Model (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- fiji.plugin.trackmate.Model

```
public class Model
extends Object
```
The model for the data managed by TrackMate trackmate.

This is a relatively large class, with a lot of public methods. This complexity arose because this class handles data storage and manipulation, through user manual editing and automatic processing. To avoid conflicting accesses to the data, some specialized methods had to be created, hopefully built in coherent sets.

Author:

Jean-Yves Tinevez <tinevez@pasteur.fr> - 2010-2013

Field Summary

Fields
Modifier and Type Field and Description

protected SpotCollection spots
The spots managed by this model.

Fields
Modifier and Type	Field and Description
`protected SpotCollection`	`spots` The spots managed by this model.

Constructor Summary

Constructors
Constructor and Description

Model()

Constructors
Constructor and Description
`Model()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`org.jgrapht.graph.DefaultWeightedEdge`	`addEdge(Spot source, Spot target, double weight)` Creates a new edge between two spots, with the specified weight.
`void`	`addModelChangeListener(ModelChangeListener listener)`
`Spot`	`addSpotTo(Spot spotToAdd, Integer toFrame)` Adds a single spot to the collections managed by this model, mark it as visible, then update its features.
`void`	`beginUpdate()`
`void`	`clearSpots(boolean doNotify)` Removes all the spots from this model.
`void`	`clearTracks(boolean doNotify)` Removes all the tracks from this model.
`protected FeatureModel`	`createFeatureModel()` Instantiates a blank `FeatureModel` to use whithin this model.
`protected TrackModel`	`createTrackModel()` Instantiates a blank `TrackModel` to use whithin this model.
`void`	`endUpdate()`
`void`	`filterSpots(Collection<FeatureFilter> spotFilters, boolean doNotify)` Filters the `SpotCollection` managed by this model with the `FeatureFilter`s specified.
`FeatureModel`	`getFeatureModel()`
`Logger`	`getLogger()` Return the logger currently set for this model.
`Set<ModelChangeListener>`	`getModelChangeListener()`
`String`	`getSpaceUnits()` Returns the spatial units for the quantities stored in this model.
`SpotCollection`	`getSpots()` Returns the spot collection managed by this model.
`String`	`getTimeUnits()` Returns the time units for the quantities stored in this model.
`TrackModel`	`getTrackModel()` Returns the `TrackModel` that manages the tracks for this model.
`Spot`	`moveSpotFrom(Spot spotToMove, Integer fromFrame, Integer toFrame)` Moves a single spot from a frame to another, make it visible if it was not, then mark it for feature update.
`void`	`notifyFeaturesComputed()` Notify the `ModelChangeListener`s of this model that feature values have been computed.
`boolean`	`removeEdge(org.jgrapht.graph.DefaultWeightedEdge edge)` Removes an existing edge from the model.
`org.jgrapht.graph.DefaultWeightedEdge`	`removeEdge(Spot source, Spot target)` Removes an edge between two spots and returns it.
`boolean`	`removeModelChangeListener(ModelChangeListener listener)`
`Spot`	`removeSpot(Spot spotToRemove)` Removes a single spot from the collections managed by this model.
`void`	`setEdgeWeight(org.jgrapht.graph.DefaultWeightedEdge edge, double weight)` Sets the weight of the specified edge.
`void`	`setLogger(Logger logger)` Set the logger that will receive the messages from the processes occurring within this trackmate.
`void`	`setPhysicalUnits(String spaceUnits, String timeUnits)` Sets the physical units for the quantities stored in this model.
`void`	`setSpots(SpotCollection spots, boolean doNotify)` Set the `SpotCollection` managed by this model.
`void`	`setTracks(org.jgrapht.graph.SimpleWeightedGraph<Spot,org.jgrapht.graph.DefaultWeightedEdge> graph, boolean doNotify)` Sets the tracks stored in this model in bulk.
`boolean`	`setTrackVisibility(Integer trackID, boolean visible)` Sets the visibility of the specified track.
`String`	`toString()`
`void`	`updateFeatures(Spot spotToUpdate)` Mark the specified spot for update.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - spots
```
protected SpotCollection spots
```
    The spots managed by this model.
- Constructor Detail
  - Model
```
public Model()
```
- Method Detail
  - createTrackModel
```
protected TrackModel createTrackModel()
```
    Instantiates a blank TrackModel to use whithin this model.
    Subclassers can override this method to have the model work with their own subclass of TrackModel.
    
    Returns:
    
    a new instance of TrackModel.
  - createFeatureModel
```
protected FeatureModel createFeatureModel()
```
    Instantiates a blank FeatureModel to use whithin this model.
    Subclassers can override this method to have the model work with their own subclass of FeatureModel.
    
