java-defects4j-math-6-cmaesoptimizer

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Before

program

block_comment "/*\n * Licensed to the Apache Software Foundation (ASF) under"...

package_declaration (+25 nodes collapsed)

import_declaration

import "import"

scoped_identifier

identifier "java"

. "."

identifier "util"

. "."

identifier "ArrayList"

; ";"

import_declaration

import "import"

scoped_identifier

identifier "java"

. "."

identifier "util"

. "."

identifier "Arrays"

; ";"

import_declaration

import "import"

scoped_identifier

identifier "java"

. "."

identifier "util"

. "."

identifier "List"

; ";"

import_declaration

import "import"

scoped_identifier

identifier "org"

. "."

identifier "apache"

. "."

identifier "commons"

. "."

identifier "math3"

. "."

identifier "exception"

. "."

identifier "DimensionMismatchException"

; ";"

import_declaration

import "import"

scoped_identifier

identifier "org"

. "."

identifier "apache"

. "."

identifier "commons"

. "."

identifier "math3"

. "."

identifier "exception"

. "."

identifier "NotPositiveException"

; ";"

import_declaration

import "import"

scoped_identifier

identifier "org"

. "."

identifier "apache"

. "."

identifier "commons"

. "."

identifier "math3"

. "."

identifier "exception"

. "."

identifier "NotStrictlyPositiveException"

; ";"

import_declaration

import "import"

scoped_identifier

identifier "org"

. "."

identifier "apache"

. "."

identifier "commons"

. "."

identifier "math3"

. "."

identifier "exception"

. "."

identifier "OutOfRangeException"

; ";"

import_declaration

import "import"

scoped_identifier

identifier "org"

. "."

identifier "apache"

. "."

identifier "commons"

. "."

identifier "math3"

. "."

identifier "exception"

. "."

identifier "TooManyEvaluationsException"

; ";"

import_declaration

import "import"

scoped_identifier

identifier "org"

. "."

identifier "apache"

. "."

identifier "commons"

. "."

identifier "math3"

. "."

identifier "linear"

. "."

identifier "Array2DRowRealMatrix"

; ";"

import_declaration

import "import"

scoped_identifier

identifier "org"

. "."

identifier "apache"

. "."

identifier "commons"

. "."

identifier "math3"

. "."

identifier "linear"

. "."

identifier "EigenDecomposition"

; ";"

import_declaration

import "import"

scoped_identifier

identifier "org"

. "."

identifier "apache"

. "."

identifier "commons"

. "."

identifier "math3"

. "."

identifier "linear"

. "."

identifier "MatrixUtils"

; ";"

import_declaration

import "import"

scoped_identifier

identifier "org"

. "."

identifier "apache"

. "."

identifier "commons"

. "."

identifier "math3"

. "."

identifier "linear"

. "."

identifier "RealMatrix"

; ";"

import_declaration

import "import"

scoped_identifier

identifier "org"

. "."

identifier "apache"

. "."

identifier "commons"

. "."

identifier "math3"

. "."

identifier "optim"

. "."

identifier "ConvergenceChecker"

; ";"

import_declaration

import "import"

scoped_identifier

identifier "org"

. "."

identifier "apache"

. "."

identifier "commons"

. "."

identifier "math3"

. "."

identifier "optim"

. "."

identifier "OptimizationData"

; ";"

import_declaration (+25 nodes collapsed)

import_declaration

import "import"

scoped_identifier

identifier "org"

. "."

identifier "apache"

. "."

identifier "commons"

. "."

identifier "math3"

. "."

identifier "optim"

. "."

identifier "PointValuePair"

; ";"

import_declaration (+25 nodes collapsed)

import_declaration

import "import"

scoped_identifier

identifier "org"

. "."

identifier "apache"

. "."

identifier "commons"

. "."

identifier "math3"

. "."

identifier "random"

. "."

identifier "RandomGenerator"

; ";"

import_declaration

import "import"

scoped_identifier

identifier "org"

. "."

identifier "apache"

. "."

identifier "commons"

. "."

identifier "math3"

. "."

identifier "util"

. "."

identifier "MathArrays"

; ";"

block_comment "/**\n * <p>An implementation of the active Covariance Matrix "...

class_declaration

modifiers

public "public"

class "class"

identifier "CMAESOptimizer"

superclass

extends "extends"

type_identifier "MultivariateOptimizer"

class_body

{ "{"

line_comment "// global search parameters"

block_comment "/**\n * Population size, offspring number. The primary st"...

field_declaration

modifiers

private "private"

integral_type

int "int"

variable_declarator

identifier "lambda"

; ";"

line_comment "// population size"

block_comment "/**\n * Covariance update mechanism, default is active CM"...

field_declaration

modifiers

private "private"

final "final"

boolean_type "boolean"

variable_declarator

identifier "isActiveCMA"

; ";"

block_comment "/**\n * Determines how often a new random offspring is ge"...

field_declaration

modifiers

private "private"

final "final"

integral_type

int "int"

variable_declarator

identifier "checkFeasableCount"

; ";"

block_comment "/**\n * @see Sigma\n */"

field_declaration

modifiers

private "private"

array_type

floating_point_type

double "double"

dimensions

[ "["

] "]"

variable_declarator

identifier "inputSigma"

; ";"

block_comment "/** Number of objective variables/problem dimension */"

field_declaration

modifiers

private "private"

integral_type

int "int"

variable_declarator

identifier "dimension"

; ";"

block_comment "/**\n * Defines the number of initial iterations, where t"...

field_declaration

modifiers

private "private"

integral_type

int "int"

variable_declarator

identifier "diagonalOnly"

; ";"

block_comment "/** Number of objective variables/problem dimension */"

field_declaration

modifiers

private "private"

boolean_type "boolean"

variable_declarator

identifier "isMinimize"

= "="

true "true"

; ";"

block_comment "/** Indicates whether statistic data is collected. */"

field_declaration

modifiers

private "private"

final "final"

boolean_type "boolean"

variable_declarator

identifier "generateStatistics"

