DP (biojava-legacy 1.9.3 API)

JavaScript is disabled on your browser.

Skip navigation links

All Classes

Summary:
Nested |
Field |
Constr |
Method

Detail:
Field |
Constr |
Method

org.biojava.bio.dp

Class DP

java.lang.Object
- org.biojava.bio.dp.DP

Direct Known Subclasses:

PairwiseDP, SingleDP
```
public abstract class DP
extends Object 
```
Objects that can perform dymamic programming operations upon sequences with HMMs.

The three main DP operations are Forwards, Backwards and Viterbi. Forwards and Backwards calculate the probability of the sequences having been made in any way by the model. Viterbi finds the most supported way that the sequence could have been made.

Each of the functions can return the dynamic-programming matrix containing the intermediate results. This may be useful for model training, or for visualisation.

Each of the funcitons can be calculated using the model probabilities, the null-model probabilities or the odds (ratio between the two). For Forwards and Backwards, the odds calculations produce numbers with questionable basis in reality. For Viterbi with odds, you will recieve the path through the model that is most different from the null model, and supported by the probabilities.

Author:

Matthew Pocock, Thomas Down

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class DP.ReverseIterator

Nested Classes
Modifier and Type	Class and Description
`static class`	`DP.ReverseIterator`

Constructor Summary

Constructors
Constructor and Description

DP ()
This method will result in a DP with no model.

DP (MarkovModel model)

Constructors
Constructor and Description
`DP ()` This method will result in a DP with no model.
`DP (MarkovModel model)`

Method Summary

All Methods
Modifier and Type	Method and Description
`abstract double`	`backward (SymbolList[] symList, ScoreType scoreType)`
`abstract DPMatrix`	`backwardMatrix (SymbolList[] symList, DPMatrix matrix, ScoreType scoreType)`
`abstract DPMatrix`	`backwardMatrix (SymbolList[] symList, ScoreType scoreType)`
`static int[][]`	`backwardTransitions (MarkovModel model, State[] states)`
`static double[][]`	`backwardTransitionScores (MarkovModel model, State[] states, int[][] transitions, ScoreType scoreType)`
`static MarkovModel`	`flatView (MarkovModel model)`
`abstract double`	`forward (SymbolList[] symList, ScoreType scoreType)`
`abstract DPMatrix`	`forwardMatrix (SymbolList[] symList, DPMatrix matrix, ScoreType scoreType)`
`abstract DPMatrix`	`forwardMatrix (SymbolList[] symList, ScoreType scoreType)`
`DPMatrix`	`forwardsBackwards (SymbolList[] symList, ScoreType scoreType)`
`static int[][]`	`forwardTransitions (MarkovModel model, State[] states)` Returns a matrix for the specified States describing all valid Transitions between those States.
`static double[][]`	`forwardTransitionScores (MarkovModel model, State[] states, int[][] transitions, ScoreType scoreType)` Compute the log(score) of all transitions between the specified States.
`StatePath`	`generate (int length)` Generates an alignment from a model.
`int[][]`	`getBackwardTransitions ()`
`double[][]`	`getBackwardTransitionScores (ScoreType scoreType)`
`int`	`getDotStatesIndex ()`
`int[][]`	`getForwardTransitions ()`
`double[][]`	`getForwardTransitionScores (ScoreType scoreType)`
`MarkovModel`	`getModel ()`
`State[]`	`getStates ()`
`void`	`lockModel ()`
`static double`	`scoreWeightMatrix (WeightMatrix matrix, SymbolList symList, int start)` Scores the SymbolList from symbol start to symbol (start+columns) with a weight matrix.
`static double`	`scoreWeightMatrix (WeightMatrix matrix, SymbolList symList, ScoreType scoreType, int start)` Scores the SymbolList from symbol start to symbol (start+columns) with a weight matrix using a particular ScoreType.
`void`	`setModel (MarkovModel model)`
`State[]`	`stateList (MarkovModel mm)`
`void`	`unlockModel ()`
`void`	`update ()`
`abstract StatePath`	`viterbi (SymbolList[] symList, ScoreType scoreType)`

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

- Constructor Detail
  - DP
```
public DP(MarkovModel model)
```
  - DP
```
public DP()
```
    This method will result in a DP with no model. Use the setModel() method to set the model before use.
- Method Detail
  - scoreWeightMatrix
```
public static double scoreWeightMatrix(WeightMatrix matrix,
 SymbolList symList,
 int start)
 throws IllegalSymbolException 
```
    Scores the SymbolList from symbol start to symbol (start+columns) with a weight matrix.
    
