Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV CLASS NEXT CLASS | FRAMES NO FRAMES
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD

## calhoun.analysis.crf.features.tricycle13
Class GeneConstraints

    java.lang.Object
      calhoun.analysis.crf.AbstractFeatureManager<java.lang.Character>
          calhoun.analysis.crf.features.tricycle13.GeneConstraints

All Implemented Interfaces:
  FeatureManager<java.lang.Character>, FeatureManagerEdge<java.lang.Character>, java.io.Serializable

    public class GeneConstraints

extends AbstractFeatureManager<java.lang.Character>
implements FeatureManagerEdge<java.lang.Character>

lmplements basic constraints on gene calls.

1. Transition from intergenic to start must occur at ATG
2. Splice sites must be canonical GT/AG or GC/AG
3. Transition from exon to stop must be followed by a stop codon

See Also:
  Serialized Form

Constructor Summary
`GeneConstraints()`

Method Summary
`void` | `evaluateEdge(InputSequence<? extends java.lang.Character> seq, int pos, int prevState, int state, FeatureList result)` Evaluates the set of features managed by this object for the given arguments.
`java.lang.String` | `getFeatureName(int featureIndex)` Returns a human identifiable name for the feature referenced by a given index.
`int` | `getNumFeatures()` This is a constraint class, so we don't return features
`void` | `train(int startingIndex, ModelManager modelInfo, java.util.List<? extends TrainingSequence<? extends java.lang.Character>> data)` Set up the matrix Depends on states starting with the words 'intergenic, intron, and exon'.

Methods inherited from class calhoun.analysis.crf.AbstractFeatureManager
`getCacheStrategy, getInputComponent, setInputComponent`

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

Methods inherited from interface calhoun.analysis.crf.FeatureManager
`getCacheStrategy, getInputComponent, setInputComponent`

Constructor Detail

### GeneConstraints

    public GeneConstraints()

Method Detail

### getFeatureName

    public java.lang.String getFeatureName(int featureIndex)

  Description copied from interface: `FeatureManager`
  Returns a human identifiable name for the feature referenced by a given index. Used for display purposes only.

  Specified by:
    `getFeatureName` in interface `FeatureManager<java.lang.Character>`
  Parameters:
    `featureIndex` - the index of this feature
  Returns:
    the human readable name of this feature

### getNumFeatures

    public int getNumFeatures()

  This is a constraint class, so we don't return features

  Specified by:
    `getNumFeatures` in interface `FeatureManager<java.lang.Character>`
  Returns:
    number of features managed by this `FeatureManager`

### train

    public void train(int startingIndex,
                      ModelManager modelInfo,
                      java.util.List<? extends TrainingSequence<? extends java.lang.Character>> data)

  Set up the matrix Depends on states starting with the words 'intergenic, intron, and exon'. Also depends on the negative strand states ending in m.

  Specified by:
    `train` in interface `FeatureManager<java.lang.Character>`
  Parameters:
    `startingIndex` - the feature index of the first feature owned by this FeatureManager. Each FeatureManager must use up consecutive indexes, so the last index used will be startingIndex + numFeatures - 1.
    `modelInfo` - the model that contains this feature
    `data` - the full list of training sequences to use to train the feature

### evaluateEdge

    public void evaluateEdge(InputSequence<? extends java.lang.Character> seq,
                             int pos,
                             int prevState,
                             int state,
                             FeatureList result)

  Description copied from interface: `FeatureManagerEdge`
  Evaluates the set of features managed by this object for the given arguments.

  Specified by:
    `evaluateEdge` in interface `FeatureManagerEdge<java.lang.Character>`

Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV CLASS NEXT CLASS | FRAMES NO FRAMES
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD