Package org.cytoscape.equations

Class FunctionUtil

java.lang.Object
org.cytoscape.equations.FunctionUtil
public final class FunctionUtil extends Object
A collection of static methods that may be useful for the implementation of built-in functions.

Cytoscape Backwards Compatibility (Static Class): This class is static and therefore can't be extended by users. This means that we may add methods for minor version updates. Methods will only be removed for major version updates.

Module: equations-api

To use this in your app, include the following dependency in your POM:

<dependency>
    <groupId>org.cytoscape</groupId>
    <artifactId>equations-api</artifactId>
</dependency>

  • Method Summary

    Modifier and Type
    Method
    Description
    static void
    addScalarArgumentTypes(List<Class> argTypes)
    Adds the scalar types that equations use internally to the argument, i.e.
    static double
    calcSampleVariance(double[] x)
    Calculates the sample variance of some numbers.
    static boolean
    getArgAsBoolean(Object arg)
    Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "boolean".
    static double
    getArgAsDouble(Object arg)
    Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "double".
    static long
    getArgAsLong(Object arg)
    Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "long".
    static String
    getArgAsString(Object arg)
    Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "String".
    static boolean[]
    getBooleans(Object[] args)
    Attempts to convert all arguments, including Lists to a uniform array of booleans.
    static double[]
    getDoubles(Object[] args)
    Attempts to convert all arguments, including Lists to a uniform array of doubles.
    static long[]
    getLongs(Object[] args)
    Attempts to convert all arguments, including Lists to a uniform array of longs.
    static String
    getOrdinal(int i)
    Converts an integer to an ordinal string.
    static String[]
    getStrings(Object[] args)
    Converts all arguments, including Lists to a uniform array of strings.
    static boolean
    isScalarArgType(Class type)
    Tests whether the argument is one of the scalar types used by equations.
    static boolean
    isTypeOfList(Class listClassCandidate)
    Tests whether the argument is some kind of List.
    static double[]
    listToArray(List<Double> a)
    Converts a List to a regular double[]
    static double
    numericallySafeSum(double[] a)
    Carefully adds the numbers in "a" minimising loss of precision.
    static Object
    translateObjectType(Object input)
    Tries to map "input" to one of Double, Long, Boolean or String.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Method Details

    • getArgAsDouble

      public static double getArgAsDouble(Object arg) throws IllegalArgumentException
      Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "double".
      Parameters:
      arg - the object instance that will be converted to a double, if possible
      Returns:
      the converted argument as a "double"
      Throws:
      IllegalArgumentException - if the argument cannot be converted to a "double"

    • getArgAsString

      public static String getArgAsString(Object arg) throws IllegalArgumentException
      Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "String".
      Parameters:
      arg - the object instance that will be converted to a String
      Returns:
      the converted argument as a "double"
      Throws:
      IllegalArgumentException - if the argument cannot be converted to a "double"

    • getArgAsLong

      public static long getArgAsLong(Object arg) throws IllegalArgumentException
      Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "long".
      Parameters:
      arg - the object instance that will be converted to a long, if possible
      Returns:
      the converted argument as a "long"
      Throws:
      IllegalArgumentException - if the argument cannot be converted to a "long"

    • getArgAsBoolean

      public static boolean getArgAsBoolean(Object arg) throws IllegalArgumentException
      Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "boolean".
      Parameters:
      arg - the object instance that will be converted to a boolean, if possible
      Returns:
      the converted argument as a "boolean"
      Throws:
      IllegalArgumentException - if the argument cannot be converted to a "boolean"

    • numericallySafeSum

      public static double numericallySafeSum(double[] a)
      Carefully adds the numbers in "a" minimising loss of precision.
      Parameters:
      a - the numbers that will be summed up
      Returns:
      the sum of the elements of "a"

    • getOrdinal

      public static String getOrdinal(int i)
      Converts an integer to an ordinal string.
      Parameters:
      i - the integer that will be converted
      Returns:
      the String representation of the ith ordinal

    • calcSampleVariance

      public static double calcSampleVariance(double[] x)
      Calculates the sample variance of some numbers.
      Parameters:
      x - the numbers whose sample variance will be calculated
      Returns:
      the sample variance of the numbers in x[]

    • listToArray

      public static double[] listToArray(List<Double> a)
      Converts a List to a regular double[]
      Parameters:
      a - the list that will be converted
      Returns:
      the converted array

    • isScalarArgType

      public static boolean isScalarArgType(Class type)
      Tests whether the argument is one of the scalar types used by equations.
      Parameters:
      type - the type that will be tested
      Returns:
      true, if type is Double.class, Long.class, String.class or Boolean.class, else false

    • isTypeOfList

      public static boolean isTypeOfList(Class listClassCandidate)
      Tests whether the argument is some kind of List.
      Parameters:
      listClassCandidate - the type that will be tested
      Returns:
      true if "listClassCandidate" is an implementer of interface List, else false

    • addScalarArgumentTypes

      public static void addScalarArgumentTypes(List<Class> argTypes)
      Adds the scalar types that equations use internally to the argument, i.e. adds Double.class, Long.class, String.class and Boolean.class to "argTypes".
      Parameters:
      argTypes - the list that will be augmented

    • getDoubles

      public static double[] getDoubles(Object[] args) throws FunctionError
      Attempts to convert all arguments, including Lists to a uniform array of doubles.
      Parameters:
      args - the objects that will be converted to doubles, if possible
      Returns:
      the converted array
      Throws:
      FunctionError
      IllegalArgumentException - if any scalar argument cannot be converted to a double or any list argument contains an element that cannot be converted to a number.

    • getLongs

      public static long[] getLongs(Object[] args) throws FunctionError
      Attempts to convert all arguments, including Lists to a uniform array of longs.
      Parameters:
      args - the objects that will be converted to longs, if possible
      Returns:
      the converted array
      Throws:
      FunctionError
      IllegalArgumentException - if any scalar argument cannot be converted to a long or any list argument contains an element that cannot be converted to a number.

    • getStrings

      public static String[] getStrings(Object[] args)
      Converts all arguments, including Lists to a uniform array of strings.
      Parameters:
      args - the objects that will be converted to Strings
      Returns:
      the converted array

    • getBooleans

      public static boolean[] getBooleans(Object[] args) throws FunctionError
      Attempts to convert all arguments, including Lists to a uniform array of booleans.
      Parameters:
      args - the objects that will be converted to booleans, if possible
      Returns:
      the converted array
      Throws:
      FunctionError
      IllegalArgumentException - if any scalar argument cannot be converted to a boolean or any list argument contains an element that cannot be converted to a number.

    • translateObjectType

      public static Object translateObjectType(Object input)
      Tries to map "input" to one of Double, Long, Boolean or String.
      Parameters:
      input - the object that will be mapped to one of the scalar types that are internally supported by equations
      Returns:
      null if the translation failed, the input object if no translation was necessary or a new object if a successful translation was possible