From a716d28cc35f5d8b090af88ceba8c901b7eb3297 Mon Sep 17 00:00:00 2001
From: Jeffrey Phillips Freeman <jeffrey.freeman@syncleus.com>
Date: Fri, 28 Nov 2014 16:13:01 -0500
Subject: [PATCH] Fixed javadocs so they compile and made pom compatable for
official repositories.
Change-Id: I05d54c1ba12df671e924cd469e4ecc9e8d17499c
---
pom.xml | 120 +++++----
.../classify/naive/bayes/package-info.java | 3 +-
.../genetics/wavelets/ExpressionFunction.java | 10 +-
.../wavelets/SignalProcessingWavelet.java | 12 +-
.../dann/graph/AbstractAdjacencyGraph.java | 8 +
.../HyperassociativeMapCanvas.java | 3 +
.../graph/topological/KnotOptimizedGraph.java | 1 +
.../topological/StructureOptimizedGraph.java | 1 +
.../dann/graph/topological/Topography.java | 58 ++++-
.../dann/math/OrderedFieldElement.java | 4 +
.../java/com/syncleus/dann/math/Vector.java | 3 +
.../math/counting/PermutationCounter.java | 5 +
.../com/syncleus/dann/math/linear/Matrix.java | 1 +
.../dann/math/linear/SimpleRealMatrix.java | 9 +-
...eskyBanachiewiczCholeskyDecomposition.java | 4 +-
.../CholeskyCroutCholeskyDecomposition.java | 4 +-
.../decomposition/CholeskyDecomposition.java | 4 +-
.../DoolittleLuDecomposition.java | 8 +-
.../HouseholderQrDecomposition.java | 6 +-
.../linear/decomposition/LuDecomposition.java | 8 +-
.../linear/decomposition/QrDecomposition.java | 6 +-
.../SingularValueDecomposition.java | 14 +-
.../StewartSingularValueDecomposition.java | 18 +-
.../TridiagonalEignevalueDecomposition.java | 4 +-
.../visualization/MathFunctionCanvas.java | 167 ------------
.../visualization/MathFunctionDataBinder.java | 239 ------------------
.../dann/neural/AbstractActivationNeuron.java | 2 +
.../dann/neural/AbstractLocalBrain.java | 8 +-
.../syncleus/dann/neural/AbstractNeuron.java | 1 +
.../syncleus/dann/neural/AbstractSynapse.java | 4 +
.../com/syncleus/dann/neural/NeuronGroup.java | 5 +-
.../syncleus/dann/neural/SimpleSynapse.java | 4 +
.../backprop/AbstractBackpropNeuron.java | 4 +
.../AbstractOutputBackpropNeuron.java | 4 +
.../neural/backprop/SimpleBackpropNeuron.java | 5 +
.../backprop/SimpleOutputBackpropNeuron.java | 4 +
.../brain/FullyConnectedFeedforwardBrain.java | 8 +
.../dann/neural/som/SimpleSomNeuron.java | 1 +
.../syncleus/dann/xml/XmlSerializable.java | 8 +
39 files changed, 257 insertions(+), 521 deletions(-)
delete mode 100644 src/main/java/com/syncleus/dann/math/visualization/MathFunctionCanvas.java
delete mode 100644 src/main/java/com/syncleus/dann/math/visualization/MathFunctionDataBinder.java
diff --git a/pom.xml b/pom.xml
index 7a8fb827..5517fda4 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,14 +4,14 @@
<modelVersion>4.0.0</modelVersion>
<parent>
- <groupId>com.syncleus</groupId>
+ <groupId>com.syncleus.dann</groupId>
<artifactId>dann</artifactId>
<version>2.1-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
<packaging>jar</packaging>
- <groupId>com.syncleus</groupId>
+ <groupId>com.syncleus.dann</groupId>
<artifactId>dann-core</artifactId>
<version>2.1-SNAPSHOT</version>
@@ -58,17 +58,19 @@
</mailingList>
</mailingLists>
+ <repositories>
+ <repository>
+ <id>ossrh.snapshots</id>
+ <url>https://oss.sonatype.org/content/repositories/snapshots</url>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ </repository>
+ </repositories>
- <distributionManagement>
- <repository>
- <id>syncleus.releases</id>
- <url>http://repo.syncleus.com/repository/releases/</url>
- </repository>
- <snapshotRepository>
- <id>syncleus.snapshots</id>
- <url>http://repo.syncleus.com/repository/snapshots/</url>
- </snapshotRepository>
- </distributionManagement>
<build>
@@ -92,6 +94,39 @@
<encoding>${project.build.resourceEncoding}</encoding>
</configuration>
</plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-source-plugin</artifactId>
+ <version>2.2.1</version>
+ <executions>
+ <execution>
+ <id>attach-sources</id>
+ <goals>
+ <goal>jar-no-fork</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-javadoc-plugin</artifactId>
+ <version>2.9.1</version>
+ <configuration>
+ <sourcepath>src/main/java/</sourcepath>
+ </configuration>
+ <executions>
+ <execution>
+ <id>attach-javadocs</id>
+ <goals>
+ <goal>jar</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-gpg-plugin</artifactId>
+ </plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
@@ -268,64 +303,25 @@
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
- <version>4.8.1</version>
+ <version>4.11</version>
<scope>test</scope>
</dependency>
-
- <dependency>
- <groupId>org.freehep</groupId>
- <artifactId>freehep-java3d</artifactId>
- <version>2.0</version>
- </dependency>
-
<dependency>
<groupId>org.jvnet.jaxb2_commons</groupId>
<artifactId>jaxb2-basics</artifactId>
- <version>0.6.0</version>
- </dependency>
-
- <dependency>
- <groupId>java3d</groupId>
- <artifactId>vecmath</artifactId>
- <version>1.3.1</version>
+ <version>0.9.1</version>
</dependency>
-
-
- </dependencies>
-
- <repositories>
- <repository>
- <id>freehep-maven</id>
- <name>Maven FreeHEP</name>
- <url>http://java.freehep.org/maven2</url>
- </repository>
-
- <repository>
- <id>snapshots</id>
- <name>Syncleus Maven Snapshot Repository</name>
- <url>http://repo.syncleus.com/repository/snapshots/</url>
- <releases>
- <enabled>true</enabled>
- </releases>
- <snapshots>
- <enabled>true</enabled>
- </snapshots>
- </repository>
-
- <repository>
- <id>dependencies</id>
- <name>Syncleus Maven Dependencies Repository</name>
- <url>http://repo.syncleus.com/repository/dependencies/</url>
- <releases>
- <enabled>true</enabled>
- </releases>
- <snapshots>
- <enabled>true</enabled>
- </snapshots>
- </repository>
+ <dependency>
+ <groupId>java3d</groupId>
+ <artifactId>j3d-core</artifactId>
+ </dependency>
- </repositories>
+ <dependency>
+ <groupId>java3d</groupId>
+ <artifactId>j3d-core-utils</artifactId>
+ </dependency>
+ </dependencies>
</project>
diff --git a/src/main/java/com/syncleus/dann/classify/naive/bayes/package-info.java b/src/main/java/com/syncleus/dann/classify/naive/bayes/package-info.java
index bdee7a7f..2806a661 100644
--- a/src/main/java/com/syncleus/dann/classify/naive/bayes/package-info.java
+++ b/src/main/java/com/syncleus/dann/classify/naive/bayes/package-info.java
@@ -20,8 +20,7 @@
/**
* This package contains naive classifiers using Bayes' theorem.
- * See <a href="
- * http://en.wikipedia.org/wiki/Statistical_classification#Bayesian_procedures">
+ * See <a href="http://en.wikipedia.org/wiki/Statistical_classification#Bayesian_procedures">
* Statistical classification - Bayesian procedures</a>.
*/
package com.syncleus.dann.classify.naive.bayes;
diff --git a/src/main/java/com/syncleus/dann/genetics/wavelets/ExpressionFunction.java b/src/main/java/com/syncleus/dann/genetics/wavelets/ExpressionFunction.java
index 2900bcf1..cde2f673 100644
--- a/src/main/java/com/syncleus/dann/genetics/wavelets/ExpressionFunction.java
+++ b/src/main/java/com/syncleus/dann/genetics/wavelets/ExpressionFunction.java
@@ -172,7 +172,9 @@ public class ExpressionFunction implements Cloneable
}
/**
- * Internally mutates.<br/> <br/> may change in any of the following ways:<br/>
+ * Internally mutates.
+ *
+ * may change in any of the following ways:
* <ul> <li>add a new bound wave</li> <li>copy an existing wave and mutates it
* adding the new mutated wave</li> <li>delete an existing wave</li>
* <li>removing a signal</li> <li>Do nothing</li> </ul>
@@ -239,8 +241,10 @@ public class ExpressionFunction implements Cloneable
}
/**
- * Mutates by incorporating a new signal into the mutated result.<br/> <br/>
- * May mutate by:<br/> <ul> <li>adding the new signal</li> </ul>
+ * Mutates by incorporating a new signal into the mutated result.
