[cilib-devel] [PATCH 0/4] Conversion of Vector to container of Numerics.

[Gary P. <gpa...@gm...>]

The Vector container class was overloaded with far too much
responsibility. The decision was made to split the classes and have the
Vector class be responsible for mathematical vector operations and that
the Vector should be specialized for Numeric types.

A companion container class "TypeList" has been added to perform the
remainder of the fucntions that the Vector was performing.

Gary Pampara (4):
  Vector for Numeric types.
  Modified Neural Networks to use Type container.
  Remainder of classes for Vector changes.
  Corrected index issue with subList().

 pom.xml                                            |    2 +-
 .../ClonedPopulationInitialisationStrategy.java    |    2 +-
 .../cilib/bioinf/rnaprediction/RNAInitialiser.java |    5 +-
 .../cilib/bioinf/rnaprediction/RNAParticle.java    |    7 +-
 .../bioinf/rnaprediction/RNAVelocityUpdate.java    |    3 +-
 .../cilib/clustering/kmeans/KMeans.java            |    2 +-
 .../cilib/cooperative/CooperativeEntity.java       |    4 +-
 .../continuous/dynamic/moo/fda1/FDA1_f2.java       |    2 +-
 .../continuous/dynamic/moo/fda1/FDA1_h.java        |    4 +-
 .../continuous/dynamic/moo/fda2/FDA2_f2.java       |    2 +-
 .../continuous/dynamic/moo/fda2/FDA2_h.java        |    6 +-
 .../discrete/LongestCommonSubsequence.java         |    4 +-
 .../sourceforge/cilib/games/agent/NeuralAgent.java |    3 +-
 .../neural/NeuralOutputInterpretationStrategy.java |    5 +-
 .../state/evaluation/NeuralStateEvaluator.java     |    6 +-
 .../predatorprey/NeuralPredatorOutputStrategy.java |   13 +-
 .../predatorprey/NeuralPreyOutputStrategy.java     |   15 +-
 .../cilib/games/items/GridLocation.java            |   11 +-
 .../measurement/RecordItemLocationMeasure.java     |    7 +-
 src/main/java/net/sourceforge/cilib/hs/HS.java     |    7 +-
 .../java/net/sourceforge/cilib/math/StatUtils.java |    6 +-
 .../net/sourceforge/cilib/math/VectorMath.java     |   29 +-
 .../measurement/multiple/CompositeMeasurement.java |    4 +-
 .../measurement/multiple/ParetoOptimalFront.java   |    6 +-
 .../measurement/multiple/ParetoOptimalSet.java     |    3 +-
 .../neuralnetwork/basicFFNN/FFNNTopology.java      |    5 +-
 .../neuralnetwork/basicFFNN/TrainAndTestNN.java    |    3 +-
 .../foundation/EvaluationMediator.java             |    5 +-
 .../cilib/neuralnetwork/foundation/NNError.java    |    4 +-
 .../foundation/NeuralNetworkProblem.java           |    3 +-
 .../foundation/NeuralNetworkTopology.java          |    3 +-
 .../BatchTrainingSetEpochStrategy.java             |    4 +-
 ...chasticTrainingGeneralisationEpochStrategy.java |    5 +-
 .../foundation/measurements/AreaUnderROC.java      |    6 +-
 .../foundation/measurements/NNOutput.java          |    4 +-
 .../neuralnetwork/generic/GenericTopology.java     |    3 +-
 .../generic/LayeredGenericTopology.java            |    7 +-
 .../DynamicPatternSelectionData.java               |    4 +-
 .../errorfunctions/ClassificationErrorReal.java    |    6 +-
 .../generic/errorfunctions/MSEErrorFunction.java   |    4 +-
 .../FFNNEvaluationMediator.java                    |    9 +-
 .../SAILAEvaluationMediator.java                   |   22 +-
 .../topologyvisitors/WeightExtractingVisitor.java  |    3 +-
 .../generic/trainingstrategies/ErrorSignal.java    |    4 +-
 .../FFNN_GD_TrainingStrategy.java                  |    8 +-
 .../trainingstrategies/SquaredErrorFunction.java   |    3 +-
 .../testarea/TestErrorINCLearnWithTrainer.java     |    3 +-
 .../testarea/TestFFNNandGDTrainer.java             |    3 +-
 .../testarea/TestNeuronAndEvaluateFFNN.java        |    5 +-
 .../testarea/TestSAILAwithTrainer.java             |    3 +-
 .../problem/changestrategy/ChangeStrategy.java     |    6 +-
 .../problem/dataset/StringDataSetBuilder.java      |    3 -
 .../pso/dynamic/ChargedVelocityUpdateStrategy.java |    3 +-
 .../net/sourceforge/cilib/type/DomainBuilder.java  |   38 +-
 .../net/sourceforge/cilib/type/types/Type.java     |   29 +-
 .../cilib/type/types/container/AbstractList.java   |  106 +---
 .../cilib/type/types/container/Randomizable.java   |   38 +
 .../cilib/type/types/container/TypeList.java       |  268 +++++++
 .../cilib/type/types/container/Vector.java         |  726 +++++++-------------
 .../sourceforge/cilib/util/ClusteringUtils.java    |    3 +-
 .../net/sourceforge/cilib/util/VectorUtils.java    |   24 +-
 src/site/site.xml                                  |   22 +-
 .../sourceforge/cilib/entity/IndividualTest.java   |    2 -
 .../measurement/multiple/MultipleFitnessTest.java  |   22 +-
 .../multiple/MultipleSolutionsTest.java            |    6 +-
 .../single/BestParticlePositionTest.java           |    8 +-
 .../cilib/measurement/single/DiameterTest.java     |   16 +-
 .../measurement/single/ParticlePositionsTest.java  |    6 +-
 .../cilib/measurement/single/SolutionTest.java     |    6 +-
 .../sourceforge/cilib/type/DomainParserTest.java   |   71 +-
 .../cilib/type/StringBasedDomainRegistryTest.java  |    8 +-
 .../cilib/type/types/container/TypeListTest.java   |   48 ++
 .../cilib/type/types/container/VectorTest.java     |  189 +-----
 .../cilib/util/ClusteringUtilsTest.java            |   12 +-
 .../sourceforge/cilib/util/VectorUtilsTest.java    |   13 -
 .../net/sourceforge/cilib/xml/XMLFileTest.java     |   11 +-
 76 files changed, 999 insertions(+), 972 deletions(-)
 create mode 100644 src/main/java/net/sourceforge/cilib/type/types/container/Randomizable.java
 create mode 100644 src/main/java/net/sourceforge/cilib/type/types/container/TypeList.java
 create mode 100644 src/test/java/net/sourceforge/cilib/type/types/container/TypeListTest.java