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extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Annotationtype.java

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Rev	Date	Author	Line
1610	23 Apr 12	nicklas	1	package net.sf.basedb.reggie.dao;
1610	23 Apr 12	nicklas	2
1610	23 Apr 12	nicklas	3	import java.lang.reflect.Field;
1610	23 Apr 12	nicklas	4	import java.util.ArrayList;
1610	23 Apr 12	nicklas	5	import java.util.Collections;
5792	16 Dec 19	nicklas	6	import java.util.HashMap;
1610	23 Apr 12	nicklas	7	import java.util.List;
5792	16 Dec 19	nicklas	8	import java.util.Map;
3942	16 May 16	nicklas	9	import java.util.Set;
1610	23 Apr 12	nicklas	10
1610	23 Apr 12	nicklas	11	import org.json.simple.JSONObject;
1610	23 Apr 12	nicklas	12
1610	23 Apr 12	nicklas	13	import net.sf.basedb.core.Annotatable;
3571	30 Oct 15	nicklas	14	import net.sf.basedb.core.Annotation;
1610	23 Apr 12	nicklas	15	import net.sf.basedb.core.AnnotationSet;
1610	23 Apr 12	nicklas	16	import net.sf.basedb.core.AnnotationType;
3618	23 Nov 15	nicklas	17	import net.sf.basedb.core.BasicItem;
1610	23 Apr 12	nicklas	18	import net.sf.basedb.core.DbControl;
1610	23 Apr 12	nicklas	19	import net.sf.basedb.core.Include;
1610	23 Apr 12	nicklas	20	import net.sf.basedb.core.InvalidDataException;
1610	23 Apr 12	nicklas	21	import net.sf.basedb.core.Item;
1610	23 Apr 12	nicklas	22	import net.sf.basedb.core.ItemNotFoundException;
1610	23 Apr 12	nicklas	23	import net.sf.basedb.core.ItemQuery;
1610	23 Apr 12	nicklas	24	import net.sf.basedb.core.Type;
1640	09 May 12	nicklas	25	import net.sf.basedb.core.query.Expression;
1610	23 Apr 12	nicklas	26	import net.sf.basedb.core.query.Expressions;
1610	23 Apr 12	nicklas	27	import net.sf.basedb.core.query.Hql;
1610	23 Apr 12	nicklas	28	import net.sf.basedb.core.query.Restrictions;
1676	31 May 12	nicklas	29	import net.sf.basedb.core.snapshot.AnnotationSnapshot;
1676	31 May 12	nicklas	30	import net.sf.basedb.core.snapshot.AnnotationTypeFilter;
1676	31 May 12	nicklas	31	import net.sf.basedb.core.snapshot.SnapshotManager;
5962	03 Jun 20	nicklas	32	import net.sf.basedb.reggie.ssp.SspModel;
3618	23 Nov 15	nicklas	33	import net.sf.basedb.util.filter.Filter;
1610	23 Apr 12	nicklas	34
1610	23 Apr 12	nicklas	35	/**
1610	23 Apr 12	nicklas	36	Used to define a annotation type items.
1610	23 Apr 12	nicklas	37
1610	23 Apr 12	nicklas	38	@author nicklas
1610	23 Apr 12	nicklas	39	@since 2.5
1610	23 Apr 12	nicklas	40	*/
1610	23 Apr 12	nicklas	41	public class Annotationtype
1610	23 Apr 12	nicklas	42	{
1610	23 Apr 12	nicklas	43
1610	23 Apr 12	nicklas	44
1610	23 Apr 12	nicklas	45	/**
1610	23 Apr 12	nicklas	46	The "PersonalNumber" annotation type, used
1610	23 Apr 12	nicklas	47	to store 12-digit personal number for biosources (Patient). The
1610	23 Apr 12	nicklas	48	number should be unique and is stored as a string.
1610	23 Apr 12	nicklas	49	*/
1610	23 Apr 12	nicklas	50	public static final Annotationtype PERSONAL_NUMBER =
2351	10 Apr 14	nicklas	51	new Annotationtype("PersonalNumber", Type.STRING, true, Item.BIOSOURCE);
1610	23 Apr 12	nicklas	52
1610	23 Apr 12	nicklas	53	/**
1610	23 Apr 12	nicklas	54	The "FamilyName" annotation type, used
1610	23 Apr 12	nicklas	55	to store the family name for biosources (Patient). It is a
1610	23 Apr 12	nicklas	56	string annotation type.
1610	23 Apr 12	nicklas	57	*/
1610	23 Apr 12	nicklas	58	public static final Annotationtype FAMILY_NAME =
2351	10 Apr 14	nicklas	59	new Annotationtype("FamilyName", Type.STRING, true, Item.BIOSOURCE);
1610	23 Apr 12	nicklas	60
1610	23 Apr 12	nicklas	61	/**
1610	23 Apr 12	nicklas	62	The "AllFirstNames" annotation type, used
1610	23 Apr 12	nicklas	63	to store the first names for biosources (Patient). It is a
1610	23 Apr 12	nicklas	64	string annotation type.
1610	23 Apr 12	nicklas	65	*/
1610	23 Apr 12	nicklas	66	public static final Annotationtype ALL_FIRST_NAMES =
2351	10 Apr 14	nicklas	67	new Annotationtype("AllFirstNames", Type.STRING, true, Item.BIOSOURCE);
1610	23 Apr 12	nicklas	68
1610	23 Apr 12	nicklas	69	/**
1610	23 Apr 12	nicklas	70	The "Gender" annotation type, used
1610	23 Apr 12	nicklas	71	to store the gender of biosources (Patient). It is an
1610	23 Apr 12	nicklas	72	enumerated string annotation type with two options: F and M.
1610	23 Apr 12	nicklas	73	*/
1610	23 Apr 12	nicklas	74	public static final Annotationtype GENDER =
2351	10 Apr 14	nicklas	75	new Annotationtype("Gender", Type.STRING, false, Item.BIOSOURCE);
1610	23 Apr 12	nicklas	76
1610	23 Apr 12	nicklas	77	/**
1610	23 Apr 12	nicklas	78	The "DateOfBirth" annotation type, used
1610	23 Apr 12	nicklas	79	to store the date of birth for biosources (Patient). It is a
1610	23 Apr 12	nicklas	80	date annotation type.
1610	23 Apr 12	nicklas	81	*/
1610	23 Apr 12	nicklas	82	public static final Annotationtype DATE_OF_BIRTH =
2351	10 Apr 14	nicklas	83	new Annotationtype("DateOfBirth", Type.DATE, false, Item.BIOSOURCE);
1610	23 Apr 12	nicklas	84
1610	23 Apr 12	nicklas	85	/**
3756	18 Feb 16	olle	86	The "RetractNaLab" annotation type, used to store a flag for
3756	18 Feb 16	olle	87	biosources (Retract or RetroNo) that the date a retract request/response
3756	18 Feb 16	olle	88	was sent/received to/from laboratory is N/A. It is a boolean annotation type.
3756	18 Feb 16	olle	89	*/
3756	18 Feb 16	olle	90	public static final Annotationtype RETRACT_NA_LAB =
3756	18 Feb 16	olle	91	new Annotationtype("RetractNaLab", Type.BOOLEAN, false, Item.BIOSOURCE);
3756	18 Feb 16	olle	92
3756	18 Feb 16	olle	93	/**
3091	15 Jan 15	olle	94	The "RetractTxLab" annotation type, used
3085	15 Jan 15	olle	95	to store the date retract request was sent to laboratory for
3085	15 Jan 15	olle	96	biosources (Retract or RetroNo). It is a date annotation type.
3085	15 Jan 15	olle	97	*/
3091	15 Jan 15	olle	98	public static final Annotationtype RETRACT_TX_LAB =
3091	15 Jan 15	olle	99	new Annotationtype("RetractTxLab", Type.DATE, false, Item.BIOSOURCE);
3085	15 Jan 15	olle	100
3085	15 Jan 15	olle	101	/**
3091	15 Jan 15	olle	102	The "RetractRxLab" annotation type, used
3085	15 Jan 15	olle	103	to store the date retract response was received from laboratory for
3085	15 Jan 15	olle	104	biosources (Retract or RetroNo). It is a date annotation type.
3085	15 Jan 15	olle	105	*/
3091	15 Jan 15	olle	106	public static final Annotationtype RETRACT_RX_LAB =
3091	15 Jan 15	olle	107	new Annotationtype("RetractRxLab", Type.DATE, false, Item.BIOSOURCE);
3085	15 Jan 15	olle	108
3085	15 Jan 15	olle	109	/**
3756	18 Feb 16	olle	110	The "RetractNaBB" annotation type, used to store a flag for
3756	18 Feb 16	olle	111	biosources (Retract or RetroNo) that the date a retract request/response
3756	18 Feb 16	olle	112	was sent/received for blood samples is N/A. It is a boolean annotation type.
3756	18 Feb 16	olle	113	*/
3756	18 Feb 16	olle	114	public static final Annotationtype RETRACT_NA_BB =
3756	18 Feb 16	olle	115	new Annotationtype("RetractNaBB", Type.BOOLEAN, false, Item.BIOSOURCE);
3756	18 Feb 16	olle	116
3756	18 Feb 16	olle	117	/**
3091	15 Jan 15	olle	118	The "RetractTxBB" annotation type, used
3085	15 Jan 15	olle	119	to store the date retract request was sent for blood samples for
3085	15 Jan 15	olle	120	biosources (Retract or RetroNo). It is a date annotation type.
3085	15 Jan 15	olle	121	*/
3091	15 Jan 15	olle	122	public static final Annotationtype RETRACT_TX_BB =
3091	15 Jan 15	olle	123	new Annotationtype("RetractTxBB", Type.DATE, false, Item.BIOSOURCE);
3085	15 Jan 15	olle	124
3085	15 Jan 15	olle	125	/**
3091	15 Jan 15	olle	126	The "RetractRxBB" annotation type, used
3085	15 Jan 15	olle	127	to store the date retract response was received for blood samples for
3085	15 Jan 15	olle	128	biosources (Retract or RetroNo). It is a date annotation type.
3085	15 Jan 15	olle	129	*/
3091	15 Jan 15	olle	130	public static final Annotationtype RETRACT_RX_BB =
3091	15 Jan 15	olle	131	new Annotationtype("RetractRxBB", Type.DATE, false, Item.BIOSOURCE);
3085	15 Jan 15	olle	132
3085	15 Jan 15	olle	133	/**
3756	18 Feb 16	olle	134	The "RetractNaFrozen" annotation type, used to store a flag for
3756	18 Feb 16	olle	135	biosources (Retract or RetroNo) that the date a retract request/response
3756	18 Feb 16	olle	136	was sent/received for frozen samples is N/A. It is a boolean annotation type.
3756	18 Feb 16	olle	137	*/
3756	18 Feb 16	olle	138	public static final Annotationtype RETRACT_NA_FROZEN =
3756	18 Feb 16	olle	139	new Annotationtype("RetractNaFrozen", Type.BOOLEAN, false, Item.BIOSOURCE);
3756	18 Feb 16	olle	140
3756	18 Feb 16	olle	141	/**
3091	15 Jan 15	olle	142	The "RetractTxFrozen" annotation type, used
3085	15 Jan 15	olle	143	to store the date retract request was sent for frozen samples for
3085	15 Jan 15	olle	144	biosources (Retract or RetroNo). It is a date annotation type.
3085	15 Jan 15	olle	145	*/
3091	15 Jan 15	olle	146	public static final Annotationtype RETRACT_TX_FROZEN =
3091	15 Jan 15	olle	147	new Annotationtype("RetractTxFrozen", Type.DATE, false, Item.BIOSOURCE);
3085	15 Jan 15	olle	148
3085	15 Jan 15	olle	149	/**
3091	15 Jan 15	olle	150	The "RetractRxFrozen" annotation type, used
3085	15 Jan 15	olle	151	to store the date retract response was received for frozen samples for
3085	15 Jan 15	olle	152	biosources (Retract or RetroNo). It is a date annotation type.
3085	15 Jan 15	olle	153	*/
3091	15 Jan 15	olle	154	public static final Annotationtype RETRACT_RX_FROZEN =
3091	15 Jan 15	olle	155	new Annotationtype("RetractRxFrozen", Type.DATE, false, Item.BIOSOURCE);
3085	15 Jan 15	olle	156
3085	15 Jan 15	olle	157	/**
3756	18 Feb 16	olle	158	The "RetractNaRccSyd" annotation type, used to store a flag for
3756	18 Feb 16	olle	159	biosources (Retract or RetroNo) that the date a retract request
3756	18 Feb 16	olle	160	was sent to RCC Syd (Regionalt cancercentrum syd) is N/A. It is a boolean annotation type.
3756	18 Feb 16	olle	161	*/
3756	18 Feb 16	olle	162	public static final Annotationtype RETRACT_NA_RCC_SYD =
3756	18 Feb 16	olle	163	new Annotationtype("RetractNaRccSyd", Type.BOOLEAN, false, Item.BIOSOURCE);
3756	18 Feb 16	olle	164
3756	18 Feb 16	olle	165	/**
3265	21 Apr 15	olle	166	The "RetractTxRccSyd" annotation type, used
3265	21 Apr 15	olle	167	to store the date retract notification was sent to RCC Syd (Regionalt cancercentrum syd)
3265	21 Apr 15	olle	168	for biosources (Retract or RetroNo). It is a date annotation type.
3265	21 Apr 15	olle	169	*/
3265	21 Apr 15	olle	170	public static final Annotationtype RETRACT_TX_RCC_SYD =
3265	21 Apr 15	olle	171	new Annotationtype("RetractTxRccSyd", Type.DATE, false, Item.BIOSOURCE);
3265	21 Apr 15	olle	172
3265	21 Apr 15	olle	173	/**
3085	15 Jan 15	olle	174	The "RetractStatus" annotation type, used for biosource item (Retract or RetroNo).
3085	15 Jan 15	olle	175	It is an enumerated string annotation type with two options: ReadyForDestruction and RetractionCompleted.
3085	15 Jan 15	olle	176	*/
3085	15 Jan 15	olle	177	public static final Annotationtype RETRACT_STATUS =
5637	03 Oct 19	nicklas	178	new Annotationtype("RetractStatus", Type.STRING, false, Item.BIOSOURCE, Item.SAMPLE, Item.EXTRACT);
3085	15 Jan 15	olle	179
3085	15 Jan 15	olle	180	/**
4512	31 May 17	nicklas	181	The "LiasonComment" annotation type, used
4512	31 May 17	nicklas	182	for comments arriving outside of regular procedure.
4512	31 May 17	nicklas	183	Used on biosource (Patient) and samples (Case, Specimen and NoSpecimen).
4512	31 May 17	nicklas	184	@since 4.9.5
4512	31 May 17	nicklas	185	*/
4512	31 May 17	nicklas	186	public static final Annotationtype LIASON_COMMENT =
4512	31 May 17	nicklas	187	new Annotationtype("LiasonComment", Type.TEXT, false, Item.BIOSOURCE, Item.SAMPLE);
4512	31 May 17	nicklas	188
4512	31 May 17	nicklas	189	/**
1610	23 Apr 12	nicklas	190	The "Laterality" annotation type, used
1610	23 Apr 12	nicklas	191	for samples (Case). It is an enumerated string annotation
1610	23 Apr 12	nicklas	192	type with two options: LEFT and RIGHT.
1610	23 Apr 12	nicklas	193	*/
1610	23 Apr 12	nicklas	194	public static final Annotationtype LATERALITY =
2351	10 Apr 14	nicklas	195	new Annotationtype("Laterality", Type.STRING, false, Item.SAMPLE);
1610	23 Apr 12	nicklas	196
1610	23 Apr 12	nicklas	197	/**
1610	23 Apr 12	nicklas	198	The "Consent" annotation type, used
1610	23 Apr 12	nicklas	199	for samples (Case and Blood). It is an enumerated string annotation
1610	23 Apr 12	nicklas	200	type with three options: Yes, No and Not asked
1610	23 Apr 12	nicklas	201	*/
1610	23 Apr 12	nicklas	202	public static final Annotationtype CONSENT =
2351	10 Apr 14	nicklas	203	new Annotationtype("Consent", Type.STRING, false, Item.SAMPLE);
1610	23 Apr 12	nicklas	204
1610	23 Apr 12	nicklas	205	/**
1610	23 Apr 12	nicklas	206	The "ConsentDate" annotation type, used
1610	23 Apr 12	nicklas	207	for samples (Case). It is a date annotation.
1610	23 Apr 12	nicklas	208	*/
1610	23 Apr 12	nicklas	209	public static final Annotationtype CONSENT_DATE =
2351	10 Apr 14	nicklas	210	new Annotationtype("ConsentDate", Type.DATE, false, Item.SAMPLE);
1610	23 Apr 12	nicklas	211
1610	23 Apr 12	nicklas	212	/**
4458	21 Apr 17	nicklas	213	The "ReferenceDate" annotation type, used
4458	21 Apr 17	nicklas	214	for samples (Case). It is a date annotation.
4458	21 Apr 17	nicklas	215	@since 4.10
4458	21 Apr 17	nicklas	216	*/
4458	21 Apr 17	nicklas	217	public static final Annotationtype REFERENCE_DATE =
4458	21 Apr 17	nicklas	218	new Annotationtype("ReferenceDate", Type.DATE, false, Item.SAMPLE);
4458	21 Apr 17	nicklas	219
4458	21 Apr 17	nicklas	220	/**
4458	21 Apr 17	nicklas	221	The "ReferenceDateSource" annotation type, used
4458	21 Apr 17	nicklas	222	for samples (Case). It is a string enumeration
4458	21 Apr 17	nicklas	223	describing the source of the ReferenceDate annotation.
4458	21 Apr 17	nicklas	224	@see ReferenceDateSource
4458	21 Apr 17	nicklas	225	@since 4.10
4458	21 Apr 17	nicklas	226	*/
4458	21 Apr 17	nicklas	227	public static final Annotationtype REFERENCE_DATE_SOURCE =
4458	21 Apr 17	nicklas	228	new Annotationtype("ReferenceDateSource", Type.STRING, false, Item.SAMPLE);
4458	21 Apr 17	nicklas	229
4458	21 Apr 17	nicklas	230	/**
6098	11 Jan 21	nicklas	231	The "LinkedCase" annotation type, used
6098	11 Jan 21	nicklas	232	for samples (Case). It is an Integer annotation.
6098	11 Jan 21	nicklas	233	@since 4.30
6098	11 Jan 21	nicklas	234	*/
6098	11 Jan 21	nicklas	235	public static final Annotationtype LINKED_CASE =
6098	11 Jan 21	nicklas	236	new Annotationtype("LinkedCase", Type.INT, false, Item.SAMPLE);
6098	11 Jan 21	nicklas	237
6098	11 Jan 21	nicklas	238	/**
3484	14 Sep 15	nicklas	239	The "FrozenTissueDate" annotation type, used
3484	14 Sep 15	nicklas	240	for samples (Case). It is a date annotation.
3484	14 Sep 15	nicklas	241	@since 3.6
3484	14 Sep 15	nicklas	242	*/
3484	14 Sep 15	nicklas	243	public static final Annotationtype FROZEN_TISSUE_DATE =
3484	14 Sep 15	nicklas	244	new Annotationtype("FrozenTissueDate", Type.DATE, false, Item.SAMPLE);
3484	14 Sep 15	nicklas	245
3786	17 Mar 16	olle	246	/**
3786	17 Mar 16	olle	247	The "IncaExportDate" annotation type, used for samples (Case).
3786	17 Mar 16	olle	248	It stores the date for the INCA export that was last imported for a case.
3786	17 Mar 16	olle	249	It is a date annotation type.
3786	17 Mar 16	olle	250	*/
3786	17 Mar 16	olle	251	public static final Annotationtype INCA_EXPORT_DATE =
3786	17 Mar 16	olle	252	new Annotationtype("IncaExportDate", Type.DATE, false, Item.SAMPLE);
3786	17 Mar 16	olle	253
3786	17 Mar 16	olle	254	/**
3786	17 Mar 16	olle	255	The "IncaImportDate" annotation type, used for samples (Case).
3786	17 Mar 16	olle	256	It stores the date the last INCA import was performed for a case.
3786	17 Mar 16	olle	257	It is a date annotation type.
3786	17 Mar 16	olle	258	*/
3786	17 Mar 16	olle	259	public static final Annotationtype INCA_IMPORT_DATE =
3786	17 Mar 16	olle	260	new Annotationtype("IncaImportDate", Type.DATE, false, Item.SAMPLE);
3484	14 Sep 15	nicklas	261
3484	14 Sep 15	nicklas	262	/**
1610	23 Apr 12	nicklas	263	The "BloodSamplingDateTime" annotation, used
1610	23 Apr 12	nicklas	264	for samples (Blood). It is a timestamp annotation.
1610	23 Apr 12	nicklas	265	*/
1610	23 Apr 12	nicklas	266	public static final Annotationtype BLOOD_SAMPLING_DATETIME =
2351	10 Apr 14	nicklas	267	new Annotationtype("BloodSamplingDateTime", Type.TIMESTAMP, false, Item.SAMPLE);
1610	23 Apr 12	nicklas	268
1610	23 Apr 12	nicklas	269	/**
1610	23 Apr 12	nicklas	270	The "BloodFreezerDateTime" annotation, used
1610	23 Apr 12	nicklas	271	for samples (Blood). It is a timestamp annotation.
1610	23 Apr 12	nicklas	272	*/
1610	23 Apr 12	nicklas	273	public static final Annotationtype BLOOD_FREEZER_DATETIME =
2351	10 Apr 14	nicklas	274	new Annotationtype("BloodFreezerDateTime", Type.TIMESTAMP, false, Item.SAMPLE);
1610	23 Apr 12	nicklas	275
1610	23 Apr 12	nicklas	276	/**
1610	23 Apr 12	nicklas	277	The "BloodSerum" annotation, used
1610	23 Apr 12	nicklas	278	for samples (Blood). It is an enumerated string annotation with
1610	23 Apr 12	nicklas	279	Yes and No as options.
1610	23 Apr 12	nicklas	280	*/
1610	23 Apr 12	nicklas	281	public static final Annotationtype BLOOD_SERUM =
2351	10 Apr 14	nicklas	282	new Annotationtype("BloodSerum", Type.STRING, false, Item.SAMPLE);
1610	23 Apr 12	nicklas	283
1610	23 Apr 12	nicklas	284	/**
1614	24 Apr 12	nicklas	285	The "BloodSample" annotation, used for samples (Blood). It
1614	24 Apr 12	nicklas	286	is an enumerated string annotation with options:
2023	19 Sep 13	olle	287	PreNeo, PreOp, FollowUp06, FollowUp12, FollowUp36
1614	24 Apr 12	nicklas	288	*/
1614	24 Apr 12	nicklas	289	public static final Annotationtype BLOOD_SAMPLE =
2351	10 Apr 14	nicklas	290	new Annotationtype("BloodSample", Type.STRING, false, Item.SAMPLE);
1614	24 Apr 12	nicklas	291
1614	24 Apr 12	nicklas	292	/**
2023	19 Sep 13	olle	293	The "BloodRccidNumber" annotation, used for follow-up samples (Blood). It
2023	19 Sep 13	olle	294	is a string annotation.
2023	19 Sep 13	olle	295	*/
2023	19 Sep 13	olle	296	public static final Annotationtype BLOOD_RCCIDNUMBER =
2351	10 Apr 14	nicklas	297	new Annotationtype("BloodRccidNumber", Type.STRING, false, Item.SAMPLE);
2023	19 Sep 13	olle	298
2023	19 Sep 13	olle	299	/**
6277	03 Jun 21	nicklas	300	The "BD47_ID" annotation, used for samples that end up in
6277	03 Jun 21	nicklas	301	the biobank. This annotation store the ID that the biobank
6277	03 Jun 21	nicklas	302	is using for the sample.
6277	03 Jun 21	nicklas	303	@since 4.31.2
6277	03 Jun 21	nicklas	304	*/
6277	03 Jun 21	nicklas	305	public static final Annotationtype BD47_ID =
6277	03 Jun 21	nicklas	306	new Annotationtype("BD47_ID", Type.STRING, false, Item.SAMPLE);
6277	03 Jun 21	nicklas	307
6277	03 Jun 21	nicklas	308
6277	03 Jun 21	nicklas	309	/**
1610	23 Apr 12	nicklas	310	The "ReasonIfNoSpecimen" annotation type, used
1610	23 Apr 12	nicklas	311	for samples (NoSpecimen). It is a string annotation.
1610	23 Apr 12	nicklas	312	*/
1610	23 Apr 12	nicklas	313	public static final Annotationtype REASON_IF_NO_SPECIMEN =
2351	10 Apr 14	nicklas	314	new Annotationtype("ReasonIfNoSpecimen", Type.STRING, false, Item.SAMPLE);
1610	23 Apr 12	nicklas	315
1610	23 Apr 12	nicklas	316	/**
6574	08 Feb 22	nicklas	317	The "ExternalSpecimenExists" annotation type, used
6574	08 Feb 22	nicklas	318	for samples (NoSpecimen). It is a string annotation.
6574	08 Feb 22	nicklas	319	@since 4.36
6574	08 Feb 22	nicklas	320	*/
6574	08 Feb 22	nicklas	321	public static final Annotationtype EXTERNAL_SPECIMEN_EXISTS =
6574	08 Feb 22	nicklas	322	new Annotationtype("ExternalSpecimenExists", Type.STRING, false, Item.SAMPLE);
6574	08 Feb 22	nicklas	323
6711	27 Apr 22	nicklas	324	/**
6918	01 Dec 22	nicklas	325	The "ExternalStorage" annotation type, used for samples and extracts
6918	01 Dec 22	nicklas	326	that are or have been stored at an external location where we don't
6918	01 Dec 22	nicklas	327	have exact information.
6918	01 Dec 22	nicklas	328	@since 4.41
6918	01 Dec 22	nicklas	329	*/
6918	01 Dec 22	nicklas	330	public static final Annotationtype EXTERNAL_STORAGE =
6918	01 Dec 22	nicklas	331	new Annotationtype("ExternalStorage", Type.STRING, false, Item.SAMPLE, Item.EXTRACT);
6918	01 Dec 22	nicklas	332
6918	01 Dec 22	nicklas	333	/**
6711	27 Apr 22	nicklas	334	The "TubeLabel" annotation type, which is used if the storage
6711	27 Apr 22	nicklas	335	tubes have a text that is different from the name of the item.
6711	27 Apr 22	nicklas	336	Typically used for Specimen, Lysate, RNA, DNA and FlowThrough
6711	27 Apr 22	nicklas	337	that has been externally handled before being delivered to SCAN-B.
6711	27 Apr 22	nicklas	338	@since 4.39
6711	27 Apr 22	nicklas	339	*/
6711	27 Apr 22	nicklas	340	public static final Annotationtype TUBE_LABEL =
6711	27 Apr 22	nicklas	341	new Annotationtype("TubeLabel", Type.STRING, false, Item.SAMPLE, Item.EXTRACT);
6574	08 Feb 22	nicklas	342
6574	08 Feb 22	nicklas	343	/**
1610	23 Apr 12	nicklas	344	The "PAD" annotation type, used
1610	23 Apr 12	nicklas	345	for samples (Specimen). It is a string annotation type.
1610	23 Apr 12	nicklas	346	*/
1610	23 Apr 12	nicklas	347	public static final Annotationtype PAD =
2351	10 Apr 14	nicklas	348	new Annotationtype("PAD", Type.STRING, true, Item.SAMPLE);
1610	23 Apr 12	nicklas	349
1610	23 Apr 12	nicklas	350	/**
6990	19 Jan 23	nicklas	351	The "AlternatePAD" annotation type, used
6990	19 Jan 23	nicklas	352	for samples (Specimen). It is a string annotation type.
