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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 org.strbio.mol.lib.pred2ary.TPSet org.strbio.mol.lib.pred2ary.PredictionSet
public class PredictionSet
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
PredClassProfile
,
Serialized FormNested Class Summary |
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Nested classes/interfaces inherited from class org.strbio.mol.lib.pred2ary.TPSet |
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TPSet.NetVars |
Nested classes/interfaces inherited from class org.strbio.mol.PolymerSet |
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PolymerSet.PolymerEnumeration |
Field Summary |
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Fields inherited from class org.strbio.mol.lib.pred2ary.TPSet |
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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 |
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capacityIncrement, elementCount, elementData |
Fields inherited from class java.util.AbstractList |
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modCount |
Constructor Summary | |
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PredictionSet()
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Method Summary | |
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void |
clear()
Clear out all information in the set. |
void |
estAccy()
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double |
fcut2ary(int sample,
Printf outfile)
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double |
fcutLvl2(int sample,
Printf outfile)
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void |
link(TrainingSet x)
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void |
predict2ary(int sample,
Printf outfile)
do 2ary prediction; train and find cutoff if necessary. |
void |
predict2aryHE()
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void |
predictClass(Printf outfile)
cutoff = 0.0 -> find correct cutoff. |
void |
predictClassRaw()
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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()
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Methods inherited from class org.strbio.mol.lib.pred2ary.TPSet |
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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 |
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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 |
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blast, blast, write, writeClustal, writeClustal, writeMSF, writeMSF, writeProf, writeProf, writeSAF, writeSAF, writeTDP |
Methods inherited from class org.strbio.mol.ProteinSet |
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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 |
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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 |
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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 |
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iterator, listIterator, listIterator |
Methods inherited from class java.lang.Object |
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finalize, getClass, notify, notifyAll, wait, wait, wait |
Methods inherited from interface java.util.List |
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iterator, listIterator, listIterator |
Constructor Detail |
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public PredictionSet()
Method Detail |
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public void clear()
TPSet
clear
in interface java.util.Collection
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)
public final void predictLvl1(int sample, Printf outfile)
public final void predictLvl2(int sample, Printf outfile)
public final void predictClass(Printf outfile)
public final void estAccy()
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