > 0 || previousChar == '\"'
-                        // || previousChar == ':')
-                        result.add(new Entry(key.trim(), last));
-
-                        if (doubleQuotes)
-                                throw new Exception(
-                                                "Double quotes expected while end of line met");
-                }
-
-                // if successfully parsed set all necessary values
-
-                //TODO: name omitting
-                Param currentParam = null;
-                boolean illegallyOmittedName = false;
-                for (Entry pair : result) {
-                        try {
-
-                                if (pair.key != null && !"".equals(pair.key)) {
-                                        Param param = getParam(pair.key);
-                                        if (param == null) {
-                                                illegallyOmittedName = true;
-                                                throw new Exception("No parameter with such id: "
-                                                                + pair.key);
-                                        } else {
-                                                currentParam = param;
-                                                illegallyOmittedName = false;
-                                        }
-                                } else if (illegallyOmittedName
-                                                || (currentParam.getFlags() & Flags.CANOMITNAME) == 0) {
-                                        throw new Exception(
-                                                        "Parameter with offset: "
-                                                                        + currentParam
-                                                                        + " is not set, "
-                                                                        + "because it's definition or definition of one of the previous params "
-                                                                        + "does not contain flag, which allow to skip the getName (flag 1024)");
-                                }
-
-                                if (pair.value != null) {
-                                        int setFlag = this.set(currentParam, pair.value);
-                                        if ((setFlag & Flags.PSET_HITMIN) != 0) {
-                                                exceptions.add(createBoundaryHitException(currentParam, pair.value, Flags.PSET_HITMIN));
-                                        }
-
-                                        if ((setFlag & Flags.PSET_HITMAX) != 0) {
-                                                exceptions.add(createBoundaryHitException(currentParam, pair.value, Flags.PSET_HITMAX));
-                                        }
-
-                                        if ((setFlag & Flags.PSET_RONLY) != 0) {
-                                                throw (new Exception(
-                                                                "Tried to set a read-only attribute \""
-                                                                                + currentParam.getId()
-                                                                                + "\" in class \"" + getId() + "\""));
-                                        }
-                                }
-
-                        } catch (Exception e) {
-                                exceptions.add(e);
-                        //} finally {
-                        //  currentProperty++;
-                        }
-                }
-                return exceptions;
-        }
-
-        private Exception createBoundaryHitException(Param param, String value, int flag) {
-                boolean minimum = (flag & Flags.PSET_HITMIN) != 0;
-                String boundary = (minimum ? param.getMin(Object.class) : param.getMax(Object.class)).toString();
-                String name =  (minimum ? "minimum" : "maximum");
-                return new Exception("Tried to set attribute \""
-                                + param.getId()
-                                + "\" in class \""
-                                + getId()
-                                + "\" to value which exceeds " + name + " ("
-                                + value
-                                + "), truncated to: "
-                                + boundary);
-        }
-        
+
+
         protected abstract <T> void internalSet(Param param, T value);
 

java/main/src/main/java/com/framsticks/params/Util.java

@@ -1 +1 @@
 package com.framsticks.params;
+
+import java.util.ArrayList;
+import java.util.List;
 
 /**
@@ -14 +17 @@
         return result.toString();
     }
+        public static List<Object> stripAccessInterface(List<AccessInterface> accesses) {
+                List<Object> result = new ArrayList<Object>();
+                for (AccessInterface a : accesses) {
+                        result.add(a.getSelected());
+                }
+                return result;
+        }
+        public static int copyParams(AccessInterface to, AccessInterface from) {
+                int copied = 0;
+                for (Param f : from.getParams()) {
+                        Param t = from.getParam(f.getId());
+                        if (t == null) {
+                                continue;
+                        }
+                        if (to.getClass() != f.getClass()) {
+                                continue;
+                        }
+                        to.set(t, from.get(f, Object.class));
+                        ++copied;
+                }
+                return copied;
+        }
 }

java/main/src/main/java/com/framsticks/parsers/FileSource.java

@@ -3 +3 @@
 import com.framsticks.params.SourceInterface;
 