6990	19 Jan 23	nicklas	353	@since 4.43
6990	19 Jan 23	nicklas	354	*/
6990	19 Jan 23	nicklas	355	public static final Annotationtype ALTERNATE_PAD =
6990	19 Jan 23	nicklas	356	new Annotationtype("AlternatePAD", Type.STRING, true, Item.SAMPLE);
6990	19 Jan 23	nicklas	357
6990	19 Jan 23	nicklas	358	/**
1610	23 Apr 12	nicklas	359	The "OtherPathNote" annotation type,
1610	23 Apr 12	nicklas	360	used for samples (Specimen). It is a string annotation type.
1610	23 Apr 12	nicklas	361	*/
1610	23 Apr 12	nicklas	362	public static final Annotationtype OTHER_PATH_NOTE =
2351	10 Apr 14	nicklas	363	new Annotationtype("OtherPathNote", Type.STRING, false, Item.SAMPLE);
1610	23 Apr 12	nicklas	364
1610	23 Apr 12	nicklas	365	/**
1610	23 Apr 12	nicklas	366	The "SamplingDateTime" annotation type, used
1610	23 Apr 12	nicklas	367	for samples (Specimen and NoSpecimen). It is a timestamp annotation.
1610	23 Apr 12	nicklas	368	*/
1610	23 Apr 12	nicklas	369	public static final Annotationtype SAMPLING_DATETIME =
2351	10 Apr 14	nicklas	370	new Annotationtype("SamplingDateTime", Type.TIMESTAMP, false, Item.SAMPLE);
1610	23 Apr 12	nicklas	371
1610	23 Apr 12	nicklas	372	/**
1610	23 Apr 12	nicklas	373	The "RNALaterDateTime" annotation type, used
1610	23 Apr 12	nicklas	374	for samples (Specimen). It is a timestamp annotation.
1610	23 Apr 12	nicklas	375	*/
1610	23 Apr 12	nicklas	376	public static final Annotationtype RNALATER_DATETIME =
2351	10 Apr 14	nicklas	377	new Annotationtype("RNALaterDateTime", Type.TIMESTAMP, false, Item.SAMPLE);
1610	23 Apr 12	nicklas	378
1610	23 Apr 12	nicklas	379	/**
1610	23 Apr 12	nicklas	380	The "ArrivalDate" annotation type, used
1610	23 Apr 12	nicklas	381	for samples (Specimen). It is a timestamp annotation.
1610	23 Apr 12	nicklas	382	*/
1610	23 Apr 12	nicklas	383	public static final Annotationtype ARRIVAL_DATE =
2351	10 Apr 14	nicklas	384	new Annotationtype("ArrivalDate", Type.DATE, false, Item.SAMPLE);
1610	23 Apr 12	nicklas	385
1610	23 Apr 12	nicklas	386	/**
1610	23 Apr 12	nicklas	387	The "NofDeliveredTubes" annotation type, used
1610	23 Apr 12	nicklas	388	for samples (Specimen). It is an Integer annotation type.
1610	23 Apr 12	nicklas	389	*/
1610	23 Apr 12	nicklas	390	public static final Annotationtype NOF_DELIVERED_TUBES =
2351	10 Apr 14	nicklas	391	new Annotationtype("NofDeliveredTubes", Type.INT, false, Item.SAMPLE);
1610	23 Apr 12	nicklas	392
1610	23 Apr 12	nicklas	393	/**
1610	23 Apr 12	nicklas	394	The "OperatorDeliveryComment" annotation type, used
1610	23 Apr 12	nicklas	395	for samples (Specimen). It is a String annotation type.
1610	23 Apr 12	nicklas	396	*/
1610	23 Apr 12	nicklas	397	public static final Annotationtype OPERATOR_DELIVERY_COMMENT =
2351	10 Apr 14	nicklas	398	new Annotationtype("OperatorDeliveryComment", Type.STRING, false, Item.SAMPLE);
1610	23 Apr 12	nicklas	399
1610	23 Apr 12	nicklas	400	/**
1610	23 Apr 12	nicklas	401	The "SpecimenType" annotation type, used for
1610	23 Apr 12	nicklas	402	samples (Specimen). It is a String enumeration annotation.
1610	23 Apr 12	nicklas	403	*/
1610	23 Apr 12	nicklas	404	public static final Annotationtype SPECIMEN_TYPE =
2351	10 Apr 14	nicklas	405	new Annotationtype("SpecimenType", Type.STRING, false, Item.SAMPLE);
1610	23 Apr 12	nicklas	406
1610	23 Apr 12	nicklas	407	/**
1610	23 Apr 12	nicklas	408	The "BiopsyType" annotation type, used for
1610	23 Apr 12	nicklas	409	samples (Specimen). It is a String enumeration annotation.
1610	23 Apr 12	nicklas	410	*/
1610	23 Apr 12	nicklas	411	public static final Annotationtype BIOPSY_TYPE =
2351	10 Apr 14	nicklas	412	new Annotationtype("BiopsyType", Type.STRING, false, Item.SAMPLE);
1610	23 Apr 12	nicklas	413
1610	23 Apr 12	nicklas	414	/**
3602	16 Nov 15	nicklas	415	The "YellowLabel" annotation type, used
3602	16 Nov 15	nicklas	416	for samples (Specimen). It is a String enumeration annotation type.
3602	16 Nov 15	nicklas	417	@since 4.0
3602	16 Nov 15	nicklas	418	*/
3602	16 Nov 15	nicklas	419	public static final Annotationtype YELLOW_LABEL =
3602	16 Nov 15	nicklas	420	new Annotationtype("YellowLabel", Type.STRING, false, Item.SAMPLE);
3602	16 Nov 15	nicklas	421
3784	16 Mar 16	nicklas	422	/**
3784	16 Mar 16	nicklas	423	The "CompletedDate" annotation type, used
3784	16 Mar 16	nicklas	424	for samples (Specimen) that are also YellowLabel.
3784	16 Mar 16	nicklas	425	It is a date annotation that when set indicates the date the
3784	16 Mar 16	nicklas	426	processing of the specimen has been completed.
3784	16 Mar 16	nicklas	427	@since 4.3
3784	16 Mar 16	nicklas	428	*/
3784	16 Mar 16	nicklas	429	public static final Annotationtype COMPLETED_DATE =
3784	16 Mar 16	nicklas	430	new Annotationtype("CompletedDate", Type.DATE, false, Item.SAMPLE);
3602	16 Nov 15	nicklas	431
3602	16 Nov 15	nicklas	432	/**
1610	23 Apr 12	nicklas	433	The "NofPieces" annotation type, used for
1610	23 Apr 12	nicklas	434	samples (Specimen). It is a Integer annotation type.
1610	23 Apr 12	nicklas	435	*/
1610	23 Apr 12	nicklas	436	public static final Annotationtype NOF_PIECES =
2351	10 Apr 14	nicklas	437	new Annotationtype("NofPieces", Type.INT, false, Item.SAMPLE);
1610	23 Apr 12	nicklas	438
1610	23 Apr 12	nicklas	439	/**
3145	25 Feb 15	nicklas	440	The "OperatorPartitionComment" annotation type, used
1610	23 Apr 12	nicklas	441	for samples (Specimen). It s a String annotation type.
1610	23 Apr 12	nicklas	442	*/
1610	23 Apr 12	nicklas	443	public static final Annotationtype OPERATOR_PARTITION_COMMENT =
2351	10 Apr 14	nicklas	444	new Annotationtype("OperatorPartitionComment", Type.STRING, false, Item.SAMPLE);
3394	12 Jun 15	nicklas	445
3394	12 Jun 15	nicklas	446	/**
3394	12 Jun 15	nicklas	447	The "LinkedSpecimen" annotation type, used for
3394	12 Jun 15	nicklas	448	samples (Specimen/NoSpecimen). It is a String enumeration annotation.
3394	12 Jun 15	nicklas	449	@since 3.5
3394	12 Jun 15	nicklas	450	*/
3394	12 Jun 15	nicklas	451	public static final Annotationtype LINKED_SPECIMEN =
3394	12 Jun 15	nicklas	452	new Annotationtype("LinkedSpecimen", Type.STRING, false, Item.SAMPLE);
3394	12 Jun 15	nicklas	453
5774	04 Dec 19	nicklas	454	/**
5774	04 Dec 19	nicklas	455	Name of TMA block were a TMASpecimen is located.
5774	04 Dec 19	nicklas	456	@since 4.25
5774	04 Dec 19	nicklas	457	*/
5774	04 Dec 19	nicklas	458	public static final Annotationtype TMA_BLOCK =
5774	04 Dec 19	nicklas	459	new Annotationtype("TMABlock", Type.STRING, false, Item.SAMPLE);
1610	23 Apr 12	nicklas	460
1610	23 Apr 12	nicklas	461	/**
5774	04 Dec 19	nicklas	462	Position on TMA block were a TMASpecimen is located.
5774	04 Dec 19	nicklas	463	@since 4.25
5774	04 Dec 19	nicklas	464	*/
5774	04 Dec 19	nicklas	465	public static final Annotationtype TMA_BLOCK_POS =
5774	04 Dec 19	nicklas	466	new Annotationtype("TMABlockPos", Type.STRING, false, Item.SAMPLE);
5799	18 Dec 19	nicklas	467
5774	04 Dec 19	nicklas	468	/**
5799	18 Dec 19	nicklas	469	PAD that was requested when creating a TMA. The actually
5799	18 Dec 19	nicklas	470	used PAD may be different in case the requested one is not
5799	18 Dec 19	nicklas	471	available. Used on TMASpecimen items.
5799	18 Dec 19	nicklas	472	@since 4.25
5799	18 Dec 19	nicklas	473	*/
5799	18 Dec 19	nicklas	474	public static final Annotationtype PAD_REQUESTED =
5799	18 Dec 19	nicklas	475	new Annotationtype("PADRequested", Type.STRING, true, Item.SAMPLE);
5799	18 Dec 19	nicklas	476
5799	18 Dec 19	nicklas	477	/**
5798	18 Dec 19	nicklas	478	Annotation to be used on samples/extracts that are
5798	18 Dec 19	nicklas	479	"owned" by an external partner. First use case is
5798	18 Dec 19	nicklas	480	TMA specimen, but could be used for other external
5798	18 Dec 19	nicklas	481	items as well.
5798	18 Dec 19	nicklas	482	@since 4.25
5798	18 Dec 19	nicklas	483	*/
5798	18 Dec 19	nicklas	484	public static final Annotationtype SAMPLE_OWNER =
5798	18 Dec 19	nicklas	485	new Annotationtype("SampleOwner", Type.STRING, false, Item.SAMPLE, Item.EXTRACT);
5798	18 Dec 19	nicklas	486
5798	18 Dec 19	nicklas	487	/**
1610	23 Apr 12	nicklas	488	The "Partition date" annotation type, used for
1610	23 Apr 12	nicklas	489	samples (Histology) and extracts (Lysate). It is a date annotation type.
1610	23 Apr 12	nicklas	490	*/
1610	23 Apr 12	nicklas	491	public static final Annotationtype PARTITION_DATE =
2351	10 Apr 14	nicklas	492	new Annotationtype("PartitionDate", Type.DATE, false, Item.SAMPLE, Item.EXTRACT);
1610	23 Apr 12	nicklas	493
1610	23 Apr 12	nicklas	494	/**
1693	08 Jun 12	nicklas	495	The "MultPieces" annotation, used for samples (Lysate). It is a
1693	08 Jun 12	nicklas	496	boolean annotation type.
1693	08 Jun 12	nicklas	497	@since 2.7
1693	08 Jun 12	nicklas	498	*/
1693	08 Jun 12	nicklas	499	public static final Annotationtype MULTIPLE_PIECES =
2351	10 Apr 14	nicklas	500	new Annotationtype("MultPieces", Type.BOOLEAN, false, Item.EXTRACT);
1693	08 Jun 12	nicklas	501
1693	08 Jun 12	nicklas	502	/**
2371	23 Apr 14	nicklas	503	The "EmbedDate" annotation type, used for histology
2371	23 Apr 14	nicklas	504	work lists. It is a date annotation type.
2371	23 Apr 14	nicklas	505	@since 2.16
2371	23 Apr 14	nicklas	506	*/
2371	23 Apr 14	nicklas	507	public static final Annotationtype EMBED_DATE =
3247	14 Apr 15	nicklas	508	new Annotationtype("EmbedDate", Type.DATE, false, Item.ITEMLIST);
2371	23 Apr 14	nicklas	509
2371	23 Apr 14	nicklas	510	/**
1668	25 May 12	nicklas	511	The "GoodStain" annotation type, used for samples
1668	25 May 12	nicklas	512	(Stained). It is a boolean annotation type.
1668	25 May 12	nicklas	513	@since 2.7
1668	25 May 12	nicklas	514	*/
1668	25 May 12	nicklas	515	public static final Annotationtype GOOD_STAIN =
2351	10 Apr 14	nicklas	516	new Annotationtype("GoodStain", Type.BOOLEAN, false, Item.SAMPLE);
2134	11 Nov 13	nicklas	517
3121	06 Feb 15	nicklas	518	/**
3121	06 Feb 15	nicklas	519	The "IHC" annotation type, used for bioplates (HE glass) to indicate the
3121	06 Feb 15	nicklas	520	type of staining. It is a string enumeration annotation type.
3121	06 Feb 15	nicklas	521	@since 3.1
3121	06 Feb 15	nicklas	522	*/
3121	06 Feb 15	nicklas	523	public static final Annotationtype IHC =
3121	06 Feb 15	nicklas	524	new Annotationtype("IHC", Type.STRING, false, Item.BIOPLATE);
3169	06 Mar 15	nicklas	525
3169	06 Mar 15	nicklas	526	/**
3169	06 Mar 15	nicklas	527	The "IHCQuality" annotation type, used for samples
3169	06 Mar 15	nicklas	528	(Stained). It is a string (enumeration) annotation type.
3169	06 Mar 15	nicklas	529	@since 3.2
3169	06 Mar 15	nicklas	530	*/
3169	06 Mar 15	nicklas	531	public static final Annotationtype IHC_QUALITY =
3169	06 Mar 15	nicklas	532	new Annotationtype("IHCQuality", Type.STRING, false, Item.SAMPLE);
1668	25 May 12	nicklas	533
1668	25 May 12	nicklas	534	/**
2134	11 Nov 13	nicklas	535	The "ScoreComplete" annotation type, used for histology samples
2134	11 Nov 13	nicklas	536	(Stained) and bioplates (HE glass). It is a boolean annotation type.
2134	11 Nov 13	nicklas	537	@since 2.14
2134	11 Nov 13	nicklas	538	*/
2134	11 Nov 13	nicklas	539	public static final Annotationtype SCORE_COMPLETE =
2351	10 Apr 14	nicklas	540	new Annotationtype("ScoreComplete", Type.BOOLEAN, false, Item.SAMPLE, Item.BIOPLATE);
2134	11 Nov 13	nicklas	541
2134	11 Nov 13	nicklas	542
2134	11 Nov 13	nicklas	543	/**
2134	11 Nov 13	nicklas	544	The "ScoreInvasiveCancer" annotation type, used for histology samples
2134	11 Nov 13	nicklas	545	(Stained). It is an integer annotation type.
2134	11 Nov 13	nicklas	546	@since 2.14
2134	11 Nov 13	nicklas	547	*/
2134	11 Nov 13	nicklas	548	public static final Annotationtype SCORE_INVASIVE_CANCER =
2351	10 Apr 14	nicklas	549	new Annotationtype("ScoreInvasiveCancer", Type.INT, false, Item.SAMPLE);
2134	11 Nov 13	nicklas	550
2134	11 Nov 13	nicklas	551	/**
2134	11 Nov 13	nicklas	552	The "ScoreInsituCancer" annotation type, used for histology samples
2134	11 Nov 13	nicklas	553	(Stained). It is an integer annotation type.
2134	11 Nov 13	nicklas	554	@since 2.14
2134	11 Nov 13	nicklas	555	*/
2134	11 Nov 13	nicklas	556	public static final Annotationtype SCORE_INSITU_CANCER =
2351	10 Apr 14	nicklas	557	new Annotationtype("ScoreInsituCancer", Type.INT, false, Item.SAMPLE);
2134	11 Nov 13	nicklas	558
2134	11 Nov 13	nicklas	559	/**
2134	11 Nov 13	nicklas	560	The "ScoreLymphocytes" annotation type, used for histology samples
2134	11 Nov 13	nicklas	561	(Stained). It is an integer annotation type.
2134	11 Nov 13	nicklas	562	@since 2.14
2134	11 Nov 13	nicklas	563	*/
2134	11 Nov 13	nicklas	564	public static final Annotationtype SCORE_LYMPHOCYTES =
2351	10 Apr 14	nicklas	565	new Annotationtype("ScoreLymphocytes", Type.INT, false, Item.SAMPLE);
2134	11 Nov 13	nicklas	566
2134	11 Nov 13	nicklas	567	/**
2134	11 Nov 13	nicklas	568	The "ScoreNormal" annotation type, used for histology samples
2134	11 Nov 13	nicklas	569	(Stained). It is an integer annotation type.
2134	11 Nov 13	nicklas	570	@since 2.14
2134	11 Nov 13	nicklas	571	*/
2134	11 Nov 13	nicklas	572	public static final Annotationtype SCORE_NORMAL =
2351	10 Apr 14	nicklas	573	new Annotationtype("ScoreNormal", Type.INT, false, Item.SAMPLE);
2134	11 Nov 13	nicklas	574
2134	11 Nov 13	nicklas	575	/**
2134	11 Nov 13	nicklas	576	The "ScoreStroma" annotation type, used for histology samples
2134	11 Nov 13	nicklas	577	(Stained). It is an integer annotation type.
2134	11 Nov 13	nicklas	578	@since 2.14
2134	11 Nov 13	nicklas	579	*/
2134	11 Nov 13	nicklas	580	public static final Annotationtype SCORE_STROMA =
2351	10 Apr 14	nicklas	581	new Annotationtype("ScoreStroma", Type.INT, false, Item.SAMPLE);
2134	11 Nov 13	nicklas	582
2134	11 Nov 13	nicklas	583	/**
2134	11 Nov 13	nicklas	584	The "ScoreFat" annotation type, used for histology samples
2134	11 Nov 13	nicklas	585	(Stained). It is an integer annotation type.
2134	11 Nov 13	nicklas	586	@since 2.14
2134	11 Nov 13	nicklas	587	*/
2134	11 Nov 13	nicklas	588	public static final Annotationtype SCORE_FAT =
2351	10 Apr 14	nicklas	589	new Annotationtype("ScoreFat", Type.INT, false, Item.SAMPLE);
2134	11 Nov 13	nicklas	590
2134	11 Nov 13	nicklas	591	/**
3469	27 Aug 15	nicklas	592	The "ReservedBy" annotation type, used for extracts (Lysate)
3469	27 Aug 15	nicklas	593	to indicate that it has been selected for processing.
3469	27 Aug 15	nicklas	594	@since 3.5
3469	27 Aug 15	nicklas	595	*/
3469	27 Aug 15	nicklas	596	public static final Annotationtype RESERVED_BY =
3469	27 Aug 15	nicklas	597	new Annotationtype("ReservedBy", Type.STRING, false, Item.EXTRACT);
3469	27 Aug 15	nicklas	598
3469	27 Aug 15	nicklas	599
3469	27 Aug 15	nicklas	600	/**
1639	09 May 12	nicklas	601	The "QiacubeDate" annotation type, used for extracts (RNA, DNA).
1639	09 May 12	nicklas	602	It is a date annotation type.
1639	09 May 12	nicklas	603	@since 2.6
1639	09 May 12	nicklas	604	*/
1639	09 May 12	nicklas	605	public static final Annotationtype QIACUBE_DATE =
2351	10 Apr 14	nicklas	606	new Annotationtype("QiacubeDate", Type.DATE, false, Item.EXTRACT);
1639	09 May 12	nicklas	607
1639	09 May 12	nicklas	608	/**
1639	09 May 12	nicklas	609	The "QiacubeOperator" annotation type, used for extracts (RNA, DNA).
1639	09 May 12	nicklas	610	It is a string annotation type.
1639	09 May 12	nicklas	611	@since 2.6
1639	09 May 12	nicklas	612	*/
1639	09 May 12	nicklas	613	public static final Annotationtype QIACUBE_OPERATOR =
2351	10 Apr 14	nicklas	614	new Annotationtype("QiacubeOperator", Type.STRING, false, Item.EXTRACT);
1639	09 May 12	nicklas	615
1639	09 May 12	nicklas	616	/**
1639	09 May 12	nicklas	617	The "QiacubePosition" annotation type, used for extracts (RNA, DNA).
1639	09 May 12	nicklas	618	It is an integer annotation type with allowed values between 1 and 12.
1639	09 May 12	nicklas	619	@since 2.6
1639	09 May 12	nicklas	620	*/
1639	09 May 12	nicklas	621	public static final Annotationtype QIACUBE_POSITION =
2351	10 Apr 14	nicklas	622	new Annotationtype("QiacubePosition", Type.INT, false, Item.EXTRACT);
1639	09 May 12	nicklas	623
1639	09 May 12	nicklas	624	/**
6510	03 Dec 21	nicklas	625	The "QiacubeRunNo" annotation type, used for extracts (RNA, DNA, FlowThrough).
1639	09 May 12	nicklas	626	It is an integer annotation type with allowed values >= 1.
1639	09 May 12	nicklas	627	@since 2.6
1639	09 May 12	nicklas	628	*/
1639	09 May 12	nicklas	629	public static final Annotationtype QIACUBE_RUN_NO =
2351	10 Apr 14	nicklas	630	new Annotationtype("QiacubeRunNo", Type.INT, false, Item.EXTRACT);
1639	09 May 12	nicklas	631
1639	09 May 12	nicklas	632	/**
6510	03 Dec 21	nicklas	633	The "QiacubeRunId" annotation type, used for extracts (RNA, DNA, FlowThrough)
6510	03 Dec 21	nicklas	634	extract by external lab. It is a string ID-like annotation
6510	03 Dec 21	nicklas	635	that group items that has been extracted in the same Qiacube run.
6510	03 Dec 21	nicklas	636	@since 4.33.5
6510	03 Dec 21	nicklas	637	*/
6510	03 Dec 21	nicklas	638	public static final Annotationtype QIACUBE_RUN_ID =
6510	03 Dec 21	nicklas	639	new Annotationtype("QiacubeRunId", Type.STRING, false, Item.EXTRACT);
6510	03 Dec 21	nicklas	640
6510	03 Dec 21	nicklas	641
6510	03 Dec 21	nicklas	642	/**
2690	24 Sep 14	nicklas	643	The "RLT_Plus" annotation type, used for extracts (Lysate).
2690	24 Sep 14	nicklas	644	@since 2.16
2690	24 Sep 14	nicklas	645	*/
2690	24 Sep 14	nicklas	646	public static final Annotationtype RLT_PLUS =
2690	24 Sep 14	nicklas	647	new Annotationtype("RLT_Plus", Type.STRING, false, Item.EXTRACT);
2690	24 Sep 14	nicklas	648
2690	24 Sep 14	nicklas	649	/**
2690	24 Sep 14	nicklas	650	The "BetaMerca" annotation type, used for extracts (Lysate).
2690	24 Sep 14	nicklas	651	@since 2.16
2690	24 Sep 14	nicklas	652	*/
2690	24 Sep 14	nicklas	653	public static final Annotationtype BETA_MERCA =
2690	24 Sep 14	nicklas	654	new Annotationtype("BetaMerca", Type.STRING, false, Item.EXTRACT);
2690	24 Sep 14	nicklas	655
2690	24 Sep 14	nicklas	656	/**
2690	24 Sep 14	nicklas	657	The "ReagentDX" annotation type, used for extracts (Lysate).
2690	24 Sep 14	nicklas	658	@since 2.16
2690	24 Sep 14	nicklas	659	*/
2690	24 Sep 14	nicklas	660	public static final Annotationtype REAGENT_DX =
2690	24 Sep 14	nicklas	661	new Annotationtype("ReagentDX", Type.STRING, false, Item.EXTRACT);
2690	24 Sep 14	nicklas	662
2690	24 Sep 14	nicklas	663	/**
2690	24 Sep 14	nicklas	664	The "QiaShredder" annotation type, used for extracts (Lysate).
2690	24 Sep 14	nicklas	665	@since 2.16
2690	24 Sep 14	nicklas	666	*/
2690	24 Sep 14	nicklas	667	public static final Annotationtype QIA_SHREDDER =
2690	24 Sep 14	nicklas	668	new Annotationtype("QiaShredder", Type.STRING, false, Item.EXTRACT);
2690	24 Sep 14	nicklas	669
2690	24 Sep 14	nicklas	670	/**
2690	24 Sep 14	nicklas	671	The "AllprepMiniKit" annotation type, used for extracts (RNA, DNA, FlowThrough).
2690	24 Sep 14	nicklas	672	@since 2.16
2690	24 Sep 14	nicklas	673	*/
2690	24 Sep 14	nicklas	674	public static final Annotationtype ALLPREP_MINI_KIT =
2690	24 Sep 14	nicklas	675	new Annotationtype("AllprepMiniKit", Type.STRING, false, Item.EXTRACT);
2690	24 Sep 14	nicklas	676
2690	24 Sep 14	nicklas	677	/**
2690	24 Sep 14	nicklas	678	The "ETOH70" annotation type, used for extracts (RNA, DNA, FlowThrough).
2690	24 Sep 14	nicklas	679	@since 2.16
2690	24 Sep 14	nicklas	680	*/
2690	24 Sep 14	nicklas	681	public static final Annotationtype ETOH70 =
2690	24 Sep 14	nicklas	682	new Annotationtype("ETOH70", Type.STRING, false, Item.EXTRACT);
2690	24 Sep 14	nicklas	683
2690	24 Sep 14	nicklas	684	/**
2690	24 Sep 14	nicklas	685	The "BufferRW1" annotation type, used for extracts (RNA, DNA, FlowThrough).
2690	24 Sep 14	nicklas	686	@since 2.16
2690	24 Sep 14	nicklas	687	*/
2690	24 Sep 14	nicklas	688	public static final Annotationtype BUFFER_RW1 =
2690	24 Sep 14	nicklas	689	new Annotationtype("BufferRW1", Type.STRING, false, Item.EXTRACT);
2690	24 Sep 14	nicklas	690
2690	24 Sep 14	nicklas	691	/**
2690	24 Sep 14	nicklas	692	The "BufferRPE" annotation type, used for extracts (RNA, DNA, FlowThrough).
2690	24 Sep 14	nicklas	693	@since 2.16
2690	24 Sep 14	nicklas	694	*/
2690	24 Sep 14	nicklas	695	public static final Annotationtype BUFFER_RPE =
2690	24 Sep 14	nicklas	696	new Annotationtype("BufferRPE", Type.STRING, false, Item.EXTRACT);
2690	24 Sep 14	nicklas	697
2690	24 Sep 14	nicklas	698	/**
2690	24 Sep 14	nicklas	699	The "BufferAW1" annotation type, used for extracts (RNA, DNA, FlowThrough).
2690	24 Sep 14	nicklas	700	@since 2.16
2690	24 Sep 14	nicklas	701	*/
2690	24 Sep 14	nicklas	702	public static final Annotationtype BUFFER_AW1 =
2690	24 Sep 14	nicklas	703	new Annotationtype("BufferAW1", Type.STRING, false, Item.EXTRACT);
2690	24 Sep 14	nicklas	704
2690	24 Sep 14	nicklas	705	/**
2690	24 Sep 14	nicklas	706	The "BufferAW2" annotation type, used for extracts (RNA, DNA, FlowThrough).
2690	24 Sep 14	nicklas	707	@since 2.16
2690	24 Sep 14	nicklas	708	*/
2690	24 Sep 14	nicklas	709	public static final Annotationtype BUFFER_AW2 =
2690	24 Sep 14	nicklas	710	new Annotationtype("BufferAW2", Type.STRING, false, Item.EXTRACT);
2690	24 Sep 14	nicklas	711
2690	24 Sep 14	nicklas	712	/**
2690	24 Sep 14	nicklas	713	The "BufferEB" annotation type, used for extracts (RNA, DNA, FlowThrough).