    Parameters:
    
    matrix - the weight matrix used to evaluate the sequences
    
    symList - the SymbolList to assess
    
    start - the index of the first symbol in the window to evaluate
    
    Returns:
    
    the log probability or likelyhood of this weight matrix having generated symbols start to (start + columns) of symList
    
    Throws:
    
    IllegalSymbolException
  - scoreWeightMatrix
```
public static double scoreWeightMatrix(WeightMatrix matrix,
 SymbolList symList,
 ScoreType scoreType,
 int start)
 throws IllegalSymbolException 
```
    Scores the SymbolList from symbol start to symbol (start+columns) with a weight matrix using a particular ScoreType.
    This method allows you to use score types such as ScoreType.ODDS. The other scoreWeightMatrix methods gives a result similar or identical to ScoreType.PROBABILITY.
    
    Parameters:
    
    matrix - the weight matrix used to evaluate the sequences
    
    symList - the SymbolList to assess
    
    scoreType - the score type to apply
    
    start - the index of the first symbol in the window to evaluate
    
    Returns:
    
    the sum of log scores of this weight matrix having generated symbols start to (start + columns) of symList
    
    Throws:
    
    IllegalSymbolException
    
    Since:
    
    1.4
  - flatView
```
public static MarkovModel flatView(MarkovModel model)
 throws IllegalAlphabetException,
 IllegalSymbolException 
```
    Throws:
    
    IllegalAlphabetException
    
    IllegalSymbolException
  - stateList
```
public State[] stateList(MarkovModel mm)
 throws IllegalSymbolException,
 IllegalTransitionException,
 BioException 
```
    Throws:
    
    IllegalSymbolException
    
    IllegalTransitionException
    
    BioException
  - forwardTransitions
```
public static int[][] forwardTransitions(MarkovModel model,
 State[] states)
 throws IllegalSymbolException 
```
    Returns a matrix for the specified States describing all valid Transitions between those States.
    The matrix is 2-dimensional. The primary array has an element corresponding to every State in the states argument. That element is itself an array the elements of which identify the States that can reach that State. The source States are identified by their index within the states [] array.
    
    Parameters:
    
    model - MarkovModel to be analysed.
    
    states - The States for which the transition matrix is to be determined.
    
    Throws:
    
    IllegalSymbolException
  - forwardTransitionScores
```
public static double[][] forwardTransitionScores(MarkovModel model,
 State[] states,
 int[][] transitions,
 ScoreType scoreType)
```
    Compute the log(score) of all transitions between the specified States. The layout of the array is identical to that of the transitions array.
    Note that all parameters MUST be consistent with each other!!!!
    
    Parameters:
    
    model - The model for which the data is to be computed.
    
    states - The States within that model for which scores are required.
    
    transitions - The transition matrix obtained by calling forwardTransitions() with the above argument values.
    
    scoreType - The type of score to be evaluated.
  - backwardTransitions
```
public static int[][] backwardTransitions(MarkovModel model,
 State[] states)
 throws IllegalSymbolException 
```
    Throws:
    
    IllegalSymbolException
  - backwardTransitionScores
```
public static double[][] backwardTransitionScores(MarkovModel model,
 State[] states,
 int[][] transitions,
 ScoreType scoreType)
```
  - getDotStatesIndex
```
public int getDotStatesIndex()
```
  - getModel
```
public MarkovModel getModel()
```
  - getStates
```
public State[] getStates()
```
  - getForwardTransitions
```
public int[][] getForwardTransitions()
```
  - getForwardTransitionScores
```
public double[][] getForwardTransitionScores(ScoreType scoreType)
```
  - getBackwardTransitions
```
public int[][] getBackwardTransitions()
```
  - getBackwardTransitionScores
```
public double[][] getBackwardTransitionScores(ScoreType scoreType)
```
  - lockModel
```
public void lockModel()
```
  - unlockModel
```
public void unlockModel()
```
  - update
```
public void update()
```
  - setModel
```
public void setModel(MarkovModel model)
```
  - forward
```
public abstract double forward(SymbolList[] symList,
 ScoreType scoreType)
 throws IllegalSymbolException,
 IllegalAlphabetException,
 IllegalTransitionException 
```
    Throws:
    