-import java.io.BufferedReader;
-import java.io.FileReader;
-import java.io.IOException;
+import java.io.*;
 
 
@@ -17 +15 @@
                 this.filename = filename;
         reader = new BufferedReader(new FileReader(filename));
+        }
+
+        public FileSource(InputStream stream) {
+                filename = "<stream>";
+                reader = new BufferedReader(new InputStreamReader(stream));
         }
 

java/main/src/main/java/com/framsticks/parsers/Schema.java

@@ -1 +1 @@
 package com.framsticks.parsers;
 
+import java.io.File;
+import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
@@ -8 +10 @@
 import java.util.Map.Entry;
 
-import com.framsticks.params.FramsClass;
-import com.framsticks.params.Param;
+import com.framsticks.params.*;
 import com.framsticks.params.types.DecimalParam;
+import com.framsticks.params.types.FloatParam;
 import com.framsticks.params.types.StringParam;
 import org.apache.log4j.Logger;
@@ -19 +21 @@
 
 import com.framsticks.leftovers.f0.NeuroClass;
-import com.framsticks.params.Group;
-import com.framsticks.params.ParamBuilder;
 import org.w3c.dom.Document;
 import org.w3c.dom.NamedNodeMap;
@@ -39 +39 @@
         private final static Logger logger = Logger.getLogger(Schema.class);
 
-        /** The main classes (such as part, joint, etc.) */
-        private Map<String, FramsClass> mainClasses = new HashMap<String, FramsClass>();
+        protected final Registry registry = new Registry();
 
         /** The neuro classes (classess representing different types of neurons). */
         private Map<String, NeuroClass> neuroClasses = new HashMap<String, NeuroClass>();
 
-        // TODO: definition can be changed
-        /**
-         * Instantiates a new schema with usage of f0def.xml file stored in
-         * resources.
-         * 
-         * @throws Exception
-         *             the exception if one occured while reading the stream
-         */
-        public Schema() throws Exception {
-                this(Thread.currentThread().getContextClassLoader()
-                                .getResourceAsStream("f0def.xml"));
+        public static InputStream getDefaultDefinitionAsStream() {
+                //return new FileInputStream(new File(Schema.class.getResource("/parsers/f0def.xml").getPath()));
+                return Schema.class.getResourceAsStream("/parsers/f0def.xml");
         }
 
@@ -61 +52 @@
          * Instantiates a new schema.
          * 
-         * @param xmlStream
+         * @param inputStream
          *            the xml stream with schema
          * @throws Exception
-         *             the exception if one occured while reading the stream
-         */
-        public Schema(InputStream xmlStream) throws Exception {
+         *             the exception if one occurred while reading the stream
+         */
+        public Schema(InputStream inputStream) throws Exception {
 
                 DocumentBuilderFactory factory;
@@ -75 +66 @@
                         db = factory.newDocumentBuilder();
 
-                        Document document = db.parse(xmlStream);
+                        Document document = db.parse(inputStream);
                         NodeList classes = document.getElementsByTagName("CLASS");
 
@@ -81 +72 @@
                                 Node classNode = classes.item(i);
                                 FramsClass framsClass = processClass(classNode);
-                                mainClasses.put(framsClass.getId(), framsClass);
+                                registry.putInfoIntoCache(framsClass);
                         }
 
@@ -106 +97 @@
                                                         symbolGlymph[j] = Integer.parseInt(sgha[j]);
                                                 } catch (NumberFormatException e) {
-                                                        logger.error("an error occured while parsing symbol glymph, class getId: "
+                                                        logger.error("an error occurred while parsing symbol glymph, class getId: "
                                                                         + framsClass.getId()
                                                                         + ", glymph offset: " + j);
@@ -119 +110 @@
 
