Class ProfilePSISet

  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
All Implemented Interfaces:, java.lang.Cloneable, java.lang.Iterable, java.util.Collection, java.util.List, java.util.RandomAccess
Direct Known Subclasses:

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

1.2, 6/7/99
See Also:
ProfilePSI, 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
 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


public ProfilePSISet()
Method Detail


public Polymer newPolymer()
Description copied from class: ProfileSet
Everything in this set should be a Profile (or subclass of it).

newPolymer in class ProfileSet