2690	24 Sep 14	nicklas	714	@since 2.16
2690	24 Sep 14	nicklas	715	*/
2690	24 Sep 14	nicklas	716	public static final Annotationtype BUFFER_EB =
2690	24 Sep 14	nicklas	717	new Annotationtype("BufferEB", Type.STRING, false, Item.EXTRACT);
2690	24 Sep 14	nicklas	718
2690	24 Sep 14	nicklas	719	/**
2690	24 Sep 14	nicklas	720	The "RNaseFreeWater" annotation type, used for extracts (RNA, DNA, FlowThrough).
2690	24 Sep 14	nicklas	721	@since 2.16
2690	24 Sep 14	nicklas	722	*/
2690	24 Sep 14	nicklas	723	public static final Annotationtype RNASE_FREE_WATER =
2690	24 Sep 14	nicklas	724	new Annotationtype("RNaseFreeWater", Type.STRING, false, Item.EXTRACT);
2690	24 Sep 14	nicklas	725
2690	24 Sep 14	nicklas	726	/**
2690	24 Sep 14	nicklas	727	The "AllPrepDNA_col" annotation type, used for extracts (RNA, DNA, FlowThrough).
2690	24 Sep 14	nicklas	728	@since 2.16
2690	24 Sep 14	nicklas	729	*/
2690	24 Sep 14	nicklas	730	public static final Annotationtype ALLPREP_DNA_COL =
2690	24 Sep 14	nicklas	731	new Annotationtype("AllPrepDNA_col", Type.STRING, false, Item.EXTRACT);
2690	24 Sep 14	nicklas	732
2690	24 Sep 14	nicklas	733	/**
2690	24 Sep 14	nicklas	734	The "RNeasy_col" annotation type, used for extracts (RNA, DNA, FlowThrough).
2690	24 Sep 14	nicklas	735	@since 2.16
2690	24 Sep 14	nicklas	736	*/
2690	24 Sep 14	nicklas	737	public static final Annotationtype RNEASY_COL =
2690	24 Sep 14	nicklas	738	new Annotationtype("RNeasy_col", Type.STRING, false, Item.EXTRACT);
2690	24 Sep 14	nicklas	739
2690	24 Sep 14	nicklas	740	/**
1610	23 Apr 12	nicklas	741	The "QCRunDate" annotation, used
1610	23 Apr 12	nicklas	742	for bioplates (RNA). It is a date annotation type.
1610	23 Apr 12	nicklas	743	*/
1610	23 Apr 12	nicklas	744	public static final Annotationtype QC_RUN_DATE =
2351	10 Apr 14	nicklas	745	new Annotationtype("QCRunDate", Type.DATE, false, Item.BIOPLATE);
1610	23 Apr 12	nicklas	746
1610	23 Apr 12	nicklas	747	/**
1610	23 Apr 12	nicklas	748	The "QCOperator" annotation, used
1610	23 Apr 12	nicklas	749	for bioplates (RNA). It is a string annotation type.
1610	23 Apr 12	nicklas	750	*/
1610	23 Apr 12	nicklas	751	public static final Annotationtype QC_OPERATOR =
2351	10 Apr 14	nicklas	752	new Annotationtype("QCOperator", Type.STRING, false, Item.BIOPLATE);
1610	23 Apr 12	nicklas	753
1610	23 Apr 12	nicklas	754	/**
1610	23 Apr 12	nicklas	755	The "BA_RIN" annotation, used
1610	23 Apr 12	nicklas	756	for extract (RNAQC). It is a float annotation type
1610	23 Apr 12	nicklas	757	*/
1610	23 Apr 12	nicklas	758	public static final Annotationtype BA_RIN =
2351	10 Apr 14	nicklas	759	new Annotationtype("BA_RIN", Type.FLOAT, false, Item.EXTRACT);
1610	23 Apr 12	nicklas	760
1610	23 Apr 12	nicklas	761	/**
1610	23 Apr 12	nicklas	762	The "CA_RQS" annotation, used
1610	23 Apr 12	nicklas	763	for extract (RNAQC). It is a float annotation type
1610	23 Apr 12	nicklas	764	*/
1610	23 Apr 12	nicklas	765	public static final Annotationtype CA_RQS =
2351	10 Apr 14	nicklas	766	new Annotationtype("CA_RQS", Type.FLOAT, false, Item.EXTRACT);
1610	23 Apr 12	nicklas	767
1610	23 Apr 12	nicklas	768	/**
1610	23 Apr 12	nicklas	769	The "NDConc" annotation, used for extract (DNA/RNA).
1610	23 Apr 12	nicklas	770	@since 2.4
1610	23 Apr 12	nicklas	771	*/
1610	23 Apr 12	nicklas	772	public static final Annotationtype ND_CONC =
2351	10 Apr 14	nicklas	773	new Annotationtype("NDConc", Type.FLOAT, false, Item.EXTRACT);
1639	09 May 12	nicklas	774
1639	09 May 12	nicklas	775	/**
1639	09 May 12	nicklas	776	The "ND260by280" annotation, used for extract (DNA/RNA).
1639	09 May 12	nicklas	777	It is a float annotation type.
1639	09 May 12	nicklas	778	@since 2.6
1639	09 May 12	nicklas	779	*/
1639	09 May 12	nicklas	780	public static final Annotationtype ND_260_BY_280 =
2351	10 Apr 14	nicklas	781	new Annotationtype("ND260by280", Type.FLOAT, false, Item.EXTRACT);
1639	09 May 12	nicklas	782
1639	09 May 12	nicklas	783	/**
1639	09 May 12	nicklas	784	The "ND260by230" annotation, used for extract (DNA/RNA).
1639	09 May 12	nicklas	785	It is a float annotation type.
1639	09 May 12	nicklas	786	@since 2.6
1639	09 May 12	nicklas	787	*/
1639	09 May 12	nicklas	788	public static final Annotationtype ND_260_BY_230 =
2351	10 Apr 14	nicklas	789	new Annotationtype("ND260by230", Type.FLOAT, false, Item.EXTRACT);
1610	23 Apr 12	nicklas	790
1610	23 Apr 12	nicklas	791	/**
1610	23 Apr 12	nicklas	792	The "QCHiSense" annotation, used for
1610	23 Apr 12	nicklas	793	extract (RNAQC). It is a boolean annotation type.
1610	23 Apr 12	nicklas	794	*/
1610	23 Apr 12	nicklas	795	public static final Annotationtype QC_HISENSE =
2351	10 Apr 14	nicklas	796	new Annotationtype("QCHiSense", Type.BOOLEAN, false, Item.EXTRACT);
1610	23 Apr 12	nicklas	797
1865	19 Feb 13	nicklas	798	/**
3269	23 Apr 15	nicklas	799	The "RNATargetAmount" annotation, used for
3269	23 Apr 15	nicklas	800	protocol (RNANormalization). It is a float annotation type.
3269	23 Apr 15	nicklas	801	@since 3.4
3269	23 Apr 15	nicklas	802	*/
3269	23 Apr 15	nicklas	803	public static final Annotationtype RNA_TARGET_AMOUNT =
5891	07 Apr 20	nicklas	804	new Annotationtype("RNATargetAmount", Type.FLOAT, false, Item.PROTOCOL, Item.BIOPLATE);
3269	23 Apr 15	nicklas	805
3269	23 Apr 15	nicklas	806	/**
3829	06 Apr 16	nicklas	807	The "RNAMinimalAmount" annotation, used for
3829	06 Apr 16	nicklas	808	protocol (RNANormalization). It is a float annotation type.
3829	06 Apr 16	nicklas	809	@since 4.3
3829	06 Apr 16	nicklas	810	*/
3829	06 Apr 16	nicklas	811	public static final Annotationtype RNA_MINIMAL_AMOUNT =
3829	06 Apr 16	nicklas	812	new Annotationtype("RNAMinimalAmount", Type.FLOAT, false, Item.PROTOCOL);
3829	06 Apr 16	nicklas	813
3829	06 Apr 16	nicklas	814	/**
3269	23 Apr 15	nicklas	815	The "RNATargetVolume" annotation, used for
3269	23 Apr 15	nicklas	816	protocol (RNANormalization). It is a float annotation type.
3269	23 Apr 15	nicklas	817	@since 3.4
3269	23 Apr 15	nicklas	818	*/
3269	23 Apr 15	nicklas	819	public static final Annotationtype RNA_TARGET_VOLUME =
5891	07 Apr 20	nicklas	820	new Annotationtype("RNATargetVolume", Type.FLOAT, false, Item.PROTOCOL, Item.BIOPLATE);
3269	23 Apr 15	nicklas	821
3269	23 Apr 15	nicklas	822	/**
5434	17 May 19	nicklas	823	Flag to set on various items to indicate which pipeline
5434	17 May 19	nicklas	824	they belong to.
5434	17 May 19	nicklas	825	@since 4.23
5434	17 May 19	nicklas	826	*/
5434	17 May 19	nicklas	827	public static final Annotationtype PIPELINE =
5470	05 Jun 19	nicklas	828	new Annotationtype("Pipeline", Type.STRING, false, Item.EXTRACT, Item.TAG,
5543	06 Aug 19	nicklas	829	Item.BIOPLATE, Item.PHYSICALBIOASSAY, Item.DERIVEDBIOASSAY, Item.RAWBIOASSAY,
6819	26 Aug 22	nicklas	830	Item.PROTOCOL, Item.SOFTWARE, Item.ARRAYDESIGN);
5434	17 May 19	nicklas	831
5434	17 May 19	nicklas	832	/**
3833	08 Apr 16	nicklas	833	Flag to set on normalization protocol to indicate the
3833	08 Apr 16	nicklas	834	target platform they can be used on. Eg. NeoPrep or manual.
3833	08 Apr 16	nicklas	835	@since 4.3
3833	08 Apr 16	nicklas	836	*/
3833	08 Apr 16	nicklas	837	public static final Annotationtype LIBPREP_TARGET =
3833	08 Apr 16	nicklas	838	new Annotationtype("LibPrepTarget", Type.STRING, false, Item.PROTOCOL);
3833	08 Apr 16	nicklas	839
3833	08 Apr 16	nicklas	840	/**
5359	12 Apr 19	nicklas	841	The "DNATargetAmount" annotation, used for
5359	12 Apr 19	nicklas	842	protocol (DNANormalization). It is a float annotation type.
5359	12 Apr 19	nicklas	843	@since 4.23
5359	12 Apr 19	nicklas	844	*/
5359	12 Apr 19	nicklas	845	public static final Annotationtype DNA_TARGET_AMOUNT =
5359	12 Apr 19	nicklas	846	new Annotationtype("DNATargetAmount", Type.FLOAT, false, Item.PROTOCOL);
5359	12 Apr 19	nicklas	847
5359	12 Apr 19	nicklas	848	/**
5359	12 Apr 19	nicklas	849	The "DNAMinimalAmount" annotation, used for
5359	12 Apr 19	nicklas	850	protocol (DNANormalization). It is a float annotation type.
5359	12 Apr 19	nicklas	851	@since 4.23
5359	12 Apr 19	nicklas	852	*/
5359	12 Apr 19	nicklas	853	public static final Annotationtype DNA_MINIMAL_AMOUNT =
5359	12 Apr 19	nicklas	854	new Annotationtype("DNAMinimalAmount", Type.FLOAT, false, Item.PROTOCOL);
5359	12 Apr 19	nicklas	855
5359	12 Apr 19	nicklas	856	/**
5359	12 Apr 19	nicklas	857	The "DNATargetVolume" annotation, used for
5359	12 Apr 19	nicklas	858	protocol (DNANormalization). It is a float annotation type.
5359	12 Apr 19	nicklas	859	@since 4.23
5359	12 Apr 19	nicklas	860	*/
5359	12 Apr 19	nicklas	861	public static final Annotationtype DNA_TARGET_VOLUME =
5359	12 Apr 19	nicklas	862	new Annotationtype("DNATargetVolume", Type.FLOAT, false, Item.PROTOCOL);
5359	12 Apr 19	nicklas	863
5402	07 May 19	nicklas	864	/**
5601	13 Sep 19	nicklas	865	The "MIPS_Panel" annotation, used for extracts
5402	07 May 19	nicklas	866	in the MIPs pipeline. It is a string annotation type.
5402	07 May 19	nicklas	867	@since 4.23
5402	07 May 19	nicklas	868	*/
5601	13 Sep 19	nicklas	869	public static final Annotationtype MIPS_PANEL =
5601	13 Sep 19	nicklas	870	new Annotationtype("MIPS_Panel", Type.STRING, false, Item.EXTRACT, Item.PROTOCOL);
5402	07 May 19	nicklas	871
5402	07 May 19	nicklas	872	/**
5447	24 May 19	nicklas	873	The "MIPS_PoolVolume" annotation, used for extracts
5461	03 Jun 19	nicklas	874	in the MIPs pipeline. It is a numeric annotation type.
5402	07 May 19	nicklas	875	@since 4.23
5402	07 May 19	nicklas	876	*/
5447	24 May 19	nicklas	877	public static final Annotationtype MIPS_POOL_VOLUME =
5461	03 Jun 19	nicklas	878	new Annotationtype("MIPS_PoolVolume", Type.FLOAT, false, Item.EXTRACT);
5447	24 May 19	nicklas	879
5447	24 May 19	nicklas	880	/**
5447	24 May 19	nicklas	881	The "MIPS_NormalTumor" annotation, used for extracts
5447	24 May 19	nicklas	882	in the MIPs pipeline. It is a string annotation type.
5447	24 May 19	nicklas	883	@since 4.23
5447	24 May 19	nicklas	884	*/
5447	24 May 19	nicklas	885	public static final Annotationtype MIPS_NORMAL_TUMOR =
5447	24 May 19	nicklas	886	new Annotationtype("MIPS_NormalTumor", Type.STRING, false, Item.EXTRACT);
5447	24 May 19	nicklas	887
5447	24 May 19	nicklas	888	/**
5447	24 May 19	nicklas	889	The "MIPS_Form" annotation, used for extracts
5447	24 May 19	nicklas	890	in the MIPs pipeline. It is a string annotation type.
5447	24 May 19	nicklas	891	@since 4.23
5447	24 May 19	nicklas	892	*/
5447	24 May 19	nicklas	893	public static final Annotationtype MIPS_FORM =
5447	24 May 19	nicklas	894	new Annotationtype("MIPS_Form", Type.STRING, false, Item.EXTRACT);
5447	24 May 19	nicklas	895
5447	24 May 19	nicklas	896	/**
5447	24 May 19	nicklas	897	The "MIPS_Variant" annotation, used for extracts
5447	24 May 19	nicklas	898	in the MIPs pipeline. It is a string annotation type.
5447	24 May 19	nicklas	899	@since 4.23
5447	24 May 19	nicklas	900	*/
5447	24 May 19	nicklas	901	public static final Annotationtype MIPS_VARIANT =
5447	24 May 19	nicklas	902	new Annotationtype("MIPS_Variant", Type.STRING, false, Item.EXTRACT);
5447	24 May 19	nicklas	903
5447	24 May 19	nicklas	904	/**
5447	24 May 19	nicklas	905	The "MIPS_VariantList annotation, used for extracts
5447	24 May 19	nicklas	906	in the MIPs pipeline. It is a string annotation type.
5447	24 May 19	nicklas	907	@since 4.23
5447	24 May 19	nicklas	908	*/
5447	24 May 19	nicklas	909	public static final Annotationtype MIPS_VARIANT_LIST =
5447	24 May 19	nicklas	910	new Annotationtype("MIPS_VariantList", Type.STRING, false, Item.EXTRACT);
5447	24 May 19	nicklas	911
5447	24 May 19	nicklas	912	/**
5447	24 May 19	nicklas	913	The "MIPS_Screening annotation, used for extracts
5447	24 May 19	nicklas	914	in the MIPs pipeline. It is a string annotation type.
5447	24 May 19	nicklas	915	@since 4.23
5447	24 May 19	nicklas	916	*/
5447	24 May 19	nicklas	917	public static final Annotationtype MIPS_SCREENING =
5447	24 May 19	nicklas	918	new Annotationtype("MIPS_Screening", Type.STRING, false, Item.EXTRACT);
5447	24 May 19	nicklas	919
5359	12 Apr 19	nicklas	920	/**
5663	11 Oct 19	nicklas	921	The "BRCA_PatientID annotation, used for extracts
5663	11 Oct 19	nicklas	922	in the MIPs pipeline. It is a string annotation type.
5663	11 Oct 19	nicklas	923	@since 4.23.2
5663	11 Oct 19	nicklas	924	*/
5663	11 Oct 19	nicklas	925	public static final Annotationtype BRCA_PATIENTID =
5663	11 Oct 19	nicklas	926	new Annotationtype("BRCA_PatientID", Type.STRING, false, Item.EXTRACT);
5663	11 Oct 19	nicklas	927
5663	11 Oct 19	nicklas	928	/**
5663	11 Oct 19	nicklas	929	The "BRCA_Provnummer annotation, used for extracts
5663	11 Oct 19	nicklas	930	in the MIPs pipeline. It is a string annotation type.
5663	11 Oct 19	nicklas	931	@since 4.23.2
5663	11 Oct 19	nicklas	932	*/
5663	11 Oct 19	nicklas	933	public static final Annotationtype BRCA_PROVNUMMER =
5663	11 Oct 19	nicklas	934	new Annotationtype("BRCA_Provnummer", Type.STRING, false, Item.EXTRACT);
5663	11 Oct 19	nicklas	935
5663	11 Oct 19	nicklas	936	/**
5407	08 May 19	nicklas	937	The "PlateProcessing" annotation which is used to control which
5407	08 May 19	nicklas	938	actions that are available for a bioplate at a given time.
5407	08 May 19	nicklas	939	It is typically used for plates that can be used multiple
5407	08 May 19	nicklas	940	times before moving on to the next state. For example,
5407	08 May 19	nicklas	941	Plates for pre-normalized DNA are filled with DNA aliquots
5407	08 May 19	nicklas	942	in multiple steps. When the plate is first used for
5407	08 May 19	nicklas	943	MIPs plate design, no more aliquots can be added, but
5407	08 May 19	nicklas	944	it may still be used for multiple MIPs plates before
5407	08 May 19	nicklas	945	finally being "used up".
5407	08 May 19	nicklas	946	@since 4.23
5407	08 May 19	nicklas	947	*/
5407	08 May 19	nicklas	948	public static final Annotationtype PLATE_PROCESSING =
5407	08 May 19	nicklas	949	new Annotationtype("PlateProcessing", Type.STRING, false, Item.BIOPLATE);
5407	08 May 19	nicklas	950
5407	08 May 19	nicklas	951
5407	08 May 19	nicklas	952	/**
1889	27 Feb 13	nicklas	953	The "AutoProcessing" annotation which, if set, is a
1889	27 Feb 13	nicklas	954	flag to indicate how the item should be handled by
1889	27 Feb 13	nicklas	955	auto-processing wizards. No value indicates normal
1889	27 Feb 13	nicklas	956	processing in the regular flow. Other values may mean
1889	27 Feb 13	nicklas	957	either disabled auto-processing (eg. "Disable") or
1889	27 Feb 13	nicklas	958	forced (re)-auto-processing (eg. "ReProcess"). The
1889	27 Feb 13	nicklas	959	support and meaning is up to each wizard.
1867	19 Feb 13	nicklas	960	@since 2.12
1865	19 Feb 13	nicklas	961	*/
1889	27 Feb 13	nicklas	962	public static final Annotationtype AUTO_PROCESSING =
7223	31 May 23	nicklas	963	new Annotationtype("AutoProcessing", Type.STRING, false, Item.BIOPLATE, Item.EXTRACT,
7223	31 May 23	nicklas	964	Item.DERIVEDBIOASSAY, Item.SAMPLE, Item.RAWBIOASSAY, Item.ITEMLIST, Item.FILESERVER);
1865	19 Feb 13	nicklas	965
1865	19 Feb 13	nicklas	966	/**
1890	01 Mar 13	nicklas	967	The "PlateProcessResult" annotation which is set after a reaction
1890	01 Mar 13	nicklas	968	plate has been proccessed to indicate the outcome of the plate as
1890	01 Mar 13	nicklas	969	a whole. A value of "Successful" typically means that the next step
1890	01 Mar 13	nicklas	970	in the process can be taken, but a value of "Failed" indicates a
1890	01 Mar 13	nicklas	971	complete failure and everything should be restarted at a previous level.
2020	13 Sep 13	nicklas	972	Can also be used on a flow cell (physical bioassay).
1890	01 Mar 13	nicklas	973	@since 2.12
1890	01 Mar 13	nicklas	974	*/
1890	01 Mar 13	nicklas	975	public static final Annotationtype PLATE_PROCESS_RESULT =
2351	10 Apr 14	nicklas	976	new Annotationtype("PlateProcessResult", Type.STRING, false, Item.BIOPLATE, Item.PHYSICALBIOASSAY);
1977	16 May 13	nicklas	977
1977	16 May 13	nicklas	978	/**
3303	04 May 15	nicklas	979	Flag that is set on mRNA items that should be used for
3303	04 May 15	nicklas	980	QC in the library preparation.
3303	04 May 15	nicklas	981	@since 3.4
3303	04 May 15	nicklas	982	*/
3303	04 May 15	nicklas	983	public static final Annotationtype USE_FOR_QC =
3303	04 May 15	nicklas	984	new Annotationtype("UseForQC", Type.BOOLEAN, false, Item.EXTRACT);
3303	04 May 15	nicklas	985
3303	04 May 15	nicklas	986	/**
3303	04 May 15	nicklas	987	Expected concentration after diluting RNA to be processed
3303	04 May 15	nicklas	988	to libraries. Used on "mRNA" and "Library" items.
3303	04 May 15	nicklas	989	@since 3.4
3303	04 May 15	nicklas	990	*/
3303	04 May 15	nicklas	991	public static final Annotationtype DILUTION_CONC =
3303	04 May 15	nicklas	992	new Annotationtype("DilutionConc", Type.FLOAT, false, Item.EXTRACT);
3303	04 May 15	nicklas	993
3303	04 May 15	nicklas	994	/**
3832	07 Apr 16	nicklas	995	Expected volume after diluting RNA to be processed
3832	07 Apr 16	nicklas	996	to libraries. Used on "mRNA" and "Library" items.
3832	07 Apr 16	nicklas	997	@since 4.3
3832	07 Apr 16	nicklas	998	*/
3832	07 Apr 16	nicklas	999	public static final Annotationtype DILUTION_VOLUME =
3832	07 Apr 16	nicklas	1000	new Annotationtype("DilutionVolume", Type.FLOAT, false, Item.EXTRACT);
3832	07 Apr 16	nicklas	1001
3833	08 Apr 16	nicklas	1002
3832	07 Apr 16	nicklas	1003	/**
2898	05 Nov 14	nicklas	1004	Annotation for mRNA and pre-normalized RNA dilution date.
2898	05 Nov 14	nicklas	1005	@since 2.12, 2.18
1998	29 May 13	nicklas	1006	*/
1998	29 May 13	nicklas	1007	public static final Annotationtype DILUTION_DATE =
2898	05 Nov 14	nicklas	1008	new Annotationtype("DilutionDate", Type.DATE, false, Item.BIOPLATE, Item.EXTRACT);
1998	29 May 13	nicklas	1009
1998	29 May 13	nicklas	1010	/**
2898	05 Nov 14	nicklas	1011	Annotation for mRNA and pre-normalized RNA dilution operator.
2898	05 Nov 14	nicklas	1012	@since 2.12, 2.18
1998	29 May 13	nicklas	1013	*/
1998	29 May 13	nicklas	1014	public static final Annotationtype DILUTION_OPERATOR =
2898	05 Nov 14	nicklas	1015	new Annotationtype("DilutionOperator", Type.STRING, false, Item.BIOPLATE, Item.EXTRACT);
1998	29 May 13	nicklas	1016
1998	29 May 13	nicklas	1017
1998	29 May 13	nicklas	1018	/**
1998	29 May 13	nicklas	1019	Annotation for mRNA purification date.
1998	29 May 13	nicklas	1020	@since 2.12
1998	29 May 13	nicklas	1021	*/
1998	29 May 13	nicklas	1022	public static final Annotationtype PURIFICATION_DATE =
2351	10 Apr 14	nicklas	1023	new Annotationtype("PurificationDate", Type.DATE, false, Item.BIOPLATE);
1998	29 May 13	nicklas	1024
1998	29 May 13	nicklas	1025	/**
1998	29 May 13	nicklas	1026	Annotation for mRNA purification operator.
1998	29 May 13	nicklas	1027	@since 2.12
1998	29 May 13	nicklas	1028	*/
1998	29 May 13	nicklas	1029	public static final Annotationtype PURIFICATION_OPERATOR =
2351	10 Apr 14	nicklas	1030	new Annotationtype("PurificationOperator", Type.STRING, false, Item.BIOPLATE);
1998	29 May 13	nicklas	1031
1998	29 May 13	nicklas	1032	/**
1998	29 May 13	nicklas	1033	Annotation for mRNA fragmentation date.
1998	29 May 13	nicklas	1034	@since 2.12
1998	29 May 13	nicklas	1035	*/
1998	29 May 13	nicklas	1036	public static final Annotationtype FRAGMENTATION_DATE =
2351	10 Apr 14	nicklas	1037	new Annotationtype("FragmentationDate", Type.DATE, false, Item.BIOPLATE);
1998	29 May 13	nicklas	1038
1998	29 May 13	nicklas	1039	/**
1998	29 May 13	nicklas	1040	Annotation for mRNA fragmentation operator.
1998	29 May 13	nicklas	1041	@since 2.12
1998	29 May 13	nicklas	1042	*/
1998	29 May 13	nicklas	1043	public static final Annotationtype FRAGMENTATION_OPERATOR =
2351	10 Apr 14	nicklas	1044	new Annotationtype("FragmentationOperator", Type.STRING, false, Item.BIOPLATE);
1998	29 May 13	nicklas	1045
1998	29 May 13	nicklas	1046	/**
1998	29 May 13	nicklas	1047	Annotation for mRNA cleanup date.
1998	29 May 13	nicklas	1048	@since 2.12
1998	29 May 13	nicklas	1049	*/
1998	29 May 13	nicklas	1050	public static final Annotationtype CLEANUP_DATE =
2351	10 Apr 14	nicklas	1051	new Annotationtype("CleanupDate", Type.DATE, false, Item.BIOPLATE);
1998	29 May 13	nicklas	1052
1998	29 May 13	nicklas	1053	/**
1998	29 May 13	nicklas	1054	Annotation for mRNA cleanup operator.
1998	29 May 13	nicklas	1055	@since 2.12
1998	29 May 13	nicklas	1056	*/
1998	29 May 13	nicklas	1057	public static final Annotationtype CLEANUP_OPERATOR =
2351	10 Apr 14	nicklas	1058	new Annotationtype("CleanupOperator", Type.STRING, false, Item.BIOPLATE);
1998	29 May 13	nicklas	1059
1999	29 May 13	nicklas	1060	/**
1999	29 May 13	nicklas	1061	Annotation for cDNA synthesis date.
1999	29 May 13	nicklas	1062	@since 2.12
1999	29 May 13	nicklas	1063	*/
1999	29 May 13	nicklas	1064	public static final Annotationtype SYNTHESIS_DATE =
2351	10 Apr 14	nicklas	1065	new Annotationtype("SynthesisDate", Type.DATE, false, Item.BIOPLATE);
1998	29 May 13	nicklas	1066
1998	29 May 13	nicklas	1067	/**
1999	29 May 13	nicklas	1068	Annotation for cDNA synthesis operator.
1999	29 May 13	nicklas	1069	@since 2.12
1999	29 May 13	nicklas	1070	*/
1999	29 May 13	nicklas	1071	public static final Annotationtype SYNTHESIS_OPERATOR =
2351	10 Apr 14	nicklas	1072	new Annotationtype("SynthesisOperator", Type.STRING, false, Item.BIOPLATE);
1999	29 May 13	nicklas	1073
2002	29 May 13	nicklas	1074	/**
2002	29 May 13	nicklas	1075	Annotation for Lib amplification date.
