ParameterSet

java.lang.Object
- de.jstacs.parameters.ParameterSet

All Implemented Interfaces:

GalaxyConvertible, Storable, Cloneable

Direct Known Subclasses:

AbstractPerformanceMeasure, ClassifierAssessmentAssessParameterSet, ConstraintParameterSet, ExpandableParameterSet, HMMTrainingParameterSet, InstanceParameterSet, SimpleParameterSet
```
public abstract class ParameterSet
extends Object
implements Storable, Cloneable, GalaxyConvertible
```
(Container) class for a set of Parameters. This is the base class for other ParameterSets that provide more specialized methods, e.g. for expanding the set of Parameters at runtime ( ExpandableParameterSet ) or defining an array of ParameterSet s from a common template ( ArrayParameterSet ).

Author:

Jan Grau, Jens Keilwagen

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`protected class`	`ParameterSet.ParameterList` Class for a `AnnotatedEntityList` that automatically sets the `Parameter.parent` field to the enclosing `ParameterSet`.

Field Summary

Fields
Modifier and Type	Field and Description
`protected String`	`errorMessage` The error message of the last error or `null`
`protected ParameterSet.ParameterList`	`parameters` The set of parameters
`protected Parameter`	`parent` If this `ParameterSet` is contained in a `Parameter`, this variable holds a reference to that `Parameter`.

Constructor Summary

Constructors
Modifier	Constructor and Description
	`ParameterSet()` Constructs a new `ParameterSet` with empty parameter values.
`protected`	`ParameterSet(ArrayList<Parameter> parameters)` Constructs a `ParameterSet` out of an `ArrayList` of `Parameter`s.
`protected`	`ParameterSet(Parameter... parameters)` Constructs a `ParameterSet` out of an array of `Parameter`s.
	`ParameterSet(StringBuffer representation)` The standard constructor for the interface `Storable`.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`ParameterSet`	`clone()` Creates a full clone (deep copy) of this `ParameterSet`.
`void`	`fromGalaxy(String namePrefix, StringBuffer command)` Parses the contents of `command` in the format defined by `configBuffer` of `GalaxyConvertible.toGalaxy(String, String, int, StringBuffer, StringBuffer, boolean)` and sets the values of the `Parameter` or `ParameterSet` accordingly.
`protected void`	`fromXML(StringBuffer representation)` Parses the instance fields of a `ParameterSet` from the XML representation as returned by `toXML()`.
`String[]`	`getAllParameterNames()` Returns the names of all `Parameter`s in this `ParameterSet`.
`static String`	`getComment(Class<? extends ParameterSet> c)` Returns a comment for the class.
`static String`	`getComment(ParameterSet p)` Returns a comment for the `ParameterSet`.
`String`	`getErrorMessage()` Returns the message of the last error that occurred.
`static int`	`getIndex(String[] names, Object[] values, Comparable current, boolean hasAlternative)` This method tries to find the correct name (`String`) for your choice.
`static String`	`getName(Class<? extends ParameterSet> c)` Returns a name for the class.
`static String`	`getName(ParameterSet p)` Returns a name for the `ParameterSet`.
`int`	`getNumberOfParameters()` Returns the number of parameters in the `ParameterSet`.
`Parameter`	`getParameterAt(int i)` Returns the `Parameter` at position `i`.
`Parameter`	`getParameterForName(String name)` Returns the `Parameter` with name `name`.
`Parameter`	`getParent()` Returns the enclosing `Parameter` of this `ParameterSet` or `null` if none exists.
`boolean`	`hasDefaultOrIsSet()` Returns `true` if all parameters in this `ParameterSet` are either set by the user or have default values.
`protected void`	`initParameterList()` Initializes the internal set of `Parameter`s, which is a `ParameterSet.ParameterList`.
`protected void`	`initParameterList(int initCapacity)` Initializes the internal set of `Parameter`s, which is a `ParameterSet.ParameterList`, with an initial number of `Parameter`s of `initCapacity`.
`boolean`	`isAtomic()` Returns `true` if this `ParameterSet` contains only atomic parameters, i.e.
`boolean`	`isComparable(ParameterSet p)` This method checks whether the given `ParameterSet` is comparable to the current instance, i.e.
`boolean`	`parametersLoaded()` Returns `true` if the parameters of this `ParameterSet` have been loaded.
`void`	`reset()` Resets all `Parameter`s in this `ParameterSet` to their default values or `null` if not default value was provided.
`void`	`setParent(Parameter parent)` Sets the enclosing `ParameterSetContainer` of this `ParameterSet` to `parent`.
`void`	`toGalaxy(String namePrefix, String configPrefix, int depth, StringBuffer descBuffer, StringBuffer configBuffer, boolean addLine)` Creates an Galaxy XML-representation of the parameters and appends it to `descBuffer` and variable configuration and appends it to `configBuffer`.
`StringBuffer`	`toXML()` This method returns an XML representation as `StringBuffer` of an instance of the implementing class.