; ";"

line_comment "// termination criteria"

block_comment "/** Maximal number of iterations allowed. */"

field_declaration

modifiers

private "private"

final "final"

integral_type

int "int"

variable_declarator

identifier "maxIterations"

; ";"

block_comment "/** Limit for fitness value. */"

field_declaration

modifiers

private "private"

final "final"

floating_point_type

double "double"

variable_declarator

identifier "stopFitness"

; ";"

block_comment "/** Stop if x-changes larger stopTolUpX. */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "stopTolUpX"

; ";"

block_comment "/** Stop if x-change smaller stopTolX. */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "stopTolX"

; ";"

block_comment "/** Stop if fun-changes smaller stopTolFun. */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "stopTolFun"

; ";"

block_comment "/** Stop if back fun-changes smaller stopTolHistFun. */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "stopTolHistFun"

; ";"

line_comment "// selection strategy parameters"

block_comment "/** Number of parents/points for recombination. */"

field_declaration

modifiers

private "private"

integral_type

int "int"

variable_declarator

identifier "mu"

; ";"

line_comment "//"

block_comment "/** log(mu + 0.5), stored for efficiency. */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "logMu2"

; ";"

block_comment "/** Array for weighted recombination. */"

field_declaration

modifiers

private "private"

type_identifier "RealMatrix"

variable_declarator

identifier "weights"

; ";"

block_comment "/** Variance-effectiveness of sum w_i x_i. */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "mueff"

; ";"

line_comment "//"

line_comment "// dynamic strategy parameters and constants"

block_comment "/** Overall standard deviation - search volume. */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "sigma"

; ";"

block_comment "/** Cumulation constant. */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "cc"

; ";"

block_comment "/** Cumulation constant for step-size. */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "cs"

; ";"

block_comment "/** Damping for step-size. */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "damps"

; ";"

block_comment "/** Learning rate for rank-one update. */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "ccov1"

; ";"

block_comment "/** Learning rate for rank-mu update' */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "ccovmu"

; ";"

block_comment "/** Expectation of ||N(0,I)|| == norm(randn(N,1)). */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "chiN"

; ";"

block_comment "/** Learning rate for rank-one update - diagonalOnly */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "ccov1Sep"

; ";"

block_comment "/** Learning rate for rank-mu update - diagonalOnly */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "ccovmuSep"

; ";"

line_comment "// CMA internal values - updated each generation"

block_comment "/** Objective variables. */"

field_declaration

modifiers

private "private"

type_identifier "RealMatrix"

variable_declarator

identifier "xmean"

; ";"

block_comment "/** Evolution path. */"

field_declaration

modifiers

private "private"

type_identifier "RealMatrix"

variable_declarator

identifier "pc"

; ";"

block_comment "/** Evolution path for sigma. */"

field_declaration

modifiers

private "private"

type_identifier "RealMatrix"

variable_declarator

identifier "ps"

; ";"

block_comment "/** Norm of ps, stored for efficiency. */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "normps"

; ";"

block_comment "/** Coordinate system. */"

field_declaration

modifiers

private "private"

type_identifier "RealMatrix"

variable_declarator

identifier "B"

; ";"

block_comment "/** Scaling. */"

field_declaration

modifiers

private "private"

type_identifier "RealMatrix"

variable_declarator

identifier "D"

; ";"

block_comment "/** B*D, stored for efficiency. */"

field_declaration

modifiers

private "private"

type_identifier "RealMatrix"

variable_declarator

identifier "BD"

; ";"

block_comment "/** Diagonal of sqrt(D), stored for efficiency. */"

field_declaration

modifiers

private "private"

type_identifier "RealMatrix"

variable_declarator

identifier "diagD"

; ";"

block_comment "/** Covariance matrix. */"

field_declaration

modifiers

private "private"

type_identifier "RealMatrix"

variable_declarator

identifier "C"

; ";"

block_comment "/** Diagonal of C, used for diagonalOnly. */"

field_declaration

modifiers

private "private"

type_identifier "RealMatrix"

variable_declarator

identifier "diagC"

; ";"

block_comment "/** Number of iterations already performed. */"

field_declaration

modifiers

private "private"

integral_type

int "int"

variable_declarator

identifier "iterations"

; ";"

block_comment "/** History queue of best values. */"

field_declaration

modifiers

private "private"

array_type

floating_point_type

double "double"

dimensions

[ "["

] "]"

variable_declarator

identifier "fitnessHistory"

; ";"

block_comment "/** Size of history queue of best values. */"

field_declaration

modifiers

private "private"

integral_type

int "int"

variable_declarator

identifier "historySize"

; ";"

block_comment "/** Random generator. */"

field_declaration

modifiers

private "private"

final "final"

type_identifier "RandomGenerator"

variable_declarator

identifier "random"

; ";"

block_comment "/** History of sigma values. */"

field_declaration (+25 nodes collapsed)

block_comment "/** History of mean matrix. */"

field_declaration (+25 nodes collapsed)

block_comment "/** History of fitness values. */"

field_declaration (+25 nodes collapsed)

block_comment "/** History of D matrix. */"

field_declaration (+25 nodes collapsed)

block_comment "/**\n * @param maxIterations Maximal number of iterations"...

constructor_declaration (+120 nodes collapsed)

block_comment "/**\n * @return History of sigma values.\n */"

method_declaration

modifiers

public "public"

generic_type

type_identifier "List"

type_arguments

< "<"

type_identifier "Double"

> ">"

identifier "getStatisticsSigmaHistory"

formal_parameters

( "("

) ")"

block

{ "{"

return_statement

return "return"

identifier "statisticsSigmaHistory"

; ";"

} "}"

block_comment "/**\n * @return History of mean matrix.\n */"

method_declaration

modifiers

public "public"

generic_type

type_identifier "List"

type_arguments

< "<"

type_identifier "RealMatrix"

> ">"

identifier "getStatisticsMeanHistory"

formal_parameters

( "("

) ")"

block

{ "{"

return_statement

return "return"

identifier "statisticsMeanHistory"

