Package org.anchoranalysis.mpp.feature.energy.marks

Class MarksWithTotalEnergy

Object
MarksWithTotalEnergy
All Implemented Interfaces:
Serializable
public class MarksWithTotalEnergy extends Object implements Serializable
A collection of marks with an associated (total) energy.
Author:
Owen Feehan
See Also:

  • Constructor Details

    • MarksWithTotalEnergy

      public MarksWithTotalEnergy(MarkCollection marks, EnergySchemeWithSharedFeatures energyScheme)
      Creates a new instance with the given marks and energy scheme.
      Parameters:
      marks - the collection of marks
      energyScheme - the energy scheme with shared features

  • Method Details

    • shallowCopy

      public MarksWithTotalEnergy shallowCopy()
      Makes a shallow copy of this instance.
      Returns:
      a newly created object with identical contents (all member fields reused)

    • deepCopy

      public MarksWithTotalEnergy deepCopy()
      Makes a deep copy of this instance (except the energyScheme which is reused).
      Returns:
      a newly created object with identical contents (some member fields duplicated, some reused)

    • add

      public void add(VoxelizedMarkMemo voxelizedMark)
      Adds a voxelized mark to the collection.
      Parameters:
      voxelizedMark - the voxelized mark to add

    • remove

      public void remove(int index)
      Removes a mark at the specified index from the collection.
      Parameters:
      index - the index of the mark to remove

    • exchange

      public void exchange(int index, VoxelizedMarkMemo newMark)
      Exchanges a mark at a particular index with a new mark.
      Parameters:
      index - the index of the mark to exchange
      newMark - the new voxelized mark to replace the existing mark

    • size

      public final int size()
      Gets the number of marks in the collection.
      Returns:
      the number of marks

    • get

      public Mark get(int index)
      Gets the mark at the specified index.
      Parameters:
      index - the index of the mark to retrieve
      Returns:
      the Mark at the specified index

    • getMarks

      public MarkCollection getMarks()
      The marks in the collection.

    • setMarks

      public void setMarks(MarkCollection marks)
      The marks in the collection.

    • getEnergyScheme

      public EnergySchemeWithSharedFeatures getEnergyScheme()
      Associated Energy Scheme, which should include the EnergySavedPairs.

    • getEnergyTotal

      public double getEnergyTotal()
      The pre-annealed total energy.

    • setEnergyTotal

      public void setEnergyTotal(double energyTotal)
      The pre-annealed total energy.