2002	29 May 13	nicklas	1076	@since 2.12
2002	29 May 13	nicklas	1077	*/
2002	29 May 13	nicklas	1078	public static final Annotationtype AMPLIFICATION_DATE =
2351	10 Apr 14	nicklas	1079	new Annotationtype("AmplificationDate", Type.DATE, false, Item.BIOPLATE);
1999	29 May 13	nicklas	1080
1999	29 May 13	nicklas	1081	/**
2002	29 May 13	nicklas	1082	Annotation for Lib amplification operator.
2002	29 May 13	nicklas	1083	@since 2.12
2002	29 May 13	nicklas	1084	*/
2002	29 May 13	nicklas	1085	public static final Annotationtype AMPLIFICATION_OPERATOR =
2351	10 Apr 14	nicklas	1086	new Annotationtype("AmplificationOperator", Type.STRING, false, Item.BIOPLATE);
2002	29 May 13	nicklas	1087
3319	11 May 15	nicklas	1088	/**
5450	27 May 19	nicklas	1089	Annotation for HybridizationDate date.
5450	27 May 19	nicklas	1090	@since 4.23
5450	27 May 19	nicklas	1091	*/
5450	27 May 19	nicklas	1092	public static final Annotationtype HYBRIDIZATION_DATE =
5450	27 May 19	nicklas	1093	new Annotationtype("HybridizationDate", Type.DATE, false, Item.BIOPLATE);
5450	27 May 19	nicklas	1094
5450	27 May 19	nicklas	1095	/**
5450	27 May 19	nicklas	1096	Annotation for Hybridization operator.
5450	27 May 19	nicklas	1097	@since 4.23
5450	27 May 19	nicklas	1098	*/
5450	27 May 19	nicklas	1099	public static final Annotationtype HYBRIDIZATION_OPERATOR =
5450	27 May 19	nicklas	1100	new Annotationtype("HybridizationOperator", Type.STRING, false, Item.BIOPLATE);
5450	27 May 19	nicklas	1101
5450	27 May 19	nicklas	1102	/**
5450	27 May 19	nicklas	1103	Annotation for PCRDate date.
5450	27 May 19	nicklas	1104	@since 4.23
5450	27 May 19	nicklas	1105	*/
5450	27 May 19	nicklas	1106	public static final Annotationtype PCR_DATE =
5450	27 May 19	nicklas	1107	new Annotationtype("PCRDate", Type.DATE, false, Item.BIOPLATE);
5450	27 May 19	nicklas	1108
5450	27 May 19	nicklas	1109	/**
5450	27 May 19	nicklas	1110	Annotation for PCR operator.
5450	27 May 19	nicklas	1111	@since 4.23
5450	27 May 19	nicklas	1112	*/
5450	27 May 19	nicklas	1113	public static final Annotationtype PCR_OPERATOR =
5450	27 May 19	nicklas	1114	new Annotationtype("PCROperator", Type.STRING, false, Item.BIOPLATE);
5450	27 May 19	nicklas	1115
5450	27 May 19	nicklas	1116
5450	27 May 19	nicklas	1117	/**
3319	11 May 15	nicklas	1118	Annotation for NeoPrep date.
3319	11 May 15	nicklas	1119	@since 3.4
3319	11 May 15	nicklas	1120	*/
3319	11 May 15	nicklas	1121	public static final Annotationtype NEOPREP_DATE =
3319	11 May 15	nicklas	1122	new Annotationtype("NeoPrepDate", Type.DATE, false, Item.BIOPLATE);
2002	29 May 13	nicklas	1123
2002	29 May 13	nicklas	1124	/**
3319	11 May 15	nicklas	1125	Annotation for NeoPrep operator.
3319	11 May 15	nicklas	1126	@since 3.4
3319	11 May 15	nicklas	1127	*/
3319	11 May 15	nicklas	1128	public static final Annotationtype NEOPREP_OPERATOR =
3319	11 May 15	nicklas	1129	new Annotationtype("NeoPrepOperator", Type.STRING, false, Item.BIOPLATE);
3319	11 May 15	nicklas	1130
3319	11 May 15	nicklas	1131	/**
2191	13 Jan 14	nicklas	1132	Annotation for pooling operator
2191	13 Jan 14	nicklas	1133	@since 2.14
1977	16 May 13	nicklas	1134	*/
2191	13 Jan 14	nicklas	1135	public static final Annotationtype POOL_OPERATOR =
5427	14 May 19	nicklas	1136	new Annotationtype("PoolOperator", Type.STRING, false, Item.EXTRACT, Item.BIOPLATE);
1977	16 May 13	nicklas	1137
1890	01 Mar 13	nicklas	1138
1890	01 Mar 13	nicklas	1139	/**
1889	27 Feb 13	nicklas	1140	The "Flag" annotation which, if set, is a
1889	27 Feb 13	nicklas	1141	flag to indicate a special condition that happened
1889	27 Feb 13	nicklas	1142	during the processing of an item. This annotation is
1889	27 Feb 13	nicklas	1143	usually set in combination with adding the item to
1889	27 Feb 13	nicklas	1144	a biomaterial list (eg. {@link BiomaterialList#FLAGGED_RNA}).
1889	27 Feb 13	nicklas	1145	@since 2.12
1889	27 Feb 13	nicklas	1146	*/
1889	27 Feb 13	nicklas	1147	public static final Annotationtype FLAG =
2351	10 Apr 14	nicklas	1148	new Annotationtype("Flag", Type.STRING, false, Item.SAMPLE, Item.EXTRACT);
1889	27 Feb 13	nicklas	1149
1889	27 Feb 13	nicklas	1150	/**
1865	19 Feb 13	nicklas	1151	The "PoolSchema" annotation which, if set, indicates the default
1865	19 Feb 13	nicklas	1152	pooling schema to use when working with mRNA, cDNA and Library
1865	19 Feb 13	nicklas	1153	plates. It an enumerated string annotation type.
1867	19 Feb 13	nicklas	1154	@since 2.12
1865	19 Feb 13	nicklas	1155	*/
1865	19 Feb 13	nicklas	1156	public static final Annotationtype POOL_SCHEMA =
2351	10 Apr 14	nicklas	1157	new Annotationtype("PoolSchema", Type.STRING, false, Item.BIOPLATE);
1865	19 Feb 13	nicklas	1158
1865	19 Feb 13	nicklas	1159	/**
1865	19 Feb 13	nicklas	1160	The "BarcodeVariant" annotation which, if set, indicates the default
1865	19 Feb 13	nicklas	1161	barcode variant to use when working with mRNA, cDNA and Library
1865	19 Feb 13	nicklas	1162	plates. It a string annotation type.
1867	19 Feb 13	nicklas	1163	@since 2.12
1865	19 Feb 13	nicklas	1164	*/
1865	19 Feb 13	nicklas	1165	public static final Annotationtype BARCODE_VARIANT =
2351	10 Apr 14	nicklas	1166	new Annotationtype("BarcodeVariant", Type.STRING, false, Item.BIOPLATE);
1865	19 Feb 13	nicklas	1167
1902	13 Mar 13	nicklas	1168	/**
1902	13 Mar 13	nicklas	1169	The "QubitConc" annotation, used for extract (Library).
1902	13 Mar 13	nicklas	1170	@since 2.12
1902	13 Mar 13	nicklas	1171	*/
1902	13 Mar 13	nicklas	1172	public static final Annotationtype QUBIT_CONC =
2351	10 Apr 14	nicklas	1173	new Annotationtype("QubitConc", Type.FLOAT, false, Item.EXTRACT);
1925	11 Apr 13	nicklas	1174
1925	11 Apr 13	nicklas	1175	/**
7286	15 Aug 23	nicklas	1176	The "QuantITConc" annotation, used for extract (Library).
7286	15 Aug 23	nicklas	1177	@since 4.48.5
7286	15 Aug 23	nicklas	1178	*/
7286	15 Aug 23	nicklas	1179	public static final Annotationtype QUANTIT_CONC =
7286	15 Aug 23	nicklas	1180	new Annotationtype("QuantITConc", Type.FLOAT, false, Item.EXTRACT);
7286	15 Aug 23	nicklas	1181
7286	15 Aug 23	nicklas	1182
7286	15 Aug 23	nicklas	1183	/**
1925	11 Apr 13	nicklas	1184	The "QubitConcAfterSpeedVac" annotation, used for extract (Library).
1925	11 Apr 13	nicklas	1185	@since 2.12
1925	11 Apr 13	nicklas	1186	*/
1925	11 Apr 13	nicklas	1187	public static final Annotationtype QUBIT_CONC_AFTER_SPEEDVAC =
2351	10 Apr 14	nicklas	1188	new Annotationtype("QubitConcAfterSpeedVac", Type.FLOAT, false, Item.EXTRACT);
1925	11 Apr 13	nicklas	1189
1610	23 Apr 12	nicklas	1190
1610	23 Apr 12	nicklas	1191	/**
1906	14 Mar 13	nicklas	1192	The "CA_Size" annotation, used for extract (Library).
2454	23 May 14	nicklas	1193	Read from Caliper well table CSV, Region[180-600] Size [BP]
1902	13 Mar 13	nicklas	1194	@since 2.12
1902	13 Mar 13	nicklas	1195	*/
1902	13 Mar 13	nicklas	1196	public static final Annotationtype CA_SIZE =
2351	10 Apr 14	nicklas	1197	new Annotationtype("CA_Size", Type.FLOAT, false, Item.EXTRACT);
1902	13 Mar 13	nicklas	1198
1906	14 Mar 13	nicklas	1199	/**
1906	14 Mar 13	nicklas	1200	The "CA_Molarity" annotation, used for extract (Library).
2454	23 May 14	nicklas	1201	Read from Caliper well table CSV, Region[180-600] Molarity (nmol/l)
2454	23 May 14	nicklas	1202	multiplied by 10. Used to store calculated values, but since 2.15.2
3571	30 Oct 15	nicklas	1203	these have move to {@link #LIBRARY_MOLARITY_EST}
2454	23 May 14	nicklas	1204	@since 2.12, 2.15.2
1906	14 Mar 13	nicklas	1205	*/
1906	14 Mar 13	nicklas	1206	public static final Annotationtype CA_MOLARITY =
2351	10 Apr 14	nicklas	1207	new Annotationtype("CA_Molarity", Type.FLOAT, false, Item.EXTRACT);
1906	14 Mar 13	nicklas	1208
1959	03 May 13	nicklas	1209	/**
2454	23 May 14	nicklas	1210	The "CA_Size_Adpt" annotation, used for extract (Library).
2454	23 May 14	nicklas	1211	Read from Caliper well table CSV, Region[120-140] Size [BP]
2454	23 May 14	nicklas	1212	@since 2.15.2
2454	23 May 14	nicklas	1213	*/
2454	23 May 14	nicklas	1214	public static final Annotationtype CA_SIZE_ADPT =
2454	23 May 14	nicklas	1215	new Annotationtype("CA_Size_Adpt", Type.FLOAT, false, Item.EXTRACT);
2454	23 May 14	nicklas	1216
2454	23 May 14	nicklas	1217	/**
2454	23 May 14	nicklas	1218	The "CA_Molarity_Adpt" annotation, used for extract (Library).
2454	23 May 14	nicklas	1219	Read from Caliper well table CSV, Region[120-140] Molarity (nmol/l)
2454	23 May 14	nicklas	1220	multiplied by 10.
2454	23 May 14	nicklas	1221	@since 2.15.2
2454	23 May 14	nicklas	1222	*/
2454	23 May 14	nicklas	1223	public static final Annotationtype CA_MOLARITY_ADPT =
2454	23 May 14	nicklas	1224	new Annotationtype("CA_Molarity_Adpt", Type.FLOAT, false, Item.EXTRACT);
2454	23 May 14	nicklas	1225
2454	23 May 14	nicklas	1226	/**
2454	23 May 14	nicklas	1227	Calculated value for library molarity.
2454	23 May 14	nicklas	1228	@since 2.15.2
2454	23 May 14	nicklas	1229	*/
2454	23 May 14	nicklas	1230	public static final Annotationtype LIBRARY_MOLARITY_EST =
2454	23 May 14	nicklas	1231	new Annotationtype("Library_Molarity_Est", Type.FLOAT, false, Item.EXTRACT);
2454	23 May 14	nicklas	1232
2454	23 May 14	nicklas	1233	/**
2454	23 May 14	nicklas	1234	Calculated value for library size. Weighted average of
2454	23 May 14	nicklas	1235	{@link #CA_SIZE} and {@link #CA_SIZE_ADPT}.
2454	23 May 14	nicklas	1236	@since 2.15.2
2454	23 May 14	nicklas	1237	*/
2454	23 May 14	nicklas	1238	public static final Annotationtype LIBRARY_SIZE_EST =
2454	23 May 14	nicklas	1239	new Annotationtype("Library_Size_Est", Type.FLOAT, false, Item.EXTRACT);
2454	23 May 14	nicklas	1240
2454	23 May 14	nicklas	1241	/**
3309	06 May 15	nicklas	1242	Calculated value for library concentration when there is no
3309	06 May 15	nicklas	1243	direct Qubit (or other) measuerment.
3309	06 May 15	nicklas	1244	@since 3.4
3309	06 May 15	nicklas	1245	*/
3309	06 May 15	nicklas	1246	public static final Annotationtype LIBRARY_CONC_EST =
3309	06 May 15	nicklas	1247	new Annotationtype("Library_Conc_Est", Type.FLOAT, false, Item.EXTRACT);
3309	06 May 15	nicklas	1248
3309	06 May 15	nicklas	1249
3309	06 May 15	nicklas	1250	/**
2454	23 May 14	nicklas	1251	Calculated value for adapter fraction (in percent). Calculated
2454	23 May 14	nicklas	1252	from {@link #CA_MOLARITY} and {@link #CA_MOLARITY_ADPT}.
2454	23 May 14	nicklas	1253	@since 2.15.2
2454	23 May 14	nicklas	1254	*/
2454	23 May 14	nicklas	1255	public static final Annotationtype LIBRARY_FRAC_ADPT =
2454	23 May 14	nicklas	1256	new Annotationtype("Library_Frac_Adpt", Type.INT, false, Item.EXTRACT);
2454	23 May 14	nicklas	1257
2454	23 May 14	nicklas	1258	/**
5870	20 Mar 20	nicklas	1259	Annotation for storing position of an item (eg. library) that
5870	20 Mar 20	nicklas	1260	is processed externally.
5870	20 Mar 20	nicklas	1261	@since 4.26
5870	20 Mar 20	nicklas	1262	*/
5870	20 Mar 20	nicklas	1263	public static final Annotationtype EXTERNAL_PLATE_POS =
5870	20 Mar 20	nicklas	1264	new Annotationtype("ExternalPlatePos", Type.STRING, false, Item.EXTRACT);
5870	20 Mar 20	nicklas	1265
5870	20 Mar 20	nicklas	1266	/**
5870	20 Mar 20	nicklas	1267	Annotation for storing the external operator.
5870	20 Mar 20	nicklas	1268	@since 4.26
5870	20 Mar 20	nicklas	1269	*/
5870	20 Mar 20	nicklas	1270	public static final Annotationtype EXTERNAL_OPERATOR =
7227	01 Jun 23	nicklas	1271	new Annotationtype("ExternalOperator", Type.STRING, false, Item.SAMPLE, Item.EXTRACT,
7227	01 Jun 23	nicklas	1272	Item.BIOPLATE, Item.FILESERVER);
5870	20 Mar 20	nicklas	1273
5870	20 Mar 20	nicklas	1274
5870	20 Mar 20	nicklas	1275	/**
1959	03 May 13	nicklas	1276	The "PoolConc" annotation, used for extracts (PooledLibrary).
1959	03 May 13	nicklas	1277	Automatically calculated from the quantities used from the
1959	03 May 13	nicklas	1278	libraries mixed in the pool.
1959	03 May 13	nicklas	1279	@since 2.12
1959	03 May 13	nicklas	1280	*/
1959	03 May 13	nicklas	1281	public static final Annotationtype POOL_CONC =
2351	10 Apr 14	nicklas	1282	new Annotationtype("PoolConc", Type.FLOAT, false, Item.EXTRACT);
1959	03 May 13	nicklas	1283
1959	03 May 13	nicklas	1284	/**
1959	03 May 13	nicklas	1285	The "PoolMolarity" annotation, used for extracts (PooledLibrary).
1959	03 May 13	nicklas	1286	Automatically calculated using the molarity from from the
1959	03 May 13	nicklas	1287	libraries mixed in the pool.
1959	03 May 13	nicklas	1288	@since 2.12
1959	03 May 13	nicklas	1289	*/
1959	03 May 13	nicklas	1290	public static final Annotationtype POOL_MOLARITY =
2351	10 Apr 14	nicklas	1291	new Annotationtype("PoolMolarity", Type.FLOAT, false, Item.EXTRACT);
2021	17 Sep 13	nicklas	1292
2021	17 Sep 13	nicklas	1293	/**
2027	30 Sep 13	nicklas	1294	The "PoolTargetVolumePerLib" annotation, used for extracts (PooledLibrary).
2027	30 Sep 13	nicklas	1295	Store the admin-defined setting for target volume per library in a
2027	30 Sep 13	nicklas	1296	pool. The actual volume may be different due to limitations implied by
2027	30 Sep 13	nicklas	1297	library concentration and rounding.
2027	30 Sep 13	nicklas	1298	@since 2.13
2027	30 Sep 13	nicklas	1299	*/
2027	30 Sep 13	nicklas	1300	public static final Annotationtype POOL_TARGET_VOLUME_PER_LIB =
2351	10 Apr 14	nicklas	1301	new Annotationtype("PoolTargetVolumePerLib", Type.FLOAT, false, Item.EXTRACT);
2140	18 Nov 13	nicklas	1302
2140	18 Nov 13	nicklas	1303	/**
2140	18 Nov 13	nicklas	1304	The "PoolTargetMolarity" annotation, used for extracts (PooledLibrary).
2140	18 Nov 13	nicklas	1305	Store the admin-defined setting for target molarity used when designing
2140	18 Nov 13	nicklas	1306	the pool. The actual molarity may different due to limitations implied by
2140	18 Nov 13	nicklas	1307	library concentration and rounding.
2140	18 Nov 13	nicklas	1308	@since 2.14
2140	18 Nov 13	nicklas	1309	*/
2140	18 Nov 13	nicklas	1310	public static final Annotationtype POOL_TARGET_MOLARITY =
2351	10 Apr 14	nicklas	1311	new Annotationtype("PoolTargetMolarity", Type.FLOAT, false, Item.EXTRACT);
2141	18 Nov 13	nicklas	1312
2141	18 Nov 13	nicklas	1313	/**
2141	18 Nov 13	nicklas	1314	The "PoolIsManual" annotation, used for extracts (PooledLibrary).
2141	18 Nov 13	nicklas	1315	Store a flag indicating if the pool is manaually created. If not set,
2141	18 Nov 13	nicklas	1316	it is asssumed that the pool is created from an entire library working plate.
2141	18 Nov 13	nicklas	1317	@since 2.14
2141	18 Nov 13	nicklas	1318	*/
2141	18 Nov 13	nicklas	1319	public static final Annotationtype POOL_IS_MANUAL =
2351	10 Apr 14	nicklas	1320	new Annotationtype("PoolIsManual", Type.BOOLEAN, false, Item.EXTRACT);
2141	18 Nov 13	nicklas	1321
2027	30 Sep 13	nicklas	1322
2027	30 Sep 13	nicklas	1323	/**
5427	14 May 19	nicklas	1324	The "PoolDate" annotation, used for extracts (PooledLibrary)
5427	14 May 19	nicklas	1325	and bioplates (Library). The date the pool was created.
2066	15 Oct 13	nicklas	1326	@since 2.13
2066	15 Oct 13	nicklas	1327	*/
2066	15 Oct 13	nicklas	1328	public static final Annotationtype POOL_DATE =
5427	14 May 19	nicklas	1329	new Annotationtype("PoolDate", Type.DATE, false, Item.EXTRACT, Item.BIOPLATE);
2066	15 Oct 13	nicklas	1330
2066	15 Oct 13	nicklas	1331
2066	15 Oct 13	nicklas	1332	/**
2041	04 Oct 13	nicklas	1333	The "PoolMixingStrategy" annotation, used for extracts (PooledLibrary).
2041	04 Oct 13	nicklas	1334	Store the admin-defined setting for the strategy to use when mixing the pool.
2041	04 Oct 13	nicklas	1335	Enumeration: fixed, dynamic. Default is fixed.
2041	04 Oct 13	nicklas	1336	@since 2.13
2041	04 Oct 13	nicklas	1337	*/
2041	04 Oct 13	nicklas	1338	public static final Annotationtype POOL_MIXING_STRATEGY =
2351	10 Apr 14	nicklas	1339	new Annotationtype("PoolMixingStrategy", Type.STRING, false, Item.EXTRACT);
2041	04 Oct 13	nicklas	1340
2041	04 Oct 13	nicklas	1341
2041	04 Oct 13	nicklas	1342	/**
7099	06 Apr 23	nicklas	1343	The "FlowCellID" annotation, used for physical bioassays (FlowCell)
7099	06 Apr 23	nicklas	1344	and also FASTQ files.
2021	17 Sep 13	nicklas	1345	@since 2.13
2021	17 Sep 13	nicklas	1346	*/
2021	17 Sep 13	nicklas	1347	public static final Annotationtype FLOWCELL_ID =
7099	06 Apr 23	nicklas	1348	new Annotationtype("FlowCellID", Type.STRING, false, Item.PHYSICALBIOASSAY, Item.FILE);
2021	17 Sep 13	nicklas	1349
1902	13 Mar 13	nicklas	1350	/**
7099	06 Apr 23	nicklas	1351	The "LaneNumber" annotation, used for FASTQ files.
7099	06 Apr 23	nicklas	1352	@since 4.46
7099	06 Apr 23	nicklas	1353	*/
7099	06 Apr 23	nicklas	1354	public static final Annotationtype LANE_NUMBER =
7099	06 Apr 23	nicklas	1355	new Annotationtype("LaneNumber", Type.INT, false, Item.FILE);
7099	06 Apr 23	nicklas	1356
7099	06 Apr 23	nicklas	1357	/**
7108	13 Apr 23	nicklas	1358	The "ReadNumber" annotation, used for FASTQ files.
7108	13 Apr 23	nicklas	1359	@since 4.46
7099	06 Apr 23	nicklas	1360	*/
7099	06 Apr 23	nicklas	1361	public static final Annotationtype READ_NUMBER =
7099	06 Apr 23	nicklas	1362	new Annotationtype("ReadNumber", Type.INT, false, Item.FILE);
7099	06 Apr 23	nicklas	1363
7099	06 Apr 23	nicklas	1364	/**
7108	13 Apr 23	nicklas	1365	The "ReadLnegth" annotation, used for FASTQ files.
7108	13 Apr 23	nicklas	1366	@since 4.46
7108	13 Apr 23	nicklas	1367	*/
7108	13 Apr 23	nicklas	1368	public static final Annotationtype READ_LENGTH =
7108	13 Apr 23	nicklas	1369	new Annotationtype("ReadLength", Type.INT, false, Item.FILE);
7108	13 Apr 23	nicklas	1370
7108	13 Apr 23	nicklas	1371	/**
5469	04 Jun 19	nicklas	1372	The "FlowCellType" annotation, used for physical bioassays (FlowCell)
7108	13 Apr 23	nicklas	1373	and hardware (Sequencer) and also FASTQ files.
2412	09 May 14	nicklas	1374	@since 2.15.1
2412	09 May 14	nicklas	1375	*/
2412	09 May 14	nicklas	1376	public static final Annotationtype FLOWCELL_TYPE =
7108	13 Apr 23	nicklas	1377	new Annotationtype("FlowCellType", Type.STRING, false, Item.PHYSICALBIOASSAY, Item.HARDWARE, Item.FILE);
2412	09 May 14	nicklas	1378
2412	09 May 14	nicklas	1379	/**
6461	01 Nov 21	nicklas	1380	The "BeadChipID" annotation, used for physical bioassays (BeadChip).
6461	01 Nov 21	nicklas	1381	@since 4.34
6461	01 Nov 21	nicklas	1382	*/
6461	01 Nov 21	nicklas	1383	public static final Annotationtype BEADCHIP_ID =
6461	01 Nov 21	nicklas	1384	new Annotationtype("BeadChipID", Type.STRING, false, Item.PHYSICALBIOASSAY);
6461	01 Nov 21	nicklas	1385
6461	01 Nov 21	nicklas	1386	/**
6461	01 Nov 21	nicklas	1387	The "BeadChipType" annotation, used for physical bioassays (BeadChip).
6461	01 Nov 21	nicklas	1388	@since 4.34
6461	01 Nov 21	nicklas	1389	*/
6461	01 Nov 21	nicklas	1390	public static final Annotationtype BEADCHIP_TYPE =
6461	01 Nov 21	nicklas	1391	new Annotationtype("BeadChipType", Type.STRING, false, Item.PHYSICALBIOASSAY);
6461	01 Nov 21	nicklas	1392
6461	01 Nov 21	nicklas	1393	/**
6461	01 Nov 21	nicklas	1394	The "BeadChipPosition" annotation, used for extracts (BloodDNA).
6461	01 Nov 21	nicklas	1395	@since 4.34
6461	01 Nov 21	nicklas	1396	*/
6461	01 Nov 21	nicklas	1397	public static final Annotationtype BEADCHIP_POSITION =
6461	01 Nov 21	nicklas	1398	new Annotationtype("BeadChipPosition", Type.STRING, false, Item.EXTRACT);
6461	01 Nov 21	nicklas	1399
6461	01 Nov 21	nicklas	1400	/**
6461	01 Nov 21	nicklas	1401	The "ScanDate" annotation, used for derived bioassays (Scan). It is
6461	01 Nov 21	nicklas	1402	a timestamp annotation.
6461	01 Nov 21	nicklas	1403	@since 4.34
6461	01 Nov 21	nicklas	1404	*/
6461	01 Nov 21	nicklas	1405	public static final Annotationtype SCAN_DATE =
6461	01 Nov 21	nicklas	1406	new Annotationtype("ScanDate", Type.TIMESTAMP, false, Item.DERIVEDBIOASSAY);
6461	01 Nov 21	nicklas	1407
6461	01 Nov 21	nicklas	1408	/**
2079	17 Oct 13	nicklas	1409	The "ClusterStart" annotation, used for physical bioassays (FlowCell).
2079	17 Oct 13	nicklas	1410	The date the flow cell was clustered.
2079	17 Oct 13	nicklas	1411	@since 2.13
2079	17 Oct 13	nicklas	1412	*/
2079	17 Oct 13	nicklas	1413	public static final Annotationtype CLUSTER_START =
2351	10 Apr 14	nicklas	1414	new Annotationtype("ClusterStart", Type.DATE, false, Item.PHYSICALBIOASSAY);
2079	17 Oct 13	nicklas	1415
2079	17 Oct 13	nicklas	1416	/**
2079	17 Oct 13	nicklas	1417	The "ClusterOperator" annotation, used for physical bioassays (FlowCell).
2079	17 Oct 13	nicklas	1418	The operator that is responsible for clustering.
2079	17 Oct 13	nicklas	1419	@since 2.13
2079	17 Oct 13	nicklas	1420	*/
2079	17 Oct 13	nicklas	1421	public static final Annotationtype CLUSTER_OPERATOR =
2351	10 Apr 14	nicklas	1422	new Annotationtype("ClusterOperator", Type.STRING, false, Item.PHYSICALBIOASSAY);
2079	17 Oct 13	nicklas	1423
2079	17 Oct 13	nicklas	1424
2079	17 Oct 13	nicklas	1425	/**
2224	12 Feb 14	nicklas	1426	The "SequencingCycles" annotation, used for physical bioassays and
2224	12 Feb 14	nicklas	1427	(FlowCell) derived bioassays (SequencingRun).