+ *
+ * May mutate by:
+ * <ul> <li>adding the new signal</li> </ul>
*
* @param newReceptor The new receptor to possibly incorporate into mutation
* @param deviation RANDOM deviation for mutation.
diff --git a/src/main/java/com/syncleus/dann/genetics/wavelets/SignalProcessingWavelet.java b/src/main/java/com/syncleus/dann/genetics/wavelets/SignalProcessingWavelet.java
index 5a2a5ea7..5a45373b 100644
--- a/src/main/java/com/syncleus/dann/genetics/wavelets/SignalProcessingWavelet.java
+++ b/src/main/java/com/syncleus/dann/genetics/wavelets/SignalProcessingWavelet.java
@@ -232,7 +232,10 @@ public class SignalProcessingWavelet implements Comparable<SignalProcessingWavel
}
/**
- * Internally mutates.<br/> <br/> may change in any of the following ways:<br/>
+ * Internally mutates.
+ *
+ * may change in any of the following ways:
+ *
* <ul> <li>add a new bound wave</li> <li>copy an existing wave and mutates it
* adding the new mutated wave</li> <li>delete an existing wave</li>
* <li>removing a signal</li> <li>Do nothing</li> </ul>
@@ -317,9 +320,12 @@ public class SignalProcessingWavelet implements Comparable<SignalProcessingWavel
}
/**
- * Mutates by incorporating a new signal into the mutated result.<br/> <br/>
- * May mutate by:<br/> <ul> <li>adding the new signal</li> </ul>
+ * Mutates by incorporating a new signal into the mutated result.
+ *
+ * May mutate by:
+ * <ul> <li>adding the new signal</li> </ul>
*
+ * @param deviation the deviation used.
* @param newSignal The new signal to incorporate.
* @return New mutated wavelet
*/
diff --git a/src/main/java/com/syncleus/dann/graph/AbstractAdjacencyGraph.java b/src/main/java/com/syncleus/dann/graph/AbstractAdjacencyGraph.java
index 90445346..4ad671ac 100644
--- a/src/main/java/com/syncleus/dann/graph/AbstractAdjacencyGraph.java
+++ b/src/main/java/com/syncleus/dann/graph/AbstractAdjacencyGraph.java
@@ -63,6 +63,9 @@ public abstract class AbstractAdjacencyGraph<N, E extends TraversableCloud<N>> i
/**
* Creates a new AbstractAdjacencyGraph with no edges and no adjacencies.
+ *
+ * @param contextEnabled determines if element context is enabled or not. If enabled then nodes and edges can
+ * be alerted to changes in their graph topology.
*/
protected AbstractAdjacencyGraph(final boolean contextEnabled)
{
@@ -82,6 +85,9 @@ public abstract class AbstractAdjacencyGraph<N, E extends TraversableCloud<N>> i
/**
* Creates a new AbstractAdjacencyGraph as a copy of the current Graph.
+ *
+ * @param contextEnabled determines if element context is enabled or not. If enabled then nodes and edges can
+ * be alerted to changes in their graph topology.
* @param copyGraph The Graph to copy
*/
protected AbstractAdjacencyGraph(final Graph<N, E> copyGraph, final boolean contextEnabled)
@@ -108,6 +114,8 @@ public abstract class AbstractAdjacencyGraph<N, E extends TraversableCloud<N>> i
* the given list of ourEdges.
* The adjacency lists are created from this structure.
*
+ * @param contextEnabled determines if element context is enabled or not. If enabled then nodes and edges can
+ * be alerted to changes in their graph topology.
* @param attemptNodes The set of all nodes
* @param attemptEdges The set of all ourEdges
*/
diff --git a/src/main/java/com/syncleus/dann/graph/drawing/hyperassociativemap/visualization/HyperassociativeMapCanvas.java b/src/main/java/com/syncleus/dann/graph/drawing/hyperassociativemap/visualization/HyperassociativeMapCanvas.java
index 1b085034..acf6e072 100644
--- a/src/main/java/com/syncleus/dann/graph/drawing/hyperassociativemap/visualization/HyperassociativeMapCanvas.java
+++ b/src/main/java/com/syncleus/dann/graph/drawing/hyperassociativemap/visualization/HyperassociativeMapCanvas.java
@@ -112,6 +112,7 @@ public class HyperassociativeMapCanvas<G extends Graph<N, ?>, N> extends JPanel
* Initializes a new HyperassociativeMapCanvas to represent the specified
* HyperassociativeMap.
*
+ * @throws ComponentUnavailableException if Java3D support is not available.
* @param ourMap The HyperassociativeMap to display.
* @since 1.0
*/
@@ -125,6 +126,7 @@ public class HyperassociativeMapCanvas<G extends Graph<N, ?>, N> extends JPanel
* HyperassociativeMap and with nodes represented graphically as spheres with
* the specified radius.
*
+ * @throws ComponentUnavailableException if Java3D support is not available.
* @param ourMap The HyperassociativeMap to display.
* @param nodeRadius The radius of the spheres representing each node.
* @since 1.0
@@ -138,6 +140,7 @@ public class HyperassociativeMapCanvas<G extends Graph<N, ?>, N> extends JPanel
* Initializes a new HyperassociativeMapCanvas to represent the specified
* HyperassociativeMap using the specified GraphicsConfiguration.
*
+ * @throws ComponentUnavailableException if Java3D support is not available.
* @param ourMap The HyperassociativeMap to display.
* @param configuration The GraphicsConfiguration to use for configuring the
* canvas.
diff --git a/src/main/java/com/syncleus/dann/graph/topological/KnotOptimizedGraph.java b/src/main/java/com/syncleus/dann/graph/topological/KnotOptimizedGraph.java
index 7533ab50..38a9f338 100644
--- a/src/main/java/com/syncleus/dann/graph/topological/KnotOptimizedGraph.java
+++ b/src/main/java/com/syncleus/dann/graph/topological/KnotOptimizedGraph.java
@@ -36,6 +36,7 @@ public interface KnotOptimizedGraph<N, E extends TraversableCloud<N>> extends Gr
* connected component of the graph it is weakly connected amongst itself.
*
* @param knotedNodes A set of nodes to check if they form a knot.
+ * @param knotedEdges A set of edges to check if they form a knot.
* @return true if the specified nodes can be traversed to from outside of the
* set, and once the set is entered there is no path to traverse
* outside of the set.
diff --git a/src/main/java/com/syncleus/dann/graph/topological/StructureOptimizedGraph.java b/src/main/java/com/syncleus/dann/graph/topological/StructureOptimizedGraph.java
index 289731ee..32dc5252 100644
--- a/src/main/java/com/syncleus/dann/graph/topological/StructureOptimizedGraph.java
+++ b/src/main/java/com/syncleus/dann/graph/topological/StructureOptimizedGraph.java
@@ -28,6 +28,7 @@ public interface StructureOptimizedGraph<N, E extends TraversableCloud<N>> exten
* also present in this graph. If graph is empty then this will always return
* true.
*
+ * @param graph The graph to check to see if it is a subgraph of this graph.
* @return true if the specified graph only contains nodes and edges that are
* also present in this graph.
* @since 2.0
diff --git a/src/main/java/com/syncleus/dann/graph/topological/Topography.java b/src/main/java/com/syncleus/dann/graph/topological/Topography.java
index 551e71e1..235baf32 100644
--- a/src/main/java/com/syncleus/dann/graph/topological/Topography.java
+++ b/src/main/java/com/syncleus/dann/graph/topological/Topography.java
@@ -52,6 +52,10 @@ public final class Topography
* connect once to this edge and to one or more other nodes, counting once towards the
* degree. However, loop edges can connect twice or more to this node counting multiple
* times.
+ *
+ * @param <N> The type of node allowed in the graph
+ * @param <E> The type of edge allowed in the graph
+ * @param graph The graph to check
* @param node The node whose degree is to be returned
* @return The degree of this node
* @see com.syncleus.dann.graph.topological.Topography#getDegree(Graph,Object)
@@ -100,6 +104,10 @@ public final class Topography
* Determines whether this graph is strongly connected.
* A graph is strongly connected if, and only if every node is strongly
* connected to every other node.
+ *
+ * @param <N> The type of node allowed in the graph
+ * @param <E> The type of edge allowed in the graph
+ * @param graph The graph to check
* @return whether this graph is strongly connected
* @see com.syncleus.dann.graph.topological.Topography#isStronglyConnected(Graph)
*/
@@ -129,6 +137,10 @@ public final class Topography
/**
* Determines whether this graph is weakly connected. A graph is weakly connected if
* there is only one node or every node is weakly connected to every other node.
+ *
+ * @param <N> The type of node allowed in the graph
+ * @param <E> The type of edge allowed in the graph
+ * @param graph The graph to check
* @return If this graph is weakly connected
* @see com.syncleus.dann.graph.topological.Topography#isWeaklyConnected(Graph)
*/
@@ -162,9 +174,13 @@ public final class Topography
/**
* Determines whether two nodes are weakly connected. Nodes are weakly connected if
* there is some path from the left node to the right node, across any adjacent nodes.
- * Assume that the hypothetical <pre>A->B</pre> graph is directional. This graph
+ * Assume that the hypothetical A->B graph is directional. This graph
* would have a strong connection from A to B, but only a weak connection from B to A.
