org.biojava.bio.structure.align.ce
Class AbstractUserArgumentProcessor

java.lang.Object
  extended by 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


Field Summary
static List<String> mandatoryArgs
           
static String newline
           
protected  StartupParameters params
           
static String PDB_DIR
          the system property PDB_DIR can be used to configure the default location for PDB files.
 
Constructor Summary
protected AbstractUserArgumentProcessor()
           
 
Method Summary
abstract  StructureAlignment getAlgorithm()
           
abstract  String getDbSearchLegend()
           
 String getDbSearchResult(AFPChain afpChain)
           
 List<String> getMandatoryArgs()
           
abstract  Object getParameters()
           
 void process(String[] argv)
          Process user arguments that have been provided from the command line
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

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
Constructor Detail

AbstractUserArgumentProcessor

protected AbstractUserArgumentProcessor()
Method Detail

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)