2085	18 Oct 13	nicklas	1428	@since 2.13
2085	18 Oct 13	nicklas	1429	*/
2087	18 Oct 13	nicklas	1430	public static final Annotationtype SEQUENCING_CYCLES =
2351	10 Apr 14	nicklas	1431	new Annotationtype("SequencingCycles", Type.STRING, false, Item.PHYSICALBIOASSAY, Item.DERIVEDBIOASSAY);
2085	18 Oct 13	nicklas	1432
2085	18 Oct 13	nicklas	1433	/**
2226	13 Feb 14	nicklas	1434	The "FailedLanes" annotation, used for physical bioassays (FlowCell).
2226	13 Feb 14	nicklas	1435	It is a multi-valued annotation type representing the index numbers
2226	13 Feb 14	nicklas	1436	of lanes that failed during sequencing of a flow cell. The index numbers
2226	13 Feb 14	nicklas	1437	go from 1 to the size of the flow cell (eg. 1-8).
2226	13 Feb 14	nicklas	1438	@since 2.15
2226	13 Feb 14	nicklas	1439	*/
2226	13 Feb 14	nicklas	1440	public static final Annotationtype FAILED_LANES =
2351	10 Apr 14	nicklas	1441	new Annotationtype("FailedLanes", Type.INT, false, Item.PHYSICALBIOASSAY);
2226	13 Feb 14	nicklas	1442
2226	13 Feb 14	nicklas	1443	/**
2224	12 Feb 14	nicklas	1444	The "HiSeqPosition" annotation, used for derived bioassays (SequencingRun).
2060	11 Oct 13	nicklas	1445	It is an enumerated string annotation type with two options: A and B
2060	11 Oct 13	nicklas	1446	@since 2.13
2060	11 Oct 13	nicklas	1447	*/
2060	11 Oct 13	nicklas	1448	public static final Annotationtype HISEQ_POSITION =
2351	10 Apr 14	nicklas	1449	new Annotationtype("HiSeqPosition", Type.STRING, false, Item.DERIVEDBIOASSAY);
2079	17 Oct 13	nicklas	1450
2028	30 Sep 13	nicklas	1451	/**
2049	07 Oct 13	nicklas	1452	The "SequencingStart" annotation, used for derived bioassays (SequencingRun).
2049	07 Oct 13	nicklas	1453	@since 2.13
2049	07 Oct 13	nicklas	1454	*/
2049	07 Oct 13	nicklas	1455	public static final Annotationtype SEQUENCING_START =
2351	10 Apr 14	nicklas	1456	new Annotationtype("SequencingStart", Type.DATE, false, Item.DERIVEDBIOASSAY);
2049	07 Oct 13	nicklas	1457
2049	07 Oct 13	nicklas	1458	/**
2196	13 Jan 14	nicklas	1459	The "SequencingTurnAround" annotation, used for derived bioassays (SequencingRun).
2196	13 Jan 14	nicklas	1460	@since 2.14
2196	13 Jan 14	nicklas	1461	*/
2196	13 Jan 14	nicklas	1462	public static final Annotationtype SEQUENCING_TURN_AROUND =
2351	10 Apr 14	nicklas	1463	new Annotationtype("SequencingTurnAround", Type.TIMESTAMP, false, Item.DERIVEDBIOASSAY);
2196	13 Jan 14	nicklas	1464
2196	13 Jan 14	nicklas	1465
2196	13 Jan 14	nicklas	1466	/**
2196	13 Jan 14	nicklas	1467	The "SequencingEnd" annotation, used for derived bioassays (SequencingRun).
2196	13 Jan 14	nicklas	1468	@since 2.14
2196	13 Jan 14	nicklas	1469	*/
2196	13 Jan 14	nicklas	1470	public static final Annotationtype SEQUENCING_END =
2351	10 Apr 14	nicklas	1471	new Annotationtype("SequencingEnd", Type.TIMESTAMP, false, Item.DERIVEDBIOASSAY);
2196	13 Jan 14	nicklas	1472
2196	13 Jan 14	nicklas	1473	/**
7099	06 Apr 23	nicklas	1474	The "SequencingRunNumber" annotation, used for derived bioassays (SequencingRun)
7099	06 Apr 23	nicklas	1475	and also FASTQ files.
2224	12 Feb 14	nicklas	1476	@since 2.15
2224	12 Feb 14	nicklas	1477	*/
2224	12 Feb 14	nicklas	1478	public static final Annotationtype SEQUENCING_RUN_NUMBER =
7099	06 Apr 23	nicklas	1479	new Annotationtype("SequencingRunNumber", Type.INT, false, Item.DERIVEDBIOASSAY, Item.FILE);
2224	12 Feb 14	nicklas	1480
2224	12 Feb 14	nicklas	1481	/**
2049	07 Oct 13	nicklas	1482	The "SequencingOperator" annotation, used for derived bioassays (SequencingRun).
2049	07 Oct 13	nicklas	1483	@since 2.13
2049	07 Oct 13	nicklas	1484	*/
2049	07 Oct 13	nicklas	1485	public static final Annotationtype SEQUENCING_OPERATOR =
2351	10 Apr 14	nicklas	1486	new Annotationtype("SequencingOperator", Type.STRING, false, Item.DERIVEDBIOASSAY);
2049	07 Oct 13	nicklas	1487
2224	12 Feb 14	nicklas	1488	/**
2224	12 Feb 14	nicklas	1489	The "DataFilesFolder" annotation, used for derived bioassays that
2224	12 Feb 14	nicklas	1490	are linked with data files on the server.
2224	12 Feb 14	nicklas	1491	@since 2.15
2224	12 Feb 14	nicklas	1492	*/
2224	12 Feb 14	nicklas	1493	public static final Annotationtype DATA_FILES_FOLDER =
2721	01 Oct 14	nicklas	1494	new Annotationtype("DataFilesFolder", Type.STRING, false, Item.DERIVEDBIOASSAY, Item.RAWBIOASSAY);
2224	12 Feb 14	nicklas	1495
2049	07 Oct 13	nicklas	1496	/**
6215	16 Apr 21	nicklas	1497	The "RawFASTQ" annotation, used for (demuxed) derived bioassays that
6209	13 Apr 21	nicklas	1498	use external FASTQ files for import. This annotation should typically
6209	13 Apr 21	nicklas	1499	have 2 values (one for R1 and one for R2).
6209	13 Apr 21	nicklas	1500	@since 4.32
6209	13 Apr 21	nicklas	1501	*/
6209	13 Apr 21	nicklas	1502	public static final Annotationtype RAW_FASTQ =
6209	13 Apr 21	nicklas	1503	new Annotationtype("RawFASTQ", Type.STRING, false, Item.DERIVEDBIOASSAY);
6209	13 Apr 21	nicklas	1504
6209	13 Apr 21	nicklas	1505	/**
2225	13 Feb 14	nicklas	1506	The "SequencingResult" annotation, used for derived bioassays (SequencingRun).
2225	13 Feb 14	nicklas	1507	A value of "Successful" typically means that the process can continue with
2225	13 Feb 14	nicklas	1508	next step (demux and merge). A value of "Failed" indicates a complete
2225	13 Feb 14	nicklas	1509	failure that require a new flow cell to be clustered. The pooled
2225	13 Feb 14	nicklas	1510	libraries on the current flow cell are flagged with "SequencingFailed".
3635	30 Nov 15	nicklas	1511	A value of "FirstBaseReportFailed" (user for HiSeq only) indicates that the
3635	30 Nov 15	nicklas	1512	first sequencing attempt
2225	13 Feb 14	nicklas	1513	failed but that it is possible to re-start with the same flow cell. The
2225	13 Feb 14	nicklas	1514	annotation is also copied to the flow cell.
2225	13 Feb 14	nicklas	1515	@since 2.15
2225	13 Feb 14	nicklas	1516	*/
2225	13 Feb 14	nicklas	1517	public static final Annotationtype SEQUENCING_RESULT =
2351	10 Apr 14	nicklas	1518	new Annotationtype("SequencingResult", Type.STRING, false, Item.PHYSICALBIOASSAY, Item.DERIVEDBIOASSAY);
2225	13 Feb 14	nicklas	1519
2225	13 Feb 14	nicklas	1520	/**
2228	14 Feb 14	nicklas	1521	The "SequencingConfirmed" annotation, used for derived bioassays (SequencingRun).
2228	14 Feb 14	nicklas	1522	Store a flag indicating that the sequencing result has been confirmed by a
3571	30 Oct 15	nicklas	1523	user with {@link ReggieRole#SECONDARY_ANALYSIS} role.
2228	14 Feb 14	nicklas	1524	@since 2.15
2228	14 Feb 14	nicklas	1525	*/
2228	14 Feb 14	nicklas	1526	public static final Annotationtype SEQUENCING_CONFIRMED =
2351	10 Apr 14	nicklas	1527	new Annotationtype("SequencingConfirmed", Type.BOOLEAN, false, Item.DERIVEDBIOASSAY);
2228	14 Feb 14	nicklas	1528
2228	14 Feb 14	nicklas	1529	/**
2320	04 Apr 14	nicklas	1530	The "ReadString" annotation, used for derived bioassays (DemuxedSequences).
2320	04 Apr 14	nicklas	1531	@since 2.13
2320	04 Apr 14	nicklas	1532	*/
2320	04 Apr 14	nicklas	1533	public static final Annotationtype READ_STRING =
2351	10 Apr 14	nicklas	1534	new Annotationtype("ReadString", Type.STRING, false, Item.DERIVEDBIOASSAY);
2320	04 Apr 14	nicklas	1535
2320	04 Apr 14	nicklas	1536	/**
2320	04 Apr 14	nicklas	1537	The "OmitLanes" annotation, used for derived bioassays (DemuxedSequences).
2320	04 Apr 14	nicklas	1538	It is a multi-valued annotation type representing the index numbers
2320	04 Apr 14	nicklas	1539	of lanes that was omitted during demulitplexing of the sequenced data.
2320	04 Apr 14	nicklas	1540	The index numbers go from 1 to the size of the flow cell (eg. 1-8).
2320	04 Apr 14	nicklas	1541	@since 2.16
2320	04 Apr 14	nicklas	1542	*/
2320	04 Apr 14	nicklas	1543	public static final Annotationtype OMIT_LANES =
2351	10 Apr 14	nicklas	1544	new Annotationtype("OmitLanes", Type.INT, false, Item.DERIVEDBIOASSAY);
2320	04 Apr 14	nicklas	1545
2350	10 Apr 14	nicklas	1546	/**
5865	12 Mar 20	nicklas	1547	The "BarcodeSet" annotation, used for tags (Barcode).
5865	12 Mar 20	nicklas	1548	It is a string annotation for grouping possible barcodes
5865	12 Mar 20	nicklas	1549	that are typically used together when sequencing.
5865	12 Mar 20	nicklas	1550	@since 4.26
5865	12 Mar 20	nicklas	1551	*/
5865	12 Mar 20	nicklas	1552	public static final Annotationtype BARCODE_SET =
5865	12 Mar 20	nicklas	1553	new Annotationtype("BarcodeSet", Type.STRING, false, Item.TAG);
5865	12 Mar 20	nicklas	1554
5865	12 Mar 20	nicklas	1555
5865	12 Mar 20	nicklas	1556	/**
5489	12 Jun 19	nicklas	1557	The "BarcodeSequence" annotation, used for tags (Barcode).
2350	10 Apr 14	nicklas	1558	It is a string annotation containing the sequence for
2350	10 Apr 14	nicklas	1559	the barcode. Typically 7 characters from ACGT.
2350	10 Apr 14	nicklas	1560	@since 2.16
2350	10 Apr 14	nicklas	1561	*/
2350	10 Apr 14	nicklas	1562	public static final Annotationtype BARCODE_SEQUENCE =
2351	10 Apr 14	nicklas	1563	new Annotationtype("BarcodeSequence", Type.STRING, false, Item.TAG);
2320	04 Apr 14	nicklas	1564
2320	04 Apr 14	nicklas	1565	/**
5489	12 Jun 19	nicklas	1566	The "BarcodeSequence2" annotation, used for tags (Barcode).
5489	12 Jun 19	nicklas	1567	It is a string annotation containing the sequence for
5489	12 Jun 19	nicklas	1568	the a second barcode when that is used in the sequencing.
5489	12 Jun 19	nicklas	1569	Typically 7 or 8 characters from ACGT.
5489	12 Jun 19	nicklas	1570	@since 4.23
5489	12 Jun 19	nicklas	1571	*/
5489	12 Jun 19	nicklas	1572	public static final Annotationtype BARCODE_SEQUENCE_2 =
5489	12 Jun 19	nicklas	1573	new Annotationtype("BarcodeSequence2", Type.STRING, false, Item.TAG);
5489	12 Jun 19	nicklas	1574
5489	12 Jun 19	nicklas	1575	/**
2364	15 Apr 14	nicklas	1576	The "AnalysisResult" annotation, used for derived bioassays.
2364	15 Apr 14	nicklas	1577	A value of "Successful" typically means that the process can continue with
2364	15 Apr 14	nicklas	1578	next step in the analysis pipeline. A value of "Failed" indicates a
2364	15 Apr 14	nicklas	1579	failure that require analysis and/or sequencing to be re-done at a
2364	15 Apr 14	nicklas	1580	higher level. The current pipeline is not continued.
2364	15 Apr 14	nicklas	1581	@since 2.16
2364	15 Apr 14	nicklas	1582	*/
2364	15 Apr 14	nicklas	1583	public static final Annotationtype ANALYSIS_RESULT =
2826	16 Oct 14	nicklas	1584	new Annotationtype("AnalysisResult", Type.STRING, false, Item.DERIVEDBIOASSAY, Item.RAWBIOASSAY);
2364	15 Apr 14	nicklas	1585
2365	16 Apr 14	nicklas	1586	/**
7099	06 Apr 23	nicklas	1587	The "READS" annotation, used for derived bioassays (MergedSequences)
7099	06 Apr 23	nicklas	1588	and FASTQ files.
2365	16 Apr 14	nicklas	1589	The annotation is the number of sequences that has been assigned to
2420	13 May 14	nicklas	1590	the library before any masking or filtering.
2365	16 Apr 14	nicklas	1591	@since 2.16
2365	16 Apr 14	nicklas	1592	*/
2420	13 May 14	nicklas	1593	public static final Annotationtype READS =
7099	06 Apr 23	nicklas	1594	new Annotationtype("READS", Type.LONG, false, Item.DERIVEDBIOASSAY, Item.FILE);
2365	16 Apr 14	nicklas	1595
2365	16 Apr 14	nicklas	1596	/**
2420	13 May 14	nicklas	1597	The "PF_READS" annotation, used for derived bioassays (MergedSequences).
2365	16 Apr 14	nicklas	1598	The annotation is the number of sequences that has been assigned to
2365	16 Apr 14	nicklas	1599	the library after filtering.
2365	16 Apr 14	nicklas	1600	@since 2.16
2365	16 Apr 14	nicklas	1601	*/
2420	13 May 14	nicklas	1602	public static final Annotationtype PF_READS =
2420	13 May 14	nicklas	1603	new Annotationtype("PF_READS", Type.LONG, false, Item.DERIVEDBIOASSAY);
2368	17 Apr 14	nicklas	1604
2364	15 Apr 14	nicklas	1605	/**
2689	23 Sep 14	nicklas	1606	The "ADAPTER_READS" annotation, used for derived bioassays (MergedSequences).
2689	23 Sep 14	nicklas	1607	The annotation is the number of sequences that was removed due to matching
2689	23 Sep 14	nicklas	1608	an Illumina adpter sequence.
2689	23 Sep 14	nicklas	1609	@since 2.16
2689	23 Sep 14	nicklas	1610	*/
2689	23 Sep 14	nicklas	1611	public static final Annotationtype ADAPTER_READS =
2689	23 Sep 14	nicklas	1612	new Annotationtype("ADAPTER_READS", Type.LONG, false, Item.DERIVEDBIOASSAY);
2689	23 Sep 14	nicklas	1613
2689	23 Sep 14	nicklas	1614	/**
2497	05 Jun 14	nicklas	1615	The "PT_READS" annotation, used for derived bioassays (MergedSequences).
2497	05 Jun 14	nicklas	1616	The annotation is the number of sequences that remains for a library after
2497	05 Jun 14	nicklas	1617	running trimmomatic.
2497	05 Jun 14	nicklas	1618	@since 2.16
2497	05 Jun 14	nicklas	1619	*/
2497	05 Jun 14	nicklas	1620	public static final Annotationtype PT_READS =
2497	05 Jun 14	nicklas	1621	new Annotationtype("PT_READS", Type.LONG, false, Item.DERIVEDBIOASSAY);
2497	05 Jun 14	nicklas	1622
2497	05 Jun 14	nicklas	1623	/**
2680	18 Sep 14	nicklas	1624	The "FragmentSizeAvg" annotation, used for derived bioassays (MergedSequences).
2680	18 Sep 14	nicklas	1625	The annotation is the average size of fragments in the library
2680	18 Sep 14	nicklas	1626	as estimated after alignment.
2680	18 Sep 14	nicklas	1627	@since 2.16
2680	18 Sep 14	nicklas	1628	*/
2680	18 Sep 14	nicklas	1629	public static final Annotationtype FRAGMENT_SIZE_AVG =
2680	18 Sep 14	nicklas	1630	new Annotationtype("FragmentSizeAvg", Type.INT, false, Item.DERIVEDBIOASSAY);
2680	18 Sep 14	nicklas	1631
2680	18 Sep 14	nicklas	1632	/**
2680	18 Sep 14	nicklas	1633	The "FragmentSizeStdev" annotation, used for derived bioassays (MergedSequences).
2680	18 Sep 14	nicklas	1634	The annotation is the standard deviation of the size of fragments in the library
2680	18 Sep 14	nicklas	1635	as estimated after alignment.
2680	18 Sep 14	nicklas	1636	@since 2.16
2680	18 Sep 14	nicklas	1637	*/
2680	18 Sep 14	nicklas	1638	public static final Annotationtype FRAGMENT_SIZE_STDEV =
2680	18 Sep 14	nicklas	1639	new Annotationtype("FragmentSizeStdev", Type.INT, false, Item.DERIVEDBIOASSAY);
2680	18 Sep 14	nicklas	1640
6421	23 Sep 21	nicklas	1641	/**
6421	23 Sep 21	nicklas	1642	The "ReadLengthAvgR1" annotation, used for derived bioassays (MergedSequences).
6421	23 Sep 21	nicklas	1643	The annotation is the average size of read length in the FASTQ file for the
6421	23 Sep 21	nicklas	1644	first read.
6421	23 Sep 21	nicklas	1645	@since 4.33
6421	23 Sep 21	nicklas	1646	*/
6421	23 Sep 21	nicklas	1647	public static final Annotationtype READLENGTH_AVG_R1 =
6421	23 Sep 21	nicklas	1648	new Annotationtype("ReadLengthAvgR1", Type.INT, false, Item.DERIVEDBIOASSAY);
6421	23 Sep 21	nicklas	1649
6421	23 Sep 21	nicklas	1650	/**
6421	23 Sep 21	nicklas	1651	The "ReadLengthAvgR2" annotation, used for derived bioassays (MergedSequences).
6421	23 Sep 21	nicklas	1652	The annotation is the average size of read length in the FASTQ file for the
6421	23 Sep 21	nicklas	1653	second read.
6421	23 Sep 21	nicklas	1654	@since 4.33
6421	23 Sep 21	nicklas	1655	*/
6421	23 Sep 21	nicklas	1656	public static final Annotationtype READLENGTH_AVG_R2 =
6421	23 Sep 21	nicklas	1657	new Annotationtype("ReadLengthAvgR2", Type.INT, false, Item.DERIVEDBIOASSAY);
2680	18 Sep 14	nicklas	1658
2680	18 Sep 14	nicklas	1659	/**
2434	19 May 14	nicklas	1660	The "PF_NNNN_PCT" annotation, used for derived bioassays (DemuxedSequences).
2434	19 May 14	nicklas	1661	The annotation is the percentage of sequences that has could not be assigned
2434	19 May 14	nicklas	1662	to any barcode when demultiplexing.
2434	19 May 14	nicklas	1663	@since 2.16
2434	19 May 14	nicklas	1664	*/
2434	19 May 14	nicklas	1665	public static final Annotationtype PF_NNNN_PCT =
2434	19 May 14	nicklas	1666	new Annotationtype("PF_NNNN_PCT", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
2434	19 May 14	nicklas	1667
2434	19 May 14	nicklas	1668	/**
2434	19 May 14	nicklas	1669	The "PF_UNUSED_PCT" annotation, used for derived bioassays (DemuxedSequences).
2434	19 May 14	nicklas	1670	The annotation is the percentage of sequences that was assigned to a barcode
2434	19 May 14	nicklas	1671	that has not been used in the pool (used to detect misatakes when pooling or
2434	19 May 14	nicklas	1672	loading the sequencer).
2434	19 May 14	nicklas	1673	@since 2.16
2434	19 May 14	nicklas	1674	*/
2434	19 May 14	nicklas	1675	public static final Annotationtype PF_UNUSED_PCT =
2434	19 May 14	nicklas	1676	new Annotationtype("PF_UNUSED_PCT", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
2434	19 May 14	nicklas	1677
2434	19 May 14	nicklas	1678	/**
2434	19 May 14	nicklas	1679	The "DemuxWarnings" annotation, used for derived bioassays (DemuxedSequences).
2434	19 May 14	nicklas	1680	Use to register warnings about things that seem strange during the demultiplexing.
2434	19 May 14	nicklas	1681	Eg. high percentage of unused barcodes.
2434	19 May 14	nicklas	1682	@since 2.16
2434	19 May 14	nicklas	1683	*/
2434	19 May 14	nicklas	1684	public static final Annotationtype DEMUX_WARNINGS =
2434	19 May 14	nicklas	1685	new Annotationtype("DemuxWarnings", Type.STRING, false, Item.DERIVEDBIOASSAY);
2434	19 May 14	nicklas	1686
2434	19 May 14	nicklas	1687	/**
3140	24 Feb 15	nicklas	1688	The "SkippedTiles" annotation, used for derived bioassays (DemuxedSequences).
3140	24 Feb 15	nicklas	1689	Use to register information about tiles that could not be demuxed. If
3140	24 Feb 15	nicklas	1690	the number of tiles is higher than a specified limit a warning will
3140	24 Feb 15	nicklas	1691	be added to "DemuxWarnings" as well.
3140	24 Feb 15	nicklas	1692	@since 3.2
3140	24 Feb 15	nicklas	1693	*/
3140	24 Feb 15	nicklas	1694	public static final Annotationtype SKIPPED_TILES =
3140	24 Feb 15	nicklas	1695	new Annotationtype("SkippedTiles", Type.STRING, false, Item.DERIVEDBIOASSAY);
3140	24 Feb 15	nicklas	1696
3140	24 Feb 15	nicklas	1697
3140	24 Feb 15	nicklas	1698	/**
2420	13 May 14	nicklas	1699	The "PM_READS" annotation, used for derived bioassays (MaskedSequences).
2420	13 May 14	nicklas	1700	The annotation is the number of sequences that has been assigned to
2420	13 May 14	nicklas	1701	the library after masking.
2420	13 May 14	nicklas	1702	@since 2.16
2420	13 May 14	nicklas	1703	*/
2420	13 May 14	nicklas	1704	public static final Annotationtype PM_READS =
2420	13 May 14	nicklas	1705	new Annotationtype("PM_READS", Type.LONG, false, Item.DERIVEDBIOASSAY);
2420	13 May 14	nicklas	1706
2420	13 May 14	nicklas	1707	/**
2420	13 May 14	nicklas	1708	The "ALIGNED_PAIRS" annotation, used for derived bioassays (AlignedSequences).
2420	13 May 14	nicklas	1709	The annotation is the number of sequences that has been assigned to
2420	13 May 14	nicklas	1710	the library after aligning.
2420	13 May 14	nicklas	1711	@since 2.16
2420	13 May 14	nicklas	1712	*/
2420	13 May 14	nicklas	1713	public static final Annotationtype ALIGNED_PAIRS =
2420	13 May 14	nicklas	1714	new Annotationtype("ALIGNED_PAIRS", Type.LONG, false, Item.DERIVEDBIOASSAY);
5843	25 Feb 20	nicklas	1715
5843	25 Feb 20	nicklas	1716	/**
5843	25 Feb 20	nicklas	1717	The "ALIGNED_BASES" annotation, used for derived bioassays (AlignedSequences).
5843	25 Feb 20	nicklas	1718	The annotation is the number of bases that has been aligned.
5843	25 Feb 20	nicklas	1719	@since 4.26
5843	25 Feb 20	nicklas	1720	*/
5843	25 Feb 20	nicklas	1721	public static final Annotationtype ALIGNED_BASES =
5843	25 Feb 20	nicklas	1722	new Annotationtype("ALIGNED_BASES", Type.LONG, false, Item.DERIVEDBIOASSAY);
5843	25 Feb 20	nicklas	1723
7113	14 Apr 23	nicklas	1724	/**
7113	14 Apr 23	nicklas	1725	The "PF_BASES" annotation, used for derived bioassays (AlignedSequences).
7113	14 Apr 23	nicklas	1726	The annotation is the number of bases that passed filter.
7113	14 Apr 23	nicklas	1727	@since 4.46
7113	14 Apr 23	nicklas	1728	*/
7113	14 Apr 23	nicklas	1729	public static final Annotationtype PF_BASES =
7113	14 Apr 23	nicklas	1730	new Annotationtype("PF_BASES", Type.LONG, false, Item.DERIVEDBIOASSAY);
7113	14 Apr 23	nicklas	1731
7113	14 Apr 23	nicklas	1732	/**
7113	14 Apr 23	nicklas	1733	The "PF_Q30_BASES" annotation, used for derived bioassays (AlignedSequences).
7113	14 Apr 23	nicklas	1734	The annotation is the number of bases that passed filter with Q30 or better
7113	14 Apr 23	nicklas	1735	quality.
7113	14 Apr 23	nicklas	1736	@since 4.46
7113	14 Apr 23	nicklas	1737	*/
7113	14 Apr 23	nicklas	1738	public static final Annotationtype PF_Q30_BASES =
7113	14 Apr 23	nicklas	1739	new Annotationtype("PF_Q30_BASES", Type.LONG, false, Item.DERIVEDBIOASSAY);
7113	14 Apr 23	nicklas	1740
2420	13 May 14	nicklas	1741
2420	13 May 14	nicklas	1742	/**
2706	29 Sep 14	nicklas	1743	The "READ_PAIRS_EXAMINED" annotation, used for derived bioassays (AlignedSequences).
2706	29 Sep 14	nicklas	1744	The annotation is the number of sequences that has been examined by picard MarkDuplicates.
2706	29 Sep 14	nicklas	1745	@since 2.16
2706	29 Sep 14	nicklas	1746	*/
2706	29 Sep 14	nicklas	1747	public static final Annotationtype READ_PAIRS_EXAMINED =
2706	29 Sep 14	nicklas	1748	new Annotationtype("READ_PAIRS_EXAMINED", Type.LONG, false, Item.DERIVEDBIOASSAY);
2706	29 Sep 14	nicklas	1749
2706	29 Sep 14	nicklas	1750	/**
2706	29 Sep 14	nicklas	1751	The "READ_PAIR_DUPLICATES" annotation, used for derived bioassays (AlignedSequences).
2706	29 Sep 14	nicklas	1752	The annotation is the number of sequences that has been found as duplicates
2706	29 Sep 14	nicklas	1753	by picard MarkDuplicates.
2706	29 Sep 14	nicklas	1754	@since 2.16
2706	29 Sep 14	nicklas	1755	*/
2706	29 Sep 14	nicklas	1756	public static final Annotationtype READ_PAIR_DUPLICATES =
2706	29 Sep 14	nicklas	1757	new Annotationtype("READ_PAIR_DUPLICATES", Type.LONG, false, Item.DERIVEDBIOASSAY);
7104	11 Apr 23	nicklas	1758
2706	29 Sep 14	nicklas	1759	/**
7104	11 Apr 23	nicklas	1760	The "READ_PAIR_OPTICAL_DUPLICATES" annotation, used for derived bioassays (AlignedSequences).
7104	11 Apr 23	nicklas	1761	The annotation is the number of sequences that has been found as duplicates.
