Class PredictionSet

  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.lib.pred2ary.PCPSet
                              extended by org.strbio.mol.lib.pred2ary.TPSet
                                  extended by org.strbio.mol.lib.pred2ary.PredictionSet
All Implemented Interfaces:, java.lang.Cloneable, java.lang.Iterable, java.util.Collection, java.util.List, java.util.RandomAccess

public class PredictionSet
extends TPSet

Class to represent a set of profiles being used in 2ary structure prediction as a prediction set.

 Version 1.1, 6/7/99 - moved to org.strbio.mol.lib.pred2ary
 Version 1.0, 5/12/98 - original version, adapted from 2ary_set.cpp

1.1, 6/7/99
See Also:
PredClassProfile, Serialized Form

Nested Class Summary
Nested classes/interfaces inherited from class org.strbio.mol.lib.pred2ary.TPSet
Nested classes/interfaces inherited from class org.strbio.mol.PolymerSet
Field Summary
Fields inherited from class org.strbio.mol.lib.pred2ary.TPSet
CLASS_2ARY, CLASS_AA, CLASS_STRONG, CSM, CSM1, cutoff_2ary, cutoff_class, cutoff_lvl2, nstats, r_SM, SM, USE_LENGTH_INFO, vars
Fields inherited from class java.util.Vector
capacityIncrement, elementCount, elementData
Fields inherited from class java.util.AbstractList
Constructor Summary
Method Summary
 void clear()
          Clear out all information in the set.
 void estAccy()
 double fcut2ary(int sample, Printf outfile)
 double fcutLvl2(int sample, Printf outfile)
 void link(TrainingSet x)
 void predict2ary(int sample, Printf outfile)
          do 2ary prediction; train and find cutoff if necessary.
 void predict2aryHE()
 void predictClass(Printf outfile)
          cutoff = 0.0 -> find correct cutoff.
 void predictClassRaw()
 void predictLvl1(int sample, Printf outfile)
          cutoff = 0.0 -> find correct cutoff.
 void predictLvl2(int sample, Printf outfile)
          cutoff = 0.0 -> find correct cutoff.
 void predictLvl2HE()
Methods inherited from class org.strbio.mol.lib.pred2ary.TPSet
addSM, clearSM, compute2arySM, computeClassSM, copyLvl1HE, copyUnreducedStats, deleteSM, estAccy, estAccyCount, fcut2ary, fcutClass, fcutLvl2, filterPred, findInputs, name2ary, newSM, predict2ary, predict2aryHE, predictClass, predictClassDirectly, predictClassRaw, predictLvl2, predictLvl2HE, print2ary, print2aryByClass, print2aryStats, print2aryUnreduced, printClass, printClassStats, printDirectClassPrediction, printDirectClassStats, smooth, translate2ary, translateClass, translateEA
Methods inherited from class org.strbio.mol.lib.pred2ary.PCPSet
addClassPred, addPred, addPred, addPredToArray, clearClassPred, clearPred, combine, divideClassPred, dividePred, loadClassPred, loadPred, newPolymer, newPolymer, pcp, predDiffs, saveClassPred, savePred
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, 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 PredictionSet()
Method Detail


public void clear()
Description copied from class: TPSet
Clear out all information in the set.

Specified by:
clear in interface java.util.Collection
Specified by:
clear in interface java.util.List
clear in class TPSet


public void link(TrainingSet x)


public final void predict2aryHE()


public final void predictLvl2HE()


public final void predictClassRaw()


public final double fcut2ary(int sample,
                             Printf outfile)


public final double fcutLvl2(int sample,
                             Printf outfile)


public final void predict2ary(int sample,
                              Printf outfile)
do 2ary prediction; train and find cutoff if necessary. if cutoff not give, best for training set used.


public final void predictLvl1(int sample,
                              Printf outfile)
cutoff = 0.0 -> find correct cutoff. cutoff = 1.0 -> just predict h and e values.


public final void predictLvl2(int sample,
                              Printf outfile)
cutoff = 0.0 -> find correct cutoff. cutoff = 1.0 -> just predict h and e values.


public final void predictClass(Printf outfile)
cutoff = 0.0 -> find correct cutoff. cutoff = 1.0 -> just predict h and e values.


public final void estAccy()