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## de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states
Class SimpleState

    java.lang.Object
      de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.SimpleState

All Implemented Interfaces:
  State, TrainableState

Direct Known Subclasses:
  SimpleDifferentiableState, SimpleSamplingState

    public class SimpleState

extends Object
implements TrainableState

This class implements a `State` based on `Emission` that allows to reuse `Emission`s for different `State`s.

Author:
  Jens Keilwagen

Field Summary
`protected Emission` | `e` The emission that is internally used for scoring subsequences.
`protected boolean` | `forward` A switch that decides whether to use the forward or the reverse complementary strand of a sequence.
`protected String` | `name` The name of the state.

Constructor Summary
`SimpleState(Emission e, String name, boolean forward)` This is the constructor of a `SimpleState`.

Method Summary
`void` | `addToStatistic(int startPos, int endPos, double weight, Sequence seq)` This method allows to add a certain `weight` to the sufficient statistic of the parameters that are used for scoring the specific subsequence(s).
`String` | `getGraphvizNodeOptions(double weight, double maxWeight, NumberFormat nf)` This method returns a `String` representation of the node options that can be used in Graphviz to create the node for this state.
`double` | `getLogScoreFor(int startPos, int endPos, Sequence seq)` This method returns the logarithm of the score for a given sequence with given start and end position.
`boolean` | `isSilent()` This method returns whether a state is silent or not.
`String` | `toString()`

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

Field Detail

### e

    protected Emission e

  The emission that is internally used for scoring subsequences.

### name

    protected String name

  The name of the state.

### forward

    protected boolean forward

  A switch that decides whether to use the forward or the reverse complementary strand of a sequence.

Constructor Detail

### SimpleState

    public SimpleState(Emission e,
                       String name,
                       boolean forward)

  This is the constructor of a `SimpleState`.

  Parameters:
    `e` - the emission that is internally used for scoring subsequences
    `name` - the name of the state
    `forward` - a switch that decides whether to use the forward or the reverse complementary strand of a sequence

Method Detail

### getGraphvizNodeOptions

    public String getGraphvizNodeOptions(double weight,
                                         double maxWeight,
                                         NumberFormat nf)

  Description copied from interface: `State`
  This method returns a `String` representation of the node options that can be used in Graphviz to create the node for this state.

  Specified by:
    `getGraphvizNodeOptions` in interface `State`
  Parameters:
    `weight` - for state
    `maxWeight` - the maximal weight for the state
    `nf` - the `NumberFormat` for the output, can be `null`
  Returns:
    `String` representation of the state

### getLogScoreFor

    public double getLogScoreFor(int startPos,
                                 int endPos,
                                 Sequence seq)
                          throws WrongLengthException,
                                 OperationNotSupportedException

  Description copied from interface: `State`
  This method returns the logarithm of the score for a given sequence with given start and end position. The method provides the basics for quantifying emission probability/density.

  Specified by:
    `getLogScoreFor` in interface `State`
  Parameters:
    `startPos` - the start position within the sequence(s)
    `endPos` - the end position within the sequence(s)
    `seq` - the sequence(s)
  Returns:
    the logarithm of score for the given sequence(s)
  Throws:
    `WrongLengthException` - if the length can not be modeled
    `OperationNotSupportedException` - if the reverse complement of the sequence can not be computed

### addToStatistic

    public void addToStatistic(int startPos,
                               int endPos,
                               double weight,
                               Sequence seq)
                        throws OperationNotSupportedException

  Description copied from interface: `TrainableState`
  This method allows to add a certain `weight` to the sufficient statistic of the parameters that are used for scoring the specific subsequence(s).

  Specified by:
    `addToStatistic` in interface `TrainableState`
  Parameters:
    `startPos` - the start position
    `endPos` - the end position
    `weight` - the weight which will be added to the sufficient statistic
    `seq` - the `Sequence`(s)
  Throws:
    `OperationNotSupportedException` - if the reverse complement of the sequence can not be computed

### isSilent

    public boolean isSilent()

  Description copied from interface: `State`
  This method returns whether a state is silent or not.

  Specified by:
    `isSilent` in interface `State`
  Returns:
    `true` if the state is silent, otherwise `false`
  See Also:
    `SilentEmission`

### toString

    public String toString()

  Overrides:
    `toString` in class `Object`

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