    IllegalSymbolException
    
    IllegalAlphabetException
    
    IllegalTransitionException
  - backward
```
public abstract double backward(SymbolList[] symList,
 ScoreType scoreType)
 throws IllegalSymbolException,
 IllegalAlphabetException,
 IllegalTransitionException 
```
    Throws:
    
    IllegalSymbolException
    
    IllegalAlphabetException
    
    IllegalTransitionException
  - forwardMatrix
```
public abstract DPMatrix forwardMatrix(SymbolList[] symList,
 ScoreType scoreType)
 throws IllegalSymbolException,
 IllegalAlphabetException,
 IllegalTransitionException 
```
    Throws:
    
    IllegalSymbolException
    
    IllegalAlphabetException
    
    IllegalTransitionException
  - backwardMatrix
```
public abstract DPMatrix backwardMatrix(SymbolList[] symList,
 ScoreType scoreType)
 throws IllegalSymbolException,
 IllegalAlphabetException,
 IllegalTransitionException 
```
    Throws:
    
    IllegalSymbolException
    
    IllegalAlphabetException
    
    IllegalTransitionException
  - forwardMatrix
```
public abstract DPMatrix forwardMatrix(SymbolList[] symList,
 DPMatrix matrix,
 ScoreType scoreType)
 throws IllegalArgumentException,
 IllegalSymbolException,
 IllegalAlphabetException,
 IllegalTransitionException 
```
    Throws:
    
    IllegalArgumentException
    
    IllegalSymbolException
    
    IllegalAlphabetException
    
    IllegalTransitionException
  - backwardMatrix
```
public abstract DPMatrix backwardMatrix(SymbolList[] symList,
 DPMatrix matrix,
 ScoreType scoreType)
 throws IllegalArgumentException,
 IllegalSymbolException,
 IllegalAlphabetException,
 IllegalTransitionException 
```
    Throws:
    
    IllegalArgumentException
    
    IllegalSymbolException
    
    IllegalAlphabetException
    
    IllegalTransitionException
  - viterbi
```
public abstract StatePath viterbi(SymbolList[] symList,
 ScoreType scoreType)
 throws IllegalSymbolException,
 IllegalArgumentException,
 IllegalAlphabetException,
 IllegalTransitionException 
```
    Throws:
    
    IllegalSymbolException
    
    IllegalArgumentException
    
    IllegalAlphabetException
    
    IllegalTransitionException
  - forwardsBackwards
```
public DPMatrix forwardsBackwards(SymbolList[] symList,
 ScoreType scoreType)
 throws BioException 
```
    Throws:
    
    BioException
  - generate
```
public StatePath generate(int length)
 throws IllegalSymbolException,
 BioException 
```
    Generates an alignment from a model.
    
    If the length is set to -1 then the model length will be sampled using the model's transition to the end state. If the length is fixed using length, then the transitions to the end state are implicitly invoked.
    
    Parameters:
    
    length - the length of the sequence to generate
    
    Returns:
    
    a StatePath generated at random
    
    Throws:
    
    IllegalSymbolException
    
    BioException

Skip navigation links

All Classes

Summary:
Nested |
Field |
Constr |
Method

Detail:
Field |
Constr |
Method

Class DP

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

DP

DP

Method Detail

scoreWeightMatrix

scoreWeightMatrix

flatView

stateList

forwardTransitions

forwardTransitionScores

backwardTransitions

backwardTransitionScores

getDotStatesIndex

getModel

getStates

getForwardTransitions

getForwardTransitionScores

getBackwardTransitions

getBackwardTransitionScores

lockModel

unlockModel

update

setModel

forward

backward

forwardMatrix

backwardMatrix

forwardMatrix

backwardMatrix

viterbi

forwardsBackwards

generate