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## org.biojava.bio
Class AnnotationType.Abstract

    java.lang.Object
      org.biojava.bio.AnnotationType.Abstract

All Implemented Interfaces:
  AnnotationType

Direct Known Subclasses:
  AnnotationType.Impl

Enclosing interface:
  AnnotationType

    public abstract static class AnnotationType.Abstract

extends Object
implements AnnotationType

An abstract base class useful for implementing AnnotationType instances.

This provides deffinitions for the logical operators (validate(), subTypeOf()), the mutators (setProperty(), getProperty() and deleteProperty()) and toString() that you may not want to write yourself. It leaves the data-related methods up to you.

Since:
  1.3
Author:
  Matthew Pocock, Thomas Down

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.AnnotationType
`AnnotationType.Abstract, AnnotationType.Impl`

Field Summary

Fields inherited from interface org.biojava.bio.AnnotationType
`ANY, NONE`

Constructor Summary
`AnnotationType.Abstract()`

Method Summary
`void` | `addProperty(Annotation ann, Object key, Object value)` Add a value to the specified property slot.
`Collection` | `getProperty(Annotation ann, Object property)` Get the Collection of values associated with an Annotation bundle according to the type we believe it to be.
`boolean` | `instanceOf(Annotation ann)` Validate an Annotation against this AnnotationType.
`void` | `removeProperty(Annotation ann, Object key, Object value)` Remove a value from the specified property slot.
`void` | `setConstraints(Object key, PropertyConstraint pc, Location cc)` Set the constraints associated with a property.
`void` | `setDefaultConstraints(PropertyConstraint pc, Location cc)` Set the constraints that will apply to all properties without an explicitly defined set of constraints.
`void` | `setProperty(Annotation ann, Object property, Object value)` Set the property in an annotation bundle according to the type we believe it should be.
`boolean` | `subTypeOf(AnnotationType subType)` See if an AnnotationType is a specialisation of this type.
`String` | `toString()`

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

Methods inherited from interface org.biojava.bio.AnnotationType
`getComment, getComment, getConstraint, getDefaultConstraint, getProperties, setComment, setComment, setConstraint, setDefaultConstraint`

Constructor Detail

### AnnotationType.Abstract

    public AnnotationType.Abstract()

Method Detail

### setConstraints

    public void setConstraints(Object key,
                               PropertyConstraint pc,
                               Location cc)

  Description copied from interface: `AnnotationType`
  Set the constraints associated with a property. This method constrains the value of the specified property such that all members must match `con`, and the number of members must match `card`. It implicitly constructs a `CollectionConstraint.AllValuesIn` instance.

  When you are building your own AnnotationType

  Specified by:
    `setConstraints` in interface `AnnotationType`
  Parameters:
    `key` - the name of the property to constrain
    `pc` - the PropertyConstraint to enforce
    `cc` - the CardinalityConstraint to enforce

### setDefaultConstraints

    public void setDefaultConstraints(PropertyConstraint pc,
                                      Location cc)

  Description copied from interface: `AnnotationType`
  Set the constraints that will apply to all properties without an explicitly defined set of constraints. This method constrains the value of the specified property such that all members must match `con`, and the number of members must match `card`. It implicitly constructs a `CollectionConstraint.AllValuesIn` instance.

  Specified by:
    `setDefaultConstraints` in interface `AnnotationType`
  Parameters:
    `pc` - the default PropertyConstraint
    `cc` - the default CardinalityConstraint

### instanceOf

    public boolean instanceOf(Annotation ann)

  Description copied from interface: `AnnotationType`
  Validate an Annotation against this AnnotationType. Any time you wish to see if an Annotation bundle conforms to a type

  Specified by:
    `instanceOf` in interface `AnnotationType`
  Parameters:
    `ann` - the Annotation to validate.
  Returns:
    true if ann conforms to this type and false if it doesn't.

### setProperty

    public final void setProperty(Annotation ann,
                                  Object property,
                                  Object value)
                           throws ChangeVetoException

  Description copied from interface: `AnnotationType`
  Set the property in an annotation bundle according to the type we believe it should be. This will take care of any neccisary packing or unpacking to Collections.

  Specified by:
    `setProperty` in interface `AnnotationType`
  Parameters:
    `ann` - the Annotation to modify
    `property` - the property key Object
    `value` - the property value Object
  Throws:
    `ChangeVetoException` - if the value could not be accepted by this annotation type for that property key, or if the Annotation could not be modified

### getProperty

    public final Collection getProperty(Annotation ann,
                                        Object property)
                                 throws ChangeVetoException

  Description copied from interface: `AnnotationType`
  Get the Collection of values associated with an Annotation bundle according to the type we believe it to be. This will take care of any neccisary packing or unpacking to Collections. Properties with no values will return empty Collections.

  Specified by:
    `getProperty` in interface `AnnotationType`
  Parameters:
    `ann` - the Annotation to access
    `property` - the property key Object
  Returns:
    a Collection of values
  Throws:
    `ChangeVetoException` - if the value could not be removed

### addProperty

    public final void addProperty(Annotation ann,
                                  Object key,
                                  Object value)
                           throws ChangeVetoException

  Description copied from interface: `AnnotationType`
  Add a value to the specified property slot.

  Specified by:
    `addProperty` in interface `AnnotationType`
  Parameters:
    `ann` - the Annotation to modify
    `key` - the property key Object
    `value` - the property value Object
  Throws:
    `ChangeVetoException` - if the value could not be accepted by this annotation type for that property key, or if the Annotation could not be modified

### removeProperty

    public final void removeProperty(Annotation ann,
                                     Object key,
                                     Object value)
                              throws ChangeVetoException

  Description copied from interface: `AnnotationType`
  Remove a value from the specified property slot.

  Specified by:
    `removeProperty` in interface `AnnotationType`
  Parameters:
    `ann` - the Annotation to modify
    `key` - the property key Object
    `value` - the property value Object
  Throws:
    `ChangeVetoException` - if the Annotation could not be modified

### toString

    public String toString()

  Overrides:
    `toString` in class `Object`

### subTypeOf

    public boolean subTypeOf(AnnotationType subType)

  Description copied from interface: `AnnotationType`

  See if an AnnotationType is a specialisation of this type.

  An AnnotationType is a sub-type if it restricts each of the properties of the super-type to a type that can be cast to the type in the super-type. Note that this is not always a cast in the pure Java sense; it may include checks on the number and type of members in collections or other criteria.

  Specified by:
    `subTypeOf` in interface `AnnotationType`
  Parameters:
    `subType` - an AnnotationType to check.
  Returns:
    true if subType is a sub-type of this type.

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