ADAM_2.12: Core 0.35.0 API < Back
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# Packages

-  package root
  Definition Classes
    root
-  package org
  Definition Classes
    root
-  package bdgenomics
  Definition Classes
    org
-  package adam
  Definition Classes
    bdgenomics
-  package algorithms
  Definition Classes
    adam
-  package converters
  Definition Classes
    adam
-  package ds
  Definition Classes
    adam
-  package io
  Definition Classes
    adam
-  package models
  Definition Classes
    adam
-  package projections
  Definition Classes
    adam
- AlignmentField
- DbxrefField
- FeatureField
- FieldEnumeration
- FieldValue
- Filter
- FragmentField
- GenotypeField
- OntologyTermField
- Projection
- ReadField
- ReadGroupField
- ReferenceField
- SampleField
- SequenceField
- SliceField
- TranscriptEffectField
- VariantAnnotationField
- VariantCallingAnnotationsField
- VariantField
-  package rich
  Definition Classes
    adam
-  package serialization
  Definition Classes
    adam
-  package sql
  Definition Classes
    adam
-  package util
  Definition Classes
    adam

p

org.bdgenomics.adam

# projections 

#### package projections

 
Ordering

1. Alphabetic

Visibility

1. Public
2. All

### Type Members

1.  abstract class FieldEnumeration extends Enumeration

   Abstract class that all record-specific enumerations extend.

2.  trait FieldValue extends AnyRef

   The FieldValue trait (and its sister abstract class, FieldEnumeration) are meant to help clean up the use of Projection when dealing with field enumeration classes like ADAMRecordField.

   The FieldValue trait (and its sister abstract class, FieldEnumeration) are meant to help clean up the use of Projection when dealing with field enumeration classes like ADAMRecordField.

   Projection is a class for turning fields from an Enumeration into a projected Avro Schema object.

   In the old way of doing this, we used a "normal" Enumeration. Projection would receive a collection of Read.Value objects, and use their names (plus the Read.SCHEMA$ static field) to turn them into a Schema for ADAMRecords. This worked fine for Read, and not at all for generalizing to other Schemas over other field enumerations.

   In the new system, we embed the Avro Schema object as an argument *in* each enumeration Value. We do this in two steps: (1) instead of ADAMRecordField (e.g.) extending Enumeration, it extends FieldEnumeration and provides the appropriate (static) Schema object as an argument. (2) instead of using the (final, non-overrideable) Value method within Enumeration to provide each enum value, it calls FieldEnumeration.SchemaValue instead, which embeds the corresponding Schema in each value.

   Finally, Projection will extract the Schema value from the first FieldValue that is given to it and produce the corresponding (projected) Schema.

   This means, of course, that Projection can't handle empty field lists -- but that was always going to be an error-filled edge-case anyway (why would you want to project to zero fields?)

### Value Members

1.  object AlignmentField extends FieldEnumeration
2.  object DbxrefField extends FieldEnumeration
3.  object FeatureField extends FieldEnumeration
4.  object Filter

   Helper object to create a projection that excludes fields from a schema.

5.  object FragmentField extends FieldEnumeration
6.  object GenotypeField extends FieldEnumeration
7.  object OntologyTermField extends FieldEnumeration
8.  object Projection

   Avro utility object to create a projection of a Schema.

9.  object ReadField extends FieldEnumeration
10.  object ReadGroupField extends FieldEnumeration
11.  object ReferenceField extends FieldEnumeration
12.  object SampleField extends FieldEnumeration
13.  object SequenceField extends FieldEnumeration
14.  object SliceField extends FieldEnumeration
15.  object TranscriptEffectField extends FieldEnumeration
16.  object VariantAnnotationField extends FieldEnumeration
17.  object VariantCallingAnnotationsField extends FieldEnumeration
18.  object VariantField extends FieldEnumeration

### Ungrouped