net.sf.basedb.plugins.executor
Class ParameterDefinition

java.lang.Object
  net.sf.basedb.plugins.executor.ParameterDefinition

public class ParameterDefinition
extends Object

Represents a parameter definition for the external program. A name and type is required. All other settings are optional. Supported values for type is:

• string: The parameter is a free-text string parameter with a maximum length of 255 characters.
• text: The parameter is a free-text string parameter with a maximum length of 64K characters.
• integer, float: The parameter is a numeric parameter. Options 'min' and 'max' can be set to restrict the range of valid values.
• boolean: The parameter is a true/false parameter.
• enumeration: The parameter is an enumeration that must take it's value from a predefined list of values. The predefined list should be set in the 'enum' option with a line break as a delimiter between values.
• factor: The parameter is an enumeration among the experimental factors that has been defined for the experiment. The default value is matched against the name/external id of the annotation types.
• spotformula: The parameter is an enumeration among the formulas that can be used with the current source bioassay set. The default value is matched against the name of the formulas.
• assays: The parameter is an enumeration among the bioassays in the current source bioassay set. The default value is matched against the name of the bioassays.

Since:

2.15

Author:

Nicklas

Field Summary

private String	defaultValue
private String	description
private static URL	dtdFile
private boolean	multiple
private String	name
private Map<String,String>	options
private boolean	required
private String	type

Constructor Summary

ParameterDefinition()
Create a new empty parameter definition.

Method Summary

String	getDefaultValue() Get the default value for this parameter.
String	getDescription() Get a description/help text about this parameter.
String	getName() Get the name of the parameter.
String	getOption(String key) Get the value for an option.
Set<String>	getOptions() Get the names of other options that are defined for this parmeter.
String	getType() Get the type of the parameter.
boolean	isMultiple() Can this parameter have multiple values or only one?
boolean	isRequired() Is this parameter a required parameter or not?
static List<ParameterDefinition>	parseXml(String xml, boolean validate) Parse an XML document containing parameter definitions.
void	setDefaultValue(String defaultValue) Set the default value for this parameter.
void	setDescription(String description) Set a description/help text for this parmeter.
void	setMultiple(boolean multiple) Set if this parameter can have multiple values or only one.
void	setName(String name) Set the name of the parameter.
void	setOption(String key, String value) Set the value for an option.
void	setRequired(boolean required) Set if this parameter should be a required or optional parameter.
void	setType(String type) Set the type of the parameter.
PluginParameter<?>	toPluginParameter(DbControl dc, BioAssaySet source) Convert this parameter definition to a PluginParameter object.
String	toXmlFragment(boolean compact) Render this parameter definition as an XML fragment.

Methods inherited from class java.lang.Object

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

Field Detail

dtdFile

private static final URL dtdFile

type

private String type

name

private String name

required

private boolean required

multiple

private boolean multiple

defaultValue

private String defaultValue

description

private String description

options

private Map<String,String> options

Constructor Detail

ParameterDefinition

public ParameterDefinition()

Create a new empty parameter definition. Before it can be used a name and type must be specified.

Method Detail

parseXml

public static List<ParameterDefinition> parseXml(String xml,
                                                 boolean validate)

Parse an XML document containing parameter definitions.

Parameters:

xml - The xml as a string (with or without a DOCTYPE declaration)

validate - TRUE to validate the XML against the dtd (external-plugin-parameters.dtd)

Returns:

A list with parameter definition

getType

public String getType()

Get the type of the parameter.

setType

public void setType(String type)

Set the type of the parameter. For supported values see the class documentation.

getName

public String getName()

Get the name of the parameter. This value is required.

setName

public void setName(String name)

Set the name of the parameter.

isRequired

public boolean isRequired()

Is this parameter a required parameter or not?

setRequired

public void setRequired(boolean required)

Set if this parameter should be a required or optional parameter.

isMultiple

public boolean isMultiple()

Can this parameter have multiple values or only one?

setMultiple

public void setMultiple(boolean multiple)

Set if this parameter can have multiple values or only one.

getDefaultValue

public String getDefaultValue()

Get the default value for this parameter.

setDefaultValue

public void setDefaultValue(String defaultValue)

Set the default value for this parameter.

getDescription

public String getDescription()

Get a description/help text about this parameter.

setDescription

public void setDescription(String description)

Set a description/help text for this parmeter.

getOptions

public Set<String> getOptions()

Get the names of other options that are defined for this parmeter. Useful options depend on the parameter type and are described in the class documentation.

getOption

public String getOption(String key)

Get the value for an option.

setOption

public void setOption(String key,
                      String value)

Set the value for an option.

toXmlFragment

public String toXmlFragment(boolean compact)

Render this parameter definition as an XML fragment. Multiple fragments can be concatenated and then wrapped with:

Parameters:
compact - If TRUE, the generated XML is compacted and without line breaks.
Returns:
An XML representation of this parameter definition

toPluginParameter

public PluginParameter<?> toPluginParameter(DbControl dc,
                                            BioAssaySet source)

Convert this parameter definition to a PluginParameter object.

Parameters:

dc - A DbControl to use for database access

source - The source bioassay set