; ";"

} "}"

block_comment "/**\n * @return History of fitness values.\n */"

method_declaration

modifiers

public "public"

generic_type

type_identifier "List"

type_arguments

< "<"

type_identifier "Double"

> ">"

identifier "getStatisticsFitnessHistory"

formal_parameters

( "("

) ")"

block

{ "{"

return_statement

return "return"

identifier "statisticsFitnessHistory"

; ";"

} "}"

block_comment "/**\n * @return History of D matrix.\n */"

method_declaration

modifiers

public "public"

generic_type

type_identifier "List"

type_arguments

< "<"

type_identifier "RealMatrix"

> ">"

identifier "getStatisticsDHistory"

formal_parameters

( "("

) ")"

block

{ "{"

return_statement

return "return"

identifier "statisticsDHistory"

; ";"

} "}"

block_comment "/**\n * Input sigma values.\n * They define the initia"...

class_declaration (+144 nodes collapsed)

block_comment "/**\n * Population size.\n * The number of offspring i"...

class_declaration (+86 nodes collapsed)

block_comment "/**\n * {@inheritDoc}\n *\n * @param optData Optimi"...

method_declaration (+36 nodes collapsed)

block_comment "/** {@inheritDoc} */"

method_declaration

modifiers

marker_annotation

@ "@"

identifier "Override"

protected "protected"

type_identifier "PointValuePair"

identifier "doOptimize"

formal_parameters

( "("

) ")"

block

{ "{"

line_comment "// -------------------- Initialization ---------------------"...

expression_statement

assignment_expression

identifier "isMinimize"

= "="

method_invocation

identifier "getGoalType"

argument_list

( "("

) ")"

. "."

identifier "equals"

argument_list

( "("

field_access

identifier "GoalType"

. "."

identifier "MINIMIZE"

) ")"

; ";"

local_variable_declaration

modifiers

final "final"

type_identifier "FitnessFunction"

variable_declarator

identifier "fitfun"

= "="

object_creation_expression

new "new"

type_identifier "FitnessFunction"

argument_list

( "("

) ")"

; ";"

local_variable_declaration

modifiers

final "final"

array_type

floating_point_type

double "double"

dimensions

[ "["

] "]"

variable_declarator

identifier "guess"

= "="

method_invocation

identifier "getStartPoint"

argument_list

( "("

) ")"

; ";"

line_comment "// number of objective variables/problem dimension"

expression_statement

assignment_expression

identifier "dimension"

= "="

field_access

identifier "guess"

. "."

identifier "length"

; ";"

expression_statement

method_invocation

identifier "initializeCMA"

argument_list

( "("

identifier "guess"

) ")"

; ";"

expression_statement

assignment_expression

identifier "iterations"

= "="

decimal_integer_literal "0"

; ";"

local_variable_declaration

floating_point_type

double "double"

variable_declarator

identifier "bestValue"

= "="

method_invocation

identifier "fitfun"

. "."

identifier "value"

argument_list

( "("

identifier "guess"

) ")"

; ";"

expression_statement

method_invocation

identifier "push"

argument_list

( "("

identifier "fitnessHistory"

, ","

identifier "bestValue"

) ")"

; ";"

local_variable_declaration (+26 nodes collapsed)

local_variable_declaration

type_identifier "PointValuePair"

variable_declarator

identifier "lastResult"

= "="

null_literal "null"

; ";"

line_comment "// -------------------- Generation Loop --------------------"...

labeled_statement

identifier "generationLoop"

: ":"

for_statement

for "for"

( "("

assignment_expression

identifier "iterations"

= "="

decimal_integer_literal "1"

; ";"

binary_expression

identifier "iterations"

<= "<="

identifier "maxIterations"

; ";"

update_expression

identifier "iterations"

++ "++"

) ")"

block

{ "{"

line_comment "// Generate and evaluate lambda offspring"

local_variable_declaration

modifiers

final "final"

type_identifier "RealMatrix"

variable_declarator

identifier "arz"

= "="

method_invocation

identifier "randn1"

argument_list

( "("

identifier "dimension"

, ","

identifier "lambda"

) ")"

; ";"

local_variable_declaration

modifiers

final "final"

type_identifier "RealMatrix"

variable_declarator

identifier "arx"

= "="

method_invocation

identifier "zeros"

argument_list

( "("

identifier "dimension"

, ","

identifier "lambda"

) ")"

; ";"

local_variable_declaration (+21 nodes collapsed)

line_comment "// generate random offspring"

for_statement (+250 nodes collapsed)

line_comment "// Sort by fitness and compute weighted mean into xmean"

local_variable_declaration

modifiers

final "final"

array_type

integral_type

int "int"

dimensions

[ "["

] "]"

variable_declarator

identifier "arindex"

= "="

method_invocation

identifier "sortedIndices"

argument_list

( "("

identifier "fitness"

) ")"

; ";"

line_comment "// Calculate new xmean, this is selection and recombination"

local_variable_declaration

modifiers

final "final"

type_identifier "RealMatrix"

variable_declarator

identifier "xold"

= "="

identifier "xmean"

; ";"

line_comment "// for speed up of Eq. (2) and (3)"

local_variable_declaration (+25 nodes collapsed)

expression_statement

assignment_expression

identifier "xmean"

= "="

method_invocation

identifier "bestArx"

. "."

identifier "multiply"

argument_list

( "("

identifier "weights"

) ")"

; ";"

local_variable_declaration (+25 nodes collapsed)

local_variable_declaration

modifiers

final "final"

type_identifier "RealMatrix"

variable_declarator

identifier "zmean"

= "="

method_invocation

identifier "bestArz"

. "."

identifier "multiply"

argument_list

( "("

identifier "weights"

) ")"

; ";"

local_variable_declaration

modifiers

final "final"

boolean_type "boolean"

variable_declarator

identifier "hsig"

= "="

method_invocation

identifier "updateEvolutionPaths"

argument_list

( "("

identifier "zmean"

, ","

identifier "xold"

) ")"