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

- Field Detail
  - parameters
```
protected ParameterSet.ParameterList parameters
```
    The set of parameters
  - errorMessage
```
protected String errorMessage
```
    The error message of the last error or null
  - parent
```
protected Parameter parent
```
    If this ParameterSet is contained in a Parameter, this variable holds a reference to that Parameter.
- Constructor Detail
  - ParameterSet
```
public ParameterSet()
```
    Constructs a new ParameterSet with empty parameter values.
  - ParameterSet
```
protected ParameterSet(Parameter... parameters)
```
    Constructs a ParameterSet out of an array of Parameters. The Parameters are not cloned, but passed by reference.
    
    Parameters:
    
    parameters - the Parameters
  - ParameterSet
```
protected ParameterSet(ArrayList<Parameter> parameters)
```
    Constructs a ParameterSet out of an ArrayList of Parameters. The Parameters are not cloned, but passed by reference.
    
    Parameters:
    
    parameters - the Parameters
  - ParameterSet
```
public ParameterSet(StringBuffer representation)
             throws NonParsableException
```
    The standard constructor for the interface Storable. Constructs a ParameterSet out of an XML representation.
    
    Parameters:
    
    representation - the XML representation as StringBuffer
    
    Throws:
    
    NonParsableException - if the ParameterSet could not be reconstructed out of the StringBuffer representation
- Method Detail
  - getName
```
public static String getName(Class<? extends ParameterSet> c)
```
    Returns a name for the class.
    
    Parameters:
    
    c - the given class.
    
    Returns:
    
    a name for the class.
    
    See Also:
    
    ParameterSetContainer.ParameterSetContainer(Class), AbstractSelectionParameter.AbstractSelectionParameter(String, String, boolean, Class...)
  - getComment
```
public static String getComment(Class<? extends ParameterSet> c)
```
    Returns a comment for the class.
    
    Parameters:
    
    c - the given class.
    
    Returns:
    
    a comment for the class.
    
    See Also:
    
    ParameterSetContainer.ParameterSetContainer(Class), AbstractSelectionParameter.AbstractSelectionParameter(String, String, boolean, Class...)
  - getName
```
public static String getName(ParameterSet p)
```
    Returns a name for the ParameterSet.
    
    Parameters:
    
    p - the given ParameterSet.
    
    Returns:
    
    a name for the ParameterSet.
    
    See Also:
    
    ParameterSetContainer.ParameterSetContainer(ParameterSet), AbstractSelectionParameter.AbstractSelectionParameter(String, String, boolean, ParameterSet...), getName(Class), Object.getClass()
  - getComment
```
public static String getComment(ParameterSet p)
```
    Returns a comment for the ParameterSet.
    
    Parameters:
    
    p - the given ParameterSet.
    
    Returns:
    
    a comment for the ParameterSet.
    
