org.biojava.bio.structure.align.gui
Class StructureAlignmentDisplay

java.lang.Object
  extended by org.biojava.bio.structure.align.gui.StructureAlignmentDisplay

public class StructureAlignmentDisplay
extends Object


Constructor Summary
StructureAlignmentDisplay()
           
 
Method Summary
static StructureAlignmentJmol display(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
          Display the alignment
static Group[] prepareGroupsForDisplay(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
          Rotate the Atoms/Groups so they are aligned for the 3D visualisation
static void shiftCA2(AFPChain afpChain, Atom[] ca2, Matrix m, Atom shift, Group[] twistedGroups)
          only shift CA positions.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

StructureAlignmentDisplay

public StructureAlignmentDisplay()
Method Detail

display

public static StructureAlignmentJmol display(AFPChain afpChain,
                                             Atom[] ca1,
                                             Atom[] ca2)
                                      throws StructureException
Display the alignment

Parameters:
afpChain -
ca1 -
ca2 -
Returns:
a StructureAlignmentJmol instance
Throws:
StructureException

prepareGroupsForDisplay

public static Group[] prepareGroupsForDisplay(AFPChain afpChain,
                                              Atom[] ca1,
                                              Atom[] ca2)
                                       throws StructureException
Rotate the Atoms/Groups so they are aligned for the 3D visualisation

Parameters:
afpChain -
ca1 -
ca2 -
Returns:
an array of Groups that are transformed for 3D display
Throws:
StructureException

shiftCA2

public static void shiftCA2(AFPChain afpChain,
                            Atom[] ca2,
                            Matrix m,
                            Atom shift,
                            Group[] twistedGroups)
only shift CA positions.