* This graph would, therefore, be weakly connected overall, but not strongly connected overall.
+ *
+ * @param <N> The type of node allowed in the graph
+ * @param <E> The type of edge allowed in the graph
+ * @param graph The graph to check
* @param leftNode The left node
* @param rightNode The right node
* @return Whether there is any connection between the two nodes
@@ -212,6 +228,10 @@ public final class Topography
* if there is some path from the left node to the right node, across any traversable
* nodes. See <code>isWeaklyConnected(N,N)</code> for an example of weak versus strong
* connections.
+ *
+ * @param <N> The type of node allowed in the graph
+ * @param <E> The type of edge allowed in the graph
+ * @param graph The graph to check
* @param leftNode The first node to check
* @param rightNode The second node to check
* @return Whether these nodes are strongly connected
@@ -254,6 +274,10 @@ public final class Topography
* Gets the set of maximally-connected components from a graph. The maximally-connected
* components are those with the most connections to other nodes.
* NOTE: This method currently returns null.
+ *
+ * @param <N> The type of node allowed in the graph
+ * @param <E> The type of edge allowed in the graph
+ * @param graph The graph to check
* @return <code>null</code>
* @see com.syncleus.dann.graph.topological.Topography#getMaximallyConnectedComponents(Graph)
*/
@@ -280,7 +304,11 @@ public final class Topography
* Determines whether the given graph is a maximal subgraph of the current graph.
* A subgraph is maximal if none of the edges of the parent graph not in the subgraph
* connect to any nodes in the subgraph.
- * @param subGraph A subgraph of this graph to be checked if maximally
+ *
+ * @param <N> The type of node allowed in the graph
+ * @param <E> The type of edge allowed in the graph
+ * @param graph The graph to check
+ * @param subGraph A subgraph of the graph to be checked if maximally
* connected.
* @return Whether this is a maximal subgraph
* @see com.syncleus.dann.graph.topological.Topography#isMaximalSubgraph(Graph, Graph)
@@ -750,6 +778,9 @@ public final class Topography
* Simple graphs can not have two nodes connected by two edges differing only
* by its direction/navigability.
*
+ * @param <N> The type of node allowed in the graph
+ * @param <E> The type of edge allowed in the graph
+ * @param graph The graph to check
* @return true if graph has no loops, and all edges have a multiplicity of 0.
* @since 2.0
* @see com.syncleus.dann.graph.topological.Topography#isSimple(Graph)
@@ -783,6 +814,9 @@ public final class Topography
* Determines if every node in this graph has the same degree. If there are no
* nodes in the graph this will return true.
*
+ * @param <N> The type of node allowed in the graph
+ * @param <E> The type of edge allowed in the graph
+ * @param graph The graph to check
* @return true if every node in this graph has the same degree or there are no
* nodes, false otherwise.
* @since 2.0
@@ -816,6 +850,10 @@ public final class Topography
/**
* Gets the degree of the regular graph.
+ *
+ * @param <N> The type of node allowed in the graph
+ * @param <E> The type of edge allowed in the graph
+ * @param graph The graph to check
* @throws IllegalStateException If this graph has no nodes, or the graph is not regular
* @return The degree of the regular graph
* @see com.syncleus.dann.graph.topological.Topography#getRegularDegree(Graph)
@@ -854,6 +892,9 @@ public final class Topography
* Determined the largest multiplicty of any node in the graph and return it.
* Returns 0 if there are no edges.
*
+ * @param <N> The type of node allowed in the graph
+ * @param <E> The type of edge allowed in the graph
+ * @param graph The graph to check
* @return the largest multiplicty of any node in the graph and return it.
* @since 2.0
* @see com.syncleus.dann.graph.topological.Topography#getMultiplicity(Graph)
@@ -887,6 +928,9 @@ public final class Topography
* Calculates the number of edges in the graph with the exact set of end nodes
* as the specified edge, not including the specified edge itself.
*
+ * @param <N> The type of node allowed in the graph
+ * @param <E> The type of edge allowed in the graph
+ * @param graph The graph to check
* @param edge the edge of which the multiplicity is to be calculated.
* @return the number of edges in the graph with the exact set of end nodes as
* the specified edge, not including the specified edge itself.
@@ -936,6 +980,9 @@ public final class Topography
* with the exact same set of nodes, no more and no less, then returns true,
* otherwise false.
*
+ * @param <N> The type of node allowed in the graph
+ * @param <E> The type of edge allowed in the graph
+ * @param graph The graph to check
* @param edge the edge to check if it is multiple.
* @return true if there is another edge in the graph with the exact same set
* of nodes.
@@ -989,6 +1036,9 @@ public final class Topography
*
* NOTE: This method always returns false.
*
+ * @param <N> The type of node allowed in the graph
+ * @param <E> The type of edge allowed in the graph
+ * @param graph The graph to check
* @param knotedNodes A set of nodes to check if they form a knot.
* @return false
* @since 2.0
@@ -1167,6 +1217,10 @@ public final class Topography
* Removes a set of nodes and a set of edges from the given graph.
* First, it removes all nodes from the graph.
* Then, it removes all edges in the edges to remove that are not connected to the given node.
+ *
+ * @param <N> The type of node allowed in the graph
+ * @param <E> The type of edge allowed in the graph
+ * @param graph The graph to check
* @param deleteNodes The nodes to remove
* @param deleteEdges The edges to remove in addition to the nodes
* @return an ImmutableAdjacencyGraph with the given nodes and edges removed
diff --git a/src/main/java/com/syncleus/dann/math/OrderedFieldElement.java b/src/main/java/com/syncleus/dann/math/OrderedFieldElement.java
index fcbf9b37..0e4033ba 100644
--- a/src/main/java/com/syncleus/dann/math/OrderedFieldElement.java
+++ b/src/main/java/com/syncleus/dann/math/OrderedFieldElement.java
@@ -26,6 +26,8 @@ public interface OrderedFieldElement<F extends OrderedFieldElement<? extends F>>
/**
* Returns a constant holding the maximum value a field of this type can
* have.
+ *
+ * @param value the field type which to evaluate
* @return the maximum value a field of this type can have.
*/
F max(F value);
@@ -33,6 +35,8 @@ public interface OrderedFieldElement<F extends OrderedFieldElement<? extends F>>
/**
* Returns a constant holding the minimum value a field of this type can
* have.
+ *
+ * @param value the field type which to evaluate
* @return the minimum value a field of this type can have.
*/
F min(F value);
diff --git a/src/main/java/com/syncleus/dann/math/Vector.java b/src/main/java/com/syncleus/dann/math/Vector.java
index ea00ce94..6a86c67d 100644
--- a/src/main/java/com/syncleus/dann/math/Vector.java
+++ b/src/main/java/com/syncleus/dann/math/Vector.java
@@ -112,6 +112,7 @@ public class Vector implements Serializable
/**
* Sets the specified coordinate.
*
+ * @return returns a new vector with the new coordinate set.
* @param coordinate The new value to set for the coordinate.
* @param dimension The dimension of the coordinate to set.
* @throws IllegalArgumentException Thrown if the coordinate is less than or
@@ -153,6 +154,7 @@ public class Vector implements Serializable
* before this method was called if the distance argument is positive. If
* the distance argument is negative it will invert the vector as well.
*
+ * @return returns a new vector with the new distance set.
* @param distance The new distance for this vector.
* @since 1.0
*/
@@ -175,6 +177,7 @@ public class Vector implements Serializable
* representation of this point. It will keep the other angles and distance
* component close to the same.
*
+ * @return returns a new vector with the new angle set.
* @param angle New angle to set.
* @param dimension Dimension of the angle you want to set.
* @throws IllegalArgumentException Thrown if dimension is less than or
diff --git a/src/main/java/com/syncleus/dann/math/counting/PermutationCounter.java b/src/main/java/com/syncleus/dann/math/counting/PermutationCounter.java
index 8214ca0a..837c8b82 100644
--- a/src/main/java/com/syncleus/dann/math/counting/PermutationCounter.java
+++ b/src/main/java/com/syncleus/dann/math/counting/PermutationCounter.java
@@ -37,6 +37,9 @@ public class PermutationCounter extends AbstractPermutationCounter
* 20! = 2,432,902,008,176,640,000 and
* 21! is too big to fit into permutation Java long, which is
* why we use BigInteger instead.
+ *
+ * @param permutationSize size of the permutation
+ * @param setSize size of the set
*/
public PermutationCounter(final int setSize, final int permutationSize)
{
@@ -47,6 +50,8 @@ public class PermutationCounter extends AbstractPermutationCounter
/**
* Generates the next permutation (algorithm from Rosen p. 284)
+ *
+ * @return true if there is another permutation to retrieve.
*/
@Override
protected boolean next()
diff --git a/src/main/java/com/syncleus/dann/math/linear/Matrix.java b/src/main/java/com/syncleus/dann/math/linear/Matrix.java
index b513a20c..adc74f4d 100644
--- a/src/main/java/com/syncleus/dann/math/linear/Matrix.java
+++ b/src/main/java/com/syncleus/dann/math/linear/Matrix.java
@@ -38,6 +38,7 @@ public interface Matrix<M extends Matrix<? extends M, ? extends F>, F extends Fi
/**
* Set a single element.
