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java.lang.Objectde.jstacs.AnnotatedEntity
de.jstacs.parameters.Parameter
de.jstacs.parameters.RangeParameter
public class RangeParameter
Class for a parameter wrapper that allows SimpleParameter
s to be set
to a set of values.
These values may be given either as a list of values separated by spaces, as
a range between a first and a last value with a given number of steps between
these values, or a single value. In the latter case a RangeParameter
works just like a plain SimpleParameter
. SimpleParameter
s
that are used to construct a RangeParameter
must be rangeable, i.e.
their method SimpleParameter.isRangeable()
must return
true
, or they will be rejected.
Nested Class Summary | |
---|---|
static class |
RangeParameter.RangeType
The possible types of defining ranges for a RangeParameter . |
static class |
RangeParameter.Scale
This enum defines possible scales, if RangeParameter.RangeType is
RangeParameter.RangeType.RANGE . |
Field Summary |
---|
Fields inherited from class de.jstacs.parameters.Parameter |
---|
parent |
Fields inherited from class de.jstacs.AnnotatedEntity |
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comment, datatype, name |
Constructor Summary | |
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RangeParameter(SimpleParameter par)
Constructs a RangeParameter from a SimpleParameter that
is rangeable. |
|
RangeParameter(StringBuffer representation)
The standard constructor for the interface Storable . |
Method Summary | |
---|---|
protected void |
appendFurtherInfos(StringBuffer buf)
This method can be used in the method Storable.toXML() to extract
further information (name, comment, datatype). |
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. |
RangeParameter |
clone()
|
protected void |
extractFurtherInfos(StringBuffer buf)
This method can be used in the constructor with parameter StringBuffer to
extract the further information. |
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. |
static EnumParameter |
getCollectionOfScales()
Returns a EnumParameter that allows the user to choose
between different scales. |
Object |
getEndValue()
Returns the last value of a range of parameter values or null if no range was specified. |
String |
getErrorMessage()
If a value could not be set successfully this method returns the corresponding error message. |
String |
getList()
Returns a list of all parameter values as a String or
null if no parameter values have been set. |
int |
getNumberOfNexts(int afterIndex)
Returns the number of calls of next() that can be done before
obtaining false . |
int |
getNumberOfValues()
Returns the number of values in a list or range of parameter values. |
String |
getScale()
Returns a description of the the scale of a range of parameter values. |
Object |
getStartValue()
Returns the start value of a range of parameter values or null if no range was specified. |
int |
getSteps()
Returns the number of steps of a range of parameter values or 0 if no range was specified. |
Object |
getValue()
Returns the value of the AnnotatedEntity . |
String |
getXMLTag()
This method returns a tag used as outer tag of the XML description. |
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 |
isRanged()
Returns true if this RangeIterator is ranging over a
set of values. |
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. |
boolean |
next()
Returns true if the next element still exists and can be
fetched using getValue() , false otherwise. |
void |
reset()
Resets the parameter and its contents to the default values or null if no defaults are given. |
void |
resetToFirst()
Resets the current value in the collection to the first value. |
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 |
setValues(Object startValue,
int steps,
Object endValue,
RangeParameter.Scale scale)
Sets the values of this RangeParameter as a range of values,
specified by a start value, a last value, a number of steps between these
values (without the last value) and a scale in that the values between
the first and the last value are chosen. |
void |
setValues(String values)
Sets a list of values from a String containing a space separated
list of values. |
void |
setValuesInLogScale(boolean log,
double radix,
Object startValue,
int steps,
Object endValue)
This method enables you to set a list of values in an easy manner. |
RangeParameter.RangeType |
shallBeRanged()
Returns one of LIST, RANGE or NO depending on
the input used to specify this RangeParameter . |
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 . |
String |
valuesToString()
Returns a String representation of the set of values. |
Methods inherited from class de.jstacs.parameters.Parameter |
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getParent, isComparable, setParent |
Methods inherited from class de.jstacs.AnnotatedEntity |
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getComment, getDatatype, getName, toXML |
Methods inherited from class java.lang.Object |
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equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public RangeParameter(SimpleParameter par) throws Exception
RangeParameter
from a SimpleParameter
that
is rangeable.
par
- the rangeable SimpleParameter
Exception
- if the SimpleParameter
is not rangeable, i.e. its
method SimpleParameter.isRangeable()
returns
false
public RangeParameter(StringBuffer representation) throws NonParsableException
Storable
.
Restores a RangeParameter
from its XML representation.
representation
- the XML representation as StringBuffer
NonParsableException
- if the StringBuffer
representation
could
not be parsedMethod Detail |
---|
public RangeParameter clone() throws CloneNotSupportedException
clone
in class Parameter
CloneNotSupportedException
public static EnumParameter getCollectionOfScales() throws ParameterException
EnumParameter
that allows the user to choose
between different scales.
EnumParameter
ParameterException
- if the EnumParameter
could, or if one of the
possible values of the SelectionParameter
was not
legalpublic String getList()
String
or
null
if no parameter values have been set.
null
public Object getStartValue()
null
if no range was specified.
null
public Object getEndValue()
null
if no range was specified.
null
public int getSteps()
0
if no range was specified.