; ";"

if_statement (+42 nodes collapsed)

line_comment "// Adapt step size sigma - Eq. (5)"

expression_statement (+37 nodes collapsed)

local_variable_declaration

modifiers

final "final"

floating_point_type

double "double"

variable_declarator

identifier "bestFitness"

= "="

array_access

identifier "fitness"

[ "["

array_access

identifier "arindex"

[ "["

decimal_integer_literal "0"

] "]"

; ";"

local_variable_declaration (+24 nodes collapsed)

if_statement (+109 nodes collapsed)

line_comment "// handle termination criteria"

line_comment "// Break, if fitness is good enough"

if_statement (+39 nodes collapsed)

local_variable_declaration (+26 nodes collapsed)

local_variable_declaration (+21 nodes collapsed)

for_statement (+84 nodes collapsed)

for_statement (+46 nodes collapsed)

local_variable_declaration

modifiers

final "final"

floating_point_type

double "double"

variable_declarator

identifier "historyBest"

= "="

method_invocation

identifier "min"

argument_list

( "("

identifier "fitnessHistory"

) ")"

; ";"

local_variable_declaration

modifiers

final "final"

floating_point_type

double "double"

variable_declarator

identifier "historyWorst"

= "="

method_invocation

identifier "max"

argument_list

( "("

identifier "fitnessHistory"

) ")"

; ";"

if_statement (+43 nodes collapsed)

if_statement (+28 nodes collapsed)

line_comment "// condition number of the covariance matrix exceeds 1e14"

if_statement (+29 nodes collapsed)

line_comment "// user defined termination"

if_statement (+87 nodes collapsed)

line_comment "// Adjust step size in case of equal function values (flat f"...

if_statement (+56 nodes collapsed)

if_statement (+61 nodes collapsed)

line_comment "// store best in history"

expression_statement

method_invocation

identifier "push"

argument_list

( "("

identifier "fitnessHistory"

, ","

identifier "bestFitness"

) ")"

; ";"

expression_statement

method_invocation

identifier "fitfun"

. "."

identifier "setValueRange"

argument_list

( "("

binary_expression

identifier "worstFitness"

- "-"

identifier "bestFitness"

) ")"

; ";"

if_statement (+68 nodes collapsed)

} "}"

return_statement

return "return"

identifier "optimum"

; ";"

} "}"

block_comment "/**\n * Scans the list of (required and optional) optimiz"...

method_declaration (+118 nodes collapsed)

block_comment "/**\n * Checks dimensions and values of boundaries and in"...

method_declaration (+195 nodes collapsed)

block_comment "/**\n * Initialization of the dynamic search parameters\n "...

method_declaration (+939 nodes collapsed)

block_comment "/**\n * Update of the evolution paths ps and pc.\n *\n "...

method_declaration (+224 nodes collapsed)

block_comment "/**\n * Update of the covariance matrix C for diagonalOnl"...

method_declaration (+201 nodes collapsed)

block_comment "/**\n * Update of the covariance matrix C.\n *\n * "...

method_declaration (+746 nodes collapsed)

block_comment "/**\n * Update B and D from C.\n *\n * @param negcc"...

method_declaration (+453 nodes collapsed)

block_comment "/**\n * Pushes the current best fitness value in a histor"...

method_declaration (+81 nodes collapsed)

block_comment "/**\n * Sorts fitness values.\n *\n * @param double"...

method_declaration (+177 nodes collapsed)

block_comment "/**\n * Used to sort fitness values. Sorting is always in"...

class_declaration (+243 nodes collapsed)

block_comment "/**\n * Normalizes fitness values to the range [0,1]. Add"...

class_declaration (+660 nodes collapsed)

line_comment "// -----Matrix utility functions similar to the Matlab build"...

block_comment "/**\n * @param m Input matrix\n * @return Matrix repre"...

method_declaration (+156 nodes collapsed)

block_comment "/**\n * @param m Input matrix.\n * @return Matrix repr"...

method_declaration (+156 nodes collapsed)

block_comment "/**\n * @param m Input matrix.\n * @return Matrix repr"...

method_declaration (+160 nodes collapsed)

block_comment "/**\n * @param m Input matrix 1.\n * @param n Input ma"...

method_declaration (+167 nodes collapsed)

block_comment "/**\n * @param m Input matrix 1.\n * @param n Input ma"...

method_declaration (+167 nodes collapsed)

block_comment "/**\n * @param m Input matrix.\n * @param cols Columns"...

method_declaration (+158 nodes collapsed)

block_comment "/**\n * @param m Input matrix.\n * @param k Diagonal p"...

method_declaration (+165 nodes collapsed)

block_comment "/**\n * @param m Input matrix.\n * @return Row matrix "...

method_declaration (+157 nodes collapsed)

block_comment "/**\n * @param m Input matrix.\n * @return the diagona"...

method_declaration (+239 nodes collapsed)

block_comment "/**\n * Copies a column from m1 to m2.\n *\n * @par"...

method_declaration (+83 nodes collapsed)

block_comment "/**\n * @param n Number of rows.\n * @param m Number o"...

method_declaration (+99 nodes collapsed)

block_comment "/**\n * @param n Number of rows.\n * @param m Number o"...

method_declaration (+109 nodes collapsed)

block_comment "/**\n * @param n Number of rows.\n * @param m Number o"...

method_declaration (+33 nodes collapsed)

block_comment "/**\n * @param mat Input matrix.\n * @param n Number o"...

method_declaration (+185 nodes collapsed)

block_comment "/**\n * @param start Start value.\n * @param end End v"...

method_declaration (+146 nodes collapsed)

block_comment "/**\n * @param m Input matrix.\n * @return the maximum"...

method_declaration (+128 nodes collapsed)

block_comment "/**\n * @param m Input matrix.\n * @return the minimum"...

method_declaration (+126 nodes collapsed)

block_comment "/**\n * @param m Input array.\n * @return the maximum "...

method_declaration (+92 nodes collapsed)

block_comment "/**\n * @param m Input array.\n * @return the minimum "...

