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public interface GalaxyConvertible
Interface for Parameter
s that can be converted to and extracted from
Galaxy representations.
The methods of this interface are used in the GalaxyAdaptor
to create
Galaxy representation, i.e., config-files, from ParameterSet
s that contain
the parameters for a specific application.
Method Summary | |
---|---|
void |
fromGalaxy(String namePrefix,
StringBuffer command)
Parses the contents of command in the format defined by configBuffer of toGalaxy(String, String, int, StringBuffer, StringBuffer)
and sets the values of the Parameter or ParameterSet accordingly. |
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 . |
Method Detail |
---|
void toGalaxy(String namePrefix, String configPrefix, int depth, StringBuffer descBuffer, StringBuffer configBuffer) throws Exception
descBuffer
and variable configuration and appends it to configBuffer
. The variable configuation
is also used to parse user-supplied values returned by Galaxy.
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 failsvoid fromGalaxy(String namePrefix, StringBuffer command) throws Exception
command
in the format defined by configBuffer
of toGalaxy(String, String, int, StringBuffer, StringBuffer)
and sets the values of the Parameter
or ParameterSet
accordingly.
namePrefix
- the prefix of the variable namecommand
- the command string
Exception
- if the command string could not be parsed
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