JaqamanLinkingCostMatrixCreator (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- fiji.plugin.trackmate.tracking.sparselap.costmatrix.JaqamanLinkingCostMatrixCreator<K,J>

Type Parameters:

K -

J -

All Implemented Interfaces:

CostMatrixCreator<K,J>, Algorithm, Benchmark, OutputAlgorithm<SparseCostMatrix>
```
public class JaqamanLinkingCostMatrixCreator<K extends Comparable<K>,J extends Comparable<J>>
extends Object
implements CostMatrixCreator<K,J>
```
A CostMatrixCreator that can generate a cost matrix from a list of sources, a list of targets and a CostFunction that can generate a cost for any combination.

Author:

Jean-Yves Tinevez - 2014

Constructor Summary

Constructors
Constructor and Description
`JaqamanLinkingCostMatrixCreator(Iterable<K> sources, Iterable<J> targets, CostFunction<K,J> costFunction, double costThreshold, double alternativeCostFactor, double percentile)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`checkInput()`
`double`	`getAlternativeCostForSource(K source)` Returns the value of the no-linking alternative cost for the specified source.
`double`	`getAlternativeCostForTarget(J target)` Returns the value of the no-linking alternative cost for the specified target.
`String`	`getErrorMessage()`
`long`	`getProcessingTime()`
`SparseCostMatrix`	`getResult()` Returns the cost matrix generated.
`List<K>`	`getSourceList()` Returns the list of sources in the generated cost matrix.
`List<J>`	`getTargetList()` Returns the list of targets in the generated cost matrix.
`boolean`	`process()`

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

- Constructor Detail
  - JaqamanLinkingCostMatrixCreator
```
public JaqamanLinkingCostMatrixCreator(Iterable<K> sources,
                                       Iterable<J> targets,
                                       CostFunction<K,J> costFunction,
                                       double costThreshold,
                                       double alternativeCostFactor,
                                       double percentile)
```
- Method Detail
  - checkInput
```
public boolean checkInput()
```
    Specified by:
    
    checkInput in interface Algorithm
  - process
```
public boolean process()
```
    Specified by:
    
    process in interface Algorithm
  - getErrorMessage
```
public String getErrorMessage()
```
    Specified by:
    
    getErrorMessage in interface Algorithm
  - getResult
```
public SparseCostMatrix getResult()
```
    Returns the cost matrix generated.
    Careful, it can be null if not acceptable costs have been found for the specified configuration. In that case, the lists returned by getSourceList() and getTargetList() are empty.
    
    Specified by:
    
    getResult in interface OutputAlgorithm<SparseCostMatrix>
    
    Returns:
    
    a new SparseCostMatrix or null.
  - getSourceList
```
public List<K> getSourceList()
```
    Description copied from interface: CostMatrixCreator
    
    Returns the list of sources in the generated cost matrix.
    
    Specified by:
    
    getSourceList in interface CostMatrixCreator<K extends Comparable<K>,J extends Comparable<J>>
    
    Returns:
    
    the list of object, such that sourceList.get( i ) is the source corresponding to the row i in the generated cost matrix.
    
    See Also:
    
    CostMatrixCreator.getTargetList(), OutputAlgorithm.getResult()
  - getTargetList
```
public List<J> getTargetList()
```
    Description copied from interface: CostMatrixCreator
    
    Returns the list of targets in the generated cost matrix.
    
    Specified by:
    
    getTargetList in interface CostMatrixCreator<K extends Comparable<K>,J extends Comparable<J>>
    
    Returns:
    
    the list of objects, such that targetList.get( j ) is the target corresponding to the column j in the generated cost matrix.
    
    See Also:
    
    CostMatrixCreator.getSourceList(), OutputAlgorithm.getResult()
  - getProcessingTime
```
public long getProcessingTime()
```
    Specified by:
    
    getProcessingTime in interface Benchmark
  - getAlternativeCostForSource
```
public double getAlternativeCostForSource(K source)
```
    Description copied from interface: CostMatrixCreator
    
    Returns the value of the no-linking alternative cost for the specified source.
    
    Specified by:
    
    getAlternativeCostForSource in interface CostMatrixCreator<K extends Comparable<K>,J extends Comparable<J>>
    
    Parameters:
    
    source - the source object.
    
    Returns:
    
    the alternative cost. Belongs to the list returned by CostMatrixCreator.getSourceList().
  - getAlternativeCostForTarget
```
public double getAlternativeCostForTarget(J target)
```
    Description copied from interface: CostMatrixCreator
    
    Returns the value of the no-linking alternative cost for the specified target.
    
    Specified by:
    
    getAlternativeCostForTarget in interface CostMatrixCreator<K extends Comparable<K>,J extends Comparable<J>>
    
    Parameters:
    
    target - the target object. Belongs to the list returned by CostMatrixCreator.getTargetList().
    
    Returns:
    
    the alternative cost.

Class JaqamanLinkingCostMatrixCreator<K extends Comparable<K>,J extends Comparable<J>>

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

JaqamanLinkingCostMatrixCreator

Method Detail

checkInput

process

getErrorMessage

getResult

getSourceList

getTargetList

getProcessingTime

getAlternativeCostForSource

getAlternativeCostForTarget