    Returns:
    
    a new instance of FeatureModel.
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - addModelChangeListener
```
public void addModelChangeListener(ModelChangeListener listener)
```
  - removeModelChangeListener
```
public boolean removeModelChangeListener(ModelChangeListener listener)
```
  - getModelChangeListener
```
public Set<ModelChangeListener> getModelChangeListener()
```
  - setPhysicalUnits
```
public void setPhysicalUnits(String spaceUnits,
                             String timeUnits)
```
    Sets the physical units for the quantities stored in this model.
    
    Parameters:
    
    spaceUnits - the spatial units (e.g. μm).
    
    timeUnits - the time units (e.g. min).
  - getSpaceUnits
```
public String getSpaceUnits()
```
    Returns the spatial units for the quantities stored in this model.
    
    Returns:
    
    the spatial units.
  - getTimeUnits
```
public String getTimeUnits()
```
    Returns the time units for the quantities stored in this model.
    
    Returns:
    
    the time units.
  - beginUpdate
```
public void beginUpdate()
```
  - endUpdate
```
public void endUpdate()
```
  - clearTracks
```
public void clearTracks(boolean doNotify)
```
    Removes all the tracks from this model.
    
    Parameters:
    
    doNotify - if true, model listeners will be notified with a ModelChangeEvent.TRACKS_COMPUTED event.
  - getTrackModel
```
public TrackModel getTrackModel()
```
    Returns the TrackModel that manages the tracks for this model.
    
    Returns:
    
    the track model.
  - setTracks
```
public void setTracks(org.jgrapht.graph.SimpleWeightedGraph<Spot,org.jgrapht.graph.DefaultWeightedEdge> graph,
                      boolean doNotify)
```
    Sets the tracks stored in this model in bulk.
    Clears the tracks of this model and replace it by the tracks found by inspecting the specified graph. All new tracks found will be made visible and will be given a default name.
    
    Parameters:
    
    graph - the graph to parse for tracks.
    
    doNotify - if true, model listeners will be notified with a ModelChangeEvent.TRACKS_COMPUTED event.
  - getSpots
```
public SpotCollection getSpots()
```
    Returns the spot collection managed by this model.
    
    Returns:
    
    the spot collection managed by this model.
  - clearSpots
```
public void clearSpots(boolean doNotify)
```
    Removes all the spots from this model.
    
    Parameters:
    
    doNotify - if true, model listeners will be notified with a ModelChangeEvent.SPOTS_COMPUTED event.
  - setSpots
```
public void setSpots(SpotCollection spots,
                     boolean doNotify)
```
    Set the SpotCollection managed by this model.
    
    Parameters:
    
    doNotify - if true, will file a ModelChangeEvent.SPOTS_COMPUTED event.
    
    spots - the SpotCollection to set.
  - filterSpots
```
public void filterSpots(Collection<FeatureFilter> spotFilters,
                        boolean doNotify)
```
    Filters the SpotCollection managed by this model with the FeatureFilters specified.
    
    Parameters:
    
    spotFilters - the FeatureFilter collection to use for filtering.
    
    doNotify - if true, will file a ModelChangeEvent.SPOTS_FILTERED event.
  - notifyFeaturesComputed
```
public void notifyFeaturesComputed()
```
    Notify the ModelChangeListeners of this model that feature values have been computed. This method serves as a manual trigger for this event.
  - setLogger
```
public void setLogger(Logger logger)
```
    Set the logger that will receive the messages from the processes occurring within this trackmate.
    
    Parameters:
    
    logger - the Logger to use.
  - getLogger
```
public Logger getLogger()
```
    Return the logger currently set for this model.
    
    Returns:
    
    the Logger used.
  - getFeatureModel
```
public FeatureModel getFeatureModel()
```
  - moveSpotFrom
```
public Spot moveSpotFrom(Spot spotToMove,
                         Integer fromFrame,
                         Integer toFrame)
```
    Moves a single spot from a frame to another, make it visible if it was not, then mark it for feature update. If the source spot could not be found in the source frame, nothing is done and null is returned.
    For the model update to happen correctly and listeners to be notified properly, a call to this method must happen within a transaction, as in:
```
 model.beginUpdate();
 try {
        ... // model modifications here
 } finally {
        model.endUpdate();
 }
 
```
    Parameters:
    
    spotToMove - the spot to move
    
    fromFrame - the frame the spot originated from
    
    toFrame - the destination frame
    
    Returns:
    
    the spot that was moved, or null if it could not be found in the source frame
  - addSpotTo
```
public Spot addSpotTo(Spot spotToAdd,
                      Integer toFrame)
```
    Adds a single spot to the collections managed by this model, mark it as visible, then update its features.
    For the model update to happen correctly and listeners to be notified properly, a call to this method must happen within a transaction, as in:
```
 model.beginUpdate();
 try {
        ... // model modifications here
 } finally {
        model.endUpdate();
 }
 
```
    Parameters:
    
    spotToAdd - the spot to add.
    
    toFrame - the frame to add it to.
    
