org.strbio.mol.lib.pred2ary
Class PCPSet

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.lib.pred2ary.PCPSet

All Implemented Interfaces:

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

Direct Known Subclasses:

TPSet

public class PCPSet
extends ProfileSet

Class to represent a set of profiles with information for 2ary structure prediction.

 Version 1.1, 6/7/99 - moved to org.strbio.mol.lib.pred2ary
 Version 1.01, 7/10/98 - added combine()
 Version 1.0, 5/12/98 - original version
 

Version:

1.1, 6/7/99

Author:

JMC

See Also:

PredClassProfile, 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

PCPSet()

PCPSet(PCPSet q)

Method Summary

void	addClassPred(double[] dp) same functions for class pred
void	addPred(double[] dp) add H and E stats together for 2 sets, using array
void	addPred(PCPSet q) add H and E stats together for 2 sets
void	addPredToArray(double[] dp)
void	clearClassPred()
void	clearPred() clear H and E to zero
void	combine() Combine all proteins in this set into one Profile.
void	divideClassPred(double d)
void	dividePred(double d) divide pred by a double
void	loadClassPred(double[] dp)
void	loadPred(double[] dp)
Polymer	newPolymer() Everything in this set should be a Profile (or subclass of it).
Polymer	newPolymer(ProteinSet q)
PredClassProfile	pcp(int i) Return the i'th protein in the set.
int	predDiffs(PCPSet b) differnces between predictions from another set returns -1 if sets different
void	saveClassPred(double[] dp)
void	savePred(double[] dp)

Methods inherited from class org.strbio.mol.ProfileSet

blast, blast, 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

PCPSet

public PCPSet()

PCPSet

public PCPSet(PCPSet q)

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

newPolymer

public Polymer newPolymer(ProteinSet q)

Overrides:

newPolymer in class ProfileSet

combine

public void combine()

Combine all proteins in this set into one Profile.

Overrides:

combine in class ProfileSet

pcp

public PredClassProfile pcp(int i)

Return the i'th protein in the set.

predDiffs

public final int predDiffs(PCPSet b)

differnces between predictions from another set returns -1 if sets different

addPred

public final void addPred(PCPSet q)

add H and E stats together for 2 sets

addPred

public final void addPred(double[] dp)

add H and E stats together for 2 sets, using array

loadPred

public final void loadPred(double[] dp)

savePred

public final void savePred(double[] dp)

addPredToArray

public final void addPredToArray(double[] dp)

clearPred

public final void clearPred()

clear H and E to zero

dividePred

public final void dividePred(double d)

divide pred by a double

addClassPred

public final void addClassPred(double[] dp)

same functions for class pred

loadClassPred

public final void loadClassPred(double[] dp)

saveClassPred

public final void saveClassPred(double[] dp)

clearClassPred

public final void clearClassPred()

divideClassPred

public final void divideClassPred(double d)