endrov.typeLineage
Class Lineage

java.lang.Object
  endrov.data.EvContainer
      endrov.data.EvObject
          endrov.typeLineage.Lineage

All Implemented Interfaces:

java.lang.Cloneable

public class Lineage
extends EvObject
implements java.lang.Cloneable

Meta object: Lineage (particles) and expression info

Nested Class Summary

static class	Lineage.InterpolatedParticle Interpolated particles, contains additional information
static class	Lineage.MeshRenderMode Render modes
class	Lineage.Particle One particle
static class	Lineage.ParticlePos Position key frame

Field Summary

static LineageParticleGrouping	cellGroups
static java.lang.String[]	connectNuc
static int	KEY_CHANGE_RADIUS
static int	KEY_DIVIDENUC
static int	KEY_MAKEPARENT
static int	KEY_SETEND
static int	KEY_SETPARENT
static int	KEY_SETSTART
static int	KEY_SETZ
static int	KEY_TRANSLATE
java.util.HashMap<java.lang.String,Lineage.Particle>	particle

Fields inherited from class endrov.data.EvContainer

author, containerIcon, coreMetadataModified, dateCreate, dateLastModify, isGeneratedData, metaObject, ostBlobID

Constructor Summary

Lineage()

Method Summary

void	associateParentChildCheckNoLoop(java.lang.String parent, java.lang.String child)
void	buildMetamenu(javax.swing.JMenu menu, EvContainer parentObject) Additions to the object-specific menu
java.lang.Object	clone() Make a deep copy
EvObject	cloneEvObject() Get a deep copy of the object, not including children
int	countParticlesAtFrame(EvDecimal frame) Count how many particles exist at a given frame
int	countParticlesUpTo(EvDecimal frame) Count how many particles exist up to and equal the frame
void	createParentChild(java.lang.String parent, java.lang.String child) Create parent-children relation based on selected particles
Tuple<EvDecimal,java.lang.String>	firstFrameOfLineage(boolean checkMesh) Find the first keyframe and particle ever mentioned in a lineage object.
void	flattenSingleChildren() Join single children with their parents.
java.util.Set<java.lang.String>	getAllExpNames() Get names of all expressions mentioned
Lineage.Particle	getCreateParticle(java.lang.String name) Get a particle; create if needed
java.util.Set<java.lang.String>	getLeafs()
Tuple<java.lang.Double,java.lang.Double>	getMaxMinExpLevel(java.lang.String expName) Get maximum and minimum level of expression
java.lang.String	getMetaTypeDesc() Description of this metatype
static java.util.Collection<Lineage>	getParticles(EvContainer meta)
java.util.Set<java.lang.String>	getRecursiveChildNames(java.lang.String name)
java.util.Set<java.lang.String>	getRoots()
java.lang.String	getUniqueParticleName() Get an unused name for a particle
static void	initPlugin() Plugin declaration
java.util.Map<LineageSelParticle,Lineage.InterpolatedParticle>	interpolateParticles(EvDecimal frame) Get all interpolated particles
Tuple<EvDecimal,java.lang.String>	lastFrameOfLineage(boolean checkMesh) Find the last keyframe and particle ever mentioned in a lineage object
void	loadColorScheme(java.io.File filename) Load color scheme from a file
void	loadColorSchemeDialog(java.awt.Component parent) Bring up dialog to save color scheme
void	loadMetadata(org.jdom.Element e) Unserialize object
void	mergeParticles(java.lang.String sourceName, java.lang.String targetName) Merge particles.
void	removeAllParentReference(java.lang.String particleName) Remove all parent references from particle
void	removeParticle(java.lang.String name) Remove a particle.
void	removePosAfter(java.lang.String name, EvDecimal frame, boolean alsoEqual) Delete all positions after or equal to the current frame.
void	removePosBefore(java.lang.String name, EvDecimal frame, boolean alsoEqual) Delete all positions before or equal to the current frame.
boolean	renameParticles(java.lang.String oldName, java.lang.String newName) Rename particles
static java.awt.Color	representativeColor(java.awt.Color nucColor)
void	saveColorScheme(java.io.File filename) Save color scheme to a file
void	saveColorSchemeDialog(java.awt.Component parent) Bring up dialog to save color scheme
java.lang.String	saveMetadata(org.jdom.Element e) Save down data

Methods inherited from class endrov.data.EvObject

cloneEvObjectRecursive, cloneUsingSerialize, getContainerIcon

Methods inherited from class endrov.data.EvContainer

addMetaObject, getChild, getChildNames, getFreeChildName, getIdObjects, getIdObjectsRecursive, getMetaContainer, getMetaObject, getObjects, isMetadataModified, putChild, removeMetaObjectByValue, setMetadataModified, setMetadataNotModified

