Class FatCatUserArgumentProcessor
- java.lang.Object
-
- org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
-
- org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor
-
- All Implemented Interfaces:
UserArgumentProcessor
public class FatCatUserArgumentProcessor extends AbstractUserArgumentProcessor
-
-
Nested Class Summary
Nested Classes Modifier and Type Class Description protected class
FatCatUserArgumentProcessor.FatCatStartupParams
-
Field Summary
-
Fields inherited from class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
mandatoryArgs, newline, params
-
-
Constructor Summary
Constructors Constructor Description FatCatUserArgumentProcessor()
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description StructureAlignment
getAlgorithm()
String
getDbSearchLegend()
Object
getParameters()
protected StartupParameters
getStartupParametersInstance()
StartupParameters is a bean to store all the possible command line parameters.-
Methods inherited from class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
getDbSearchResult, printAboutMe, printHelp, process
-
-
-
-
Constructor Detail
-
FatCatUserArgumentProcessor
public FatCatUserArgumentProcessor()
-
-
Method Detail
-
getStartupParametersInstance
protected StartupParameters getStartupParametersInstance()
Description copied from class:AbstractUserArgumentProcessor
StartupParameters is a bean to store all the possible command line parameters. The `StartupParameter` class contains the basic set of CLI parameters common to all `StructureAligmnent`s. This method should return a subclass of StartupParameters which has been extended to store values for all additional parameters.- Specified by:
getStartupParametersInstance
in classAbstractUserArgumentProcessor
- Returns:
- A new instance of the correct StartupParameters subclass
-
getAlgorithm
public StructureAlignment getAlgorithm()
- Specified by:
getAlgorithm
in classAbstractUserArgumentProcessor
-
getParameters
public Object getParameters()
- Specified by:
getParameters
in classAbstractUserArgumentProcessor
-
getDbSearchLegend
public String getDbSearchLegend()
- Specified by:
getDbSearchLegend
in classAbstractUserArgumentProcessor
-
-