Class FoldLibrary

  extended by java.util.AbstractCollection<E>
      extended by java.util.AbstractList<E>
          extended by java.util.Vector
              extended by org.strbio.mol.PolymerSet
                  extended by org.strbio.mol.ProteinSet
                      extended by org.strbio.mol.ProfileSet
                          extended by org.strbio.mol.ProfilePSISet
                              extended by org.strbio.mol.lib.FoldLibrary
All Implemented Interfaces:, java.lang.Cloneable, java.lang.Iterable, java.util.Collection, java.util.List, java.util.RandomAccess, Description
Direct Known Subclasses:
TOMFoldLibrary, UserFoldLibrary

public class FoldLibrary
extends ProfilePSISet
implements Description

A standard fold library for threading; i.e. the TOM fold library, or the Fischer fold library.

1.0, 7/8/99
See Also:
Serialized Form

Nested Class Summary
Nested classes/interfaces inherited from class org.strbio.mol.PolymerSet
Field Summary
Fields inherited from class java.util.Vector
capacityIncrement, elementCount, elementData
Fields inherited from class java.util.AbstractList
Constructor Summary
Method Summary
 void describe(Printf outfile)
          The default fold library description just prints the name of the class.
 java.lang.String getFileName()
          Every local fold library must have a name that it can be loaded from; other ways of getting a fold library still need to be implemented.
 void loadFromClassPath()
          Load in the fold library, silently, from the CLASSPATH.
Methods inherited from class org.strbio.mol.ProfilePSISet
Methods inherited from class org.strbio.mol.ProfileSet
blast, blast, combine, newPolymer, write, writeClustal, writeClustal, writeMSF, writeMSF, writeProf, writeProf, writeSAF, writeSAF, writeTDP
Methods inherited from class org.strbio.mol.ProteinSet
findDSSP, findPDB, fixDistanceGaps, predictSS, predictSS, protein, residues, thread, thread, writeCASP, writeCASP, writeConv, writeConv, writeEA, writeEA, writePDB, writePDB, writePDB, writePDB, writeVar2, writeVar2
Methods inherited from class org.strbio.mol.PolymerSet
add, add, add, addReversedCopies, clear, clearPolymers, clearProperties, clearProperty, ensureNames, findClosest, getNames, getPropertyAll, getPropertyOne, isEqual, keepOnlyChainID, keepOnlyNames, keepOnlyNamesFuzzy, load, n, nMonomers, noSpaceNames, nPolymersInFile, p, polymer, polymers, polymersInFile, polymersInFile, polymersInFile, polymersInFile, printNames, read, read, read, readList, remove, remove, removeRedundantSequences, save, searchByName, searchByNameFuzzy, searchByNameFuzzy, searchByNameFuzzyIndex, searchByNameFuzzyIndex, searchByNameIndex, setPolymerAt, setProperty, stripNoAtoms, writeFasta, writeFasta, writeList, writeList, writePTS, writePTS, writeYAPF, writeYAPF
Methods inherited from class java.util.Vector
add, add, addAll, addAll, addElement, capacity, clone, contains, containsAll, copyInto, elementAt, elements, ensureCapacity, equals, firstElement, get, hashCode, indexOf, indexOf, insertElementAt, isEmpty, lastElement, lastIndexOf, lastIndexOf, remove, removeAll, removeAllElements, removeElement, removeElementAt, removeRange, retainAll, set, setElementAt, setSize, size, subList, toArray, toArray, toString, trimToSize
Methods inherited from class java.util.AbstractList
iterator, listIterator, listIterator
Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait
Methods inherited from interface java.util.List
iterator, listIterator, listIterator

Constructor Detail


public FoldLibrary()
Method Detail


public java.lang.String getFileName()
Every local fold library must have a name that it can be loaded from; other ways of getting a fold library still need to be implemented. This should be specified relative to the CLASSPATH.


public void loadFromClassPath()
Load in the fold library, silently, from the CLASSPATH.


public void describe(Printf outfile)
The default fold library description just prints the name of the class.

Specified by:
describe in interface Description