Atom

java.lang.Object
- net.richarddawkins.watchmaker.genome.SimpleGene
- - net.richarddawkins.watchmaker.morphs.arthro.genome.Atom

All Implemented Interfaces:

java.util.EventListener, Gene, GeneManipulationListener
```
public class Atom
extends SimpleGene
```

Field Summary

Fields
Modifier and Type	Field and Description
`double`	`angle` Original documentation: also used in an AnimalTrunk to store the number of atoms in the animal. also used in SectionTrunk to store the Overlap of segments also used in SegmentTrunk to store the rank number of the segment
`Atom`	`firstBelowMe` Original documentation: where to look in the BoneYard for the next atom.
`int`	`gradientGene`
`double`	`height` Original documentation: Also used for Thickness of a Joint
`AtomKind`	`kind`
`Atom`	`nextLikeMe` Original documentation: Where to look in the BoneYard for the next atom.
`int`	`segmentNumber`
`double`	`width` Original documentation: Also used for Length of a Joint

Constructor Summary

Constructors
Constructor and Description
`Atom(ArthromorphGenome genome)`
`Atom(ArthromorphGenome genome, AtomKind kind)`
`Atom(ArthromorphGenome genome, AtomKind kind, double height, double width, double angle, int gradientGene, Atom nextLikeMe, Atom firstBelowMe)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`Atom`	`copy(Genome genome)`
`Atom`	`copyExceptNext(Genome genome)`
`int`	`countAtoms()` Recursively traverse tree of atoms to calculate the total number of atoms in the tree.
`int`	`depthBelow(Atom ancestor, Atom descendent)`
`boolean`	`doDelete()` Original Documentation
`void`	`geneManipulated(GeneManipulationEvent gbme)`
`boolean`	`genomicallyEquals(Gene gene)`
`double`	`getAngle()`
`Atom`	`getFirstBelowMe()`
`int`	`getGradientGene()`
`double`	`getHeight()`
`AtomKind`	`getKind()`
`Atom`	`getNextLikeMe()`
`double`	`getWidth()`
`void`	`kill()` Original Documentation
`void`	`readValueFromByteBuffer(java.nio.ByteBuffer byteBuffer)`
`void`	`setAngle(double angle)`
`void`	`setFirstBelowMe(Atom firstBelowMe)`
`void`	`setGradientGene(int gradientGene)`
`void`	`setHeight(double newValue)`
`void`	`setKind(AtomKind kind)`
`void`	`setNextLikeMe(Atom nextLikeMe)`
`void`	`setWidth(double newValue)`
`java.lang.String`	`toString()`
`java.util.Vector<Atom>`	`toVector()`
`void`	`writeValueToByteBuffer(java.nio.ByteBuffer byteBuffer)`

Methods inherited from class net.richarddawkins.watchmaker.genome.SimpleGene
addPropertyChangeListener, copy, getDoubleGooseSize, getGenome, getGooseSize, getName, readIndexedValueFromByteBuffer, removePropertyChangeListener, setGenome, setName, writeIndexedValueToByteBuffer

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail
- angle
```
public double angle
```
  Original documentation:
  - also used in an AnimalTrunk to store the number of atoms in the animal.
  - also used in SectionTrunk to store the Overlap of segments
  - also used in SegmentTrunk to store the rank number of the segment
- firstBelowMe
```
public Atom firstBelowMe
```
  Original documentation: where to look in the BoneYard for the next atom. 0 means end of chain
- gradientGene
```
public int gradientGene
```
- height
```
public double height
```
  Original documentation: Also used for Thickness of a Joint
- kind
```
public AtomKind kind
```
- nextLikeMe
```
public Atom nextLikeMe
```
  Original documentation: Where to look in the BoneYard for the next atom. 0 means end of chain. Also used in AnimalTrunk to store Gradient gene, slightly more or less than 100. Treat as Percentage
- segmentNumber
```
public int segmentNumber
```
- width
```
public double width
```
  Original documentation: Also used for Length of a Joint

Constructor Detail

Atom
```
public Atom(ArthromorphGenome genome)
```

Atom

public Atom(ArthromorphGenome genome,
            AtomKind kind)

Atom

public Atom(ArthromorphGenome genome,
            AtomKind kind,
            double height,
            double width,
            double angle,
            int gradientGene,
            Atom nextLikeMe,
            Atom firstBelowMe)

Method Detail

copy
```
public Atom copy(Genome genome)
```

copyExceptNext

public Atom copyExceptNext(Genome genome)

countAtoms

public int countAtoms()

Recursively traverse tree of atoms to calculate the total number of atoms in the tree.

