scripps.vvm.manager
Class SetOperations

java.lang.Object
  |
  +--scripps.vvm.manager.SetOperations

public class SetOperations

extends java.lang.Object

Constructor Summary

SetOperations()

Method Summary

static TreeNodeSet	clone(TreeNodeSet set)
static TreeNodeSet	cloneSeed(TreeNodeSet set)
static java.util.Hashtable	coerse(java.util.Hashtable table, Molecule mol, java.lang.String fromDomain, java.lang.String toDomain)
static TreeNodeSet	coerse(TreeNodeSet defSet, java.lang.String domainType)
static AtomSet	coerseToAtoms(TreeNodeSet defSet)
static BondSet	coerseToBonds(TreeNodeSet defSet)
static ChainSet	coerseToChains(TreeNodeSet defSet)
static MoleculeSet	coerseToMolecules(TreeNodeSet defSet)
static ResidueSet	coerseToResidues(TreeNodeSet defSet)
static void	filterResidueSet(ResidueSet out, ResidueSet in, java.util.Vector sets, boolean pass)
static Chain	findChain(ChainSet chainSet, java.lang.String id)
static Residue	findResidue(ResidueSet residueSet, java.lang.String number)
static AtomSet	getAllAtoms(Molecule mol)
static BondSet	getAllBonds(Molecule mol)
static ChainSet	getAllChains(Molecule mol)
static ResidueSet	getAllResidues(Molecule mol)
static java.lang.String	getDomain(TreeNodeSet set)
static java.lang.String[]	getDomains(VVM_RepShape def)
static TreeNodeSet	getDomainSet(Molecule mol, java.lang.String domainName)
static java.lang.String	getElementDomain(java.lang.Object element)
static java.util.Vector[]	getPropSets(VVM_RepShape def)
static TreeNodeSet	newSet(java.lang.String domainName)
static java.lang.String	rangeStringFromTable(Molecule mol, TreeNodeSet domainSet, java.util.Hashtable table)
static void	rangeStringToTable(java.lang.String selString, Molecule mol, TreeNodeSet set, java.util.Hashtable table)
static java.lang.String	residueSelectionString(ResidueSet set)
static java.lang.String	selectionString(TreeNodeSet set)
static void	setFromTable(TreeNodeSet ret, Molecule mol, java.util.Hashtable table, TreeNodeSet domainSet)
static void	sortSet(TreeNodeSet set)
static void	tableFromSet(TreeNodeSet set, Molecule mol, java.util.Hashtable table)
static java.util.Vector	uniqeTypeSets(java.util.Vector sets)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SetOperations

public SetOperations()

Method Detail

getAllAtoms

public static AtomSet getAllAtoms(Molecule mol)

getAllResidues

public static ResidueSet getAllResidues(Molecule mol)

getAllChains

public static ChainSet getAllChains(Molecule mol)

getAllBonds

public static BondSet getAllBonds(Molecule mol)

getDomains

public static java.lang.String[] getDomains(VVM_RepShape def)

getDomain

public static java.lang.String getDomain(TreeNodeSet set)

getElementDomain

public static java.lang.String getElementDomain(java.lang.Object element)

getDomainSet

public static TreeNodeSet getDomainSet(Molecule mol,
                                       java.lang.String domainName)

newSet

public static TreeNodeSet newSet(java.lang.String domainName)

getPropSets

public static java.util.Vector[] getPropSets(VVM_RepShape def)

cloneSeed

public static TreeNodeSet cloneSeed(TreeNodeSet set)

clone

public static TreeNodeSet clone(TreeNodeSet set)

findResidue

public static Residue findResidue(ResidueSet residueSet,
                                  java.lang.String number)

findChain

public static Chain findChain(ChainSet chainSet,
                              java.lang.String id)

coerseToMolecules

public static MoleculeSet coerseToMolecules(TreeNodeSet defSet)

coerseToChains

public static ChainSet coerseToChains(TreeNodeSet defSet)

coerseToResidues

public static ResidueSet coerseToResidues(TreeNodeSet defSet)

coerseToAtoms

public static AtomSet coerseToAtoms(TreeNodeSet defSet)

coerseToBonds

public static BondSet coerseToBonds(TreeNodeSet defSet)

coerse

public static TreeNodeSet coerse(TreeNodeSet defSet,
                                 java.lang.String domainType)

coerse

public static java.util.Hashtable coerse(java.util.Hashtable table,
                                         Molecule mol,
                                         java.lang.String fromDomain,
                                         java.lang.String toDomain)

sortSet

public static void sortSet(TreeNodeSet set)

uniqeTypeSets

public static java.util.Vector uniqeTypeSets(java.util.Vector sets)

filterResidueSet

public static void filterResidueSet(ResidueSet out,
                                    ResidueSet in,
                                    java.util.Vector sets,
                                    boolean pass)

tableFromSet

public static void tableFromSet(TreeNodeSet set,
                                Molecule mol,
                                java.util.Hashtable table)

setFromTable

public static void setFromTable(TreeNodeSet ret,
                                Molecule mol,
                                java.util.Hashtable table,
                                TreeNodeSet domainSet)

rangeStringFromTable

public static java.lang.String rangeStringFromTable(Molecule mol,
                                                    TreeNodeSet domainSet,
                                                    java.util.Hashtable table)

rangeStringToTable

public static void rangeStringToTable(java.lang.String selString,
                                      Molecule mol,
                                      TreeNodeSet set,
                                      java.util.Hashtable table)

selectionString

public static java.lang.String selectionString(TreeNodeSet set)

residueSelectionString

public static java.lang.String residueSelectionString(ResidueSet set)