7104	11 Apr 23	nicklas	1762	@since 4.46
7104	11 Apr 23	nicklas	1763	*/
7104	11 Apr 23	nicklas	1764	public static final Annotationtype READ_PAIR_OPTICAL_DUPLICATES =
7104	11 Apr 23	nicklas	1765	new Annotationtype("READ_PAIR_OPTICAL_DUPLICATES", Type.LONG, false, Item.DERIVEDBIOASSAY);
7104	11 Apr 23	nicklas	1766
7104	11 Apr 23	nicklas	1767	/**
7106	12 Apr 23	nicklas	1768	The "MEAN_COVERAGE" annotation, used for derived bioassays (AlignedSequences).
7106	12 Apr 23	nicklas	1769	@since 4.46
7106	12 Apr 23	nicklas	1770	*/
7106	12 Apr 23	nicklas	1771	public static final Annotationtype MEAN_COVERAGE =
7106	12 Apr 23	nicklas	1772	new Annotationtype("MEAN_COVERAGE", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
7106	12 Apr 23	nicklas	1773
7106	12 Apr 23	nicklas	1774	/**
7106	12 Apr 23	nicklas	1775	The "SD_COVERAGE" annotation, used for derived bioassays (AlignedSequences).
7106	12 Apr 23	nicklas	1776	@since 4.46
7106	12 Apr 23	nicklas	1777	*/
7106	12 Apr 23	nicklas	1778	public static final Annotationtype SD_COVERAGE =
7106	12 Apr 23	nicklas	1779	new Annotationtype("SD_COVERAGE", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
7106	12 Apr 23	nicklas	1780
7106	12 Apr 23	nicklas	1781	/**
2706	29 Sep 14	nicklas	1782	The "FRACTION_DUPLICATION" annotation, used for derived bioassays (AlignedSequences).
2706	29 Sep 14	nicklas	1783	The annotation is the fraction of sequences that has been found as duplicates
2706	29 Sep 14	nicklas	1784	by picard MarkDuplicates (PERCENT_DUPLICATION field).
2706	29 Sep 14	nicklas	1785	@since 2.16
2706	29 Sep 14	nicklas	1786	*/
2706	29 Sep 14	nicklas	1787	public static final Annotationtype FRACTION_DUPLICATION =
2706	29 Sep 14	nicklas	1788	new Annotationtype("FRACTION_DUPLICATION", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
4620	16 Nov 17	nicklas	1789
4620	16 Nov 17	nicklas	1790	/**
7104	11 Apr 23	nicklas	1791	The "FRACTION_OPTICAL_DUPLICATION" annotation, used for derived bioassays (AlignedSequences).
7104	11 Apr 23	nicklas	1792	The annotation is the fraction of sequences that has been found as duplicates.
7104	11 Apr 23	nicklas	1793	@since 4.46
7104	11 Apr 23	nicklas	1794	*/
7104	11 Apr 23	nicklas	1795	public static final Annotationtype FRACTION_OPTICAL_DUPLICATION =
7104	11 Apr 23	nicklas	1796	new Annotationtype("FRACTION_OPTICAL_DUPLICATION", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
7104	11 Apr 23	nicklas	1797
7104	11 Apr 23	nicklas	1798	/**
4620	16 Nov 17	nicklas	1799	The "QC_GenoTypeCount" annotation, used for derived bioassays (AlignedSequences).
4620	16 Nov 17	nicklas	1800	The annotation is the number of genotypes available for QC checks.
4620	16 Nov 17	nicklas	1801	@since 4.13
4620	16 Nov 17	nicklas	1802	*/
4620	16 Nov 17	nicklas	1803	public static final Annotationtype QC_GENOTYPE_COUNT =
4620	16 Nov 17	nicklas	1804	new Annotationtype("QC_GenoTypeCount", Type.INT, false, Item.DERIVEDBIOASSAY);
4620	16 Nov 17	nicklas	1805
4620	16 Nov 17	nicklas	1806	/**
4658	26 Jan 18	nicklas	1807	The "QC_GenoTypeHET_PCT" annotation, used for derived bioassays (AlignedSequences).
4658	26 Jan 18	nicklas	1808	The annotation is the percentage of genotypes found to be heterozygous.
4658	26 Jan 18	nicklas	1809	@since 4.14
4620	16 Nov 17	nicklas	1810	*/
4658	26 Jan 18	nicklas	1811	public static final Annotationtype QC_GENOTYPE_HET_PCT =
4658	26 Jan 18	nicklas	1812	new Annotationtype("QC_GenoTypeHET_PCT", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
4642	28 Nov 17	nicklas	1813
4642	28 Nov 17	nicklas	1814	/**
4642	28 Nov 17	nicklas	1815	The "QC_GenoTypeStatus" annotation, used for derived bioassays (AlignedSequences).
4642	28 Nov 17	nicklas	1816	The annotation is an enum indicating if qc has been done or not or if it should
4642	28 Nov 17	nicklas	1817	be disabled.
4642	28 Nov 17	nicklas	1818	@since 4.14
4642	28 Nov 17	nicklas	1819	*/
4642	28 Nov 17	nicklas	1820	public static final Annotationtype QC_GENOTYPE_STATUS =
4642	28 Nov 17	nicklas	1821	new Annotationtype("QC_GenoTypeStatus", Type.STRING, false, Item.DERIVEDBIOASSAY);
4642	28 Nov 17	nicklas	1822
4648	15 Dec 17	nicklas	1823	/**
4710	20 Mar 18	nicklas	1824	The "QC_GenoTypeVerified" annotation, used for derived bioassays (AlignedSequences).
4710	20 Mar 18	nicklas	1825	The annotation is an enum indicating if the genotypes of alignment has been verified
4710	20 Mar 18	nicklas	1826	to match another alignment from a different sample.
4710	20 Mar 18	nicklas	1827	@since 4.16
4710	20 Mar 18	nicklas	1828	*/
4710	20 Mar 18	nicklas	1829	public static final Annotationtype QC_GENOTYPE_VERIFIED =
4710	20 Mar 18	nicklas	1830	new Annotationtype("QC_GenoTypeVerified", Type.STRING, false, Item.DERIVEDBIOASSAY);
4710	20 Mar 18	nicklas	1831
4710	20 Mar 18	nicklas	1832
4710	20 Mar 18	nicklas	1833	/**
4648	15 Dec 17	nicklas	1834	The "QC_GenoTypeComment" annotation type, used for comments about
4648	15 Dec 17	nicklas	1835	genotype comparisons. Used on derived bioassays (AlignedSequences).
4648	15 Dec 17	nicklas	1836	@since 4.14
4648	15 Dec 17	nicklas	1837	*/
4648	15 Dec 17	nicklas	1838	public static final Annotationtype QC_GENOTYPE_COMMENT =
4648	15 Dec 17	nicklas	1839	new Annotationtype("QC_GenoTypeComment", Type.STRING, false, Item.DERIVEDBIOASSAY);
2706	29 Sep 14	nicklas	1840
6476	05 Nov 21	nicklas	1841
2706	29 Sep 14	nicklas	1842	/**
6476	05 Nov 21	nicklas	1843	The "CallDate" annotation type, used for derived bioassays (GenotypeCall).
6476	05 Nov 21	nicklas	1844	@since 4.34
6476	05 Nov 21	nicklas	1845	*/
6476	05 Nov 21	nicklas	1846	public static final Annotationtype CALL_DATE =
6476	05 Nov 21	nicklas	1847	new Annotationtype("CallDate", Type.TIMESTAMP, false, Item.DERIVEDBIOASSAY);
6476	05 Nov 21	nicklas	1848
6476	05 Nov 21	nicklas	1849	/**
6476	05 Nov 21	nicklas	1850	The "NumCalls" annotation type, used for derived bioassays (GenotypeCall).
6476	05 Nov 21	nicklas	1851	@since 4.34
6476	05 Nov 21	nicklas	1852	*/
6476	05 Nov 21	nicklas	1853	public static final Annotationtype NUM_CALLS =
6476	05 Nov 21	nicklas	1854	new Annotationtype("NumCalls", Type.INT, false, Item.DERIVEDBIOASSAY);
6476	05 Nov 21	nicklas	1855
6476	05 Nov 21	nicklas	1856	/**
6476	05 Nov 21	nicklas	1857	The "NumNoCalls" annotation type, used for derived bioassays (GenotypeCall).
6476	05 Nov 21	nicklas	1858	@since 4.34
6476	05 Nov 21	nicklas	1859	*/
6476	05 Nov 21	nicklas	1860	public static final Annotationtype NUM_NO_CALLS =
6476	05 Nov 21	nicklas	1861	new Annotationtype("NumNoCalls", Type.INT, false, Item.DERIVEDBIOASSAY);
6476	05 Nov 21	nicklas	1862
6476	05 Nov 21	nicklas	1863	/**
6476	05 Nov 21	nicklas	1864	The "CallRate" annotation type, used for derived bioassays (GenotypeCall).
6476	05 Nov 21	nicklas	1865	@since 4.34
6476	05 Nov 21	nicklas	1866	*/
6476	05 Nov 21	nicklas	1867	public static final Annotationtype CALL_RATE =
6476	05 Nov 21	nicklas	1868	new Annotationtype("CallRate", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
6476	05 Nov 21	nicklas	1869
6476	05 Nov 21	nicklas	1870	/**
6476	05 Nov 21	nicklas	1871	The "GC10" annotation type, used for derived bioassays (GenotypeCall).
6476	05 Nov 21	nicklas	1872	@since 4.34
6476	05 Nov 21	nicklas	1873	*/
6476	05 Nov 21	nicklas	1874	public static final Annotationtype GC10 =
6476	05 Nov 21	nicklas	1875	new Annotationtype("GC10", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
6476	05 Nov 21	nicklas	1876
6476	05 Nov 21	nicklas	1877	/**
6476	05 Nov 21	nicklas	1878	The "GC50" annotation type, used for derived bioassays (GenotypeCall).
6476	05 Nov 21	nicklas	1879	@since 4.34
6476	05 Nov 21	nicklas	1880	*/
6476	05 Nov 21	nicklas	1881	public static final Annotationtype GC50 =
6476	05 Nov 21	nicklas	1882	new Annotationtype("GC50", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
6476	05 Nov 21	nicklas	1883
6476	05 Nov 21	nicklas	1884	/**
6476	05 Nov 21	nicklas	1885	The "LogRDev" annotation type, used for derived bioassays (GenotypeCall).
6476	05 Nov 21	nicklas	1886	@since 4.34
6476	05 Nov 21	nicklas	1887	*/
6476	05 Nov 21	nicklas	1888	public static final Annotationtype LOG_R_DEV =
6476	05 Nov 21	nicklas	1889	new Annotationtype("LogRDev", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
6476	05 Nov 21	nicklas	1890
6557	31 Jan 22	nicklas	1891
6476	05 Nov 21	nicklas	1892	/**
6557	31 Jan 22	nicklas	1893	The "GenotypeCount" annotation type, used for raw bioassays (GenotypeCall).
6557	31 Jan 22	nicklas	1894	@since 4.35
6557	31 Jan 22	nicklas	1895	*/
6557	31 Jan 22	nicklas	1896	public static final Annotationtype GENOTYPE_COUNT =
6557	31 Jan 22	nicklas	1897	new Annotationtype("GenotypeCount", Type.INT, false, Item.RAWBIOASSAY);
6557	31 Jan 22	nicklas	1898
6557	31 Jan 22	nicklas	1899	/**
6557	31 Jan 22	nicklas	1900	The "GenoTypeREF_PCT" annotation, used for raw bioassays (GenotypeCall).
6557	31 Jan 22	nicklas	1901	The annotation is the percentage of genotypes found to be homozygous
6557	31 Jan 22	nicklas	1902	for the reference allele.
6557	31 Jan 22	nicklas	1903	@since 4.35
6557	31 Jan 22	nicklas	1904	*/
6557	31 Jan 22	nicklas	1905	public static final Annotationtype GENOTYPE_REF_PCT =
6557	31 Jan 22	nicklas	1906	new Annotationtype("GenoTypeREF_PCT", Type.FLOAT, false, Item.RAWBIOASSAY);
6557	31 Jan 22	nicklas	1907
6557	31 Jan 22	nicklas	1908	/**
6557	31 Jan 22	nicklas	1909	The "GenoTypeHET_PCT" annotation, used for raw bioassays (GenotypeCall).
6557	31 Jan 22	nicklas	1910	The annotation is the percentage of genotypes found to be heterozygous.
6557	31 Jan 22	nicklas	1911	@since 4.35
6557	31 Jan 22	nicklas	1912	*/
6557	31 Jan 22	nicklas	1913	public static final Annotationtype GENOTYPE_HET_PCT =
6557	31 Jan 22	nicklas	1914	new Annotationtype("GenoTypeHET_PCT", Type.FLOAT, false, Item.RAWBIOASSAY);
6557	31 Jan 22	nicklas	1915
6557	31 Jan 22	nicklas	1916	/**
6557	31 Jan 22	nicklas	1917	The "GenoTypeALT_PCT" annotation, used for raw bioassays (GenotypeCall).
6557	31 Jan 22	nicklas	1918	The annotation is the percentage of genotypes found to be homozygous
6557	31 Jan 22	nicklas	1919	for the alternate allele.
6557	31 Jan 22	nicklas	1920	@since 4.35
6557	31 Jan 22	nicklas	1921	*/
6557	31 Jan 22	nicklas	1922	public static final Annotationtype GENOTYPE_ALT_PCT =
6557	31 Jan 22	nicklas	1923	new Annotationtype("GenoTypeALT_PCT", Type.FLOAT, false, Item.RAWBIOASSAY);
6557	31 Jan 22	nicklas	1924
6557	31 Jan 22	nicklas	1925	/**
6876	18 Nov 22	nicklas	1926	The "NumProbesRaw" annotation type, used for derived bioassays (Methylation).
6876	18 Nov 22	nicklas	1927	@since 4.41
6876	18 Nov 22	nicklas	1928	*/
6876	18 Nov 22	nicklas	1929	public static final Annotationtype NUM_PROBES =
6876	18 Nov 22	nicklas	1930	new Annotationtype("NumProbesRaw", Type.INT, false, Item.DERIVEDBIOASSAY);
6876	18 Nov 22	nicklas	1931
6876	18 Nov 22	nicklas	1932	/**
6876	18 Nov 22	nicklas	1933	The "NumProbesBadPVal" annotation type, used for derived bioassays (Methylation).
6876	18 Nov 22	nicklas	1934	@since 4.41
6876	18 Nov 22	nicklas	1935	*/
6876	18 Nov 22	nicklas	1936	public static final Annotationtype NUM_PROBES_BAD_PVAL =
6876	18 Nov 22	nicklas	1937	new Annotationtype("NumProbesBadPVal", Type.INT, false, Item.DERIVEDBIOASSAY);
6876	18 Nov 22	nicklas	1938
6876	18 Nov 22	nicklas	1939	/**
6876	18 Nov 22	nicklas	1940	The "NumProbes_I" annotation type, used for derived bioassays (Methylation).
6876	18 Nov 22	nicklas	1941	@since 4.41
6876	18 Nov 22	nicklas	1942	*/
6876	18 Nov 22	nicklas	1943	public static final Annotationtype NUM_PROBES_I =
6876	18 Nov 22	nicklas	1944	new Annotationtype("NumProbes_I", Type.INT, false, Item.DERIVEDBIOASSAY);
6876	18 Nov 22	nicklas	1945
6876	18 Nov 22	nicklas	1946	/**
6876	18 Nov 22	nicklas	1947	The "NumProbes_II" annotation type, used for derived bioassays (Methylation).
6876	18 Nov 22	nicklas	1948	@since 4.41
6876	18 Nov 22	nicklas	1949	*/
6876	18 Nov 22	nicklas	1950	public static final Annotationtype NUM_PROBES_II =
6876	18 Nov 22	nicklas	1951	new Annotationtype("NumProbes_II", Type.INT, false, Item.DERIVEDBIOASSAY);
6876	18 Nov 22	nicklas	1952
6876	18 Nov 22	nicklas	1953	/**
6876	18 Nov 22	nicklas	1954	The "ProbesRate" annotation type, used for derived bioassays (Methylation).
6876	18 Nov 22	nicklas	1955	@since 4.41
6876	18 Nov 22	nicklas	1956	*/
6876	18 Nov 22	nicklas	1957	public static final Annotationtype PROBES_RATE =
6876	18 Nov 22	nicklas	1958	new Annotationtype("ProbesRate", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
6876	18 Nov 22	nicklas	1959
6876	18 Nov 22	nicklas	1960	/**
6876	18 Nov 22	nicklas	1961	The "MedianMeth" annotation type, used for derived bioassays (Methylation).
6876	18 Nov 22	nicklas	1962	@since 4.41
6876	18 Nov 22	nicklas	1963	*/
6876	18 Nov 22	nicklas	1964	public static final Annotationtype MEDIAN_METH =
6876	18 Nov 22	nicklas	1965	new Annotationtype("MedianMeth", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
6876	18 Nov 22	nicklas	1966
6876	18 Nov 22	nicklas	1967	/**
6876	18 Nov 22	nicklas	1968	The "MedianUnmeth" annotation type, used for derived bioassays (Methylation).
6876	18 Nov 22	nicklas	1969	@since 4.41
6876	18 Nov 22	nicklas	1970	*/
6876	18 Nov 22	nicklas	1971	public static final Annotationtype MEDIAN_UNMETH =
6876	18 Nov 22	nicklas	1972	new Annotationtype("MedianUnmeth", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
6876	18 Nov 22	nicklas	1973
6876	18 Nov 22	nicklas	1974	/**
6876	18 Nov 22	nicklas	1975	The "PeakMeth_I" annotation type, used for derived bioassays (Methylation).
6876	18 Nov 22	nicklas	1976	@since 4.41
6876	18 Nov 22	nicklas	1977	*/
6876	18 Nov 22	nicklas	1978	public static final Annotationtype PEAK_METH_I =
6876	18 Nov 22	nicklas	1979	new Annotationtype("PeakMeth_I", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
6876	18 Nov 22	nicklas	1980
6876	18 Nov 22	nicklas	1981	/**
6876	18 Nov 22	nicklas	1982	The "PeakUnmeth_I" annotation type, used for derived bioassays (Methylation).
6876	18 Nov 22	nicklas	1983	@since 4.41
6876	18 Nov 22	nicklas	1984	*/
6876	18 Nov 22	nicklas	1985	public static final Annotationtype PEAK_UNMETH_I =
6876	18 Nov 22	nicklas	1986	new Annotationtype("PeakUnmeth_I", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
6876	18 Nov 22	nicklas	1987
6876	18 Nov 22	nicklas	1988	/**
6876	18 Nov 22	nicklas	1989	The "PeakMeth_II" annotation type, used for derived bioassays (Methylation).
6876	18 Nov 22	nicklas	1990	@since 4.41
6876	18 Nov 22	nicklas	1991	*/
6876	18 Nov 22	nicklas	1992	public static final Annotationtype PEAK_METH_II =
6876	18 Nov 22	nicklas	1993	new Annotationtype("PeakMeth_II", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
6876	18 Nov 22	nicklas	1994
6876	18 Nov 22	nicklas	1995	/**
6876	18 Nov 22	nicklas	1996	The "PeakUnmeth_II" annotation type, used for derived bioassays (Methylation).
6876	18 Nov 22	nicklas	1997	@since 4.41
6876	18 Nov 22	nicklas	1998	*/
6876	18 Nov 22	nicklas	1999	public static final Annotationtype PEAK_UNMETH_II =
6876	18 Nov 22	nicklas	2000	new Annotationtype("PeakUnmeth_II", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
6878	18 Nov 22	nicklas	2001
6876	18 Nov 22	nicklas	2002	/**
6878	18 Nov 22	nicklas	2003	The "PeakUnmeth_II" annotation type, used for derived bioassays (Methylation).
6878	18 Nov 22	nicklas	2004	@since 4.41
6878	18 Nov 22	nicklas	2005	*/
6878	18 Nov 22	nicklas	2006	public static final Annotationtype ANALYSIS_FLAG =
6878	18 Nov 22	nicklas	2007	new Annotationtype("AnalysisFlag", Type.STRING, false, Item.DERIVEDBIOASSAY);
6878	18 Nov 22	nicklas	2008
6878	18 Nov 22	nicklas	2009	/**
7287	15 Aug 23	nicklas	2010	The "TauManual" annotation type, used for derived bioassays (CopyNumber).
7287	15 Aug 23	nicklas	2011	@since 4.49
7287	15 Aug 23	nicklas	2012	*/
7287	15 Aug 23	nicklas	2013	public static final Annotationtype TAU_MANUAL =
7287	15 Aug 23	nicklas	2014	new Annotationtype("TauManual", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
7287	15 Aug 23	nicklas	2015	/**
7287	15 Aug 23	nicklas	2016	The "RhoManual" annotation type, used for derived bioassays (CopyNumber).
7287	15 Aug 23	nicklas	2017	@since 4.49
7287	15 Aug 23	nicklas	2018	*/
7287	15 Aug 23	nicklas	2019	public static final Annotationtype RHO_MANUAL =
7287	15 Aug 23	nicklas	2020	new Annotationtype("RhoManual", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
7287	15 Aug 23	nicklas	2021	/**
7287	15 Aug 23	nicklas	2022	The "PsiManual" annotation type, used for derived bioassays (CopyNumber).
7287	15 Aug 23	nicklas	2023	@since 4.49
7287	15 Aug 23	nicklas	2024	*/
7287	15 Aug 23	nicklas	2025	public static final Annotationtype PSI_MANUAL =
7287	15 Aug 23	nicklas	2026	new Annotationtype("PsiManual", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
7287	15 Aug 23	nicklas	2027	/**
7341	11 Sep 23	nicklas	2028	The "Penalty" annotation type, used for derived bioassays (CopyNumber).
7341	11 Sep 23	nicklas	2029	@since 4.49.1
7341	11 Sep 23	nicklas	2030	*/
7341	11 Sep 23	nicklas	2031	public static final Annotationtype PENALTY =
7341	11 Sep 23	nicklas	2032	new Annotationtype("Penalty", Type.INT, false, Item.DERIVEDBIOASSAY);
7341	11 Sep 23	nicklas	2033	/**
7341	11 Sep 23	nicklas	2034	The "MinDepth" annotation type, used for derived bioassays (CopyNumber).
7341	11 Sep 23	nicklas	2035	@since 4.49.1
7341	11 Sep 23	nicklas	2036	*/
7341	11 Sep 23	nicklas	2037	public static final Annotationtype MIN_DEPTH =
7341	11 Sep 23	nicklas	2038	new Annotationtype("MinDepth", Type.INT, false, Item.DERIVEDBIOASSAY);
7341	11 Sep 23	nicklas	2039	/**
7287	15 Aug 23	nicklas	2040	The "ImbalanceTest" annotation type, used for derived bioassays (CopyNumber).
7287	15 Aug 23	nicklas	2041	@since 4.49
7287	15 Aug 23	nicklas	2042	*/
7287	15 Aug 23	nicklas	2043	public static final Annotationtype IMBALANCE_TEST =
7287	15 Aug 23	nicklas	2044	new Annotationtype("ImbalanceTest", Type.STRING, false, Item.DERIVEDBIOASSAY);
7287	15 Aug 23	nicklas	2045	/**
7287	15 Aug 23	nicklas	2046	The "NormalContamination" annotation type, used for derived bioassays (CopyNumber).
7287	15 Aug 23	nicklas	2047	@since 4.49
7287	15 Aug 23	nicklas	2048	*/
7287	15 Aug 23	nicklas	2049	public static final Annotationtype NORMAL_CONTAMINATION =
7287	15 Aug 23	nicklas	2050	new Annotationtype("NormalContamination", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
7287	15 Aug 23	nicklas	2051	/**
7287	15 Aug 23	nicklas	2052	The "Ploidy" annotation type, used for derived bioassays (CopyNumber).
7287	15 Aug 23	nicklas	2053	@since 4.49
7287	15 Aug 23	nicklas	2054	*/
7287	15 Aug 23	nicklas	2055	public static final Annotationtype PLOIDY =
7287	15 Aug 23	nicklas	2056	new Annotationtype("Ploidy", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
7287	15 Aug 23	nicklas	2057	/**
7287	15 Aug 23	nicklas	2058	The "Purity" annotation type, used for derived bioassays (CopyNumber).
7287	15 Aug 23	nicklas	2059	@since 4.49
7287	15 Aug 23	nicklas	2060	*/
7287	15 Aug 23	nicklas	2061	public static final Annotationtype PURITY =
7287	15 Aug 23	nicklas	2062	new Annotationtype("Purity", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
7287	15 Aug 23	nicklas	2063	/**
7287	15 Aug 23	nicklas	2064	The "GoodnessOfFit" annotation type, used for derived bioassays (CopyNumber).
7287	15 Aug 23	nicklas	2065	@since 4.49
7287	15 Aug 23	nicklas	2066	*/
7287	15 Aug 23	nicklas	2067	public static final Annotationtype GOODNESS_OF_FIT =
7287	15 Aug 23	nicklas	2068	new Annotationtype("GoodnessOfFit", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
7287	15 Aug 23	nicklas	2069
7287	15 Aug 23	nicklas	2070	/**
7341	11 Sep 23	nicklas	2071	The "NonAberrant" annotation type, used for derived bioassays (CopyNumber).
7341	11 Sep 23	nicklas	2072	@since 4.49.1
7341	11 Sep 23	nicklas	2073	*/
7341	11 Sep 23	nicklas	2074	public static final Annotationtype NON_ABERRANT =
7341	11 Sep 23	nicklas	2075	new Annotationtype("NonAberrant", Type.STRING, false, Item.DERIVEDBIOASSAY);
7341	11 Sep 23	nicklas	2076
7341	11 Sep 23	nicklas	2077	/**
7405	08 Nov 23	nicklas	2078	The "NumberOfSegments" annotation type, used for derived bioassays (CopyNumber).
7405	08 Nov 23	nicklas	2079	@since 4.49.4
7405	08 Nov 23	nicklas	2080	*/
7405	08 Nov 23	nicklas	2081	public static final Annotationtype NUMBER_OF_SEGMENTS =
7405	08 Nov 23	nicklas	2082	new Annotationtype("NumberOfSegments", Type.INT, false, Item.DERIVEDBIOASSAY);
7405	08 Nov 23	nicklas	2083
7405	08 Nov 23	nicklas	2084	/**
7405	08 Nov 23	nicklas	2085	The "LOH_fraction" annotation type, used for derived bioassays (CopyNumber).
7405	08 Nov 23	nicklas	2086	@since 4.49.4
7405	08 Nov 23	nicklas	2087	*/
7405	08 Nov 23	nicklas	2088	public static final Annotationtype LOH_FRACTION =
7405	08 Nov 23	nicklas	2089	new Annotationtype("LOH_fraction", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
7405	08 Nov 23	nicklas	2090
7405	08 Nov 23	nicklas	2091	/**
7405	08 Nov 23	nicklas	2092	The "GI_score" annotation type, used for derived bioassays (CopyNumber).
7405	08 Nov 23	nicklas	2093	@since 4.49.4
7405	08 Nov 23	nicklas	2094	*/
7405	08 Nov 23	nicklas	2095	public static final Annotationtype GI_SCORE =
7405	08 Nov 23	nicklas	2096	new Annotationtype("GI_score", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
7405	08 Nov 23	nicklas	2097
7405	08 Nov 23	nicklas	2098	/**
7293	22 Aug 23	nicklas	2099	The "AscatResult" annotation type, used for derived bioassays (CopyNumber).
7293	22 Aug 23	nicklas	2100	@since 4.49
7293	22 Aug 23	nicklas	2101	*/
7293	22 Aug 23	nicklas	2102	public static final Annotationtype ASCAT_RESULT =
7293	22 Aug 23	nicklas	2103	new Annotationtype("AscatResult", Type.STRING, false, Item.DERIVEDBIOASSAY);
7293	22 Aug 23	nicklas	2104
7293	22 Aug 23	nicklas	2105	/**
5046	22 Oct 18	nicklas	2106	The "mBAF_SNPCount" annotation, used for derived bioassays (AlignedSequences).
