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## de.jstacs.parameters
Class FileParameter

    java.lang.Object
      de.jstacs.parameters.Parameter
          de.jstacs.parameters.FileParameter

All Implemented Interfaces:
  GalaxyConvertible, Storable, Cloneable

    public class FileParameter

extends Parameter
implements GalaxyConvertible

Class for a `Parameter` that represents a local file.

Author:
  Jan Grau

Nested Class Summary
`static class` | `FileParameter.FileRepresentation` Class that represents a file.

Field Summary

Fields inherited from class de.jstacs.parameters.Parameter
`neededReference, neededReferenceId, parent`

Constructor Summary
`FileParameter(StringBuffer buf)` The standard constructor for the interface `Storable`.
`FileParameter(String name, String comment, String mime, boolean required)` Creates a `FileParameter`.
`FileParameter(String name, String comment, String mime, boolean required, ParameterValidator validator)` Constructs a `FileParameter`.

Method Summary
`boolean` | `checkValue(Object value)` Checks the value for correctness, e.g. for numerical parameters this might be checking if the value is within specified bounds.
`FileParameter` | `clone()`
`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)` and sets the values of the `Parameter` or `ParameterSet` accordingly.
`protected void` | `fromXML(StringBuffer representation)` Parses a `Parameter` from a XML representation as returned by `Parameter.toXML()`.
`String` | `getAcceptedMimeType()` Returns the MIME-type of the allowed files.
`String` | `getComment()` Returns a comment on this `Parameter` that tells something about useful values, domains, usage of this parameter, etc.
`DataType` | `getDatatype()` Returns the data type of the `Parameter`.
`String` | `getErrorMessage()` If a value could not be set successfully this method returns the corresponding error message.
`FileParameter.FileRepresentation` | `getFileContents()` Returns the content of the file.
`String` | `getName()` Returns the name of the `Parameter`.
`Object` | `getValue()` Returns the current value of this `Parameter`.
`boolean` | `hasDefaultOrIsSet()` Returns `true` if the parameter either has a default value or the value was set by the user, `false` otherwise.
`boolean` | `isAtomic()` Returns `true` if the parameter is of an atomic data type, `false` otherwise.
`boolean` | `isRequired()` Returns `true` if the `Parameter` is required, `false` otherwise.
`boolean` | `isSet()` Returns `true` if the parameter was set by the user, `false` otherwise.
`void` | `reset()` Resets the `FileParameter` to its original state.
`void` | `setDefault(Object defaultValue)` Sets the default value of the `Parameter` to `defaultValue`.
`void` | `setValue(Object value)` Sets the value of this `Parameter` to `value`.
`void` | `simplify()` Simplifies the `Parameter` and its contents to the relevant information.
`void` | `toGalaxy(String namePrefix, String configPrefix, int depth, StringBuffer descBuffer, StringBuffer configBuffer)` 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 de.jstacs.parameters.Parameter
`getId, getNeededReference, getNeededReferenceId, getParent, setNeededReference, setParent`

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

Constructor Detail

### FileParameter

    public FileParameter(StringBuffer buf)
                  throws NonParsableException

  The standard constructor for the interface `Storable`. Restores a `FileParameter` from an XML representation.

  Parameters:
    `buf` - the XML representation as `StringBuffer`
  Throws:
    `NonParsableException` - if the XML code could not be parsed
  See Also:
    `fromXML(StringBuffer)`

### FileParameter

    public FileParameter(String name,
                         String comment,
                         String mime,
                         boolean required)

  Creates a `FileParameter`.

  Parameters:
    `name` - the name of the parameter
    `comment` - a comment on the parameter
    `mime` - the MIME-type of allowed files
    `required` - `true` if this `FileParameter` is required to continue, `false` otherwise

### FileParameter

    public FileParameter(String name,
                         String comment,
                         String mime,
                         boolean required,
                         ParameterValidator validator)

  Constructs a `FileParameter`.

  Parameters:
    `name` - the name of the parameter
    `comment` - a comment on the parameter
    `mime` - the MIME-type of allowed files
    `required` - `true` if this `FileParameter` is required
    `validator` - a validator that validates e.g. the contents of the file

Method Detail

### clone

    public FileParameter clone()
                        throws CloneNotSupportedException

  Overrides:
    `clone` in class `Parameter`
  Throws:
    `CloneNotSupportedException`

### getName

    public String getName()

  Description copied from class: `Parameter`
  Returns the name of the `Parameter`.

  Specified by:
    `getName` in class `Parameter`
  Returns:
    the name of the `Parameter`

### isAtomic

    public boolean isAtomic()

  Description copied from class: `Parameter`
  Returns `true` if the parameter is of an atomic data type, `false` otherwise.