*
+ * @return a matrix of the specified dimensions.
* @param heightIndex Row index.
* @param widthIndex Column index.
* @param fillValue value to set
diff --git a/src/main/java/com/syncleus/dann/math/linear/SimpleRealMatrix.java b/src/main/java/com/syncleus/dann/math/linear/SimpleRealMatrix.java
index ed00c0c8..689eb719 100644
--- a/src/main/java/com/syncleus/dann/math/linear/SimpleRealMatrix.java
+++ b/src/main/java/com/syncleus/dann/math/linear/SimpleRealMatrix.java
@@ -42,13 +42,15 @@ import org.apache.log4j.Logger;
* Methods for reading and printing matrices are also included. All the
* operations in this version of the SimpleRealMatrix Class involve real
* matrices. Complex matrices may be handled in a future version.
- * <p/>
+ *
* Five fundamental matrix decompositions, which consist of pairs or triples of
* matrices, permutation vectors, and the like, produce results in five
* decomposition classes. These decompositions are accessed by the
* SimpleRealMatrix class to compute solutions of simultaneous linear equations,
* determinants, inverses and other matrix functions. The five decompositions
- * are: <P><UL> <LI>Cholesky Decomposition of symmetric, positive definite
+ * are:
+ *
+ * <UL> <LI>Cholesky Decomposition of symmetric, positive definite
* matrices. <LI>LU Decomposition of rectangular matrices. <LI>QR Decomposition
* of rectangular matrices. <LI>Singular Value Decomposition of rectangular
* matrices. <LI>Eigenvalue Decomposition of both symmetric and non-symmetric
@@ -165,6 +167,7 @@ public class SimpleRealMatrix implements Cloneable, Serializable, RealMatrix
/**
* Construct a matrix from a copy of a 2-D array.
*
+ * @return a new matrix copying the elements specified.
* @param matrixElements Two-dimensional array of doubles.
* @throws IllegalArgumentException All rows must have the same length
*/
@@ -175,6 +178,8 @@ public class SimpleRealMatrix implements Cloneable, Serializable, RealMatrix
/**
* Creates a deep copy of a matrix.
+ *
+ * @return A new RealMatrix representing a deep copy of this matrix.
*/
public RealMatrix copy()
{
diff --git a/src/main/java/com/syncleus/dann/math/linear/decomposition/CholeskyBanachiewiczCholeskyDecomposition.java b/src/main/java/com/syncleus/dann/math/linear/decomposition/CholeskyBanachiewiczCholeskyDecomposition.java
index ec8de13b..862a8d72 100644
--- a/src/main/java/com/syncleus/dann/math/linear/decomposition/CholeskyBanachiewiczCholeskyDecomposition.java
+++ b/src/main/java/com/syncleus/dann/math/linear/decomposition/CholeskyBanachiewiczCholeskyDecomposition.java
@@ -28,10 +28,10 @@ import com.syncleus.dann.math.linear.Matrix;
/**
* Cholesky Decomposition.
- * <p/>
+ *
* For a symmetric, positive definite matrix A, the Cholesky decomposition is an
* lower triangular matrix L so that A = L*L'.
- * <p/>
+ *
* If the matrix is not symmetric or positive definite, the constructor returns
* a partial decomposition and sets an internal flag that may be queried by the
* isSpd() method.
diff --git a/src/main/java/com/syncleus/dann/math/linear/decomposition/CholeskyCroutCholeskyDecomposition.java b/src/main/java/com/syncleus/dann/math/linear/decomposition/CholeskyCroutCholeskyDecomposition.java
index fd241317..822fd46b 100644
--- a/src/main/java/com/syncleus/dann/math/linear/decomposition/CholeskyCroutCholeskyDecomposition.java
+++ b/src/main/java/com/syncleus/dann/math/linear/decomposition/CholeskyCroutCholeskyDecomposition.java
@@ -37,9 +37,9 @@ public class CholeskyCroutCholeskyDecomposition<M extends Matrix<M, F>, F extend
/**
* Right Triangular Cholesky Decomposition.
- * <p/>
+ *
* Cholesky algorithm for symmetric and positive definite matrix.
- * <p/>
+ *
* For a symmetric, positive definite matrix A, the Right Cholesky
* decomposition is an upper triangular matrix R so that A = R'*R. This
* constructor computes R with the Fortran inspired column oriented algorithm
diff --git a/src/main/java/com/syncleus/dann/math/linear/decomposition/CholeskyDecomposition.java b/src/main/java/com/syncleus/dann/math/linear/decomposition/CholeskyDecomposition.java
index 708ce264..1b4432c7 100644
--- a/src/main/java/com/syncleus/dann/math/linear/decomposition/CholeskyDecomposition.java
+++ b/src/main/java/com/syncleus/dann/math/linear/decomposition/CholeskyDecomposition.java
@@ -23,10 +23,10 @@ import com.syncleus.dann.math.linear.Matrix;
/**
* Cholesky Decomposition.
- * <p/>
+ *
* For a symmetric, positive definite matrix A, the Cholesky decomposition is an
* lower triangular matrix L so that A = L*L'.
- * <p/>
+ *
* If the matrix is not symmetric or positive definite, the constructor returns
* a partial decomposition and sets an internal flag that may be queried by the
* isSpd() method.
diff --git a/src/main/java/com/syncleus/dann/math/linear/decomposition/DoolittleLuDecomposition.java b/src/main/java/com/syncleus/dann/math/linear/decomposition/DoolittleLuDecomposition.java
index 8c52c62a..985e3a4a 100644
--- a/src/main/java/com/syncleus/dann/math/linear/decomposition/DoolittleLuDecomposition.java
+++ b/src/main/java/com/syncleus/dann/math/linear/decomposition/DoolittleLuDecomposition.java
@@ -32,14 +32,14 @@ import com.syncleus.dann.math.linear.Matrix;
/**
* matrixToDecomposeElements Decomposition.
- * <p/>
- * For an height-by-width matrix matrixToDecompose with height >= width, the
+ *
+ * For an height-by-width matrix matrixToDecompose with height >= width, the
* matrixToDecomposeElements decomposition is an height-by-width unit lower
* triangular matrix lowerTriangularFactor, an width-by-width upper triangular
* matrix U, and a permutation vector pivot of length height so that
- * matrixToDecompose(pivot,:) = lowerTriangularFactor*U. If height < width, then
+ * matrixToDecompose(pivot,:) = lowerTriangularFactor*U. If height < width, then
* lowerTriangularFactor is height-by-height and U is height-by-width.
- * <p/>
+ *
* The matrixToDecomposeElements decomposition with pivoting always exists, even
* if the matrix is singular, so the constructor will never fail. The primary
* use of the matrixToDecomposeElements decomposition is in the solution of
diff --git a/src/main/java/com/syncleus/dann/math/linear/decomposition/HouseholderQrDecomposition.java b/src/main/java/com/syncleus/dann/math/linear/decomposition/HouseholderQrDecomposition.java
index 2cfdd5b8..96478cb3 100644
--- a/src/main/java/com/syncleus/dann/math/linear/decomposition/HouseholderQrDecomposition.java
+++ b/src/main/java/com/syncleus/dann/math/linear/decomposition/HouseholderQrDecomposition.java
@@ -32,11 +32,11 @@ import com.syncleus.dann.math.linear.Matrix;
/**
* QR Decomposition.
- * <p/>
- * For an m-by-n matrix matrixToDecompose with m >= n, the QR decomposition is
+ *
+ * For an m-by-n matrix matrixToDecompose with m >= n, the QR decomposition is
* an m-by-n orthogonal matrix factor and an n-by-n upper triangular matrix
* factor so that matrixToDecompose = factor*factor.
- * <p/>
+ *
* The QR decomposition always exists, even if the matrix does not have full
* rank, so the constructor will never fail. The primary use of the QR
* decomposition is in the least squares solution of non-square systems of
diff --git a/src/main/java/com/syncleus/dann/math/linear/decomposition/LuDecomposition.java b/src/main/java/com/syncleus/dann/math/linear/decomposition/LuDecomposition.java
index 0f97ca5b..6eb78837 100644
--- a/src/main/java/com/syncleus/dann/math/linear/decomposition/LuDecomposition.java
+++ b/src/main/java/com/syncleus/dann/math/linear/decomposition/LuDecomposition.java
@@ -23,14 +23,14 @@ import com.syncleus.dann.math.linear.Matrix;
/**
* matrixToDecomposeElements Decomposition.
- * <p/>
- * For an height-by-width matrix matrixToDecompose with height >= width, the
+ *
+ * For an height-by-width matrix matrixToDecompose with height >= width, the
* matrixToDecomposeElements decomposition is an height-by-width unit lower
* triangular matrix lowerTriangularFactor, an width-by-width upper triangular
* matrix U, and a permutation vector pivot of length height so that
- * matrixToDecompose(pivot,:) = lowerTriangularFactor*U. If height < width, then
+ * matrixToDecompose(pivot,:) = lowerTriangularFactor*U. If height < width, then
* lowerTriangularFactor is height-by-height and U is height-by-width.