                 } catch (IOException e) {
-                        logger.fatal("unexpected exception occured: ", e);
+                        logger.fatal("unexpected exception occurred: ", e);
                         throw e;
                 } catch (ParserConfigurationException e) {
-                        logger.fatal("unexpected exception occured: ", e);
+                        logger.fatal("unexpected exception occurred: ", e);
                         throw e;
                 } catch (SAXException e) {
-                        logger.fatal("unexpected exception occured: ", e);
+                        logger.fatal("unexpected exception occurred: ", e);
                         throw e;
                 }
@@ -140 +131 @@
          */
         private static int getIntAttribute(NamedNodeMap attributes, String name) {
+                String v = getAttribute(attributes, name);
+                if (v == null) {
+                        return 0;
+                }
                 try {
-                        return Integer.parseInt(getAttribute(attributes, name));
+                        return Integer.parseInt(v);
                 } catch (NullPointerException e) {
                         return 0;
                 } catch (NumberFormatException e) {
                         logger.fatal("attribute " + name
-                                        + " should be numeric (it is not)");
+                                        + " should be numeric: " + v);
                         return 0;
                 }
@@ -186 +181 @@
          *             the exception in case of any error
          */
-        private FramsClass processClass(Node classNode) throws Exception {
+        private static FramsClass processClass(Node classNode) throws Exception {
                 String classId = null;
                 String className = "";
@@ -200 +195 @@
                 classDescription = getAttributeFromNode("DESCRIPTION", classNode);
 
-                FramsClass framsClass = new FramsClass(classId, className,
-                                classDescription);
+                FramsClass framsClass = new FramsClass(classId, className, classDescription);
 
                 NodeList classProperties = classNode.getChildNodes();
@@ -210 +204 @@
                         if ("GROUP".equals(node.getNodeName())) {
                                 NamedNodeMap attributes = node.getAttributes();
-                                String name = attributes.getNamedItem("NAME") == null ? null
-                                                : attributes.getNamedItem("NAME").getNodeValue();
-                                if (name == null)
-                                        logger.warn("Group getName in class \"" + classId + "\" ("
+                                String name = getAttribute(attributes, "NAME");
+                                if (name == null) {
+                                        logger.warn("Group name in class \"" + classId + "\" ("
                                                         + className + ") is undefined");
-                                else
+                                } else {
                                         framsClass.appendGroup(new Group(name));
-
+                                }
                         } else if ("PROP".equals(node.getNodeName())
                                         || "NEUROPROP".equals(node.getNodeName())) {
@@ -232 +225 @@
 
         /**
-         * It analyses the single property within the clas
+         * It analyses the single property within the class
          * 
          * @param attributes
@@ -242 +235 @@
          *             the exception in case of any error
          */
-        private Param processParameter(NamedNodeMap attributes, String classId)
+        private static Param processParameter(NamedNodeMap attributes, String classId)
                         throws Exception {
 
@@ -315 +308 @@
                                 }
                         }
-                        builder.setType(DecimalParam.class);
+                        builder.setType(FloatParam.class);
                         builder.setMin(minMaxDefDouble.get("MIN"));
                         builder.setMax(minMaxDefDouble.get("MAX"));
@@ -330 +323 @@
         }
 
-        public Map<String, FramsClass> getMainClasses() {
-                return Collections.unmodifiableMap(mainClasses);
-        }
 
         public Map<String, NeuroClass> getNeuroClasses() {
@@ -338 +328 @@
         }
 
+        public final Registry getRegistry() {
+                return registry;
+        }
+
+
 }

java/main/src/main/java/com/framsticks/portals/Portal.java

@@ -36 +36 @@
 
     @Override
-    protected void configure() {
+    protected void configure() throws Exception {
         super.configure();
     }

java/main/src/main/java/com/framsticks/util/Orientation.java

@@ -9 +9 @@
     public final Point3d z;
 
