ffe.lang
Class Polymer

java.lang.Object
  javax.swing.tree.DefaultMutableTreeNode
      ffe.lang.FNode
          ffe.lang.FGroup
              ffe.lang.Polymer

All Implemented Interfaces:

java.lang.Cloneable, javax.swing.tree.MutableTreeNode, java.io.Serializable, javax.swing.tree.TreeNode

public final class Polymer

extends FGroup

The Polymer class encapsulates a polypeptide or polynucleotide chain.

See Also:

Serialized Form

Nested Class Summary

Nested classes inherited from class javax.swing.tree.DefaultMutableTreeNode

Field Summary

Fields inherited from class ffe.lang.FNode

selected

Fields inherited from class javax.swing.tree.DefaultMutableTreeNode

allowsChildren, children, EMPTY_ENUMERATION, parent, userObject

Constructor Summary

Polymer()
Default Polymer Construtor

Polymer(java.lang.String n, boolean bk)

Polymer(java.lang.String n, boolean bk, boolean l)
Polymer Constructor

Polymer(java.lang.String n, FNode residues, boolean bk)
Polymer Constructor

Method Summary

void	addFNode(FNode o) A generic method for adding a FNode to the Polymer.
boolean	equals(java.lang.Object object) Overidden equals method.
void	finalize(boolean finalizeGroups) Finalize should be called after all the Residues have been added to the Polymer.
boolean	getLink()
Residue	getResidue(int resNum)
Residue	getResidue(java.lang.String resName, int resNum, boolean create)
void	setLink(boolean t)
void	switchColor(int colortype, javax.vecmath.Color3f color, javax.media.j3d.Material mat)

Methods inherited from class ffe.lang.FGroup

collectBonds, ConstructGeometry, destroy, findCenter, findDangelingAtoms, getAngles, getBond, getBond, getBonds, getBondsKnown, getCenter, getDangelingAtoms, getDihedrals, getFGroupList, getFGroups, getFNode, getFNode, getTerms, isFinalized, joiner, joiner, print, reInit, removeLeaves, setAngles, setBonds, setBondsKnown, setCenter, setDangelingAtoms, setDihedrals, setFGroups, setFinalized, setTerms, toString, updateAtoms, updateBonds

Methods inherited from class ffe.lang.FNode

drawLabel, getAtomList, getBondList, getFSystemNode, getList, getListIterator, getMoleculeNode, getMW, getName, getPolymerNode, getResidueNode, getTermList, isSelected, setName, setSelected, switchView

Methods inherited from class javax.swing.tree.DefaultMutableTreeNode

add, breadthFirstEnumeration, children, clone, depthFirstEnumeration, getAllowsChildren, getChildAfter, getChildAt, getChildBefore, getChildCount, getDepth, getFirstChild, getFirstLeaf, getIndex, getLastChild, getLastLeaf, getLeafCount, getLevel, getNextLeaf, getNextNode, getNextSibling, getParent, getPath, getPathToRoot, getPreviousLeaf, getPreviousNode, getPreviousSibling, getRoot, getSharedAncestor, getSiblingCount, getUserObject, getUserObjectPath, insert, isLeaf, isNodeAncestor, isNodeChild, isNodeDescendant, isNodeRelated, isNodeSibling, isRoot, pathFromAncestorEnumeration, postorderEnumeration, preorderEnumeration, remove, remove, removeAllChildren, removeFromParent, setAllowsChildren, setParent, setUserObject

Methods inherited from class java.lang.Object

finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Polymer

public Polymer()

Default Polymer Construtor

Polymer

public Polymer(java.lang.String n,
               boolean bk)

Polymer

public Polymer(java.lang.String n,
               boolean bk,
               boolean l)

Polymer Constructor

Parameters:

n - Polymer indentifier, generally a letter in PDB files (ie A,B,C,etc)

Polymer

public Polymer(java.lang.String n,
               FNode residues,
               boolean bk)

Polymer Constructor

Parameters:

n - Polymer indentifier, generally a letter in PDB files (ie A,B,C,etc)

residues - Represents a FNode where the Polymer's residues have been attached

Method Detail

equals

public boolean equals(java.lang.Object object)

Overidden equals method.

Overrides:

equals in class FNode

Parameters:

object - Object to compare

Returns:

True if object is not this Polymer, is of Class Polymer, and both object and this Polymer have identical names

addFNode

public void addFNode(FNode o)

A generic method for adding a FNode to the Polymer.

Specified by:

addFNode in class FGroup

Parameters:

o - If the FNode is an Atom, an attempt is made to pass it to the residue to which it belongs. Otherwise, if the FNode is a Residue, it will be added to the Polymer, so long as its sequence number is not already in use

finalize

public void finalize(boolean finalizeGroups)

Finalize should be called after all the Residues have been added to the Polymer. This method in turn calls the Finalize method of each Residue, then forms Joints between adjacent Residues in the Polymer

Specified by:

finalize in class FGroup

getResidue

public Residue getResidue(int resNum)

getResidue

public Residue getResidue(java.lang.String resName,
                          int resNum,
                          boolean create)

setLink

public void setLink(boolean t)

getLink

public boolean getLink()

switchColor

public void switchColor(int colortype,
                        javax.vecmath.Color3f color,
                        javax.media.j3d.Material mat)

Overrides:

switchColor in class FGroup