- * <p/>
+ *
* The matrixToDecomposeElements decompostion with pivoting always exists, even
* if the matrix is singular, so the constructor will never fail. The primary
* use of the matrixToDecomposeElements decomposition is in the solution of
diff --git a/src/main/java/com/syncleus/dann/math/linear/decomposition/QrDecomposition.java b/src/main/java/com/syncleus/dann/math/linear/decomposition/QrDecomposition.java
index e02ee2b1..7d83fab8 100644
--- a/src/main/java/com/syncleus/dann/math/linear/decomposition/QrDecomposition.java
+++ b/src/main/java/com/syncleus/dann/math/linear/decomposition/QrDecomposition.java
@@ -23,11 +23,11 @@ import com.syncleus.dann.math.linear.Matrix;
/**
* QR Decomposition.
- * <p/>
- * For an m-by-n matrix matrixToDecompose with m >= n, the QR decomposition is
+ *
+ * For an m-by-n matrix matrixToDecompose with m >= n, the QR decomposition is
* an m-by-n orthogonal matrix factor and an n-by-n upper triangular matrix
* factor so that matrixToDecompose = factor*factor.
- * <p/>
+ *
* The QR decompostion always exists, even if the matrix does not have full
* rank, so the constructor will never fail. The primary use of the QR
* decomposition is in the least squares solution of nonsquare systems of
diff --git a/src/main/java/com/syncleus/dann/math/linear/decomposition/SingularValueDecomposition.java b/src/main/java/com/syncleus/dann/math/linear/decomposition/SingularValueDecomposition.java
index 5b89790b..fc85164f 100644
--- a/src/main/java/com/syncleus/dann/math/linear/decomposition/SingularValueDecomposition.java
+++ b/src/main/java/com/syncleus/dann/math/linear/decomposition/SingularValueDecomposition.java
@@ -24,17 +24,17 @@ import com.syncleus.dann.math.linear.RealMatrix;
/**
* Singular Value Decomposition.
- * <p/>
- * For an m-by-n matrix A with m >= n, the singular value decomposition is an
+ *
+ * For an m-by-n matrix A with m >= n, the singular value decomposition is an
* m-by-n orthogonal matrix U, an n-by-n diagonal matrix S, and an n-by-n
* orthogonal matrix V so that A = U*S*V'.
- * <p/>
- * The singular values, sigma[k] = S[k][k], are ordered so that sigma[0] >=
- * sigma[1] >= ... >= sigma[n-1].
- * <p/>
+ *
+ * The singular values, sigma[k] = S[k][k], are ordered so that sigma[0] >=
+ * sigma[1] >= ... >= sigma[n-1].
+ *
* The singular value decompostion always exists, so the constructor will never
* fail. The matrix condition number and the effective numerical rank can be
- * computed from this decomposition.<br/>
+ * computed from this decomposition.
*/
public interface SingularValueDecomposition extends Decomposition<RealMatrix>
{
diff --git a/src/main/java/com/syncleus/dann/math/linear/decomposition/StewartSingularValueDecomposition.java b/src/main/java/com/syncleus/dann/math/linear/decomposition/StewartSingularValueDecomposition.java
index 7b71650f..ca146bae 100644
--- a/src/main/java/com/syncleus/dann/math/linear/decomposition/StewartSingularValueDecomposition.java
+++ b/src/main/java/com/syncleus/dann/math/linear/decomposition/StewartSingularValueDecomposition.java
@@ -31,20 +31,20 @@ import com.syncleus.dann.math.linear.SimpleRealMatrix;
/**
* Singular Value Decomposition.
- * <p/>
- * For an m-by-n matrix A with m >= n, the singular value decomposition is an
+ *
+ * For an m-by-n matrix A with m >= n, the singular value decomposition is an
* m-by-n orthogonal matrix leftSingularMatrix, an n-by-n diagonal matrix S, and
* an n-by-n orthogonal matrix rightSingularMatrix so that A =
* leftSingularMatrix*S*rightSingularMatrix'.
- * <p/>
- * The singular values, sigma[k] = S[k][k], are ordered so that sigma[0] >=
- * sigma[1] >= ... >= sigma[n-1].
- * <p/>
+ *
+ * The singular values, sigma[k] = S[k][k], are ordered so that sigma[0] >=
+ * sigma[1] >= ... >= sigma[n-1].
+ *
* The singular value decomposition always exists, so the constructor will never
* fail. The matrix condition number and the effective numerical rank can be
- * computed from this decomposition.<br/> Algorithm taken from: G.W. Stewart,
- * university of Maryland, Argonne national lab. C
- * @author Jeffrey Phillips Freeman
+ * computed from this decomposition.
+ *
+ * Algorithm taken from: G.W. Stewart. university of Maryland, Argonne national lab. C
*/
public class StewartSingularValueDecomposition implements java.io.Serializable, SingularValueDecomposition
{
diff --git a/src/main/java/com/syncleus/dann/math/linear/decomposition/TridiagonalEignevalueDecomposition.java b/src/main/java/com/syncleus/dann/math/linear/decomposition/TridiagonalEignevalueDecomposition.java
index b9b9b5a3..c320b130 100644
--- a/src/main/java/com/syncleus/dann/math/linear/decomposition/TridiagonalEignevalueDecomposition.java
+++ b/src/main/java/com/syncleus/dann/math/linear/decomposition/TridiagonalEignevalueDecomposition.java
@@ -32,14 +32,14 @@ import com.syncleus.dann.math.linear.SimpleRealMatrix;
/**
* Eigenvalues and eigenvectors of a real matrix.
- * <p/>
+ *
* If matrixToDecomposeElements is symmetric, then matrixToDecomposeElements =
* matrixElements*D*matrixElements' where the eigenvalue matrix D is diagonal
* and the eigenvector matrix matrixElements is orthogonal. I.e.
* matrixToDecomposeElements = matrixElements.times(D.times(matrixElements.transpose()))
* and matrixElements.times(matrixElements.transpose()) equals the identity
* matrix.
- * <p/>
+ *
* If matrixToDecomposeElements is not symmetric, then the eigenvalue matrix D
* is block diagonal with the real eigenvalues in 1-by-1 blocks and any complex
* eigenvalues, lambda + i*mu, in 2-by-2 blocks, [lambda, mu; -mu, lambda]. The
diff --git a/src/main/java/com/syncleus/dann/math/visualization/MathFunctionCanvas.java b/src/main/java/com/syncleus/dann/math/visualization/MathFunctionCanvas.java
deleted file mode 100644
index 5e47db58..00000000
--- a/src/main/java/com/syncleus/dann/math/visualization/MathFunctionCanvas.java
+++ /dev/null
@@ -1,167 +0,0 @@
-/******************************************************************************
- * *
- * Copyright: (c) Syncleus, Inc. *
- * *
- * You may redistribute and modify this source code under the terms and *
- * conditions of the Open Source Community License - Type C version 1.0 *
- * or any later version as published by Syncleus, Inc. at www.syncleus.com. *
- * There should be a copy of the license included with this file. If a copy *
- * of the license is not included you are granted no right to distribute or *
- * otherwise use this file except through a legal and valid license. You *
- * should also contact Syncleus, Inc. at the information below if you cannot *
- * find a license: *
- * *
- * Syncleus, Inc. *
- * 2604 South 12th Street *
- * Philadelphia, PA 19148 *
- * *
- ******************************************************************************/
-package com.syncleus.dann.math.visualization;
-
-import com.syncleus.dann.math.Function;
-import org.freehep.j3d.plot.Binned2DData;
-import org.freehep.j3d.plot.SurfacePlot;
-
-public class MathFunctionCanvas extends SurfacePlot
-{
- private static final long serialVersionUID = -6107827702991178553L;
- private Function function;
- private int xIndex;
- private int yIndex;
- private float xMin;
- private float xMax;
- private float yMin;
- private float yMax;
- private int resolution;
-
- public MathFunctionCanvas(final Function function, final String xParameter, final String yParameter, final float xMin, final float xMax, final float yMin, final float yMax, final int resolution)
- {
- super();
-
- this.function = function;
- this.xIndex = this.function.getParameterNameIndex(xParameter);
- this.yIndex = this.function.getParameterNameIndex(yParameter);
- this.xMin = xMin;
- this.xMax = xMax;
- this.yMin = yMin;
- this.yMax = yMax;
- this.resolution = resolution;
- this.setLogZscaling(false);
- this.refresh();
- }
-
- private void refresh()
- {
- final MathFunctionDataBinder dataBinder = new MathFunctionDataBinder(
- this.function,
- this.function.getParameterName(this.xIndex),
- this.function.getParameterName(this.yIndex),
- this.xMin,
- this.xMax,
- this.yMin,
- this.yMax,
- this.resolution);
- super.setData(dataBinder);
- }
-
- public void setFunction(final Function newFunction, final String xParameter, final String yParameter)
- {
- this.function = newFunction;