method_declaration (+90 nodes collapsed)

block_comment "/**\n * @param indices Input index array.\n * @return "...

method_declaration (+95 nodes collapsed)

block_comment "/**\n * @param indices Input index array.\n * @return "...

method_declaration (+104 nodes collapsed)

block_comment "/**\n * @param size Length of random array.\n * @retur"...

method_declaration (+84 nodes collapsed)

block_comment "/**\n * @param size Number of rows.\n * @param popSize"...

method_declaration (+125 nodes collapsed)

} "}"

After

program

block_comment "/*\n * Licensed to the Apache Software Foundation (ASF) under"...

package_declaration (+25 nodes collapsed)

import_declaration

import "import"

scoped_identifier

identifier "java"

. "."

identifier "util"

. "."

identifier "ArrayList"

; ";"

import_declaration

import "import"

scoped_identifier

identifier "java"

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identifier "util"

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import_declaration

import "import"

scoped_identifier

identifier "java"

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import_declaration

import "import"

scoped_identifier

identifier "org"

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identifier "apache"

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identifier "commons"

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identifier "math3"

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identifier "exception"

. "."

identifier "DimensionMismatchException"

; ";"

import_declaration

import "import"

scoped_identifier

identifier "org"

. "."

identifier "apache"

. "."

identifier "commons"

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identifier "math3"

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identifier "exception"

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identifier "NotPositiveException"

; ";"

import_declaration

import "import"

scoped_identifier

identifier "org"

. "."

identifier "apache"

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identifier "commons"

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identifier "math3"

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identifier "exception"

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identifier "NotStrictlyPositiveException"

; ";"

import_declaration

import "import"

scoped_identifier

identifier "org"

. "."

identifier "apache"

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identifier "commons"

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identifier "math3"

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identifier "exception"

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identifier "OutOfRangeException"

; ";"

import_declaration

import "import"

scoped_identifier

identifier "org"

. "."

identifier "apache"

. "."

identifier "commons"

. "."

identifier "math3"

. "."

identifier "exception"

. "."

identifier "TooManyEvaluationsException"

; ";"

import_declaration

import "import"

scoped_identifier

identifier "org"

. "."

identifier "apache"

. "."

identifier "commons"

. "."

identifier "math3"

. "."

identifier "linear"

. "."

identifier "Array2DRowRealMatrix"

; ";"

import_declaration

import "import"

scoped_identifier

identifier "org"

. "."

identifier "apache"

. "."

identifier "commons"

. "."

identifier "math3"

. "."

identifier "linear"

. "."

identifier "EigenDecomposition"

; ";"

import_declaration

import "import"

scoped_identifier

identifier "org"

. "."

identifier "apache"

. "."

identifier "commons"

. "."

identifier "math3"

. "."

identifier "linear"

. "."

identifier "MatrixUtils"

; ";"

import_declaration

import "import"

scoped_identifier

identifier "org"

. "."

identifier "apache"

. "."

identifier "commons"

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identifier "math3"

. "."

identifier "linear"

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identifier "RealMatrix"

; ";"

import_declaration

import "import"

scoped_identifier

identifier "org"

. "."

identifier "apache"

. "."

identifier "commons"

. "."

identifier "math3"

. "."

identifier "optim"

. "."

identifier "ConvergenceChecker"

; ";"

import_declaration

import "import"

scoped_identifier

identifier "org"

. "."

identifier "apache"

. "."

identifier "commons"

. "."

identifier "math3"

. "."

identifier "optim"

. "."

identifier "OptimizationData"

; ";"

import_declaration (+25 nodes collapsed)

import_declaration

import "import"

scoped_identifier

identifier "org"

. "."

identifier "apache"

. "."

identifier "commons"

. "."

identifier "math3"

. "."

identifier "optim"

. "."

identifier "PointValuePair"

; ";"

import_declaration (+25 nodes collapsed)

import_declaration

import "import"

scoped_identifier

identifier "org"

. "."

identifier "apache"

. "."

identifier "commons"

. "."

identifier "math3"

. "."

identifier "random"

. "."

identifier "RandomGenerator"

; ";"

import_declaration

import "import"

scoped_identifier

identifier "org"

. "."

identifier "apache"

. "."

identifier "commons"

. "."

identifier "math3"

. "."

identifier "util"

. "."

identifier "MathArrays"

; ";"

block_comment "/**\n * <p>An implementation of the active Covariance Matrix "...

class_declaration

modifiers

public "public"

class "class"

identifier "CMAESOptimizer"

superclass

extends "extends"

type_identifier "MultivariateOptimizer"

class_body

{ "{"

line_comment "// global search parameters"

block_comment "/**\n * Population size, offspring number. The primary st"...

field_declaration

modifiers

private "private"

integral_type

int "int"

variable_declarator

identifier "lambda"

; ";"

line_comment "// population size"

block_comment "/**\n * Covariance update mechanism, default is active CM"...

field_declaration

modifiers

private "private"

final "final"

boolean_type "boolean"

variable_declarator

identifier "isActiveCMA"

; ";"

block_comment "/**\n * Determines how often a new random offspring is ge"...

field_declaration

modifiers

private "private"

final "final"

integral_type

int "int"

variable_declarator

identifier "checkFeasableCount"

; ";"

block_comment "/**\n * @see Sigma\n */"

field_declaration

modifiers

private "private"

array_type

floating_point_type

double "double"

dimensions

[ "["

] "]"

variable_declarator

identifier "inputSigma"

; ";"

block_comment "/** Number of objective variables/problem dimension */"

field_declaration

modifiers

private "private"

integral_type

int "int"

variable_declarator

identifier "dimension"

; ";"

block_comment "/**\n * Defines the number of initial iterations, where t"...

field_declaration

modifiers

private "private"

integral_type

int "int"

variable_declarator

identifier "diagonalOnly"

; ";"

block_comment "/** Number of objective variables/problem dimension */"

field_declaration

modifiers

private "private"

boolean_type "boolean"

variable_declarator

identifier "isMinimize"

