org.strbio.mol.lib
Class UserFoldLibrary

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
                                  org.strbio.mol.lib.UserFoldLibrary

All Implemented Interfaces:

java.io.Serializable, 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.

Version:

1.0, 11/1/99

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

UserFoldLibrary()

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(java.io.BufferedReader 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

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, 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

UserFoldLibrary

public UserFoldLibrary()

UserFoldLibrary

public UserFoldLibrary(java.lang.String filename)

UserFoldLibrary

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

Method Detail

read

public void read(java.io.BufferedReader infile,
                 Printf outfile)
          throws java.io.IOException

Reads proteins in, making sure they have the correct info.

Overrides:

read in class PolymerSet

Throws:

java.io.IOException

See Also:

Polymer.read(java.io.BufferedReader, org.strbio.io.Printf, boolean)

describe

public void describe(Printf outfile)

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

Specified by:

describe in interface Description

Overrides:

describe in class FoldLibrary