org.biojava.bio.structure.align.fatcat
Class FatCat

java.lang.Object
  extended by org.biojava.bio.structure.align.fatcat.FatCat
Direct Known Subclasses:
FatCatFlexible, FatCatRigid

public class FatCat
extends Object


Field Summary
static String newline
           
static float VERSION
           
 
Constructor Summary
FatCat()
           
 
Method Summary
protected  AFPChain align(Atom[] ca1, Atom[] ca2, FatCatParameters params, boolean doRigid)
           
 AFPChain alignFlexible(Atom[] ca1, Atom[] ca2, FatCatParameters params)
           
 AFPChain alignRigid(Atom[] ca1, Atom[] ca2)
           
 AFPChain alignRigid(Atom[] ca1, Atom[] ca2, FatCatParameters params)
           
 FatCatAligner getFatCatAligner()
           
static void main(String[] argv)
          See demo/FatCatDemo.java for an example how to run.
 String printHelp()
          print the -h help text.
 String toString()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

VERSION

public static final float VERSION
See Also:
Constant Field Values

newline

public static String newline
Constructor Detail

FatCat

public FatCat()
Method Detail

main

public static void main(String[] argv)
See demo/FatCatDemo.java for an example how to run. Launch FatCat from command line. Parameters are:

Parameters:
argv -

toString

public String toString()
Overrides:
toString in class Object

printHelp

public String printHelp()
print the -h help text.


alignRigid

public AFPChain alignRigid(Atom[] ca1,
                           Atom[] ca2)
                    throws StructureException
Throws:
StructureException

alignRigid

public AFPChain alignRigid(Atom[] ca1,
                           Atom[] ca2,
                           FatCatParameters params)
                    throws StructureException
Throws:
StructureException

alignFlexible

public AFPChain alignFlexible(Atom[] ca1,
                              Atom[] ca2,
                              FatCatParameters params)
                       throws StructureException
Throws:
StructureException

align

protected AFPChain align(Atom[] ca1,
                         Atom[] ca2,
                         FatCatParameters params,
                         boolean doRigid)
                  throws StructureException
Throws:
StructureException

getFatCatAligner

public FatCatAligner getFatCatAligner()