Methods inherited from class java.lang.Object

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

Field Detail

cellGroups

public static LineageParticleGrouping cellGroups

KEY_TRANSLATE

public static final int KEY_TRANSLATE

KEY_CHANGE_RADIUS

public static final int KEY_CHANGE_RADIUS

KEY_SETZ

public static final int KEY_SETZ

KEY_DIVIDENUC

public static final int KEY_DIVIDENUC

KEY_SETEND

public static final int KEY_SETEND

KEY_SETSTART

public static final int KEY_SETSTART

KEY_MAKEPARENT

public static final int KEY_MAKEPARENT

KEY_SETPARENT

public static final int KEY_SETPARENT

connectNuc

public static final java.lang.String[] connectNuc

particle

public java.util.HashMap<java.lang.String,Lineage.Particle> particle

Constructor Detail

Lineage

public Lineage()

Method Detail

getParticles

public static java.util.Collection<Lineage> getParticles(EvContainer meta)

createParentChild

public void createParentChild(java.lang.String parent,
                              java.lang.String child)

Create parent-children relation based on selected particles

loadColorScheme

public void loadColorScheme(java.io.File filename)
                     throws java.lang.Exception

Load color scheme from a file

Throws:

java.lang.Exception

saveColorScheme

public void saveColorScheme(java.io.File filename)
                     throws java.lang.Exception

Save color scheme to a file

Throws:

java.lang.Exception

saveColorSchemeDialog

public void saveColorSchemeDialog(java.awt.Component parent)

Bring up dialog to save color scheme

loadColorSchemeDialog

public void loadColorSchemeDialog(java.awt.Component parent)

Bring up dialog to save color scheme

clone

public java.lang.Object clone()

Make a deep copy

Overrides:

clone in class java.lang.Object

getMetaTypeDesc

public java.lang.String getMetaTypeDesc()

Description of this metatype

Specified by:

getMetaTypeDesc in class EvObject

saveMetadata

public java.lang.String saveMetadata(org.jdom.Element e)

Save down data

Specified by:

saveMetadata in class EvObject

loadMetadata

public void loadMetadata(org.jdom.Element e)

Description copied from class: EvObject

Unserialize object

Specified by:

loadMetadata in class EvObject

getCreateParticle

public Lineage.Particle getCreateParticle(java.lang.String name)

Get a particle; create if needed

removePosAfter

public void removePosAfter(java.lang.String name,
                           EvDecimal frame,
                           boolean alsoEqual)

Delete all positions after or equal to the current frame. If there are no more positions, remove the particle as well

removePosBefore

public void removePosBefore(java.lang.String name,
                            EvDecimal frame,
                            boolean alsoEqual)

Delete all positions before or equal to the current frame. If there are no more positions, remove the particle as well

removeParticle

public void removeParticle(java.lang.String name)

Remove a particle. Cleans up child references

interpolateParticles

public java.util.Map<LineageSelParticle,Lineage.InterpolatedParticle> interpolateParticles(EvDecimal frame)

Get all interpolated particles

getUniqueParticleName

public java.lang.String getUniqueParticleName()

Get an unused name for a particle

renameParticles

public boolean renameParticles(java.lang.String oldName,
                               java.lang.String newName)

Rename particles

mergeParticles

public void mergeParticles(java.lang.String sourceName,
                           java.lang.String targetName)

Merge particles. The target is removed, source stays and contains everything from the target TODO also handle expression pattern?

associateParentChildCheckNoLoop

public void associateParentChildCheckNoLoop(java.lang.String parent,
                                            java.lang.String child)

removeAllParentReference

public void removeAllParentReference(java.lang.String particleName)

Remove all parent references from particle

firstFrameOfLineage

public Tuple<EvDecimal,java.lang.String> firstFrameOfLineage(boolean checkMesh)

Find the first keyframe and particle ever mentioned in a lineage object. Can optionally also check mesh frames

lastFrameOfLineage

public Tuple<EvDecimal,java.lang.String> lastFrameOfLineage(boolean checkMesh)

Find the last keyframe and particle ever mentioned in a lineage object

representativeColor

public static java.awt.Color representativeColor(java.awt.Color nucColor)

countParticlesUpTo

public int countParticlesUpTo(EvDecimal frame)

Count how many particles exist up to and equal the frame

countParticlesAtFrame

public int countParticlesAtFrame(EvDecimal frame)

Count how many particles exist at a given frame

flattenSingleChildren

public void flattenSingleChildren()

Join single children with their parents. Useful if an algorithm generates one cell for each time point

getAllExpNames

public java.util.Set<java.lang.String> getAllExpNames()

Get names of all expressions mentioned

getMaxMinExpLevel

public Tuple<java.lang.Double,java.lang.Double> getMaxMinExpLevel(java.lang.String expName)

Get maximum and minimum level of expression

cloneEvObject

public EvObject cloneEvObject()

Description copied from class: EvObject

Get a deep copy of the object, not including children

Specified by:

cloneEvObject in class EvObject

buildMetamenu

public void buildMetamenu(javax.swing.JMenu menu,
                          EvContainer parentObject)

Additions to the object-specific menu

Specified by:

buildMetamenu in class EvObject

parentObject - TODO

getRecursiveChildNames

public java.util.Set<java.lang.String> getRecursiveChildNames(java.lang.String name)

getRoots

public java.util.Set<java.lang.String> getRoots()

getLeafs

public java.util.Set<java.lang.String> getLeafs()

initPlugin

public static void initPlugin()

Plugin declaration