org.biojava.bio.structure.align.ce
Class AbstractUserArgumentProcessor
java.lang.Object
org.biojava.bio.structure.align.ce.AbstractUserArgumentProcessor
- All Implemented Interfaces:
- UserArgumentProcessor
- Direct Known Subclasses:
- CeSideChainUserArgumentProcessor, CeUserArgumentProcessor, FatCatUserArgumentProcessor, SmithWatermanUserArgumentProcessor
public abstract class AbstractUserArgumentProcessor
- extends Object
- implements UserArgumentProcessor
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
newline
public static String newline
params
protected StartupParameters params
mandatoryArgs
public static final List<String> mandatoryArgs
PDB_DIR
public static final String PDB_DIR
- the system property PDB_DIR can be used to configure the
default location for PDB files.
- See Also:
- Constant Field Values
AbstractUserArgumentProcessor
protected AbstractUserArgumentProcessor()
getAlgorithm
public abstract StructureAlignment getAlgorithm()
getParameters
public abstract Object getParameters()
getDbSearchLegend
public abstract String getDbSearchLegend()
process
public void process(String[] argv)
- Description copied from interface:
UserArgumentProcessor
- Process user arguments that have been provided from the command line
- Specified by:
process
in interface UserArgumentProcessor
getMandatoryArgs
public List<String> getMandatoryArgs()
getDbSearchResult
public String getDbSearchResult(AFPChain afpChain)