Original Pascal Source

In Classic Arthromorphs, the NextLikeMe field for AnimalTrunk was used to store the gradient gene. In the Java version, gradient is separately tracked in the Arthromorph class. For this reason, the "kind != AnimalTrunk" check is not needed.

        function CountAtoms (which: integer): integer;
        {travel over the Animal, counting Atoms}
                var
                        count: integer;
        begin
                count := 1;     {count me}
                with BoneYard[which]^^ do
                        begin
                                if FirstBelowMe <> 0 then
                                        count := count + CountAtoms(FirstBelowMe);
                                if (NextLikeMe <> 0) and (kind <> AnimalTrunk) then
                                        count := count + CountAtoms(NextLikeMe);
                        end;
                CountAtoms := count;    {Me and all below me}
        end;

Returns:: the number of atoms in the tree.

depthBelow

public int depthBelow(Atom ancestor,
                      Atom descendent)

doDelete

public boolean doDelete()

Original Documentation

Delete a section of the animal somewhere near the atom which.

Caller must correct the AtomCount of the whole animal. Return false if failed

Must have a hold on the atom above what we delete. If chosen atom is:

AnimalTrunk   delete first Sec
        AnimalJoint   delete first Sec
        AnimalClaw      delete first Sec
                SectionTrunk    delete next Sec
                        SectionJoint            delete first Seg
                        SectionClaw             delete first Seg
                                SegmentTrunk            delete next Seg
                                        SegmentJoint            delete first Joint
                                        SegmentClaw             delete first Joint
                                                Joint                           delete next Joint
                                                Joint                           delete next Joint
                                                Joint                           delete Claw
                                                        Claw                            fail

Also fail if trying to delete last example of a Kind

Returns:: whether the delete succeeded.

geneManipulated

public void geneManipulated(GeneManipulationEvent gbme)

getAngle
```
public double getAngle()
```

getFirstBelowMe
```
public Atom getFirstBelowMe()
```

getGradientGene
```
public int getGradientGene()
```

getHeight
```
public double getHeight()
```

getKind
```
public AtomKind getKind()
```

getNextLikeMe
```
public Atom getNextLikeMe()
```

getWidth
```
public double getWidth()
```

kill
```
public void kill()
```
Original Documentation

Destroy this animal. Mark all of its Atoms as Free again.

Recursively step through the animal

Specified by:

kill in interface Gene

Overrides:

kill in class SimpleGene

setAngle
```
public void setAngle(double angle)
```

setFirstBelowMe

public void setFirstBelowMe(Atom firstBelowMe)

setGradientGene

public void setGradientGene(int gradientGene)

setHeight

public void setHeight(double newValue)

setKind
```
public void setKind(AtomKind kind)
```

setNextLikeMe

public void setNextLikeMe(Atom nextLikeMe)

setWidth

public void setWidth(double newValue)

toString
```
public java.lang.String toString()
```
Overrides:

toString in class java.lang.Object

toVector

public java.util.Vector<Atom> toVector()

readValueFromByteBuffer
```
public void readValueFromByteBuffer(java.nio.ByteBuffer byteBuffer)
```
Specified by:

readValueFromByteBuffer in interface Gene

Overrides:

readValueFromByteBuffer in class SimpleGene

writeValueToByteBuffer
```
public void writeValueToByteBuffer(java.nio.ByteBuffer byteBuffer)
```
Specified by:

writeValueToByteBuffer in interface Gene

Overrides:

writeValueToByteBuffer in class SimpleGene

genomicallyEquals

public boolean genomicallyEquals(Gene gene)

Class Atom

Field Summary

Constructor Summary

Method Summary

Methods inherited from class net.richarddawkins.watchmaker.genome.SimpleGene

Methods inherited from class java.lang.Object

Field Detail

angle

firstBelowMe

gradientGene

height

kind

nextLikeMe

segmentNumber

width

Constructor Detail

Atom

Atom

Atom

Method Detail

copy

copyExceptNext

countAtoms

Original Pascal Source

depthBelow

doDelete

Original Documentation

geneManipulated

getAngle

getFirstBelowMe

getGradientGene

getHeight

getKind

getNextLikeMe

getWidth

kill

Original Documentation

setAngle

setFirstBelowMe

setGradientGene

setHeight

setKind

setNextLikeMe

setWidth

toString

toVector

readValueFromByteBuffer

writeValueToByteBuffer

genomicallyEquals