= "="

true "true"

; ";"

block_comment "/** Indicates whether statistic data is collected. */"

field_declaration

modifiers

private "private"

final "final"

boolean_type "boolean"

variable_declarator

identifier "generateStatistics"

; ";"

line_comment "// termination criteria"

block_comment "/** Maximal number of iterations allowed. */"

field_declaration

modifiers

private "private"

final "final"

integral_type

int "int"

variable_declarator

identifier "maxIterations"

; ";"

block_comment "/** Limit for fitness value. */"

field_declaration

modifiers

private "private"

final "final"

floating_point_type

double "double"

variable_declarator

identifier "stopFitness"

; ";"

block_comment "/** Stop if x-changes larger stopTolUpX. */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "stopTolUpX"

; ";"

block_comment "/** Stop if x-change smaller stopTolX. */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "stopTolX"

; ";"

block_comment "/** Stop if fun-changes smaller stopTolFun. */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "stopTolFun"

; ";"

block_comment "/** Stop if back fun-changes smaller stopTolHistFun. */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "stopTolHistFun"

; ";"

line_comment "// selection strategy parameters"

block_comment "/** Number of parents/points for recombination. */"

field_declaration

modifiers

private "private"

integral_type

int "int"

variable_declarator

identifier "mu"

; ";"

line_comment "//"

block_comment "/** log(mu + 0.5), stored for efficiency. */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "logMu2"

; ";"

block_comment "/** Array for weighted recombination. */"

field_declaration

modifiers

private "private"

type_identifier "RealMatrix"

variable_declarator

identifier "weights"

; ";"

block_comment "/** Variance-effectiveness of sum w_i x_i. */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "mueff"

; ";"

line_comment "//"

line_comment "// dynamic strategy parameters and constants"

block_comment "/** Overall standard deviation - search volume. */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "sigma"

; ";"

block_comment "/** Cumulation constant. */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "cc"

; ";"

block_comment "/** Cumulation constant for step-size. */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "cs"

; ";"

block_comment "/** Damping for step-size. */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "damps"

; ";"

block_comment "/** Learning rate for rank-one update. */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "ccov1"

; ";"

block_comment "/** Learning rate for rank-mu update' */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "ccovmu"

; ";"

block_comment "/** Expectation of ||N(0,I)|| == norm(randn(N,1)). */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "chiN"

; ";"

block_comment "/** Learning rate for rank-one update - diagonalOnly */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "ccov1Sep"

; ";"

block_comment "/** Learning rate for rank-mu update - diagonalOnly */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "ccovmuSep"

; ";"

line_comment "// CMA internal values - updated each generation"

block_comment "/** Objective variables. */"

field_declaration

modifiers

private "private"

type_identifier "RealMatrix"

variable_declarator

identifier "xmean"

; ";"

block_comment "/** Evolution path. */"

field_declaration

modifiers

private "private"

type_identifier "RealMatrix"

variable_declarator

identifier "pc"

; ";"

block_comment "/** Evolution path for sigma. */"

field_declaration

modifiers

private "private"

type_identifier "RealMatrix"

variable_declarator

identifier "ps"

; ";"

block_comment "/** Norm of ps, stored for efficiency. */"

field_declaration

modifiers

private "private"

floating_point_type

double "double"

variable_declarator

identifier "normps"

; ";"

block_comment "/** Coordinate system. */"

field_declaration

modifiers

private "private"

type_identifier "RealMatrix"

variable_declarator

identifier "B"

; ";"

block_comment "/** Scaling. */"

field_declaration

modifiers

private "private"

type_identifier "RealMatrix"

variable_declarator

identifier "D"

; ";"

block_comment "/** B*D, stored for efficiency. */"

field_declaration

modifiers

private "private"

type_identifier "RealMatrix"

variable_declarator

identifier "BD"

; ";"

block_comment "/** Diagonal of sqrt(D), stored for efficiency. */"

field_declaration

modifiers

private "private"

type_identifier "RealMatrix"

variable_declarator

identifier "diagD"

; ";"

block_comment "/** Covariance matrix. */"

field_declaration

modifiers

private "private"

type_identifier "RealMatrix"

variable_declarator

identifier "C"

; ";"

block_comment "/** Diagonal of C, used for diagonalOnly. */"

field_declaration

modifiers

private "private"

type_identifier "RealMatrix"

variable_declarator

identifier "diagC"

; ";"

block_comment "/** Number of iterations already performed. */"

field_declaration

modifiers

private "private"

integral_type

int "int"

variable_declarator

identifier "iterations"

; ";"

block_comment "/** History queue of best values. */"

field_declaration

modifiers

private "private"

array_type

floating_point_type

double "double"

dimensions

[ "["

] "]"

variable_declarator

identifier "fitnessHistory"

; ";"

block_comment "/** Size of history queue of best values. */"

field_declaration

modifiers

private "private"

integral_type

int "int"

variable_declarator

identifier "historySize"

; ";"

block_comment "/** Random generator. */"

field_declaration

modifiers

private "private"

final "final"

type_identifier "RandomGenerator"

variable_declarator

identifier "random"

; ";"

block_comment "/** History of sigma values. */"

field_declaration (+25 nodes collapsed)

block_comment "/** History of mean matrix. */"

field_declaration (+25 nodes collapsed)

block_comment "/** History of fitness values. */"

field_declaration (+25 nodes collapsed)

block_comment "/** History of D matrix. */"

field_declaration (+25 nodes collapsed)

block_comment "/**\n * @param maxIterations Maximal number of iterations"...

constructor_declaration (+120 nodes collapsed)

block_comment "/**\n * @return History of sigma values.\n */"

method_declaration

modifiers

public "public"

generic_type

type_identifier "List"

type_arguments

< "<"

type_identifier "Double"

> ">"

identifier "getStatisticsSigmaHistory"

formal_parameters

( "("

) ")"

block

{ "{"

return_statement

return "return"

identifier "statisticsSigmaHistory"

; ";"

