Serialized Form (molgenis-omx-das 1.1.0 API)

Package org.molgenis

Class org.molgenis.JDBCMetaDatabase extends Model implements Serializable

serialVersionUID:

1L

Class org.molgenis.MolgenisOptions extends Object implements Serializable

serialVersionUID:: 1L

Serialized Fields

molgenis_properties
```
String molgenis_properties
```
model_database
```
ArrayList<E> model_database
```
import_model_database
```
ArrayList<E> import_model_database
```
output_dir
```
String output_dir
```
output_src
```
String output_src
```
output_hand
```
String output_hand
```
output_sql
```
String output_sql
```
output_doc
```
String output_doc
```
output_web
```
String output_web
```
decorator_overriders
```
String decorator_overriders
```
db_filepath
```
String db_filepath
```
object_relational_mapping
```
String object_relational_mapping
```
generate_persistence
```
boolean generate_persistence
```
generate_jpa
```
boolean generate_jpa
```
jpa_use_sequence
```
boolean jpa_use_sequence
```
generate_db
```
boolean generate_db
```
exclude_system
```
boolean exclude_system
```
generate_doc
```
boolean generate_doc
```
generate_entityio
```
boolean generate_entityio
```
generate_tests
```
boolean generate_tests
```
generate_model
```
boolean generate_model
```
delete_generated_folder
```
boolean delete_generated_folder
```
authorizable
```
ArrayList<E> authorizable
```
disable_decorators
```
boolean disable_decorators
```
block_webspiders
```
boolean block_webspiders
```
generate_jpa_repository_source
```
boolean generate_jpa_repository_source
```
path
```
String path
```

Package org.molgenis.omx.das.impl
- Class org.molgenis.omx.das.impl.MolgenisDasTarget extends uk.ac.ebi.mydas.model.DasTarget implements Serializable
  
  serialVersionUID:
  
  1L
Package org.molgenis.omx.patient
- Class org.molgenis.omx.patient.Patient extends Individual implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - allele1
```
Variant allele1
```
    - allele2
```
Variant allele2
```
    - pheno
```
String pheno
```
    - pubMedID
```
String pubMedID
```
    - reference
```
String reference
```
Package org.molgenis.omx.xgap
- Class org.molgenis.omx.xgap.Chromosome extends ObservationTarget implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - orderNr
```
Integer orderNr
```
    - isAutosomal
```
Boolean isAutosomal
```
    - bpLength
```
Integer bpLength
```
    - species
```
OntologyTerm species
```
- Class org.molgenis.omx.xgap.Clone extends ObservationTarget implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - chromosome
```
Chromosome chromosome
```
    - cM
```
Double cM
```
    - bpStart
```
Long bpStart
```
    - bpEnd
```
Long bpEnd
```
    - seq
```
String seq
```
    - symbol
```
String symbol
```
- Class org.molgenis.omx.xgap.DerivedTrait extends ObservationTarget implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.molgenis.omx.xgap.EnvironmentalFactor extends ObservationTarget implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.molgenis.omx.xgap.Gene extends ObservationTarget implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - chromosome
```
Chromosome chromosome
```
    - cM
```
Double cM
```
    - bpStart
```
Long bpStart
```
    - bpEnd
```
Long bpEnd
```
    - seq
```
String seq
```
    - symbol
```
String symbol
```
    - orientation
```
String orientation
```
    - orientation_label
```
String orientation_label
```
    - control
```
Boolean control
```
- Class org.molgenis.omx.xgap.Marker extends ObservationTarget implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - chromosome
```
Chromosome chromosome
```
    - cM
```
Double cM
```
    - bpStart
```
Long bpStart
```
    - bpEnd
```
Long bpEnd
```
    - seq
```
String seq
```
    - symbol
```
String symbol
```
    - reportsFor
```
List<E> reportsFor
```
    - reportsForMarkerCollection
```
Collection<E> reportsForMarkerCollection
```
- Class org.molgenis.omx.xgap.Marker_ReportsFor extends AbstractEntity implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - autoid
```
Integer autoid
```
    - reportsFor
```
Marker reportsFor
```
    - marker
```
Marker marker
```
- Class org.molgenis.omx.xgap.MassPeak extends ObservationTarget implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - mZ
```
Double mZ
```
    - retentionTime
```
Double retentionTime
```
- Class org.molgenis.omx.xgap.Metabolite extends ObservationTarget implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - formula
```
String formula
```
    - mass
```
Double mass
```
    - structure
```
String structure
```
- Class org.molgenis.omx.xgap.NMRBin extends ObservationTarget implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.molgenis.omx.xgap.PairedSample extends ObservationTarget implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - subject1
```
Individual subject1
```
    - label1
```
OntologyTerm label1
```
    - subject2
```
Individual subject2
```
    - label2
```
OntologyTerm label2
```
- Class org.molgenis.omx.xgap.Polymorphism extends ObservationTarget implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - base
```
String base
```
    - base_label
```
String base_label
```
    - value
```
String value
```
    - polymorphismSNPCollection
```
Collection<E> polymorphismSNPCollection
```
- Class org.molgenis.omx.xgap.Probe extends ObservationTarget implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - chromosome
```
Chromosome chromosome
```
    - cM
```
Double cM
```
    - bpStart
```
Long bpStart
```
    - bpEnd
```
Long bpEnd
```
    - seq
```
String seq
```
    - symbol
```
String symbol
```
    - mismatch
```
Boolean mismatch
```
    - probeSet
```
ProbeSet probeSet
```
    - reportsFor
```
Gene reportsFor
```
- Class org.molgenis.omx.xgap.ProbeSet extends ObservationTarget implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - chromosome
```
Chromosome chromosome
```
    - cM
```
Double cM
```
    - bpStart
```
Long bpStart
```
    - bpEnd
```
Long bpEnd
```
    - seq
```
String seq
```
    - symbol
```
String symbol
```
- Class org.molgenis.omx.xgap.Protein extends ObservationTarget implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - gene
```
Gene gene
```
    - transcript
```
Transcript transcript
```
    - aminoSequence
```
String aminoSequence
```
    - mass
```
Double mass
```
- Class org.molgenis.omx.xgap.Sample extends ObservationTarget implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - individual
```
Individual individual
```
    - tissue
```
OntologyTerm tissue
```
- Class org.molgenis.omx.xgap.SNP extends Marker implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - status
```
String status
```
    - polymorphism
```
List<E> polymorphism
```
- Class org.molgenis.omx.xgap.SNP_Polymorphism extends AbstractEntity implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - autoid
```
Integer autoid
```
    - polymorphism
```
Polymorphism polymorphism
```
    - sNP
```
SNP sNP
```
- Class org.molgenis.omx.xgap.Spot extends Probe implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - x
```
Integer x
```
    - y
```
Integer y
```
    - gridX
```
Integer gridX
```
    - gridY
```
Integer gridY
```
- Class org.molgenis.omx.xgap.Track extends Characteristic implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.molgenis.omx.xgap.Transcript extends ObservationTarget implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - gene
```
Gene gene
```
- Class org.molgenis.omx.xgap.Variant extends ObservationTarget implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - chromosome
```
Chromosome chromosome
```
    - cM
```
Double cM
```
    - bpStart
```
Long bpStart
```
    - bpEnd
```
Long bpEnd
```
    - seq
```
String seq
```
    - symbol
```
String symbol
```
    - mutationPosition
```
Integer mutationPosition
```
    - cdnaPosition
```
Integer cdnaPosition
```
    - aaPosition
```
Integer aaPosition
```
    - variantLength
```
Integer variantLength
```
    - event
```
String event
```
    - ntChange
```
String ntChange
```
    - codonchange
```
String codonchange
```
    - cdnaNotation
```
String cdnaNotation
```
    - gdnaNotation
```
String gdnaNotation
```
    - aaNotation
```
String aaNotation
```
    - exon
```
String exon
```
    - consequence
```
String consequence
```
    - inheritance
```
String inheritance
```
    - reportedSNP
```
Boolean reportedSNP
```
    - effectOnSplicing
```
Boolean effectOnSplicing
```
    - pathogenicity
```
String pathogenicity
```
    - gene
```
String gene
```
    - idMutation
```
Integer idMutation
```
    - detailsForMutation
```
String detailsForMutation
```
    - track
```
Track track
```