  Specified by:
    `isAtomic` in class `Parameter`
  Returns:
    `true` if the parameter is atomic, `false` otherwise

### getDatatype

    public DataType getDatatype()

  Description copied from class: `Parameter`
  Returns the data type of the `Parameter`.

  Specified by:
    `getDatatype` in class `Parameter`
  Returns:
    the data type of the `Parameter`

### getComment

    public String getComment()

  Description copied from class: `Parameter`
  Returns a comment on this `Parameter` that tells something about useful values, domains, usage of this parameter, etc.

  Specified by:
    `getComment` in class `Parameter`
  Returns:
    the comment

### isRequired

    public boolean isRequired()

  Description copied from class: `Parameter`
  Returns `true` if the `Parameter` is required, `false` otherwise.

  Specified by:
    `isRequired` in class `Parameter`
  Returns:
    `true` if the `Parameter` is required, `false` otherwise

### reset

    public void reset()

  Resets the `FileParameter` to its original state.

  Specified by:
    `reset` in class `Parameter`

### getFileContents

    public FileParameter.FileRepresentation getFileContents()

  Returns the content of the file.

  Returns:
    the content of the file

### getErrorMessage

    public String getErrorMessage()

  Description copied from class: `Parameter`
  If a value could not be set successfully this method returns the corresponding error message.

  Specified by:
    `getErrorMessage` in class `Parameter`
  Returns:
    an error message if a value could not be set successfully

### checkValue

    public boolean checkValue(Object value)

  Description copied from class: `Parameter`
  Checks the value for correctness, e.g. for numerical parameters this might be checking if the value is within specified bounds.

  Specified by:
    `checkValue` in class `Parameter`
  Parameters:
    `value` - the value to be checked
  Returns:
    `true` if the value is valid, `false` otherwise

### setDefault

    public void setDefault(Object defaultValue)
                    throws SimpleParameter.IllegalValueException

  Description copied from class: `Parameter`
  Sets the default value of the `Parameter` to `defaultValue`.

  Specified by:
    `setDefault` in class `Parameter`
  Parameters:
    `defaultValue` - the default value
  Throws:
    `SimpleParameter.IllegalValueException`

### simplify

    public void simplify()

  Description copied from class: `Parameter`
  Simplifies the `Parameter` and its contents to the relevant information. This could be e.g. to reset the contents of those values of a `CollectionParameter` that are not selected.

  Specified by:
    `simplify` in class `Parameter`

### setValue

    public void setValue(Object value)
                  throws SimpleParameter.IllegalValueException

  Description copied from class: `Parameter`
  Sets the value of this `Parameter` to `value`.

  Specified by:
    `setValue` in class `Parameter`
  Parameters:
    `value` - the new value of the `Parameter`
  Throws:
    `SimpleParameter.IllegalValueException` - if the specified value is not valid for this `Parameter`

### getValue

    public Object getValue()

  Description copied from class: `Parameter`
  Returns the current value of this `Parameter`.

  Specified by:
    `getValue` in class `Parameter`
  Returns:
    the current value of the `Parameter`

### hasDefaultOrIsSet

    public boolean hasDefaultOrIsSet()

  Description copied from class: `Parameter`
  Returns `true` if the parameter either has a default value or the value was set by the user, `false` otherwise.

  Specified by:
    `hasDefaultOrIsSet` in class `Parameter`
  Returns:
    `true` if value has a default value or was set, `false` otherwise

### isSet

    public boolean isSet()

  Description copied from class: `Parameter`
  Returns `true` if the parameter was set by the user, `false` otherwise.

  Specified by:
    `isSet` in class `Parameter`
  Returns:
    `true` if the parameter was set, `false` otherwise

### 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`
  Overrides:
    `toXML` in class `Parameter`
  Returns:
    the XML representation

### fromXML

    protected void fromXML(StringBuffer representation)
                    throws NonParsableException

  Description copied from class: `Parameter`
  Parses a `Parameter` from a XML representation as returned by `Parameter.toXML()`.

  Overrides:
    `fromXML` in class `Parameter`
  Parameters:
    `representation` - the XML representation as `StringBuffer`
  Throws:
    `NonParsableException` - if the XML code could not be parsed
  See Also:
    `Parameter.toXML()`

### getAcceptedMimeType

    public String getAcceptedMimeType()

  Returns the MIME-type of the allowed files.

  Returns:
    the MIME-type of the allowed files

### toGalaxy

    public void toGalaxy(String namePrefix,
                         String configPrefix,
                         int depth,
                         StringBuffer descBuffer,
                         StringBuffer configBuffer)

  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 configuation 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

### 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)` 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

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