meshi.applications.prediction
Class ModelData

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.ArrayList<Pair>
              meshi.applications.prediction.ModelData

All Implemented Interfaces:

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

public class ModelData
extends java.util.ArrayList<Pair>

See Also:

Serialized Form

Nested Class Summary

private static class

ModelData.TermComparator

Field Summary

private static int	AVG_ENERGY_INDEX
private static int	BASE_INDEX
private static int	GDT_INDEX
private static int	NAME_INDEX
private static int	RMS_INDEX

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

ModelData()

ModelData(ModelData source)

ModelData(Protein model, Protein reference, TotalEnergy totalEnergy)

ModelData(Protein model, Protein reference, TotalEnergy totalEnergy, java.lang.String fileName)

Method Summary

static ModelData	avgModel(java.util.List<ModelData> models, ModelData sum)
private static double	getCoolAtomsEnergy(Protein model, int numberOfAtoms)
private static double	getWeightedEnergy(Protein model, int numberOfAtoms)
static ModelData	processProtein(Protein protein, Protein reference, CommandList commands, EnergyCreator[] energyCreators)
static ModelData	stdModel(ModelData avg, ModelData avg2)
static ModelData	sum2Model(java.util.List<ModelData> models)
static ModelData	sumModel(java.util.List<ModelData> models)
static java.util.Comparator<ModelData>	termComparator(java.lang.String key)
static ModelData[]	toArray(java.util.List<ModelData> list)
java.lang.String	toString()
java.lang.String	toString(boolean headerFlag, boolean nameFlag, boolean zScoresFlag, java.lang.String lable)
static java.util.List<ModelData>	zScoreOfModels(java.util.List<ModelData> models)

Methods inherited from class java.util.ArrayList

add, add, addAll, addAll, clear, clone, contains, ensureCapacity, get, indexOf, isEmpty, lastIndexOf, remove, remove, removeRange, set, size, toArray, toArray, trimToSize

Methods inherited from class java.util.AbstractList

equals, hashCode, iterator, listIterator, listIterator, subList

Methods inherited from class java.util.AbstractCollection

containsAll, removeAll, retainAll

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.List

containsAll, equals, hashCode, iterator, listIterator, listIterator, removeAll, retainAll, subList

Field Detail

NAME_INDEX

private static final int NAME_INDEX

See Also:

Constant Field Values

AVG_ENERGY_INDEX

private static final int AVG_ENERGY_INDEX

See Also:

Constant Field Values

RMS_INDEX

private static final int RMS_INDEX

See Also:

Constant Field Values

GDT_INDEX

private static final int GDT_INDEX

See Also:

Constant Field Values

BASE_INDEX

private static final int BASE_INDEX

See Also:

Constant Field Values

Constructor Detail

ModelData

public ModelData()

ModelData

public ModelData(Protein model,
                 Protein reference,
                 TotalEnergy totalEnergy)

ModelData

public ModelData(Protein model,
                 Protein reference,
                 TotalEnergy totalEnergy,
                 java.lang.String fileName)

ModelData

public ModelData(ModelData source)

Method Detail

processProtein

public static ModelData processProtein(Protein protein,
                                       Protein reference,
                                       CommandList commands,
                                       EnergyCreator[] energyCreators)

getWeightedEnergy

private static double getWeightedEnergy(Protein model,
                                        int numberOfAtoms)

getCoolAtomsEnergy

private static double getCoolAtomsEnergy(Protein model,
                                         int numberOfAtoms)

toString

public java.lang.String toString(boolean headerFlag,
                                 boolean nameFlag,
                                 boolean zScoresFlag,
                                 java.lang.String lable)

toString

public java.lang.String toString()

Overrides:

toString in class java.util.AbstractCollection<Pair>

sumModel

public static ModelData sumModel(java.util.List<ModelData> models)

sum2Model

public static ModelData sum2Model(java.util.List<ModelData> models)

avgModel

public static ModelData avgModel(java.util.List<ModelData> models,
                                 ModelData sum)

stdModel

public static ModelData stdModel(ModelData avg,
                                 ModelData avg2)

zScoreOfModels

public static java.util.List<ModelData> zScoreOfModels(java.util.List<ModelData> models)

toArray

public static ModelData[] toArray(java.util.List<ModelData> list)

termComparator

public static java.util.Comparator<ModelData> termComparator(java.lang.String key)