} "}"

block_comment "/**\n * @return History of mean matrix.\n */"

method_declaration

modifiers

public "public"

generic_type

type_identifier "List"

type_arguments

< "<"

type_identifier "RealMatrix"

> ">"

identifier "getStatisticsMeanHistory"

formal_parameters

( "("

) ")"

block

{ "{"

return_statement

return "return"

identifier "statisticsMeanHistory"

; ";"

} "}"

block_comment "/**\n * @return History of fitness values.\n */"

method_declaration

modifiers

public "public"

generic_type

type_identifier "List"

type_arguments

< "<"

type_identifier "Double"

> ">"

identifier "getStatisticsFitnessHistory"

formal_parameters

( "("

) ")"

block

{ "{"

return_statement

return "return"

identifier "statisticsFitnessHistory"

; ";"

} "}"

block_comment "/**\n * @return History of D matrix.\n */"

method_declaration

modifiers

public "public"

generic_type

type_identifier "List"

type_arguments

< "<"

type_identifier "RealMatrix"

> ">"

identifier "getStatisticsDHistory"

formal_parameters

( "("

) ")"

block

{ "{"

return_statement

return "return"

identifier "statisticsDHistory"

; ";"

} "}"

block_comment "/**\n * Input sigma values.\n * They define the initia"...

class_declaration (+144 nodes collapsed)

block_comment "/**\n * Population size.\n * The number of offspring i"...

class_declaration (+86 nodes collapsed)

block_comment "/**\n * {@inheritDoc}\n *\n * @param optData Optimi"...

method_declaration (+36 nodes collapsed)

block_comment "/** {@inheritDoc} */"

method_declaration

modifiers

marker_annotation

@ "@"

identifier "Override"

protected "protected"

type_identifier "PointValuePair"

identifier "doOptimize"

formal_parameters

( "("

) ")"

block

{ "{"

line_comment "// -------------------- Initialization ---------------------"...

expression_statement

assignment_expression

identifier "isMinimize"

= "="

method_invocation

identifier "getGoalType"

argument_list

( "("

) ")"

. "."

identifier "equals"

argument_list

( "("

field_access

identifier "GoalType"

. "."

identifier "MINIMIZE"

) ")"

; ";"

local_variable_declaration

modifiers

final "final"

type_identifier "FitnessFunction"

variable_declarator

identifier "fitfun"

= "="

object_creation_expression

new "new"

type_identifier "FitnessFunction"

argument_list

( "("

) ")"

; ";"

local_variable_declaration

modifiers

final "final"

array_type

floating_point_type

double "double"

dimensions

[ "["

] "]"

variable_declarator

identifier "guess"

= "="

method_invocation

identifier "getStartPoint"

argument_list

( "("

) ")"

; ";"

line_comment "// number of objective variables/problem dimension"

expression_statement

assignment_expression

identifier "dimension"

= "="

field_access

identifier "guess"

. "."

identifier "length"

; ";"

expression_statement

method_invocation

identifier "initializeCMA"

argument_list

( "("

identifier "guess"

) ")"

; ";"

expression_statement

assignment_expression

identifier "iterations"

= "="

decimal_integer_literal "0"

; ";"

local_variable_declaration

floating_point_type

double "double"

variable_declarator

identifier "bestValue"

= "="

method_invocation

identifier "fitfun"

. "."

identifier "value"

argument_list

( "("

identifier "guess"

) ")"

; ";"

expression_statement

method_invocation

identifier "push"

argument_list

( "("

identifier "fitnessHistory"

, ","

identifier "bestValue"

) ")"

; ";"

local_variable_declaration (+26 nodes collapsed)

local_variable_declaration

type_identifier "PointValuePair"

variable_declarator

identifier "lastResult"

= "="

null_literal "null"

; ";"

line_comment "// -------------------- Generation Loop --------------------"...

labeled_statement

identifier "generationLoop"

: ":"

for_statement

for "for"

( "("

assignment_expression

identifier "iterations"

= "="

decimal_integer_literal "1"

; ";"

binary_expression

identifier "iterations"

<= "<="

identifier "maxIterations"

; ";"

update_expression

identifier "iterations"

++ "++"

) ")"

block

{ "{"

expression_statement

method_invocation

identifier "incrementIterationCount"

argument_list

( "("

) ")"

; ";"

line_comment "// Generate and evaluate lambda offspring"

local_variable_declaration

modifiers

final "final"

type_identifier "RealMatrix"

variable_declarator

identifier "arz"

= "="

method_invocation

identifier "randn1"

argument_list

( "("

identifier "dimension"

, ","

identifier "lambda"

) ")"

; ";"

local_variable_declaration

modifiers

final "final"

type_identifier "RealMatrix"

variable_declarator

identifier "arx"

= "="

method_invocation

identifier "zeros"

argument_list

( "("

identifier "dimension"

, ","

identifier "lambda"

) ")"

; ";"

local_variable_declaration (+21 nodes collapsed)

line_comment "// generate random offspring"

for_statement (+250 nodes collapsed)

line_comment "// Sort by fitness and compute weighted mean into xmean"

local_variable_declaration

modifiers

final "final"

array_type

integral_type

int "int"

dimensions

[ "["

] "]"

variable_declarator

identifier "arindex"

= "="

method_invocation

identifier "sortedIndices"

argument_list

( "("

identifier "fitness"

) ")"

; ";"

line_comment "// Calculate new xmean, this is selection and recombination"

local_variable_declaration

modifiers

final "final"

type_identifier "RealMatrix"

variable_declarator

identifier "xold"

= "="

identifier "xmean"

; ";"

line_comment "// for speed up of Eq. (2) and (3)"

local_variable_declaration (+25 nodes collapsed)

expression_statement

assignment_expression

identifier "xmean"

= "="

method_invocation

identifier "bestArx"

. "."

identifier "multiply"

argument_list

( "("

identifier "weights"

) ")"

; ";"

local_variable_declaration (+25 nodes collapsed)

local_variable_declaration

modifiers

final "final"

type_identifier "RealMatrix"

variable_declarator

identifier "zmean"