5046	22 Oct 18	nicklas	2107	The annotation is the number of SNPs that was available for mBAF analysis.
5046	22 Oct 18	nicklas	2108	@since 4.20
5046	22 Oct 18	nicklas	2109	*/
5046	22 Oct 18	nicklas	2110	public static final Annotationtype MBAF_SNP_COUNT =
5046	22 Oct 18	nicklas	2111	new Annotationtype("mBAF_SNPCount", Type.INT, false, Item.DERIVEDBIOASSAY);
5046	22 Oct 18	nicklas	2112
5046	22 Oct 18	nicklas	2113	/**
5046	22 Oct 18	nicklas	2114	The "mBAF_SNPCountFiltered" annotation, used for derived bioassays (AlignedSequences).
5046	22 Oct 18	nicklas	2115	The annotation is the number of SNPs that was actually used for mBAF analysis
5046	22 Oct 18	nicklas	2116	after filtering away homozygous SNPs and those with too few reads.
5046	22 Oct 18	nicklas	2117	@since 4.20
5046	22 Oct 18	nicklas	2118	*/
5046	22 Oct 18	nicklas	2119	public static final Annotationtype MBAF_SNP_COUNT_FILTERED =
5046	22 Oct 18	nicklas	2120	new Annotationtype("mBAF_SNPCountFiltered", Type.INT, false, Item.DERIVEDBIOASSAY);
5046	22 Oct 18	nicklas	2121
5046	22 Oct 18	nicklas	2122	/**
5046	22 Oct 18	nicklas	2123	The "mBAF_MinPValue" annotation, used for derived bioassays (AlignedSequences).
5046	22 Oct 18	nicklas	2124	The annotation is the p-value for the region with the lowest p-value.
5046	22 Oct 18	nicklas	2125	@since 4.20
5046	22 Oct 18	nicklas	2126	*/
5046	22 Oct 18	nicklas	2127	public static final Annotationtype MBAF_MIN_PVALUE =
5046	22 Oct 18	nicklas	2128	new Annotationtype("mBAF_MinPValue", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
5046	22 Oct 18	nicklas	2129
5046	22 Oct 18	nicklas	2130	/**
5046	22 Oct 18	nicklas	2131	The "mBAF_MinPRegion" annotation, used for derived bioassays (AlignedSequences).
5046	22 Oct 18	nicklas	2132	The annotation is the region with the lowest p-value.
5046	22 Oct 18	nicklas	2133	@since 4.20
5046	22 Oct 18	nicklas	2134	*/
5046	22 Oct 18	nicklas	2135	public static final Annotationtype MBAF_MIN_PREGION =
5046	22 Oct 18	nicklas	2136	new Annotationtype("mBAF_MinPRegion", Type.STRING, false, Item.DERIVEDBIOASSAY);
5046	22 Oct 18	nicklas	2137
5050	24 Oct 18	nicklas	2138	/**
5050	24 Oct 18	nicklas	2139	The "mBAF_NumRegions" annotation, used for derived bioassays (AlignedSequences).
5050	24 Oct 18	nicklas	2140	The annotation is the number of regions with a mBAF value.
5050	24 Oct 18	nicklas	2141	@since 4.20
5050	24 Oct 18	nicklas	2142	*/
5050	24 Oct 18	nicklas	2143	public static final Annotationtype MBAF_NUM_REGIONS =
5050	24 Oct 18	nicklas	2144	new Annotationtype("mBAF_NumRegions", Type.INT, false, Item.DERIVEDBIOASSAY);
5050	24 Oct 18	nicklas	2145
5050	24 Oct 18	nicklas	2146	/**
5050	24 Oct 18	nicklas	2147	The "mBAF_SignificantRegions" annotation, used for derived bioassays (AlignedSequences).
5050	24 Oct 18	nicklas	2148	The annotation is the number of regions with a mBAF value that has a significant deviation
5050	24 Oct 18	nicklas	2149	from the normal reference.
5050	24 Oct 18	nicklas	2150	@since 4.20
5050	24 Oct 18	nicklas	2151	*/
5050	24 Oct 18	nicklas	2152	public static final Annotationtype MBAF_SIGNIFICANT_REGIONS =
5050	24 Oct 18	nicklas	2153	new Annotationtype("mBAF_SignificantRegions", Type.INT, false, Item.DERIVEDBIOASSAY);
5046	22 Oct 18	nicklas	2154
5046	22 Oct 18	nicklas	2155	/**
4972	20 Sep 18	nicklas	2156	The "DoNotUse" annotation type which is a flag to indicate that
4972	20 Sep 18	nicklas	2157	a biomaterial (sample or extract) is not correct and it should
4972	20 Sep 18	nicklas	2158	not be used. The typical problems are mixups in the QiaCube or
4972	20 Sep 18	nicklas	2159	contamination in the lib-prep. The flag is also put on all child items.
4972	20 Sep 18	nicklas	2160	The value is an enumeration that indicates the topmost item type.
4972	20 Sep 18	nicklas	2161	@since 4.20
4972	20 Sep 18	nicklas	2162	*/
4972	20 Sep 18	nicklas	2163	public static final Annotationtype DO_NOT_USE =
4972	20 Sep 18	nicklas	2164	new Annotationtype("DoNotUse", Type.STRING, false, Item.SAMPLE, Item.EXTRACT, Item.DERIVEDBIOASSAY, Item.RAWBIOASSAY);
4972	20 Sep 18	nicklas	2165
4972	20 Sep 18	nicklas	2166	/**
4972	20 Sep 18	nicklas	2167	A comment that goes with the "DoNotUse" annotations.
4972	20 Sep 18	nicklas	2168	@since 4.20
4972	20 Sep 18	nicklas	2169	*/
4972	20 Sep 18	nicklas	2170	public static final Annotationtype DO_NOT_USE_COMMENT =
4972	20 Sep 18	nicklas	2171	new Annotationtype("DoNotUseComment", Type.STRING, false, Item.SAMPLE, Item.EXTRACT, Item.DERIVEDBIOASSAY, Item.RAWBIOASSAY);
4972	20 Sep 18	nicklas	2172
4972	20 Sep 18	nicklas	2173	/**
7099	06 Apr 23	nicklas	2174	The "SerialNumber" annotation, used for hardware items
7099	06 Apr 23	nicklas	2175	and FASTQ files.
2368	17 Apr 14	nicklas	2176	It is a string annotation containing a typically unique
2368	17 Apr 14	nicklas	2177	value for each hardware item.
2368	17 Apr 14	nicklas	2178	@since 2.16
2368	17 Apr 14	nicklas	2179	*/
2368	17 Apr 14	nicklas	2180	public static final Annotationtype SERIAL_NUMBER =
7099	06 Apr 23	nicklas	2181	new Annotationtype("SerialNumber", Type.STRING, false, Item.HARDWARE, Item.FILE);
2368	17 Apr 14	nicklas	2182
2368	17 Apr 14	nicklas	2183	/**
6010	18 Sep 20	nicklas	2184	The "Model" annotation, used for hardware items.
6010	18 Sep 20	nicklas	2185	It is a string annotation containing the generic name of
6010	18 Sep 20	nicklas	2186	the model of the hardware.
6010	18 Sep 20	nicklas	2187	@since 4.27.4
6010	18 Sep 20	nicklas	2188	*/
6010	18 Sep 20	nicklas	2189	public static final Annotationtype HARDWARE_MODEL =
6010	18 Sep 20	nicklas	2190	new Annotationtype("Model", Type.STRING, false, Item.HARDWARE);
6010	18 Sep 20	nicklas	2191
6010	18 Sep 20	nicklas	2192
6010	18 Sep 20	nicklas	2193	/**
3114	05 Feb 15	nicklas	2194	The "ParameterSet" annotation, used for software items.
3114	05 Feb 15	nicklas	2195	It is a string annotation containing a named set of alternate
3114	05 Feb 15	nicklas	2196	parameter to use in the secondary analysis pipeline.
3114	05 Feb 15	nicklas	2197	@since 3.1
3114	05 Feb 15	nicklas	2198	*/
3114	05 Feb 15	nicklas	2199	public static final Annotationtype PARAMETER_SET =
3114	05 Feb 15	nicklas	2200	new Annotationtype("ParameterSet", Type.STRING, false, Item.SOFTWARE);
3114	05 Feb 15	nicklas	2201
3114	05 Feb 15	nicklas	2202	/**
3616	23 Nov 15	nicklas	2203	The "ReportTemplate" annotation, used for software items.
3616	23 Nov 15	nicklas	2204	It is a string enum annotation containing the name of the
3616	23 Nov 15	nicklas	2205	report template/software used for generating a report.
3616	23 Nov 15	nicklas	2206	@since 4.0
3616	23 Nov 15	nicklas	2207	*/
3616	23 Nov 15	nicklas	2208	public static final Annotationtype REPORT_TEMPLATE =
3616	23 Nov 15	nicklas	2209	new Annotationtype("ReportTemplate", Type.STRING, false, Item.SOFTWARE);
3616	23 Nov 15	nicklas	2210
4138	29 Sep 16	nicklas	2211	/**
6213	15 Apr 21	nicklas	2212	The "DemuxType" annotation, used for software/protocol items
6213	15 Apr 21	nicklas	2213	of type Demuxing. It is a string enum annotation containing the
6213	15 Apr 21	nicklas	2214	name of the merge software used.
6213	15 Apr 21	nicklas	2215	@since 4.32
6213	15 Apr 21	nicklas	2216	*/
6213	15 Apr 21	nicklas	2217	public static final Annotationtype DEMUX_TYPE =
6213	15 Apr 21	nicklas	2218	new Annotationtype("DemuxType", Type.STRING, false, Item.SOFTWARE, Item.PROTOCOL);
6213	15 Apr 21	nicklas	2219
6213	15 Apr 21	nicklas	2220	/**
6213	15 Apr 21	nicklas	2221	The "MergeType" annotation, used for software/protocol items
6213	15 Apr 21	nicklas	2222	of type Merging. It is a string enum annotation containing the
6213	15 Apr 21	nicklas	2223	name of the merge software used.
6213	15 Apr 21	nicklas	2224	@since 4.32
6213	15 Apr 21	nicklas	2225	*/
6213	15 Apr 21	nicklas	2226	public static final Annotationtype MERGE_TYPE =
6213	15 Apr 21	nicklas	2227	new Annotationtype("MergeType", Type.STRING, false, Item.SOFTWARE, Item.PROTOCOL);
6213	15 Apr 21	nicklas	2228
6213	15 Apr 21	nicklas	2229	/**
4602	29 Sep 17	nicklas	2230	The "AlignmentType" annotation, used for software/protocol items
4602	29 Sep 17	nicklas	2231	of type Alignment. It is a string enum annotation containing the
4602	29 Sep 17	nicklas	2232	name of the align software used.
4602	29 Sep 17	nicklas	2233	@since 4.12
4602	29 Sep 17	nicklas	2234	*/
4602	29 Sep 17	nicklas	2235	public static final Annotationtype ALIGNMENT_TYPE =
4602	29 Sep 17	nicklas	2236	new Annotationtype("AlignmentType", Type.STRING, false, Item.SOFTWARE, Item.PROTOCOL);
4602	29 Sep 17	nicklas	2237
4602	29 Sep 17	nicklas	2238	/**
5057	29 Oct 18	nicklas	2239	The "VariantCallType" annotation, used for software items
5057	29 Oct 18	nicklas	2240	of type "Variant calling". It is a string enum annotation
5057	29 Oct 18	nicklas	2241	containing the intended usage for the variant calling.
5057	29 Oct 18	nicklas	2242	@since 4.20
5057	29 Oct 18	nicklas	2243	*/
5057	29 Oct 18	nicklas	2244	public static final Annotationtype VARIANT_CALL_TYPE =
5057	29 Oct 18	nicklas	2245	new Annotationtype("VariantCallType", Type.STRING, false, Item.SOFTWARE);
5057	29 Oct 18	nicklas	2246
5057	29 Oct 18	nicklas	2247	/**
4662	29 Jan 18	nicklas	2248	The "ExpressionType" annotation, used for software/protocol items
4662	29 Jan 18	nicklas	2249	of type Feature extrations. It is a string enum annotation containing the
4662	29 Jan 18	nicklas	2250	name of the software used.
4662	29 Jan 18	nicklas	2251	@since 4.15
4662	29 Jan 18	nicklas	2252	*/
4662	29 Jan 18	nicklas	2253	public static final Annotationtype EXPRESSION_TYPE =
4662	29 Jan 18	nicklas	2254	new Annotationtype("ExpressionType", Type.STRING, false, Item.SOFTWARE, Item.PROTOCOL);
4662	29 Jan 18	nicklas	2255
4662	29 Jan 18	nicklas	2256	/**
4138	29 Sep 16	nicklas	2257	Annotation for marking a sample outtake as completed in the
4138	29 Sep 16	nicklas	2258	lab. Eg. tubes and boxes has been prepared and are ready
4138	29 Sep 16	nicklas	2259	for delivery.
4138	29 Sep 16	nicklas	2260	@since 4.8
4138	29 Sep 16	nicklas	2261	*/
4138	29 Sep 16	nicklas	2262	public static final Annotationtype OUTTAKE_COMPLETED_DATE =
4138	29 Sep 16	nicklas	2263	new Annotationtype("OuttakeCompleted", Type.DATE, false, Item.ITEMLIST);
3616	23 Nov 15	nicklas	2264
3616	23 Nov 15	nicklas	2265	/**
4138	29 Sep 16	nicklas	2266	Annotation for marking a sample outtake as delivered
4138	29 Sep 16	nicklas	2267	to the external party.
4138	29 Sep 16	nicklas	2268	@since 4.8
4138	29 Sep 16	nicklas	2269	*/
4138	29 Sep 16	nicklas	2270	public static final Annotationtype OUTTAKE_DELIVERED_DATE =
4138	29 Sep 16	nicklas	2271	new Annotationtype("OuttakeDelivered", Type.DATE, false, Item.ITEMLIST);
4179	27 Oct 16	nicklas	2272
4138	29 Sep 16	nicklas	2273	/**
4179	27 Oct 16	nicklas	2274	The "OuttakeResult" annotation which is set after finalizing an
4179	27 Oct 16	nicklas	2275	outtake. A value of "Successful" typically means that the outtake was
4179	27 Oct 16	nicklas	2276	successful. "Failed" indicates that the outtake could not be completed.
4179	27 Oct 16	nicklas	2277	@since 4.8
4179	27 Oct 16	nicklas	2278	*/
4179	27 Oct 16	nicklas	2279	public static final Annotationtype OUTTAKE_RESULT =
4179	27 Oct 16	nicklas	2280	new Annotationtype("OuttakeResult", Type.STRING, false, Item.ITEMLIST);
4179	27 Oct 16	nicklas	2281
4179	27 Oct 16	nicklas	2282	/**
4154	06 Oct 16	nicklas	2283	Target amount that is aimed for when making an outtake of
4154	06 Oct 16	nicklas	2284	biomaterial.
4154	06 Oct 16	nicklas	2285	@since 4.8
4154	06 Oct 16	nicklas	2286	*/
4154	06 Oct 16	nicklas	2287	public static final Annotationtype OUTTAKE_TARGET_AMOUNT =
4154	06 Oct 16	nicklas	2288	new Annotationtype("OuttakeTargetAmount", Type.FLOAT, false, Item.ITEMLIST);
4154	06 Oct 16	nicklas	2289
4154	06 Oct 16	nicklas	2290	/**
4154	06 Oct 16	nicklas	2291	Target amount that is aimed for when making an outtake of
4154	06 Oct 16	nicklas	2292	biomaterial.
4154	06 Oct 16	nicklas	2293	@since 4.8
4154	06 Oct 16	nicklas	2294	*/
4154	06 Oct 16	nicklas	2295	public static final Annotationtype OUTTAKE_TARGET_VOLUME =
6326	14 Jun 21	nicklas	2296	new Annotationtype("OuttakeTargetVolume", Type.FLOAT, false, Item.ITEMLIST);
4154	06 Oct 16	nicklas	2297
4154	06 Oct 16	nicklas	2298	/**
6326	14 Jun 21	nicklas	2299	Subtype of the parent items for the outtake aliquots.
6326	14 Jun 21	nicklas	2300	@since 4.31.3
6326	14 Jun 21	nicklas	2301	*/
6326	14 Jun 21	nicklas	2302	public static final Annotationtype OUTTAKE_PARENT_TYPE =
6326	14 Jun 21	nicklas	2303	new Annotationtype("OuttakeParentType", Type.STRING, false, Item.ITEMLIST);
6326	14 Jun 21	nicklas	2304
6326	14 Jun 21	nicklas	2305	/**
4699	15 Mar 18	nicklas	2306	INCA2 diagnosis date annotation (provtagningsdatum). We need this to
4699	15 Mar 18	nicklas	2307	be able to set {@link #REFERENCE_DATE} in the INCA import.
4699	15 Mar 18	nicklas	2308	@since 4.16
4699	15 Mar 18	nicklas	2309	*/
4699	15 Mar 18	nicklas	2310	public static final Annotationtype INCA2_a_diag_dat =
4699	15 Mar 18	nicklas	2311	new Annotationtype("INCA2_a_diag_dat", Type.DATE, false, Item.SAMPLE);
4699	15 Mar 18	nicklas	2312
4699	15 Mar 18	nicklas	2313	/**
4536	21 Jun 17	nicklas	2314	Calculated subtype from pilot report. String enum.
4536	21 Jun 17	nicklas	2315	@since 4.11
4536	21 Jun 17	nicklas	2316	*/
4536	21 Jun 17	nicklas	2317	public static final Annotationtype PILOT_SUBTYPE =
4536	21 Jun 17	nicklas	2318	new Annotationtype("PILOT_Subtype", Type.STRING, false, Item.RAWBIOASSAY);
4536	21 Jun 17	nicklas	2319
4536	21 Jun 17	nicklas	2320	/**
4536	21 Jun 17	nicklas	2321	Calculated GGI value from pilot report. String enum.
4536	21 Jun 17	nicklas	2322	@since 4.11
4536	21 Jun 17	nicklas	2323	*/
4536	21 Jun 17	nicklas	2324	public static final Annotationtype PILOT_GGI =
4536	21 Jun 17	nicklas	2325	new Annotationtype("PILOT_GGI", Type.STRING, false, Item.RAWBIOASSAY);
4536	21 Jun 17	nicklas	2326
4536	21 Jun 17	nicklas	2327	/**
4536	21 Jun 17	nicklas	2328	Calculated ER value from pilot report. String enum.
4536	21 Jun 17	nicklas	2329	@since 4.11
4536	21 Jun 17	nicklas	2330	*/
4536	21 Jun 17	nicklas	2331	public static final Annotationtype PILOT_ER =
4536	21 Jun 17	nicklas	2332	new Annotationtype("PILOT_ER", Type.STRING, false, Item.RAWBIOASSAY);
4536	21 Jun 17	nicklas	2333
4536	21 Jun 17	nicklas	2334	/**
4536	21 Jun 17	nicklas	2335	Calculated PGR value from pilot report. String enum.
4536	21 Jun 17	nicklas	2336	@since 4.11
4536	21 Jun 17	nicklas	2337	*/
4536	21 Jun 17	nicklas	2338	public static final Annotationtype PILOT_PGR =
4536	21 Jun 17	nicklas	2339	new Annotationtype("PILOT_PGR", Type.STRING, false, Item.RAWBIOASSAY);
4536	21 Jun 17	nicklas	2340
4536	21 Jun 17	nicklas	2341	/**
4536	21 Jun 17	nicklas	2342	Calculated HER2 value from pilot report. String enum.
4536	21 Jun 17	nicklas	2343	@since 4.11
4536	21 Jun 17	nicklas	2344	*/
4536	21 Jun 17	nicklas	2345	public static final Annotationtype PILOT_HER2 =
4536	21 Jun 17	nicklas	2346	new Annotationtype("PILOT_HER2", Type.STRING, false, Item.RAWBIOASSAY);
4536	21 Jun 17	nicklas	2347
4536	21 Jun 17	nicklas	2348	/**
4536	21 Jun 17	nicklas	2349	Calculated KI67 value from pilot report. String enum.
4536	21 Jun 17	nicklas	2350	@since 4.11
4536	21 Jun 17	nicklas	2351	*/
4536	21 Jun 17	nicklas	2352	public static final Annotationtype PILOT_KI67 =
4536	21 Jun 17	nicklas	2353	new Annotationtype("PILOT_KI67", Type.STRING, false, Item.RAWBIOASSAY);
4536	21 Jun 17	nicklas	2354
4536	21 Jun 17	nicklas	2355	/**
4536	21 Jun 17	nicklas	2356	Calculated Luminal A score from pilot report. Float.
4536	21 Jun 17	nicklas	2357	@since 4.11
4536	21 Jun 17	nicklas	2358	*/
4536	21 Jun 17	nicklas	2359	public static final Annotationtype PILOT_SCORE_LUMA =
4536	21 Jun 17	nicklas	2360	new Annotationtype("PILOT_SCORE_LumA", Type.FLOAT, false, Item.RAWBIOASSAY);
4536	21 Jun 17	nicklas	2361
4536	21 Jun 17	nicklas	2362	/**
4536	21 Jun 17	nicklas	2363	Calculated Luminal B score from pilot report. Float.
4536	21 Jun 17	nicklas	2364	@since 4.11
4536	21 Jun 17	nicklas	2365	*/
4536	21 Jun 17	nicklas	2366	public static final Annotationtype PILOT_SCORE_LUMB =
4536	21 Jun 17	nicklas	2367	new Annotationtype("PILOT_SCORE_LumB", Type.FLOAT, false, Item.RAWBIOASSAY);
4536	21 Jun 17	nicklas	2368
4536	21 Jun 17	nicklas	2369	/**
4536	21 Jun 17	nicklas	2370	Calculated HER2 score from pilot report. Float.
4536	21 Jun 17	nicklas	2371	@since 4.11
4536	21 Jun 17	nicklas	2372	*/
4536	21 Jun 17	nicklas	2373	public static final Annotationtype PILOT_SCORE_HER2 =
4536	21 Jun 17	nicklas	2374	new Annotationtype("PILOT_SCORE_HER2", Type.FLOAT, false, Item.RAWBIOASSAY);
4536	21 Jun 17	nicklas	2375
4536	21 Jun 17	nicklas	2376	/**
4536	21 Jun 17	nicklas	2377	Calculated Basal score from pilot report. Float.
4536	21 Jun 17	nicklas	2378	@since 4.11
4536	21 Jun 17	nicklas	2379	*/
4536	21 Jun 17	nicklas	2380	public static final Annotationtype PILOT_SCORE_BASAL =
4536	21 Jun 17	nicklas	2381	new Annotationtype("PILOT_SCORE_Basal", Type.FLOAT, false, Item.RAWBIOASSAY);
4536	21 Jun 17	nicklas	2382
4536	21 Jun 17	nicklas	2383	/**
4536	21 Jun 17	nicklas	2384	Calculated Normal score from pilot report. Float.
4536	21 Jun 17	nicklas	2385	@since 4.11
4536	21 Jun 17	nicklas	2386	*/
4536	21 Jun 17	nicklas	2387	public static final Annotationtype PILOT_SCORE_NORMAL =
4536	21 Jun 17	nicklas	2388	new Annotationtype("PILOT_SCORE_Normal", Type.FLOAT, false, Item.RAWBIOASSAY);
4536	21 Jun 17	nicklas	2389
4536	21 Jun 17	nicklas	2390	/**
5721	13 Nov 19	nicklas	2391	Number of callable bases. Integer. Belongs to the alignment.
7397	06 Nov 23	nicklas	2392	@since 4.24, In 4.50 changed from INT to LONG
5706	07 Nov 19	nicklas	2393	*/
5706	07 Nov 19	nicklas	2394	public static final Annotationtype CALLABLE_BASES =
7410	10 Nov 23	nicklas	2395	new Annotationtype("CallableBases", Type.LONG, false, Item.DERIVEDBIOASSAY, Item.RAWBIOASSAY);
7390	02 Nov 23	nicklas	2396
7390	02 Nov 23	nicklas	2397	/**
7439	16 Nov 23	nicklas	2398	The panel-of-normal used in WGS paired variant calling.
7439	16 Nov 23	nicklas	2399	It is an enum with string values.
7439	16 Nov 23	nicklas	2400	@since 4.50
7439	16 Nov 23	nicklas	2401	*/
7439	16 Nov 23	nicklas	2402	public static final Annotationtype PANEL_OF_NORMALS =
7440	16 Nov 23	nicklas	2403	new Annotationtype("PanelOfNormals", Type.STRING, false, Item.DERIVEDBIOASSAY, Item.RAWBIOASSAY);
7439	16 Nov 23	nicklas	2404
7439	16 Nov 23	nicklas	2405	/**
5721	13 Nov 19	nicklas	2406	Number of raw variants found. Integer. Belongs to the alignment.
5706	07 Nov 19	nicklas	2407	@since 4.24
5706	07 Nov 19	nicklas	2408	*/
5721	13 Nov 19	nicklas	2409	public static final Annotationtype VARIANTS_RAW =
7410	10 Nov 23	nicklas	2410	new Annotationtype("VariantsRaw", Type.INT, false, Item.DERIVEDBIOASSAY, Item.RAWBIOASSAY);
5706	07 Nov 19	nicklas	2411
5706	07 Nov 19	nicklas	2412	/**
5721	13 Nov 19	nicklas	2413	Number of variants passed filter. Integer. Belongs to the child raw bioassay.
5706	07 Nov 19	nicklas	2414	@since 4.24
5706	07 Nov 19	nicklas	2415	*/
5706	07 Nov 19	nicklas	2416	public static final Annotationtype VARIANTS_PASSED_FILTER =
5706	07 Nov 19	nicklas	2417	new Annotationtype("VariantsPassedFilter", Type.INT, false, Item.RAWBIOASSAY);
5706	07 Nov 19	nicklas	2418
6197	06 Apr 21	nicklas	2419	/**
6197	06 Apr 21	nicklas	2420	The "ExternalRef" annotation is used to store an ID reference on
6197	06 Apr 21	nicklas	2421	items that have been handled externally.
6197	06 Apr 21	nicklas	2422	@since 4.32
6197	06 Apr 21	nicklas	2423	*/
6197	06 Apr 21	nicklas	2424	public static final Annotationtype EXTERNAL_REF =
6203	09 Apr 21	nicklas	2425	new Annotationtype("ExternalRef", Type.STRING, false, Item.SAMPLE, Item.EXTRACT,
7174	17 May 23	nicklas	2426	Item.BIOPLATE, Item.SOFTWARE, Item.PROTOCOL, Item.ITEMLIST);
6387	15 Sep 21	nicklas	2427
6387	15 Sep 21	nicklas	2428	/**
6910	30 Nov 22	nicklas	2429	The "ImportWarnings" annotation is used to store warnings when importing
6910	30 Nov 22	nicklas	2430	data for externally processed samples.
6910	30 Nov 22	nicklas	2431	@since 4.41
6910	30 Nov 22	nicklas	2432	*/
6910	30 Nov 22	nicklas	2433	public static final Annotationtype IMPORT_WARNINGS =
6926	02 Dec 22	nicklas	2434	new Annotationtype("ImportWarnings", Type.STRING, true, Item.SAMPLE, Item.EXTRACT);
7168	12 May 23	nicklas	2435
7168	12 May 23	nicklas	2436	/**
7168	12 May 23	nicklas	2437	The "TransportMessages" annotation is used to store messages about
7168	12 May 23	nicklas	2438	the transfer of biomaterial from transport boxes to new storage locations.
7168	12 May 23	nicklas	2439	Messages are linked to the item list and typically have information about
7168	12 May 23	nicklas	2440	biomaterial that should not be transfered (eg. due to missing consent).
