endrov.typeLineage.util
Class MakeParticleContactMap

java.lang.Object
  endrov.typeLineage.util.MakeParticleContactMap

public class MakeParticleContactMap
extends java.lang.Object

Calculate a particle contact map

Constructor Summary

MakeParticleContactMap()

Method Summary

void	calcneigh(java.util.Set<java.lang.String> nucNames, EvDecimal startFrame, EvDecimal endFrame, EvDecimal frameInc)
static LineageVoronoi	calcneighOneFrame(java.util.Set<java.lang.String> nucNames, java.util.Map<LineageSelParticle,Lineage.InterpolatedParticle> inter, boolean selfContact) Calculate neighbours for one frame.
static NeighMap	calculateCellMap(Lineage lin, java.util.Set<java.lang.String> nucNames, EvDecimal startFrame, EvDecimal endFrame, EvDecimal frameInc) Calculate cell contact map from a lineage, from startFrames <= f <= endFrame.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MakeParticleContactMap

public MakeParticleContactMap()

Method Detail

calcneighOneFrame

public static LineageVoronoi calcneighOneFrame(java.util.Set<java.lang.String> nucNames,
                                               java.util.Map<LineageSelParticle,Lineage.InterpolatedParticle> inter,
                                               boolean selfContact)
                                        throws java.lang.Exception

Calculate neighbours for one frame. Adds particles at a distance to avoid some really nonbiological contacts. These are also returned (starts with :::)

Throws:

java.lang.Exception

calcneigh

public void calcneigh(java.util.Set<java.lang.String> nucNames,
                      EvDecimal startFrame,
                      EvDecimal endFrame,
                      EvDecimal frameInc)

calculateCellMap

public static NeighMap calculateCellMap(Lineage lin,
                                        java.util.Set<java.lang.String> nucNames,
                                        EvDecimal startFrame,
                                        EvDecimal endFrame,
                                        EvDecimal frameInc)

Calculate cell contact map from a lineage, from startFrames <= f <= endFrame. Contacts for one frame can be obtained by letting startframe=endframe.