- this.xIndex = this.function.getParameterNameIndex(xParameter);
- this.yIndex = this.function.getParameterNameIndex(yParameter);
-
- this.refresh();
- }
-
- public Function getFunction()
- {
- return this.function;
- }
-
- public int getXIndex()
- {
- return this.xIndex;
- }
-
- public int getYIndex()
- {
- return this.yIndex;
- }
-
- public int getResolution()
- {
- return this.resolution;
- }
-
- public float getXMax()
- {
- return this.xMax;
- }
-
- public float getXMin()
- {
- return this.xMin;
- }
-
- public float getYMax()
- {
- return this.yMax;
- }
-
- public float getYMin()
- {
- return this.yMin;
- }
-
- @Override
- public void setData(final Binned2DData data)
- {
- if( data instanceof MathFunctionDataBinder )
- {
- final MathFunctionDataBinder mathFunctionData = (MathFunctionDataBinder) data;
-
- this.function = mathFunctionData.getFunction();
- this.xIndex = mathFunctionData.getXIndex();
- this.yIndex = mathFunctionData.getYIndex();
- this.setXMin(mathFunctionData.xMin());
- this.setXMax(mathFunctionData.xMax());
- this.setYMin(mathFunctionData.yMin());
- this.setYMax(mathFunctionData.yMax());
- this.setResolution(mathFunctionData.getResolution());
-
- this.refresh();
- }
- else
- throw new IllegalArgumentException("data must be a MathFunction3dDataBinder");
- }
-
- public void setXMin(final float xMin)
- {
- this.xMin = xMin;
- this.refresh();
- }
-
- public void setXMax(final float xMax)
- {
- this.xMax = xMax;
- this.refresh();
- }
-
- public void setYMin(final float yMin)
- {
- this.yMin = yMin;
- this.refresh();
- }
-
- public void setYMax(final float yMax)
- {
- this.yMax = yMax;
- this.refresh();
- }
-
- public void setResolution(final int resolution)
- {
- this.resolution = resolution;
- this.refresh();
- }
-}
diff --git a/src/main/java/com/syncleus/dann/math/visualization/MathFunctionDataBinder.java b/src/main/java/com/syncleus/dann/math/visualization/MathFunctionDataBinder.java
deleted file mode 100644
index 38e06d0c..00000000
--- a/src/main/java/com/syncleus/dann/math/visualization/MathFunctionDataBinder.java
+++ /dev/null
@@ -1,239 +0,0 @@
-/******************************************************************************
- * *
- * Copyright: (c) Syncleus, Inc. *
- * *
- * You may redistribute and modify this source code under the terms and *
- * conditions of the Open Source Community License - Type C version 1.0 *
- * or any later version as published by Syncleus, Inc. at www.syncleus.com. *
- * There should be a copy of the license included with this file. If a copy *
- * of the license is not included you are granted no right to distribute or *
- * otherwise use this file except through a legal and valid license. You *
- * should also contact Syncleus, Inc. at the information below if you cannot *
- * find a license: *
- * *
- * Syncleus, Inc. *
- * 2604 South 12th Street *
- * Philadelphia, PA 19148 *
- * *
- ******************************************************************************/
-package com.syncleus.dann.math.visualization;
-
-import java.awt.Color;
-import javax.vecmath.Color3b;
-import org.freehep.j3d.plot.Binned2DData;
-import com.syncleus.dann.math.Function;
-
-public final class MathFunctionDataBinder implements Binned2DData
-{
- private final Function function;
- private final int functionXIndex;
- private final int functionYIndex;
- private final float minX;
- private final float maxX;
- private final float minY;
- private final float maxY;
- private final float minZ;
- private final float maxZ;
- private final int resolution;
-
- public MathFunctionDataBinder(final Function function,
- final String functionXParam,
- final String functionYParam,
- final float xMin,
- final float xMax,
- final float yMin,
- final float yMax,
- final int resolution)
- {
- if( resolution <= 0 )
- throw new IllegalArgumentException("resolution must be greater than 0");
- this.function = function;
- this.functionXIndex = this.function.getParameterNameIndex(functionXParam);
- this.functionYIndex = this.function.getParameterNameIndex(functionYParam);
- this.minX = xMin;
- this.maxX = xMax;
- this.minY = yMin;
- this.maxY = yMax;
- this.resolution = resolution;
- boolean zMaxSet = false;
- boolean zMinSet = false;
- float newZMax = 1.0f;
- float newZMin = -1.0f;
- for(int xIndex = 0; xIndex < this.xBins(); xIndex++)
- {
- this.setX(this.convertFromXIndex(xIndex));
- for(int yIndex = 0; yIndex < this.yBins(); yIndex++)
- {
- this.setY(this.convertFromYIndex(yIndex));
- final float currentZ = (float) this.calculateZ();
- if( !Float.isNaN(currentZ) )
- {
- if( (newZMax < currentZ) || (!zMaxSet) )
- {
- newZMax = currentZ;
- zMaxSet = true;
- }
- if( (newZMin > currentZ) || (!zMinSet) )
- {
- newZMin = currentZ;
- zMinSet = true;
- }
- }
- }
- }
- if( newZMax == newZMin )
- {
- newZMax += (float) 1.0;
- newZMin -= (float) 1.0;
- }
- this.maxZ = newZMax;
- this.minZ = newZMin;
- assert ((!Float.isNaN(this.maxZ)) && (!Float.isNaN(this.minZ)));
- }
-
- private float convertFromXIndex(final int xCoord)
- {
- final float xSize = this.maxX - this.minX;
- return (((float) xCoord) / ((float) this.xBins())) * xSize + this.minX;
- }
-
- private float convertFromYIndex(final int yCoord)
- {
- final float ySize = this.maxY - this.minY;
- return (((float) (this.yBins() - yCoord)) / ((float) this.yBins())) * ySize + this.minY;
- }
-
- public Function getFunction()
- {
- return this.function;
- }
-
- public int getXIndex()
- {
- return this.functionXIndex;
- }
-
- public int getYIndex()
- {
- return this.functionYIndex;
- }
-
- public int getResolution()
- {
- return this.resolution;
- }
-
- private void setX(final double xCoord)
- {
- this.function.setParameter(this.functionXIndex, xCoord);
- }
-
- private void setY(final double yCoord)
- {
- this.function.setParameter(this.functionYIndex, yCoord);
- }
-
- private double calculateZ()
- {
- return this.function.calculate();
- }
-
- private Color colorAtPoint(final int xIndex, final int yIndex)
- {
- final float xCoord = this.convertFromXIndex(xIndex);
- final float yCoord = this.convertFromYIndex(yIndex);
-
- this.setX(xCoord);
- this.setY(yCoord);
- final double zCoord = this.calculateZ();
-
-
- if( zCoord > this.maxZ )
- return new Color(0.0f, 0.0f, 0.0f);
- else if( zCoord < this.minZ )
- return new Color(0.0f, 0.0f, 0.0f);
- else
- {
- final float redValue = (float) (zCoord - this.minZ) / (this.maxZ - this.minZ);
- final float blueValue = 1.0f - redValue;
- final float greenValue = 0.0f;
-
- return new Color(redValue, greenValue, blueValue);
- }
- }
-
- @Override
- public Color3b colorAt(final int xIndex, final int yIndex)
- {
- return new Color3b(colorAtPoint(xIndex, yIndex));
- }
-
- @Override
- public int xBins()
- {
- return this.resolution;
- }
-
- @Override
- public float xMax()
- {
- return this.maxX;
- }
-
- @Override
- public float xMin()
- {
- return this.minX;
- }
-
- @Override
- public int yBins()
- {
- return this.resolution;
- }
-
- @Override
- public float yMax()
- {
- return this.maxY;
- }
-
- @Override
- public float yMin()
- {
- return this.minY;
- }
-
- @Override
- public float zAt(final int xIndex, final int yIndex)
- {
- final float xCoord = this.convertFromXIndex(xIndex);
- final float yCoord = this.convertFromYIndex(yIndex);
-
- this.setX(xCoord);
- this.setY(yCoord);
- final float zCoord = (float) this.calculateZ();
-
-
- if( zCoord < this.minZ )
- return this.minZ;
- else if( zCoord > this.maxZ )
- return this.maxZ;
- else if( Float.isNaN(zCoord) )
- return 0.0f;
- else
- return zCoord;
- }
-
- @Override
- public float zMax()
- {
- return this.maxZ;
- }
-
- @Override
- public float zMin()
- {
- return this.minZ;
- }
-}
diff --git a/src/main/java/com/syncleus/dann/neural/AbstractActivationNeuron.java b/src/main/java/com/syncleus/dann/neural/AbstractActivationNeuron.java
index 8a62331c..3d2183e6 100644
--- a/src/main/java/com/syncleus/dann/neural/AbstractActivationNeuron.java
+++ b/src/main/java/com/syncleus/dann/neural/AbstractActivationNeuron.java
@@ -55,6 +55,7 @@ public abstract class AbstractActivationNeuron extends AbstractNeuron
* Creates a new instance of NeuronImpl with a RANDOM bias weight and
* HyperbolicTangentActivationFunction as the activation function.
*
+ * @param brain The brain which contains this neuron.
