org.strbio.mol.lib
Class FoldLibrary

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.Vector
              org.strbio.mol.PolymerSet
                  org.strbio.mol.ProteinSet
                      org.strbio.mol.ProfileSet
                          org.strbio.mol.ProfilePSISet
                              org.strbio.mol.lib.FoldLibrary

All Implemented Interfaces:

java.io.Serializable, 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.

Version:

1.0, 7/8/99

Author:

JMC

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class org.strbio.mol.PolymerSet

PolymerSet.PolymerEnumeration

Field Summary

Fields inherited from class java.util.Vector

capacityIncrement, elementCount, elementData

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

FoldLibrary()

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

newPolymer

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

FoldLibrary

public FoldLibrary()

Method Detail

getFileName

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.

loadFromClassPath

public void loadFromClassPath()

Load in the fold library, silently, from the CLASSPATH.

describe

public void describe(Printf outfile)

The default fold library description just prints the name of the class.

Specified by:

describe in interface Description