= "="

method_invocation

identifier "bestArz"

. "."

identifier "multiply"

argument_list

( "("

identifier "weights"

) ")"

; ";"

local_variable_declaration

modifiers

final "final"

boolean_type "boolean"

variable_declarator

identifier "hsig"

= "="

method_invocation

identifier "updateEvolutionPaths"

argument_list

( "("

identifier "zmean"

, ","

identifier "xold"

) ")"

; ";"

if_statement (+42 nodes collapsed)

line_comment "// Adapt step size sigma - Eq. (5)"

expression_statement (+37 nodes collapsed)

local_variable_declaration

modifiers

final "final"

floating_point_type

double "double"

variable_declarator

identifier "bestFitness"

= "="

array_access

identifier "fitness"

[ "["

array_access

identifier "arindex"

[ "["

decimal_integer_literal "0"

] "]"

; ";"

local_variable_declaration (+24 nodes collapsed)

if_statement (+109 nodes collapsed)

line_comment "// handle termination criteria"

line_comment "// Break, if fitness is good enough"

if_statement (+39 nodes collapsed)

local_variable_declaration (+26 nodes collapsed)

local_variable_declaration (+21 nodes collapsed)

for_statement (+84 nodes collapsed)

for_statement (+46 nodes collapsed)

local_variable_declaration

modifiers

final "final"

floating_point_type

double "double"

variable_declarator

identifier "historyBest"

= "="

method_invocation

identifier "min"

argument_list

( "("

identifier "fitnessHistory"

) ")"

; ";"

local_variable_declaration

modifiers

final "final"

floating_point_type

double "double"

variable_declarator

identifier "historyWorst"

= "="

method_invocation

identifier "max"

argument_list

( "("

identifier "fitnessHistory"

) ")"

; ";"

if_statement (+43 nodes collapsed)

if_statement (+28 nodes collapsed)

line_comment "// condition number of the covariance matrix exceeds 1e14"

if_statement (+29 nodes collapsed)

line_comment "// user defined termination"

if_statement (+87 nodes collapsed)

line_comment "// Adjust step size in case of equal function values (flat f"...

if_statement (+56 nodes collapsed)

if_statement (+61 nodes collapsed)

line_comment "// store best in history"

expression_statement

method_invocation

identifier "push"

argument_list

( "("

identifier "fitnessHistory"

, ","

identifier "bestFitness"

) ")"

; ";"

expression_statement

method_invocation

identifier "fitfun"

. "."

identifier "setValueRange"

argument_list

( "("

binary_expression

identifier "worstFitness"

- "-"

identifier "bestFitness"

) ")"

; ";"

if_statement (+68 nodes collapsed)

} "}"

return_statement

return "return"

identifier "optimum"

; ";"

} "}"

block_comment "/**\n * Scans the list of (required and optional) optimiz"...

method_declaration (+118 nodes collapsed)

block_comment "/**\n * Checks dimensions and values of boundaries and in"...

method_declaration (+195 nodes collapsed)

block_comment "/**\n * Initialization of the dynamic search parameters\n "...

method_declaration (+939 nodes collapsed)

block_comment "/**\n * Update of the evolution paths ps and pc.\n *\n "...

method_declaration (+224 nodes collapsed)

block_comment "/**\n * Update of the covariance matrix C for diagonalOnl"...

method_declaration (+201 nodes collapsed)

block_comment "/**\n * Update of the covariance matrix C.\n *\n * "...

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block_comment "/**\n * Update B and D from C.\n *\n * @param negcc"...

method_declaration (+453 nodes collapsed)

block_comment "/**\n * Pushes the current best fitness value in a histor"...

method_declaration (+81 nodes collapsed)

block_comment "/**\n * Sorts fitness values.\n *\n * @param double"...

method_declaration (+177 nodes collapsed)

block_comment "/**\n * Used to sort fitness values. Sorting is always in"...

class_declaration (+243 nodes collapsed)

block_comment "/**\n * Normalizes fitness values to the range [0,1]. Add"...

class_declaration (+660 nodes collapsed)

line_comment "// -----Matrix utility functions similar to the Matlab build"...

block_comment "/**\n * @param m Input matrix\n * @return Matrix repre"...

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block_comment "/**\n * @param m Input matrix.\n * @return Matrix repr"...

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block_comment "/**\n * @param m Input matrix.\n * @return Matrix repr"...

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block_comment "/**\n * @param m Input matrix 1.\n * @param n Input ma"...

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block_comment "/**\n * @param m Input matrix 1.\n * @param n Input ma"...

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block_comment "/**\n * @param m Input matrix.\n * @param cols Columns"...

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block_comment "/**\n * @param m Input matrix.\n * @param k Diagonal p"...

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block_comment "/**\n * @param m Input matrix.\n * @return Row matrix "...

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block_comment "/**\n * @param m Input matrix.\n * @return the diagona"...

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block_comment "/**\n * Copies a column from m1 to m2.\n *\n * @par"...

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block_comment "/**\n * @param n Number of rows.\n * @param m Number o"...

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block_comment "/**\n * @param n Number of rows.\n * @param m Number o"...

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block_comment "/**\n * @param n Number of rows.\n * @param m Number o"...

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block_comment "/**\n * @param mat Input matrix.\n * @param n Number o"...

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block_comment "/**\n * @param start Start value.\n * @param end End v"...

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block_comment "/**\n * @param m Input matrix.\n * @return the maximum"...

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block_comment "/**\n * @param m Input matrix.\n * @return the minimum"...

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block_comment "/**\n * @param m Input array.\n * @return the maximum "...

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block_comment "/**\n * @param m Input array.\n * @return the minimum "...

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block_comment "/**\n * @param indices Input index array.\n * @return "...

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block_comment "/**\n * @param indices Input index array.\n * @return "...

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block_comment "/**\n * @param size Length of random array.\n * @retur"...

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block_comment "/**\n * @param size Number of rows.\n * @param popSize"...

method_declaration (+125 nodes collapsed)

} "}"