    Returns:
    
    the spot just added.
  - removeSpot
```
public Spot removeSpot(Spot spotToRemove)
```
    Removes a single spot from the collections managed by this model. If the spot cannot be found, nothing is done and null is returned.
    For the model update to happen correctly and listeners to be notified properly, a call to this method must happen within a transaction, as in:
```
 model.beginUpdate();
 try {
        ... // model modifications here
 } finally {
        model.endUpdate();
 }
 
```
    Parameters:
    
    spotToRemove - the spot to remove.
    
    Returns:
    
    the spot removed, or null if it could not be found.
  - updateFeatures
```
public void updateFeatures(Spot spotToUpdate)
```
    Mark the specified spot for update. At the end of the model transaction, its features will be recomputed, and other edge and track features that depends on it will be as well.
    For the model update to happen correctly and listeners to be notified properly, a call to this method must happen within a transaction, as in:
```
 model.beginUpdate();
 try {
        ... // model modifications here
 } finally {
        model.endUpdate();
 }
 
```
    Parameters:
    
    spotToUpdate - the spot to mark for update
  - addEdge
```
public org.jgrapht.graph.DefaultWeightedEdge addEdge(Spot source,
                                                     Spot target,
                                                     double weight)
```
    Creates a new edge between two spots, with the specified weight.
    For the model update to happen correctly and listeners to be notified properly, a call to this method must happen within a transaction, as in:
```
 model.beginUpdate();
 try {
        ... // model modifications here
 } finally {
        model.endUpdate();
 }
 
```
    Parameters:
    
    source - the source spot.
    
    target - the target spot.
    
    weight - the weight of the edge.
    
    Returns:
    
    the edge created.
  - removeEdge
```
public org.jgrapht.graph.DefaultWeightedEdge removeEdge(Spot source,
                                                        Spot target)
```
    Removes an edge between two spots and returns it. Returns null and do nothing to the tracks if the edge did not exist.
    
    Parameters:
    
    source - the source spot.
    
    target - the target spot.
    
    Returns:
    
    the edge between the two spots, if it existed.
  - removeEdge
```
public boolean removeEdge(org.jgrapht.graph.DefaultWeightedEdge edge)
```
    Removes an existing edge from the model.
    For the model update to happen correctly and listeners to be notified properly, a call to this method must happen within a transaction, as in:
```
 model.beginUpdate();
 try {
        ... // model modifications here
 } finally {
        model.endUpdate();
 }
 
```
    Parameters:
    
    edge - the edge to remove.
    
    Returns:
    
    true if the edge existed in the model and was successfully, false otherwise.
  - setEdgeWeight
```
public void setEdgeWeight(org.jgrapht.graph.DefaultWeightedEdge edge,
                          double weight)
```
    Sets the weight of the specified edge.
    For the model update to happen correctly and listeners to be notified properly, a call to this method must happen within a transaction, as in:
```
 model.beginUpdate();
 try {
        ... // model modifications here
 } finally {
        model.endUpdate();
 }
 
```
    Parameters:
    
    edge - the edge.
    
    weight - the weight to set.
  - setTrackVisibility
```
public boolean setTrackVisibility(Integer trackID,
                                  boolean visible)
```
    Sets the visibility of the specified track. Throws a NullPointerException if the track ID is unknown to the model.
    For the model update to happen correctly and listeners to be notified properly, a call to this method must happen within a transaction, as in:
```
 model.beginUpdate();
 try {
        ... // model modifications here
 } finally {
        model.endUpdate();
 }
 
```
    Parameters:
    
    trackID - the track ID.
    
    visible - the desired visibility.
    
    Returns:
    
    the specified track visibility prior to calling this method.

Class Model

The model for the data managed by TrackMate trackmate.

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

spots

Constructor Detail

Model

Method Detail

createTrackModel

createFeatureModel

toString

addModelChangeListener

removeModelChangeListener

getModelChangeListener

setPhysicalUnits

getSpaceUnits

getTimeUnits

beginUpdate

endUpdate

clearTracks

getTrackModel

setTracks

getSpots

clearSpots

setSpots

filterSpots

notifyFeaturesComputed

setLogger

getLogger

getFeatureModel

moveSpotFrom

addSpotTo

removeSpot

updateFeatures

addEdge

removeEdge

removeEdge

setEdgeWeight

setTrackVisibility