* @since 1.0
*/
protected AbstractActivationNeuron(final Brain<InputNeuron, OutputNeuron, Neuron, Synapse<Neuron>> brain)
@@ -67,6 +68,7 @@ public abstract class AbstractActivationNeuron extends AbstractNeuron
* Creates a new instance of NeuronImpl with a RANDOM bias weight and the
* specified activation function.
*
+ * @param brain The brain which contains this neuron.
* @param activationFunction The activation function used to calculate the
* output from the neuron's activity.
* @since 1.0
diff --git a/src/main/java/com/syncleus/dann/neural/AbstractLocalBrain.java b/src/main/java/com/syncleus/dann/neural/AbstractLocalBrain.java
index 3635ba26..7460e3b0 100644
--- a/src/main/java/com/syncleus/dann/neural/AbstractLocalBrain.java
+++ b/src/main/java/com/syncleus/dann/neural/AbstractLocalBrain.java
@@ -37,8 +37,9 @@ import com.syncleus.dann.graph.topological.StrongConnectivityOptimizedGraph;
/**
* Represents a single artificial brain typically belonging to a single
* artificial organism. It will contain a set of input and output neurons which
- * corelate to a specific dataset pattern.<br/> <br/> This class is abstract
- * and must be extended in order to be used.
+ * corelate to a specific dataset pattern.
+ *
+ * This class is abstract and must be extended in order to be used.
*
* @author Jeffrey Phillips Freeman
* @since 1.0
@@ -118,6 +119,7 @@ public abstract class AbstractLocalBrain<IN extends InputNeuron, ON extends Outp
* Adds a new neuron to the brain. The construction of the brain is done by
* the child class so this method is protected.
*
+ * @return true if neuron was added to the graph, false otherwise.
* @param newNeuron The neuron to add to the brain.
* @since 1.0
*/
@@ -145,6 +147,7 @@ public abstract class AbstractLocalBrain<IN extends InputNeuron, ON extends Outp
* Adds a new collection of neurons to the brain. The construction of the brain
* is done by the child class so this method is protected.
*
+ * @return true if neuron was added to the graph, false otherwise.
* @param newNeurons The collection of neurons to add.
* @since 1.0
*/
@@ -238,6 +241,7 @@ public abstract class AbstractLocalBrain<IN extends InputNeuron, ON extends Outp
* Removes the specified neuron from the brain. This only removes it from
* the collection of neurons it does not disconnect it from other neurons.
*
+ * @return true if neuron was removed from the graph, false otherwise.
* @param removeNeuron The neuron to remove.
* @since 1.0
*/
diff --git a/src/main/java/com/syncleus/dann/neural/AbstractNeuron.java b/src/main/java/com/syncleus/dann/neural/AbstractNeuron.java
index eb60c99d..b50bc7c8 100644
--- a/src/main/java/com/syncleus/dann/neural/AbstractNeuron.java
+++ b/src/main/java/com/syncleus/dann/neural/AbstractNeuron.java
@@ -34,6 +34,7 @@ public abstract class AbstractNeuron implements Neuron
* Creates a new instance of NeuronImpl with a RANDOM bias weight and
* HyperbolicTangentActivationFunction as the activation function.
*
+ * @param brain The brain which contains this neuron.
* @since 1.0
*/
protected AbstractNeuron(final Brain<InputNeuron, OutputNeuron, Neuron, Synapse<Neuron>> brain)
diff --git a/src/main/java/com/syncleus/dann/neural/AbstractSynapse.java b/src/main/java/com/syncleus/dann/neural/AbstractSynapse.java
index bbbd790b..8559e4f0 100644
--- a/src/main/java/com/syncleus/dann/neural/AbstractSynapse.java
+++ b/src/main/java/com/syncleus/dann/neural/AbstractSynapse.java
@@ -69,6 +69,8 @@ public abstract class AbstractSynapse<N> extends AbstractDirectedEdge<N> impleme
/**
* Creates a new instance of AbstractSynapse.
*
+ * @param contextEnabled true if context awareness is enabled in this synapse
+ * @param allowJoiningMultipleGraphs True if the synapse is allowed to exist in more than one graph at a time.
* @param sourceToSet The incoming neuron connection.
* @param destinationToSet The outgoing neuron connection.
* @param initialWeight The initial weight of the synapse
@@ -83,6 +85,8 @@ public abstract class AbstractSynapse<N> extends AbstractDirectedEdge<N> impleme
/**
* Creates a new instance of AbstractSynapse.
*
+ * @param contextEnabled true if context awareness is enabled in this synapse
+ * @param allowJoiningMultipleGraphs True if the synapse is allowed to exist in more than one graph at a time.
* @param sourceToSet The incoming neuron connection.
* @param destinationToSet The outgoing neuron connection.
* @since 1.0
diff --git a/src/main/java/com/syncleus/dann/neural/NeuronGroup.java b/src/main/java/com/syncleus/dann/neural/NeuronGroup.java
index 8f0be7ee..70907b0c 100644
--- a/src/main/java/com/syncleus/dann/neural/NeuronGroup.java
+++ b/src/main/java/com/syncleus/dann/neural/NeuronGroup.java
@@ -111,6 +111,7 @@ public class NeuronGroup<N extends Neuron> implements java.io.Serializable
/**
* Obtains all the Neurons directly owned by this NeuronGroup.
*
+ * @return A set of all neurons directly owned by this group.
* @since 1.0
*/
public Set<N> getChildrenNeurons()
@@ -121,6 +122,7 @@ public class NeuronGroup<N extends Neuron> implements java.io.Serializable
/**
* Obtains all the NeuronGroups directly owned by this NeuronGroup.
*
+ * @return A set of all NeuronGroups owned directly by this group.
* @since 1.0
*/
public Set<NeuronGroup<? extends N>> getChildrenNeuronGroups()
@@ -130,8 +132,9 @@ public class NeuronGroup<N extends Neuron> implements java.io.Serializable
/**
* Obtains all the NetworkNodes owned recursively excluding
- * NeuronGroups.<BR>
+ * NeuronGroups.
*
+ * @return a set of all the NetworkNodes owned recursively by this group, excluding NeuronGroups.
* @since 1.0
*/
public Set<N> getChildrenNeuronsRecursivly()
diff --git a/src/main/java/com/syncleus/dann/neural/SimpleSynapse.java b/src/main/java/com/syncleus/dann/neural/SimpleSynapse.java
index b302f6bf..3750ac7c 100644
--- a/src/main/java/com/syncleus/dann/neural/SimpleSynapse.java
+++ b/src/main/java/com/syncleus/dann/neural/SimpleSynapse.java
@@ -59,6 +59,8 @@ public final class SimpleSynapse<N> extends AbstractSynapse<N>
/**
* Creates a new instance of SimpleSynapse.
*
+ * @param contextEnabled true if context awareness is enabled in this synapse
+ * @param allowJoiningMultipleGraphs True if the synapse is allowed to exist in more than one graph at a time.
* @param sourceToSet The incoming neuron connection.
* @param destinationToSet The outgoing neuron connection.
* @param initialWeight The initial weight of the synapse
@@ -72,6 +74,8 @@ public final class SimpleSynapse<N> extends AbstractSynapse<N>
/**
* Creates a new instance of SimpleSynapse.
*
+ * @param contextEnabled true if context awareness is enabled in this synapse
+ * @param allowJoiningMultipleGraphs True if the synapse is allowed to exist in more than one graph at a time.
* @param sourceToSet The incoming neuron connection.
* @param destinationToSet The outgoing neuron connection.
* @since 1.0
diff --git a/src/main/java/com/syncleus/dann/neural/backprop/AbstractBackpropNeuron.java b/src/main/java/com/syncleus/dann/neural/backprop/AbstractBackpropNeuron.java
index 1cbb3dab..458bada8 100644
--- a/src/main/java/com/syncleus/dann/neural/backprop/AbstractBackpropNeuron.java
+++ b/src/main/java/com/syncleus/dann/neural/backprop/AbstractBackpropNeuron.java
@@ -50,6 +50,7 @@ public abstract class AbstractBackpropNeuron extends AbstractActivationNeuron im
/**
* Creates a new default instance of SimpleBackpropNeuron.
*
+ * @param brain The brain which contains this neuron.
* @since 1.0
*/
protected AbstractBackpropNeuron(final Brain brain)
@@ -61,6 +62,7 @@ public abstract class AbstractBackpropNeuron extends AbstractActivationNeuron im
* Creates a new instance of SimpleBackpropNeuron with the specified
* activation function.
*
+ * @param brain The brain which contains this neuron.
* @param activationFunction The Neuron's activation function.
* @since 1.0
*/
@@ -73,6 +75,7 @@ public abstract class AbstractBackpropNeuron extends AbstractActivationNeuron im
* Creates a new instance of a SimpleBackpropNeuron using the default
* activation function with the specified learning rate.
*
+ * @param brain The brain which contains this neuron.
* @param learningRate learning rate of this neuron.
* @since 1.0
*/
@@ -86,6 +89,7 @@ public abstract class AbstractBackpropNeuron extends AbstractActivationNeuron im
* Creates a new instance of a SimpleBackpropNeuron with the specified
* activation function and learning rate.