0
public String getScale()
RangeParameter.Scale
public boolean isRequired()
Parameter
true
if the Parameter
is required,
false
otherwise.
isRequired
in class Parameter
true
if the Parameter
is required,
false
otherwisepublic boolean checkValue(Object value)
Parameter
checkValue
in class Parameter
value
- the value to be checked
true
if the value is valid, false
otherwisepublic void setValue(Object value) throws SimpleParameter.IllegalValueException
Parameter
Parameter
to value
.
setValue
in class Parameter
value
- the new value of the Parameter
SimpleParameter.IllegalValueException
- if the specified value is not valid for this
Parameter
public void setValues(String values) throws SimpleParameter.IllegalValueException
String
containing a space separated
list of values. After this method has been called,
shallBeRanged()
returns RangeParameter.RangeType.LIST
.
values
- the space separated list of values
SimpleParameter.IllegalValueException
- if at least one of the values in the list is not suitable for
this RangeParameter
public void setValues(Object startValue, int steps, Object endValue, RangeParameter.Scale scale) throws SimpleParameter.IllegalValueException
RangeParameter
as a range of values,
specified by a start value, a last value, a number of steps between these
values (without the last value) and a scale in that the values between
the first and the last value are chosen. This scale must be one of
those listed in RangeParameter.Scale
.
startValue
- the first value of the rangesteps
- the number of steps between startValue
and
endValue
(exclusive)endValue
- the last value of the rangescale
- the RangeParameter.Scale
SimpleParameter.IllegalValueException
- if one of the values is not suitable for this
RangeParameter
, e.g. is out of a specified range of
allowed valuesRangeParameter.Scale
public void setValuesInLogScale(boolean log, double radix, Object startValue, int steps, Object endValue) throws SimpleParameter.IllegalValueException
[startValue,endValue]
in (inverse) logarithmic scale.
log
- if true
a logarithmic scale is used, otherwise
the inverse logarithmic scaleradix
- the radix for the scalestartValue
- the first value of the rangesteps
- the number of steps between startValue
and
endValue
(exclusive)endValue
- the last value of the range
SimpleParameter.IllegalValueException
- if some constraints are not fulfilledpublic Object getValue()
AnnotatedEntity
AnnotatedEntity
.
getValue
in class AnnotatedEntity
AnnotatedEntity
public boolean next() throws SimpleParameter.IllegalValueException
true
if the next element still exists and can be
fetched using getValue()
, false
otherwise.
next
in interface RangeIterator
true
if the next element exists and can be fetched,
false
otherwise
SimpleParameter.IllegalValueException
- if the next value to be fetched is not validsetValue(Object)
public int getNumberOfValues()
getNumberOfValues
in interface RangeIterator
public int getNumberOfNexts(int afterIndex)
next()
that can be done before
obtaining false
.
afterIndex
- the index after which next()
shall be called
next()
after
afterIndex
public RangeParameter.RangeType shallBeRanged()
LIST, RANGE
or NO
depending on
the input used to specify this RangeParameter
.
RangeParameter.RangeType
public boolean hasDefaultOrIsSet()
Parameter
true
if the parameter either has a default value or
the value was set by the user, false
otherwise.
hasDefaultOrIsSet
in class Parameter
true
if value has a default value or was set,
false
otherwisepublic boolean isSet()
Parameter
true
if the parameter was set by the user,
false
otherwise.
isSet
in class Parameter
true
if the parameter was set, false
otherwisepublic boolean isAtomic()
Parameter
true
if the parameter is of an atomic data type,
false
otherwise.
isAtomic
in class Parameter
true
if the parameter is atomic, false
otherwisepublic String getErrorMessage()
Parameter
getErrorMessage
in class Parameter
public String getXMLTag()
AnnotatedEntity
getXMLTag
in class AnnotatedEntity
protected void appendFurtherInfos(StringBuffer buf)
AnnotatedEntity
Storable.toXML()
to extract
further information (name, comment, datatype).
appendFurtherInfos
in class Parameter
buf
- a XML representation of the main information as
StringBuffer
Storable.toXML()
protected void extractFurtherInfos(StringBuffer buf) throws NonParsableException
AnnotatedEntity
StringBuffer
to
extract the further information.
extractFurtherInfos
in class Parameter
buf
- a XML represenation of the main information as
StringBuffer
NonParsableException
- if the XML representation is not parsableAnnotatedEntity.AnnotatedEntity(StringBuffer)
public void reset()
Parameter
null
if no defaults are given.
reset
in class Parameter
public void resetToFirst()
RangeIterator
resetToFirst
in interface RangeIterator
public void setDefault(Object defaultValue) throws Exception
Parameter
Parameter
to
defaultValue
. This method also sets the current
value of this Parameter
to the default.
setDefault
in class Parameter
defaultValue
- the default value
Exception
- if the default value is not an appropriate value for this
Parameter
public String valuesToString()
RangeIterator
String
representation of the set of values.
valuesToString
in interface RangeIterator
String
representationpublic boolean isRanged()
RangeIterator
true
if this RangeIterator
is ranging over a
set of values.
isRanged
in interface RangeIterator
true
if this RangeIterator
is ranging over a
set of values, false
otherwisepublic void toGalaxy(String namePrefix, String configPrefix, int depth, StringBuffer descBuffer, StringBuffer configBuffer) throws Exception
GalaxyConvertible
descBuffer
and variable configuration and appends it to configBuffer
. The variable configuation
is also used to parse user-supplied values returned by Galaxy.
toGalaxy
in interface GalaxyConvertible
namePrefix
- the prefix of the variable name used in GalaxyconfigPrefix
- the prefix for conditionalsdepth
- the depth in the parameter hierarchy, used for graphical representation of nestingdescBuffer
- the buffer for the parameter descriptionconfigBuffer
- the buffer for the configuration line
Exception
- if the conversion failspublic void fromGalaxy(String namePrefix, StringBuffer command) throws Exception
GalaxyConvertible
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.
fromGalaxy
in interface GalaxyConvertible
namePrefix
- the prefix of the variable namecommand
- the command string
Exception
- if the command string could not be parsed
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