    See Also:
    
    ParameterSetContainer.ParameterSetContainer(ParameterSet), AbstractSelectionParameter.AbstractSelectionParameter(String, String, boolean, ParameterSet...), getComment(Class), Object.getClass()
  - getIndex
```
public static int getIndex(String[] names,
                           Object[] values,
                           Comparable current,
                           boolean hasAlternative)
                    throws IllegalArgumentException
```
    This method tries to find the correct name (String) for your choice. This method is useful if you handle AbstractSelectionParameters.
    
    Parameters:
    
    names - the names
    
    values - the values that can be set
    
    current - the value to be set
    
    hasAlternative - indicates whether the last entry of names is an alternative parameter
    
    Returns:
    
    the StringIndexOutOfBoundsException that has to be used
    
    Throws:
    
    IllegalArgumentException - if no match could be found
    
    See Also:
    
    AbstractSelectionParameter
  - clone
```
public ParameterSet clone()
                   throws CloneNotSupportedException
```
    Creates a full clone (deep copy) of this ParameterSet. As a convenience-method the user can use fillWithStandardFieldsForClone(ParameterSet) on a newly created instance of a subclass of ParameterSet to obtain a clone/copy of all standard member variables (those already defined in ParameterSet) in the passed ParameterSet. Using this method, the cloning process becomes merely three-step:
    - Create a new instance of your subclass of ParameterSet, most likely with an empty constructor or the one taking just the instance class.
    - Call this.fillWithStandardFieldsForClone on this instance.
    - Return the instance.
    This method fulfills the conventions of Object's method Object.clone().
    Overrides:
    
    clone in class Object
    
    Returns:
    
    a deep clone/copy of this ParameterSet
    
    Throws:
    
    CloneNotSupportedException
  - initParameterList
```
protected final void initParameterList()
```
    Initializes the internal set of Parameters, which is a ParameterSet.ParameterList.
  - initParameterList
```
protected final void initParameterList(int initCapacity)
```
    Initializes the internal set of Parameters, which is a ParameterSet.ParameterList, with an initial number of Parameters of initCapacity.
    
    Parameters:
    
    initCapacity - the initial number of Parameters
  - parametersLoaded
```
public boolean parametersLoaded()
```
    Returns true if the parameters of this ParameterSet have been loaded.
    
    Returns:
    
    the state of the parameters (loaded or not)
  - isAtomic
```
public boolean isAtomic()
```
    Returns true if this ParameterSet contains only atomic parameters, i.e. the parameters do not contain ParameterSets themselves.
    
    Returns:
    
    true if the ParameterSet contains only atomic parameters, false otherwise
  - hasDefaultOrIsSet
```
public boolean hasDefaultOrIsSet()
```
    Returns true if all parameters in this ParameterSet are either set by the user or have default values. If any additional constraints are required on your parameters you should either specify some ParameterValidator on these parameters or implement these constraints by overriding this method in your implementation of ParameterSet. It is recommended to specify a useful remark which constraint failed in the member-variable errorMessage, which will be displayed to the user. In the overriding method super.hasDefaultOrIsSet() should be called prior to checking specific constraints.
    
    Returns:
    
    true if all parameters have some allowed value set, false otherwise
  - getErrorMessage
```
public String getErrorMessage()
```
    Returns the message of the last error that occurred. If no error occurred this method returns null.
    
    Returns:
    
    the error message of the last error or null
  - getNumberOfParameters
```
public int getNumberOfParameters()
```
    Returns the number of parameters in the ParameterSet.
    
    Returns:
    
    the number of parameters in the ParameterSet
  - getAllParameterNames
```
public String[] getAllParameterNames()
```
    Returns the names of all Parameters in this ParameterSet.
    
    Returns:
    
    an array containing the names of all Parameters in this ParameterSet
  - getParameterForName
```
public Parameter getParameterForName(String name)
```
    Returns the Parameter with name name.
    
    Parameters:
    
    name - the name of the Parameter
    
    Returns:
    
    the Parameter with name name
  - getParameterAt
```
public Parameter getParameterAt(int i)
```
    Returns the Parameter at position i.
    