*
+ * @param brain The brain which contains this neuron.
* @param activationFunction Activation function for this neuron.
* @param learningRate Learning rate for this neuron.
*/
diff --git a/src/main/java/com/syncleus/dann/neural/backprop/AbstractOutputBackpropNeuron.java b/src/main/java/com/syncleus/dann/neural/backprop/AbstractOutputBackpropNeuron.java
index 0d99d092..16c0af14 100644
--- a/src/main/java/com/syncleus/dann/neural/backprop/AbstractOutputBackpropNeuron.java
+++ b/src/main/java/com/syncleus/dann/neural/backprop/AbstractOutputBackpropNeuron.java
@@ -35,6 +35,7 @@ public abstract class AbstractOutputBackpropNeuron extends AbstractBackpropNeuro
/**
* Creates a new instance of OutputBackpropNeuron.
*
+ * @param brain The brain which contains this neuron.
* @since 1.0
*/
protected AbstractOutputBackpropNeuron(final Brain brain)
@@ -46,6 +47,7 @@ public abstract class AbstractOutputBackpropNeuron extends AbstractBackpropNeuro
* Creates a new instance of OutputBackpropNeuron using the specified
* activation function.
*
+ * @param brain The brain which contains this neuron.
* @param activationFunction The activation function to use.
* @since 1.0
*/
@@ -57,6 +59,7 @@ public abstract class AbstractOutputBackpropNeuron extends AbstractBackpropNeuro
/**
* Creates a new instance of this class using the specified learning rate.
*
+ * @param brain The brain which contains this neuron.
* @param learningRate The learning rate for this neuron.
* @since 1.0
*/
@@ -69,6 +72,7 @@ public abstract class AbstractOutputBackpropNeuron extends AbstractBackpropNeuro
* Creates a new instance of this class with the specified activation
* function and learning rate.
*
+ * @param brain The brain which contains this neuron.
* @param activationFunction The activation used by this neuron.
* @param learningRate The learning rate for this neuron.
* @since 1.0
diff --git a/src/main/java/com/syncleus/dann/neural/backprop/SimpleBackpropNeuron.java b/src/main/java/com/syncleus/dann/neural/backprop/SimpleBackpropNeuron.java
index aa9c94ae..62f1847f 100644
--- a/src/main/java/com/syncleus/dann/neural/backprop/SimpleBackpropNeuron.java
+++ b/src/main/java/com/syncleus/dann/neural/backprop/SimpleBackpropNeuron.java
@@ -38,6 +38,7 @@ public final class SimpleBackpropNeuron extends AbstractBackpropNeuron
/**
* Creates a new default instance of SimpleBackpropNeuron.
*
+ * @param brain The brain which contains this neuron.
* @since 1.0
*/
public SimpleBackpropNeuron(final Brain brain)
@@ -49,6 +50,7 @@ public final class SimpleBackpropNeuron extends AbstractBackpropNeuron
* Creates a new instance of SimpleBackpropNeuron with the specified
* activation function.
*
+ * @param brain The brain which contains this neuron.
* @param activationFunction The Neuron's activation function.
* @since 1.0
*/
@@ -61,6 +63,7 @@ public final class SimpleBackpropNeuron extends AbstractBackpropNeuron
* Creates a new instance of a SimpleBackpropNeuron using the default
* activation function with the specified learning rate.
*
+ * @param brain The brain which contains this neuron.
* @param learningRate learning rate of this neuron.
* @since 1.0
*/
@@ -73,6 +76,8 @@ public final class SimpleBackpropNeuron extends AbstractBackpropNeuron
* Creates a new instance of a SimpleBackpropNeuron with the specified
* activation function and learning rate.
*
+ *
+ * @param brain The brain which contains this neuron.
* @param activationFunction Activation function for this neuron.
* @param learningRate Learning rate for this neuron.
*/
diff --git a/src/main/java/com/syncleus/dann/neural/backprop/SimpleOutputBackpropNeuron.java b/src/main/java/com/syncleus/dann/neural/backprop/SimpleOutputBackpropNeuron.java
index f15cd658..38e1f3bc 100644
--- a/src/main/java/com/syncleus/dann/neural/backprop/SimpleOutputBackpropNeuron.java
+++ b/src/main/java/com/syncleus/dann/neural/backprop/SimpleOutputBackpropNeuron.java
@@ -35,6 +35,7 @@ public final class SimpleOutputBackpropNeuron extends AbstractOutputBackpropNeur
/**
* Creates a new instance of OutputBackpropNeuron.
*
+ * @param brain The brain which contains this neuron.
* @since 1.0
*/
public SimpleOutputBackpropNeuron(final Brain brain)
@@ -46,6 +47,7 @@ public final class SimpleOutputBackpropNeuron extends AbstractOutputBackpropNeur
* Creates a new instance of OutputBackpropNeuron using the specified
* activation function.
*
+ * @param brain The brain which contains this neuron.
* @param activationFunction The activation function to use.
* @since 1.0
*/
@@ -57,6 +59,7 @@ public final class SimpleOutputBackpropNeuron extends AbstractOutputBackpropNeur
/**
* Creates a new instance of this class using the specified learning rate.
*
+ * @param brain The brain which contains this neuron.
* @param learningRate The learning rate for this neuron.
* @since 1.0
*/
@@ -69,6 +72,7 @@ public final class SimpleOutputBackpropNeuron extends AbstractOutputBackpropNeur
* Creates a new instance of this class with the specified activation function
* and learning rate.
*
+ * @param brain The brain which contains this neuron.
* @param activationFunction The activation used by this neuron.
* @param learningRate The learning rate for this neuron.
* @since 1.0
diff --git a/src/main/java/com/syncleus/dann/neural/backprop/brain/FullyConnectedFeedforwardBrain.java b/src/main/java/com/syncleus/dann/neural/backprop/brain/FullyConnectedFeedforwardBrain.java
index 8e85c5d4..83ad6082 100644
--- a/src/main/java/com/syncleus/dann/neural/backprop/brain/FullyConnectedFeedforwardBrain.java
+++ b/src/main/java/com/syncleus/dann/neural/backprop/brain/FullyConnectedFeedforwardBrain.java
@@ -37,6 +37,10 @@ public final class FullyConnectedFeedforwardBrain<IN extends InputBackpropNeuron
/**
* Uses the given threadExecutor for executing tasks.
*
+ * @param neuronsPerLayer an array of integers, each element in the array specifies a layer and the value of the
+ * integer for that element is the number of neurons in that layer
+ * @param learningRate the learning rate for the network.
+ * @param activationFunction the activation function to use for all neurons in the network.
* @param threadExecutor executor to use for executing tasks.
* @since 2.0
*/
@@ -53,6 +57,10 @@ public final class FullyConnectedFeedforwardBrain<IN extends InputBackpropNeuron
* Default constructor initializes a default threadExecutor based on the number
* of processors.
*
+ * @param neuronsPerLayer an array of integers, each element in the array specifies a layer and the value of the
+ * integer for that element is the number of neurons in that layer
+ * @param learningRate the learning rate for the network.
+ * @param activationFunction the activation function to use for all neurons in the network.
* @since 2.0
*/
public FullyConnectedFeedforwardBrain(final int[] neuronsPerLayer, final double learningRate, final ActivationFunction activationFunction)
diff --git a/src/main/java/com/syncleus/dann/neural/som/SimpleSomNeuron.java b/src/main/java/com/syncleus/dann/neural/som/SimpleSomNeuron.java
index 6ec5f27f..bc0beba8 100644
--- a/src/main/java/com/syncleus/dann/neural/som/SimpleSomNeuron.java
+++ b/src/main/java/com/syncleus/dann/neural/som/SimpleSomNeuron.java
@@ -42,6 +42,7 @@ public class SimpleSomNeuron extends AbstractNeuron implements SomOutputNeuron
/**
* Creates a default SimpleSomNeuron.
*
+ * @param brain The brain which contains this neuron.
* @since 2.0
*/
public SimpleSomNeuron(final Brain brain)
diff --git a/src/main/java/com/syncleus/dann/xml/XmlSerializable.java b/src/main/java/com/syncleus/dann/xml/XmlSerializable.java
index bcb2274e..9784eb5f 100644
--- a/src/main/java/com/syncleus/dann/xml/XmlSerializable.java
+++ b/src/main/java/com/syncleus/dann/xml/XmlSerializable.java
@@ -22,18 +22,26 @@ public interface XmlSerializable<T, N>
{
/**
* Write stand alone element, including all instances.
+ *
+ * @return returns a serialized XML version of the object
*/
T toXml();
/**
* Write nested element assuming recurring instances of components are
* already named.
+ *
+ * @param namer a class responsible for naming repeated occurances of the same object
+ * @return returns a serialized XML version of the object
*/
T toXml(Namer<N> namer);
/**
* Write nested element assuming recurring instances of components are
* already named, use preexisting XML objects.
+ *
+ * @param jaxbObject The jaxbObject that will hold the serialization
+ * @param namer a class responsible for naming repeated occurances of the same object
*/
void toXml(T jaxbObject, Namer<N> namer);
}
--
GitLab