org.strbio.mol.lib.pred2ary
Class PredictionSet

java.lang.Object
  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.io.Serializable, 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
 

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.lib.pred2ary.TPSet
TPSet.NetVars
 
Nested classes/interfaces inherited from class org.strbio.mol.PolymerSet
PolymerSet.PolymerEnumeration
 
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
modCount
 
Constructor Summary
PredictionSet()
           
 
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

PredictionSet

public PredictionSet()
Method Detail

clear

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
Overrides:
clear in class TPSet

link

public void link(TrainingSet x)

predict2aryHE

public final void predict2aryHE()

predictLvl2HE

public final void predictLvl2HE()

predictClassRaw

public final void predictClassRaw()

fcut2ary

public final double fcut2ary(int sample,
                             Printf outfile)

fcutLvl2

public final double fcutLvl2(int sample,
                             Printf outfile)

predict2ary

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.


predictLvl1

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


predictLvl2

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


predictClass

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


estAccy

public final void estAccy()