org.strbio.mol
Class ProfilePSISet

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

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Iterable, java.util.Collection, java.util.List, java.util.RandomAccess

Direct Known Subclasses:

FoldLibrary

public class ProfilePSISet
extends ProfileSet

Class to represent a set of profiles with position specific information (PSI), such as PSI-BLAST info and JMC's backbone potential.

  Version 1.2, 6/7/99 - changed name from JMCProteinSet to ProfilePSISet
  Version 1.1, 2/17/99 - made ProfileSet instead of ProteinSet
  Version 1.0, 4/23/98 - original version
  

Version:

1.2, 6/7/99

Author:

JMC

See Also:

ProfilePSI, 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

ProfilePSISet()

Method Summary

Polymer

newPolymer() Everything in this set should be a Profile (or subclass of it).

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

ProfilePSISet

public ProfilePSISet()

Method Detail

newPolymer

public Polymer newPolymer()

Description copied from class: ProfileSet

Everything in this set should be a Profile (or subclass of it).

Overrides:

newPolymer in class ProfileSet