-    public Orientation() {
-        x = new Point3d();
-        y = new Point3d();
-        z = new Point3d();
-    }
+        public Orientation(Point3d x, Point3d y, Point3d z) {
+                this.x = x;
+                this.y = y;
+                this.z = z;
+        }
+
+        public Orientation() {
+                x = new Point3d(1, 0, 0);
+                y = new Point3d(0, 1, 0);
+                z = new Point3d(0, 0, 1);
+        }
+
+        /** based on c++ void Orient::transform(Pt3D& target,const Pt3D &s) const */
+        public Point3d transform(Point3d source) {
+                Point3d.Builder b = new Point3d.Builder();
+                for (int i = 0; i < 3; ++i) {
+                        double v = 0;
+                        for (int j = 0; j < 3; ++j) {
+                                v += source.get(j) * this.get(j).get(i);
+                        }
+                        b.set(i, v);
+                }
+                return b.build();
+        }
+
+        /** based on c++ void Orient::transform(Orient& target,const Orient& src) const */
+        public Orientation transform(Orientation source) {
+                return new Orientation(transform(source.x), transform(source.y), transform(source.z));
+        }
+
+        protected static Point3d rotate2D(double sin, double cos, Point3d p, int a0, int a1, int im) {
+                Point3d.Builder b = new Point3d.Builder();
+                b.set(a0, cos * p.get(a0) - sin * p.get(a1));
+                b.set(a1, sin * p.get(a0) + cos * p.get(a1));
+                b.set(im, p.get(im));
+                return b.build();
+        }
+
+        /** based on c++ Orient::rotate(const Pt3D &v) */
+        public Orientation rotate(Point3d v) {
+                Point3d[] p = new Point3d[] {x, y, z};
+
+                for (int i = 0; i < 3; ++i) {
+                        double sin = Math.sin(v.get(i));
+                        double cos = Math.cos(v.get(i));
+
+                        for (int j = 0; j < 3; ++j) {
+                                p[j] = rotate2D(sin, cos, p[j], i == 0 ? 1 : 0, i == 2 ? 1 : 2, i);
+                        }
+                }
+                return new Orientation(p[0], p[1], p[2]);
+        }
+
+        final Point3d get(int i) {
+                switch (i) {
+                        case 0: return x;
+                        case 1: return y;
+                        case 2: return z;
+                }
+                assert false;
+                return null;
+        }
 
 
+        @Override
+        public final String toString() {
+                return x + " | " + y + " | " + z;
+        }
 }

java/main/src/main/java/com/framsticks/util/Point3d.java

@@ -6 +6 @@
 public class Point3d
 {
-        public Double x;
-        public Double y;
-        public Double z;
+        public final double x;
+        public final double y;
+        public final double z;
 
         public Point3d() {
@@ -16 +16 @@
         }
 
-        public Point3d(Double x, Double y, Double z) {
+        public Point3d(double x, double y, double z) {
                 this.x = x;
                 this.y = y;
@@ -22 +22 @@
         }
 
+        public Point3d(Point3d p) {
+                x = p.x;
+                y = p.y;
+                z = p.z;
+        }
+
         @Override
-        public String toString() {
-                //return new StringBuilder().append(x).append(" ").append(y).append(" ").append("z").toString();
+        public final String toString() {
                 return x + " " + y + " " + z;
         }
+
+        public final double get(int i) {
+                switch (i) {
+                        case 0: return x;
+                        case 1: return y;
+                        case 2: return z;
+                }
+                assert false;
+                return 0;
+        }
+
+
+        public final Point3d add(Point3d p) {
+                return new Point3d(x + p.x, y + p.y, z + p.z);
+        }
+
+        public final Point3d sub(Point3d p) {
+                return new Point3d(x - p.x, y - p.y, z - p.z);
+        }
+
+        public final double length() {
+                return Math.sqrt(x * x + y * y + z * z);
+        }
+
+        public static class Builder {
+                double[] a = new double[3];
+
+                public Point3d build() { return new Point3d(a[0], a[1], a[2]); }
+
+                public final void set(int i, double v) {
+                        a[i] = v;
+                }
+        }
 }

java/main/src/main/java/com/framsticks/visualization/Viewer.java

@@ -1 +1 @@
 package com.framsticks.visualization;
 
