Class UserFoldLibrary

  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
                                  extended by org.strbio.mol.lib.UserFoldLibrary
All Implemented Interfaces:, java.lang.Cloneable, java.lang.Iterable, java.util.Collection, java.util.List, java.util.RandomAccess, Description

public class UserFoldLibrary
extends FoldLibrary

A standard fold library for threading, loaded in by the user.

1.0, 11/1/99
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
UserFoldLibrary(java.lang.String filename)
UserFoldLibrary(java.lang.String filename, Printf outfile)
Method Summary
 void describe(Printf outfile)
          The default fold library description just prints the name of the class.
 void read( infile, Printf outfile)
          Reads proteins in, making sure they have the correct info.
Methods inherited from class org.strbio.mol.lib.FoldLibrary
getFileName, loadFromClassPath
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, 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 UserFoldLibrary()


public UserFoldLibrary(java.lang.String filename)


public UserFoldLibrary(java.lang.String filename,
                       Printf outfile)
Method Detail


public void read( infile,
                 Printf outfile)
Reads proteins in, making sure they have the correct info.

read in class PolymerSet
See Also:,, boolean)


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

Specified by:
describe in interface Description
describe in class FoldLibrary