Serialized Form

Package org.molgenis

Class org.molgenis.JDBCMetaDatabase extends Model implements Serializable

Class org.molgenis.MolgenisOptions extends Object implements Serializable

Serialized Fields

molgenis_properties

model_database

import_model_database

output_dir

output_src

output_hand

output_sql

output_doc

output_web

decorator_overriders

db_filepath

object_relational_mapping

generate_persistence

generate_jpa

jpa_use_sequence

generate_db

exclude_system

generate_doc

generate_entityio

generate_tests

generate_model

delete_generated_folder

authorizable

disable_decorators

block_webspiders

generate_jpa_repository_source

path

Package org.molgenis.omx.das.impl

Class org.molgenis.omx.das.impl.MolgenisDasTarget extends uk.ac.ebi.mydas.model.DasTarget implements Serializable

Package org.molgenis.omx.patient

Class org.molgenis.omx.patient.Patient extends Individual implements Serializable

Serialized Fields

allele1

allele2

pheno

pubMedID

reference

Package org.molgenis.omx.xgap

Class org.molgenis.omx.xgap.Chromosome extends ObservationTarget implements Serializable

Serialized Fields

orderNr

isAutosomal

bpLength

species

Class org.molgenis.omx.xgap.Clone extends ObservationTarget implements Serializable

Serialized Fields

chromosome

cM

bpStart

bpEnd

seq

symbol

Class org.molgenis.omx.xgap.DerivedTrait extends ObservationTarget implements Serializable

Class org.molgenis.omx.xgap.EnvironmentalFactor extends ObservationTarget implements Serializable

Class org.molgenis.omx.xgap.Gene extends ObservationTarget implements Serializable

Serialized Fields

chromosome

cM

bpStart

bpEnd

seq

symbol

orientation

orientation_label

control

Class org.molgenis.omx.xgap.Marker extends ObservationTarget implements Serializable

Serialized Fields

chromosome

cM

bpStart

bpEnd

seq

symbol

reportsFor

reportsForMarkerCollection