    Parameters:
    
    i - the position in the ParameterSet
    
    Returns:
    
    the Parameter at position i
  - toXML
```
public StringBuffer toXML()
```
    Description copied from interface: Storable
    
    This method returns an XML representation as StringBuffer of an instance of the implementing class.
    
    Specified by:
    
    toXML in interface Storable
    
    Returns:
    
    the XML representation
  - reset
```
public void reset()
```
    Resets all Parameters in this ParameterSet to their default values or null if not default value was provided.
    
    See Also:
    
    Parameter.reset()
  - fromXML
```
protected void fromXML(StringBuffer representation)
                throws NonParsableException
```
    Parses the instance fields of a ParameterSet from the XML representation as returned by toXML().
    
    Parameters:
    
    representation - the XML representation as StringBuffer
    
    Throws:
    
    NonParsableException - if the XML code could not be parsed
    
    See Also:
    
    toXML()
  - getParent
```
public Parameter getParent()
```
    Returns the enclosing Parameter of this ParameterSet or null if none exists.
    
    Returns:
    
    the enclosing Parameter (parent)
  - setParent
```
public void setParent(Parameter parent)
```
    Sets the enclosing ParameterSetContainer of this ParameterSet to parent.
    
    Parameters:
    
    parent - the new parent
  - toGalaxy
```
public void toGalaxy(String namePrefix,
                     String configPrefix,
                     int depth,
                     StringBuffer descBuffer,
                     StringBuffer configBuffer,
                     boolean addLine)
              throws Exception
```
    Description copied from interface: GalaxyConvertible
    
    Creates an Galaxy XML-representation of the parameters and appends it to descBuffer and variable configuration and appends it to configBuffer. The variable configuration is also used to parse user-supplied values returned by Galaxy.
    
    Specified by:
    
    toGalaxy in interface GalaxyConvertible
    
    Parameters:
    
    namePrefix - the prefix of the variable name used in Galaxy
    
    configPrefix - the prefix for conditionals
    
    depth - the depth in the parameter hierarchy, used for graphical representation of nesting
    
    descBuffer - the buffer for the parameter description
    
    configBuffer - the buffer for the configuration line
    
    addLine - if true, a line is added before the title of a parameter
    
    Throws:
    
    Exception - if the conversion fails
  - fromGalaxy
```
public void fromGalaxy(String namePrefix,
                       StringBuffer command)
                throws Exception
```
    Description copied from interface: GalaxyConvertible
    
    Parses the contents of command in the format defined by configBuffer of GalaxyConvertible.toGalaxy(String, String, int, StringBuffer, StringBuffer, boolean) and sets the values of the Parameter or ParameterSet accordingly.
    
    Specified by:
    
    fromGalaxy in interface GalaxyConvertible
    
    Parameters:
    
    namePrefix - the prefix of the variable name
    
    command - the command string
    
    Throws:
    
    Exception - if the command string could not be parsed
  - isComparable
```
public boolean isComparable(ParameterSet p)
```
    This method checks whether the given ParameterSet is comparable to the current instance, i.e. whether the Class and the number of parameters are identical, and the individual Parameters are comparable. In other words, the method returns true if the ParameterSets only differ in their specific raw values.
    
    Parameters:
    
    p - the ParameterSet for the comparison
    
    Returns:
    
    true if the ParameterSets only differ in their values, otherwise false
    
    See Also:
    
    Object.getClass(), getNumberOfParameters(), Parameter.isComparable(Parameter)

Class ParameterSet

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

parameters

errorMessage

parent

Constructor Detail

ParameterSet

ParameterSet

ParameterSet

ParameterSet

Method Detail

getName

getComment

getName

getComment

getIndex

clone

initParameterList

initParameterList

parametersLoaded

isAtomic

hasDefaultOrIsSet

getErrorMessage

getNumberOfParameters

getAllParameterNames

getParameterForName

getParameterAt

toXML

reset

fromXML

getParent

setParent

toGalaxy

fromGalaxy

isComparable