-import com.framsticks.communication.Connection;
 import com.framsticks.model.World;
 import com.sun.j3d.loaders.IncorrectFormatException;
@@ -22 +21 @@
 import java.awt.event.ActionListener;
 import java.io.FileNotFoundException;
-import java.util.ArrayList;
 
 import org.apache.log4j.Logger;
 
-
-
 public class Viewer {
-    static final long serialVersionUID = 1;
-
-    private static Logger logger = Logger.getLogger(Viewer.class);
+
+    private static Logger LOGGER = Logger.getLogger(Viewer.class);
 
     Canvas3D canvas3d;
@@ -45 +40 @@
     private JCheckBoxMenuItem autorefreshItem;
 
-        private Connection connection;
-    ArrayList<String> args;
-
-    public Viewer(ArrayList<String> args, JMenuBar menuBar) {
+    public Viewer(JMenuBar menuBar) {
         super();
-        this.args = args;
         this.menuBar = menuBar;
         loggingItem = new JCheckBoxMenuItem("Logging");
@@ -56 +47 @@
 
         init();
-
     }
 
@@ -261 +251 @@
     }
 
-
-
-
-    public void setCommunication(Connection connection) {
-        this.connection = connection;
-    }
-
     public void rebuildViewMenu(Object creatures) {
 

java/main/src/main/resources/configs/framsticks.properties

@@ -1 +1 @@
 com.framsticks.entities.browser.class=com.framsticks.gui.Browser
-#com.framsticks.entities.browser.endpoints=localhost,dump,remote_portal
 com.framsticks.entities.browser.size.width=1500
 com.framsticks.entities.browser.size.height=800
-com.framsticks.entities.browser.endpoints=localhost,dump
+com.framsticks.entities.browser.endpoints=localhost,dump,genotype_browser
 com.framsticks.entities.browser.endpoints.dump.entity.class=com.framsticks.dumping.FileInstance
 com.framsticks.entities.browser.endpoints.dump.entity.filename=dumps/localhost:9009__.param
 com.framsticks.entities.browser.endpoints.localhost.entity.mount=com.framsticks.entities.localhost
 com.framsticks.entities.browser.endpoints.remote_portal.entity.mount=com.framsticks.entities.remote_portal
+com.framsticks.entities.browser.endpoints.genotype_browser.entity.mount=com.framsticks.entities.genotype_browser
 
 com.framsticks.entities.diagnostics.class=com.framsticks.diagnostics.Diagnostics
@@ -30 +30 @@
 com.framsticks.entities.hosted_portal.hosted.entity.mount=com.framsticks.entities.portal
 
-#com.framsticks.entity=browser
+com.framsticks.entities.genotype_browser.class=com.framsticks.examples.GenotypeBrowser
+
+com.framsticks.entity.mount = com.framsticks.entities.browser

java/main/src/main/resources/configs/log4j.properties

@@ -3 +3 @@
 # -------------------------------------------------------------------
 #log4j.rootLogger=INFO, STDOUT, FILE
-log4j.rootLogger=DEBUG, STDOUT, FILE
+log4j.rootLogger=DEBUG, STDOUT
 
 
@@ -27 +27 @@
 log4j.appender.STDOUT.layout.ConversionPattern=%d{ABSOLUTE} [%-5p] [%t] %c -- %m%n
 
-# File appender
-log4j.appender.FILE=org.apache.log4j.FileAppender
-log4j.appender.FILE.File=${user.home}/frams_network_client.log
-log4j.appender.FILE.layout=org.apache.log4j.PatternLayout
-log4j.appender.FILE.layout.ConversionPattern=%d{ABSOLUTE} [%-5p] [%t] %c -- %m%n
 
 log4j.logger.com.framsticks=INFO