7168	12 May 23	nicklas	2441	@since 4.47
7168	12 May 23	nicklas	2442	*/
7168	12 May 23	nicklas	2443	public static final Annotationtype TRANSPORT_MESSAGES =
7168	12 May 23	nicklas	2444	new Annotationtype("TransportMessages", Type.STRING, true, Item.ITEMLIST);
7168	12 May 23	nicklas	2445
7186	22 May 23	nicklas	2446	/**
7186	22 May 23	nicklas	2447	The "MoveDate" annotation type, used for item lists that are representing
7186	22 May 23	nicklas	2448	transport boxes.
7186	22 May 23	nicklas	2449	@since 4.47
7186	22 May 23	nicklas	2450	*/
7186	22 May 23	nicklas	2451	public static final Annotationtype MOVE_DATE =
7186	22 May 23	nicklas	2452	new Annotationtype("MoveDate", Type.DATE, false, Item.ITEMLIST);
6910	30 Nov 22	nicklas	2453
6910	30 Nov 22	nicklas	2454	/**
7186	22 May 23	nicklas	2455	The "MoveOperator" annotation type, used for item lists that are representing
7186	22 May 23	nicklas	2456	transport boxes.
7186	22 May 23	nicklas	2457	@since 4.47
7186	22 May 23	nicklas	2458	*/
7186	22 May 23	nicklas	2459	public static final Annotationtype MOVE_OPERATOR =
7186	22 May 23	nicklas	2460	new Annotationtype("MoveOperator", Type.STRING, false, Item.ITEMLIST);
7186	22 May 23	nicklas	2461
7186	22 May 23	nicklas	2462	/**
6387	15 Sep 21	nicklas	2463	The "TargetedGenotype" annotation is used VCF files that
6387	15 Sep 21	nicklas	2464	are the result of targeted genotyping.
6389	15 Sep 21	nicklas	2465	@since 4.32
6387	15 Sep 21	nicklas	2466	*/
6387	15 Sep 21	nicklas	2467	public static final Annotationtype TARGETED_GENOTYPE =
6387	15 Sep 21	nicklas	2468	new Annotationtype("TargetedGenotype", Type.STRING, false, Item.FILE);
6387	15 Sep 21	nicklas	2469
5706	07 Nov 19	nicklas	2470	/**
6388	15 Sep 21	nicklas	2471	The "NumTargetedGenotypes" annotation is used VCF files that
6388	15 Sep 21	nicklas	2472	are the result of targeted genotyping.
6389	15 Sep 21	nicklas	2473	@since 4.32
6388	15 Sep 21	nicklas	2474	*/
6388	15 Sep 21	nicklas	2475	public static final Annotationtype NUM_TARGETED_GENOTYPES =
6388	15 Sep 21	nicklas	2476	new Annotationtype("NumTargetedGenotypes", Type.INT, false, Item.FILE);
6388	15 Sep 21	nicklas	2477
6388	15 Sep 21	nicklas	2478	/**
6388	15 Sep 21	nicklas	2479	The "NumTargetedVariants" annotation is used VCF files that
6388	15 Sep 21	nicklas	2480	are the result of targeted genotyping.
6389	15 Sep 21	nicklas	2481	@since 4.32
6388	15 Sep 21	nicklas	2482	*/
6388	15 Sep 21	nicklas	2483	public static final Annotationtype NUM_TARGETED_VARIANTS =
6388	15 Sep 21	nicklas	2484	new Annotationtype("NumTargetedVariants", Type.INT, false, Item.FILE);
6388	15 Sep 21	nicklas	2485
6388	15 Sep 21	nicklas	2486	/**
6864	04 Nov 22	nicklas	2487	The "ZipPassword" annotation is used on files with Referral ID
6864	04 Nov 22	nicklas	2488	that have been downloaded as encrypted ZIP files with the
6864	04 Nov 22	nicklas	2489	"Remember password" option enabled.
6864	04 Nov 22	nicklas	2490	@since 4.40.1
6864	04 Nov 22	nicklas	2491	*/
6864	04 Nov 22	nicklas	2492	public static final Annotationtype ZIP_PASSWORD =
6864	04 Nov 22	nicklas	2493	new Annotationtype("ZipPassword", Type.STRING, true, Item.FILE);
6864	04 Nov 22	nicklas	2494
7224	31 May 23	nicklas	2495	/**
7224	31 May 23	nicklas	2496	This annotation is used by the IMPORT_GATEWAY file server
7224	31 May 23	nicklas	2497	to store files that failed auto-import so that they
7224	31 May 23	nicklas	2498	are not checked again.
7224	31 May 23	nicklas	2499	@since 4.48
7224	31 May 23	nicklas	2500	*/
7224	31 May 23	nicklas	2501	public static final Annotationtype FILES_TO_IGNORE =
7224	31 May 23	nicklas	2502	new Annotationtype("FilesToIgnore", Type.STRING, false, Item.FILESERVER);
6864	04 Nov 22	nicklas	2503
6864	04 Nov 22	nicklas	2504	/**
5792	16 Dec 19	nicklas	2505	Number of mutation signatures.
5792	16 Dec 19	nicklas	2506	*/
5792	16 Dec 19	nicklas	2507	public static final int NUM_MUTATION_SIGNATURES = 30;
5792	16 Dec 19	nicklas	2508
5792	16 Dec 19	nicklas	2509	private static Map<Integer, Annotationtype> mutationSignatures = new HashMap<>();
5792	16 Dec 19	nicklas	2510	/**
5792	16 Dec 19	nicklas	2511	Get the "MutationSignatureNN" annotation type. The value is a score
5792	16 Dec 19	nicklas	2512	belonging to a variant call raw bioassay.
5792	16 Dec 19	nicklas	2513	@since 4.25
5792	16 Dec 19	nicklas	2514	*/
5792	16 Dec 19	nicklas	2515	public static final Annotationtype mutationSignature(int index)
5792	16 Dec 19	nicklas	2516	{
5792	16 Dec 19	nicklas	2517	Annotationtype signature = mutationSignatures.get(index);
5792	16 Dec 19	nicklas	2518	if (signature == null)
5792	16 Dec 19	nicklas	2519	{
5792	16 Dec 19	nicklas	2520	if (index < 1 \|\| index > NUM_MUTATION_SIGNATURES)
5792	16 Dec 19	nicklas	2521	{
5792	16 Dec 19	nicklas	2522	throw new InvalidDataException("Index must be between 1 and " + NUM_MUTATION_SIGNATURES);
5792	16 Dec 19	nicklas	2523	}
5792	16 Dec 19	nicklas	2524	synchronized(mutationSignatures)
5792	16 Dec 19	nicklas	2525	{
5793	16 Dec 19	nicklas	2526	signature = new Annotationtype("MutationSignature"+(index < 10 ? "0" : "")+index, Type.FLOAT, false, Item.RAWBIOASSAY);
5792	16 Dec 19	nicklas	2527	mutationSignatures.put(index, signature);
5792	16 Dec 19	nicklas	2528	}
5792	16 Dec 19	nicklas	2529	}
5792	16 Dec 19	nicklas	2530	return signature;
5792	16 Dec 19	nicklas	2531	}
5792	16 Dec 19	nicklas	2532
5872	23 Mar 20	nicklas	2533
5872	23 Mar 20	nicklas	2534	private static Map<String, Annotationtype> geneVariantAnnotations = new HashMap<>();
5792	16 Dec 19	nicklas	2535	/**
5872	23 Mar 20	nicklas	2536	Get the "<GENE>_Variants" annotation type, with special case for ESR1 that
5872	23 Mar 20	nicklas	2537	is ESR1_Resistance_Variants.
5872	23 Mar 20	nicklas	2538
5872	23 Mar 20	nicklas	2539	@since 4.26
5872	23 Mar 20	nicklas	2540	*/
5872	23 Mar 20	nicklas	2541	public static final Annotationtype geneVariantAnnotation(String gene)
5872	23 Mar 20	nicklas	2542	{
5872	23 Mar 20	nicklas	2543	Annotationtype at = geneVariantAnnotations.get(gene);
5872	23 Mar 20	nicklas	2544	if (at == null)
5872	23 Mar 20	nicklas	2545	{
5872	23 Mar 20	nicklas	2546	synchronized(geneVariantAnnotations)
5872	23 Mar 20	nicklas	2547	{
5872	23 Mar 20	nicklas	2548	String suffix = "ESR1".equals(gene) ? "_ResistanceVariants" : "_Variants";
5915	22 Apr 20	nicklas	2549	at = new Annotationtype(gene + suffix, Type.TEXT, false, Item.RAWBIOASSAY);
5872	23 Mar 20	nicklas	2550	geneVariantAnnotations.put(gene, at);
5872	23 Mar 20	nicklas	2551	}
5872	23 Mar 20	nicklas	2552	}
5872	23 Mar 20	nicklas	2553	return at;
5872	23 Mar 20	nicklas	2554	}
5872	23 Mar 20	nicklas	2555
5962	03 Jun 20	nicklas	2556	/**
5962	03 Jun 20	nicklas	2557	Get the SSP result class annotation.
5962	03 Jun 20	nicklas	2558	@since 4.27.1
5962	03 Jun 20	nicklas	2559	*/
5962	03 Jun 20	nicklas	2560	public static final Annotationtype sspResultAnnotation(SspModel m)
5962	03 Jun 20	nicklas	2561	{
5962	03 Jun 20	nicklas	2562	return new Annotationtype(m.getAnnotationTypeName(), Type.STRING, false, m.getDescription(), Item.RAWBIOASSAY);
5962	03 Jun 20	nicklas	2563	}
5872	23 Mar 20	nicklas	2564
5872	23 Mar 20	nicklas	2565	/**
5962	03 Jun 20	nicklas	2566	Get the SSP score annotation.
5962	03 Jun 20	nicklas	2567	@since 4.27.1
5962	03 Jun 20	nicklas	2568	*/
5962	03 Jun 20	nicklas	2569	public static final Annotationtype sspScoreAnnotation(SspModel m)
5962	03 Jun 20	nicklas	2570	{
5962	03 Jun 20	nicklas	2571	if (m.getAnnotationTypeNameScores() == null) return null;
5998	09 Sep 20	nicklas	2572	return new Annotationtype(m.getAnnotationTypeNameScores(), Type.TEXT, false, m.getDescription(), Item.RAWBIOASSAY);
5962	03 Jun 20	nicklas	2573	}
5962	03 Jun 20	nicklas	2574
5962	03 Jun 20	nicklas	2575	/**
1610	23 Apr 12	nicklas	2576	Get the annotation type by name of the static constant defined in this class.
1610	23 Apr 12	nicklas	2577
3571	30 Oct 15	nicklas	2578	@param cName The name of the static constant
1610	23 Apr 12	nicklas	2579	@return An annotationtype object or null if not found
1610	23 Apr 12	nicklas	2580	*/
1610	23 Apr 12	nicklas	2581	public static Annotationtype getByCName(String cName)
1610	23 Apr 12	nicklas	2582	{
1610	23 Apr 12	nicklas	2583	if (cName == null) return null;
1610	23 Apr 12	nicklas	2584	Annotationtype type = null;
1610	23 Apr 12	nicklas	2585	try
1610	23 Apr 12	nicklas	2586	{
1610	23 Apr 12	nicklas	2587	Field f = Annotationtype.class.getDeclaredField(cName);
1610	23 Apr 12	nicklas	2588	type = (Annotationtype)f.get(null);
1610	23 Apr 12	nicklas	2589	}
1610	23 Apr 12	nicklas	2590	catch (NoSuchFieldException ex)
1610	23 Apr 12	nicklas	2591	{}
1610	23 Apr 12	nicklas	2592	catch (IllegalAccessException ex)
1610	23 Apr 12	nicklas	2593	{}
1610	23 Apr 12	nicklas	2594	catch (ClassCastException ex)
1610	23 Apr 12	nicklas	2595	{}
1610	23 Apr 12	nicklas	2596	return type;
1610	23 Apr 12	nicklas	2597	}
1610	23 Apr 12	nicklas	2598
1610	23 Apr 12	nicklas	2599	private final String name;
5962	03 Jun 20	nicklas	2600	private final String description;
2351	10 Apr 14	nicklas	2601	private final boolean disableLog;
1610	23 Apr 12	nicklas	2602	private final Item[] mainType;
1610	23 Apr 12	nicklas	2603	private final Type valueType;
1610	23 Apr 12	nicklas	2604
1610	23 Apr 12	nicklas	2605	private int id;
1676	31 May 12	nicklas	2606	private AnnotationTypeFilter snapshotFilter;
1610	23 Apr 12	nicklas	2607	private JSONObject json;
1610	23 Apr 12	nicklas	2608
1610	23 Apr 12	nicklas	2609
1610	23 Apr 12	nicklas	2610	/**
3942	16 May 16	nicklas	2611	Get the AnnotationType as an instance of this class. Useful
3942	16 May 16	nicklas	2612	when there is need for using the helper methods for getting/setting
3942	16 May 16	nicklas	2613	annotation values.
3942	16 May 16	nicklas	2614	@since 4.5
3942	16 May 16	nicklas	2615	*/
3942	16 May 16	nicklas	2616	public static Annotationtype get(AnnotationType at)
3942	16 May 16	nicklas	2617	{
3942	16 May 16	nicklas	2618	Set<Item> items = at.getEnabledItems();
3942	16 May 16	nicklas	2619	Annotationtype a = new Annotationtype(at.getName(), at.getValueType(),
5962	03 Jun 20	nicklas	2620	at.getDisableLogOfValues(), at.getDescription(), items.toArray(new Item[items.size()]));
3942	16 May 16	nicklas	2621	a.id = at.getId();
3942	16 May 16	nicklas	2622	return a;
3942	16 May 16	nicklas	2623	}
3942	16 May 16	nicklas	2624
3942	16 May 16	nicklas	2625	/**
1610	23 Apr 12	nicklas	2626	Create a new definition of an annotation type.
1610	23 Apr 12	nicklas	2627
1610	23 Apr 12	nicklas	2628	@param name The name of the subtype
1610	23 Apr 12	nicklas	2629	@param valueType The date type of values that can be stored
2351	10 Apr 14	nicklas	2630	@param disableLog TRUE if change history logging of annotation values should be disabled
1610	23 Apr 12	nicklas	2631	@param mainType The main item type(s) of the annotation type
1610	23 Apr 12	nicklas	2632	*/
2351	10 Apr 14	nicklas	2633	private Annotationtype(String name, Type valueType, boolean disableLog, Item... mainType)
1610	23 Apr 12	nicklas	2634	{
1610	23 Apr 12	nicklas	2635	this.name = name;
5962	03 Jun 20	nicklas	2636	this.description = null;
1610	23 Apr 12	nicklas	2637	this.valueType = valueType;
2351	10 Apr 14	nicklas	2638	this.disableLog = disableLog;
1610	23 Apr 12	nicklas	2639	this.mainType = mainType;
1610	23 Apr 12	nicklas	2640	}
1610	23 Apr 12	nicklas	2641
1610	23 Apr 12	nicklas	2642	/**
5962	03 Jun 20	nicklas	2643	Create a new definition of an annotation type.
5962	03 Jun 20	nicklas	2644
5962	03 Jun 20	nicklas	2645	@param name The name of the subtype
5962	03 Jun 20	nicklas	2646	@param valueType The date type of values that can be stored
5962	03 Jun 20	nicklas	2647	@param disableLog TRUE if change history logging of annotation values should be disabled
5962	03 Jun 20	nicklas	2648	@param mainType The main item type(s) of the annotation type
5962	03 Jun 20	nicklas	2649	*/
5962	03 Jun 20	nicklas	2650	private Annotationtype(String name, Type valueType, boolean disableLog, String description, Item... mainType)
5962	03 Jun 20	nicklas	2651	{
5962	03 Jun 20	nicklas	2652	this.name = name;
5962	03 Jun 20	nicklas	2653	this.description = description;
5962	03 Jun 20	nicklas	2654	this.valueType = valueType;
5962	03 Jun 20	nicklas	2655	this.disableLog = disableLog;
5962	03 Jun 20	nicklas	2656	this.mainType = mainType;
5962	03 Jun 20	nicklas	2657	}
5962	03 Jun 20	nicklas	2658
5962	03 Jun 20	nicklas	2659	/**
1610	23 Apr 12	nicklas	2660	Get the name of the subtype.
1610	23 Apr 12	nicklas	2661	*/
1610	23 Apr 12	nicklas	2662	public String getName()
1610	23 Apr 12	nicklas	2663	{
1610	23 Apr 12	nicklas	2664	return name;
1610	23 Apr 12	nicklas	2665	}
1610	23 Apr 12	nicklas	2666
5962	03 Jun 20	nicklas	2667	public String getDescription()
5962	03 Jun 20	nicklas	2668	{
5962	03 Jun 20	nicklas	2669	return description;
5962	03 Jun 20	nicklas	2670	}
5962	03 Jun 20	nicklas	2671
1610	23 Apr 12	nicklas	2672	/**
1610	23 Apr 12	nicklas	2673	Get the data type of the values that can be stored.
1610	23 Apr 12	nicklas	2674	*/
1610	23 Apr 12	nicklas	2675	public Type getValueType()
1610	23 Apr 12	nicklas	2676	{
1610	23 Apr 12	nicklas	2677	return valueType;
1610	23 Apr 12	nicklas	2678	}
1610	23 Apr 12	nicklas	2679
1610	23 Apr 12	nicklas	2680	/**
2351	10 Apr 14	nicklas	2681	Should change history logging be disabled or not for annotation values.
2351	10 Apr 14	nicklas	2682	@since 2.16
2351	10 Apr 14	nicklas	2683	*/
2351	10 Apr 14	nicklas	2684	public boolean getDisableChangeHistoryLog()
2351	10 Apr 14	nicklas	2685	{
2351	10 Apr 14	nicklas	2686	return disableLog;
2351	10 Apr 14	nicklas	2687	}
2351	10 Apr 14	nicklas	2688
2351	10 Apr 14	nicklas	2689	/**
1610	23 Apr 12	nicklas	2690	Get the item type on which this annotation type can be used.
1610	23 Apr 12	nicklas	2691	*/
1610	23 Apr 12	nicklas	2692	public Item[] getMainType()
1610	23 Apr 12	nicklas	2693	{
1610	23 Apr 12	nicklas	2694	return mainType;
1610	23 Apr 12	nicklas	2695	}
1610	23 Apr 12	nicklas	2696
1610	23 Apr 12	nicklas	2697	/**
1610	23 Apr 12	nicklas	2698	Get the annotation type information as a JSON object ready to be sent as an AJAX response.
1610	23 Apr 12	nicklas	2699	*/
1610	23 Apr 12	nicklas	2700	public JSONObject asJSONObject(DbControl dc)
1610	23 Apr 12	nicklas	2701	{
1610	23 Apr 12	nicklas	2702	if (json == null)
1610	23 Apr 12	nicklas	2703	{
1610	23 Apr 12	nicklas	2704	if (id==0) load(dc); // Ensure that the annotationtype has been loaded
1610	23 Apr 12	nicklas	2705	json = new JSONObject();
1610	23 Apr 12	nicklas	2706	json.put("id", id);
1610	23 Apr 12	nicklas	2707	json.put("name", getName());
1610	23 Apr 12	nicklas	2708	}
1610	23 Apr 12	nicklas	2709	return json;
1610	23 Apr 12	nicklas	2710	}
1610	23 Apr 12	nicklas	2711
1610	23 Apr 12	nicklas	2712	/**
1610	23 Apr 12	nicklas	2713	Load the underlying annotation type. If it doesn't exists and exception is thrown.
1610	23 Apr 12	nicklas	2714
1610	23 Apr 12	nicklas	2715	@param dc The DbControl to use for database access
1610	23 Apr 12	nicklas	2716	@return An AnnotationType object
1610	23 Apr 12	nicklas	2717	*/
1610	23 Apr 12	nicklas	2718	public AnnotationType load(DbControl dc)
1610	23 Apr 12	nicklas	2719	{
1610	23 Apr 12	nicklas	2720	AnnotationType type = null;
1610	23 Apr 12	nicklas	2721	if (id == 0)
1610	23 Apr 12	nicklas	2722	{
1610	23 Apr 12	nicklas	2723	List<AnnotationType> result = list(dc);
1610	23 Apr 12	nicklas	2724	if (result.size() == 0)
1610	23 Apr 12	nicklas	2725	{
1610	23 Apr 12	nicklas	2726	throw new ItemNotFoundException("AnnotationType["+name+"]");
1610	23 Apr 12	nicklas	2727	}
1610	23 Apr 12	nicklas	2728	else if (result.size() > 1)
1610	23 Apr 12	nicklas	2729	{
1610	23 Apr 12	nicklas	2730	throw new InvalidDataException("Found > 1 AnnotationType["+name+"]");
1610	23 Apr 12	nicklas	2731	}
1610	23 Apr 12	nicklas	2732	type = result.get(0);
1610	23 Apr 12	nicklas	2733	id = type.getId();
1610	23 Apr 12	nicklas	2734	}
1610	23 Apr 12	nicklas	2735	else
1610	23 Apr 12	nicklas	2736	{
1610	23 Apr 12	nicklas	2737	type = AnnotationType.getById(dc, id);
1610	23 Apr 12	nicklas	2738	}
1610	23 Apr 12	nicklas	2739	return type;
1610	23 Apr 12	nicklas	2740	}
2350	10 Apr 14	nicklas	2741
1610	23 Apr 12	nicklas	2742	/**
2350	10 Apr 14	nicklas	2743	Load the annotation type as a BASE item. Same as {@link #load(DbControl)} but return null
2350	10 Apr 14	nicklas	2744	if no BASE item is found instead of throwing an exception.
2350	10 Apr 14	nicklas	2745	@param dc The DbControl to use for database access
2350	10 Apr 14	nicklas	2746	@return An ItemSubtype object
2350	10 Apr 14	nicklas	2747	@since 2.16
2350	10 Apr 14	nicklas	2748	*/
2350	10 Apr 14	nicklas	2749	public AnnotationType get(DbControl dc)
2350	10 Apr 14	nicklas	2750	{
2350	10 Apr 14	nicklas	2751	AnnotationType type = null;
2350	10 Apr 14	nicklas	2752	if (id == 0)
2350	10 Apr 14	nicklas	2753	{
2350	10 Apr 14	nicklas	2754	List<AnnotationType> result = list(dc);
2350	10 Apr 14	nicklas	2755	if (result.size() == 1)
2350	10 Apr 14	nicklas	2756	{
2350	10 Apr 14	nicklas	2757	type = result.get(0);
2350	10 Apr 14	nicklas	2758	id = type.getId();
2350	10 Apr 14	nicklas	2759	}
2350	10 Apr 14	nicklas	2760	}
2350	10 Apr 14	nicklas	2761	else
2350	10 Apr 14	nicklas	2762	{
2350	10 Apr 14	nicklas	2763	type = AnnotationType.getById(dc, id);
2350	10 Apr 14	nicklas	2764	}
2350	10 Apr 14	nicklas	2765	return type;
2350	10 Apr 14	nicklas	2766	}
2350	10 Apr 14	nicklas	2767
2350	10 Apr 14	nicklas	2768	/**
1640	09 May 12	nicklas	2769	List all annotation types registered in BASE with a name and main item type
1640	09 May 12	nicklas	2770	matching this annotation type definition. Normally, only a single annotation
1640	09 May 12	nicklas	2771	type should be returned.
1610	23 Apr 12	nicklas	2772	*/
1610	23 Apr 12	nicklas	2773	public List<AnnotationType> list(DbControl dc)
1610	23 Apr 12	nicklas	2774	{
1610	23 Apr 12	nicklas	2775	ItemQuery<AnnotationType> query = AnnotationType.getQuery(null);
1610	23 Apr 12	nicklas	2776	query.restrict(Restrictions.eq(Hql.property("name"), Expressions.parameter("name", name, Type.STRING)));
1640	09 May 12	nicklas	2777
1640	09 May 12	nicklas	2778	Item[] mt = getMainType();
1640	09 May 12	nicklas	2779	Expression[] mainTypes = new Expression[mt.length];
1640	09 May 12	nicklas	2780	for (int i = 0; i < mainTypes.length; ++i)
1640	09 May 12	nicklas	2781	{
1640	09 May 12	nicklas	2782	mainTypes[i] = Expressions.integer(mt[i].getValue());
1640	09 May 12	nicklas	2783	}
2102	25 Oct 13	nicklas	2784	if (mainTypes.length > 0)
2102	25 Oct 13	nicklas	2785	{
2102	25 Oct 13	nicklas	2786	query.joinPermanent(Hql.innerJoin("itemTypes", "it"));
2102	25 Oct 13	nicklas	2787	query.restrictPermanent(Restrictions.in(Hql.alias("it"), mainTypes));
2102	25 Oct 13	nicklas	2788	}
1640	09 May 12	nicklas	2789
1610	23 Apr 12	nicklas	2790	query.include(Include.ALL);
1640	09 May 12	nicklas	2791	query.setDistinct(true);
1610	23 Apr 12	nicklas	2792	return query.list(dc);
1610	23 Apr 12	nicklas	2793	}
1610	23 Apr 12	nicklas	2794
1610	23 Apr 12	nicklas	2795	/**
3484	14 Sep 15	nicklas	2796	Check if the item already has an annotation value for this
3484	14 Sep 15	nicklas	2797	annotation type.
3484	14 Sep 15	nicklas	2798	@since 3.6
3484	14 Sep 15	nicklas	2799	*/
3484	14 Sep 15	nicklas	2800	public boolean hasAnnotation(DbControl dc, Annotatable item)
3484	14 Sep 15	nicklas	2801	{
3484	14 Sep 15	nicklas	2802	if (item == null) return false;
3484	14 Sep 15	nicklas	2803	AnnotationType at = load(dc);
3484	14 Sep 15	nicklas	2804	if (!item.isAnnotated()) return false;
3484	14 Sep 15	nicklas	2805	AnnotationSet as = item.getAnnotationSet();
3571	30 Oct 15	nicklas	2806	return as.hasAnnotation(at, Annotation.Source.PRIMARY);
3484	14 Sep 15	nicklas	2807	}
3484	14 Sep 15	nicklas	2808
3484	14 Sep 15	nicklas	2809	/**
1610	23 Apr 12	nicklas	2810	Get the annotation value (single) for this annotation type from the
1610	23 Apr 12	nicklas	2811	annotatable item.
1610	23 Apr 12	nicklas	2812	@return The value, or null if the item is not annotated
1610	23 Apr 12	nicklas	2813	*/
1610	23 Apr 12	nicklas	2814	public Object getAnnotationValue(DbControl dc, Annotatable item)
1610	23 Apr 12	nicklas	2815	{
2348	10 Apr 14	nicklas	2816	if (item == null) return null;
1610	23 Apr 12	nicklas	2817	AnnotationType at = load(dc);
1610	23 Apr 12	nicklas	2818	if (!item.isAnnotated()) return null;
1610	23 Apr 12	nicklas	2819	AnnotationSet as = item.getAnnotationSet();
3571	30 Oct 15	nicklas	2820	if (!as.hasAnnotation(at, Annotation.Source.PRIMARY)) return null;
1610	23 Apr 12	nicklas	2821	return as.getAnnotation(at).getValues().get(0);
1610	23 Apr 12	nicklas	2822	}
1610	23 Apr 12	nicklas	2823
1610	23 Apr 12	nicklas	2824	/**
1676	31 May 12	nicklas	2825	Get the annotation value (single) for this annotation type from the
1676	31 May 12	nicklas	2826	annotatable item using a snapshot stored on the disk if available.
1676	31 May 12	nicklas	2827	@return The value, or null if the item is not annotated
1676	31 May 12	nicklas	2828	@since 2.7
1676	31 May 12	nicklas	2829	*/
1676	31 May 12	nicklas	2830	public Object getAnnotationValue(DbControl dc, SnapshotManager manager, Annotatable item)
1676	31 May 12	nicklas	2831	{
3166	05 Mar 15	nicklas	2832	if (manager == null) return getAnnotationValue(dc, item);
1676	31 May 12	nicklas	2833	if (snapshotFilter == null)
1676	31 May 12	nicklas	2834	{
1676	31 May 12	nicklas	2835	snapshotFilter = new AnnotationTypeFilter(load(dc));
1676	31 May 12	nicklas	2836	}
1676	31 May 12	nicklas	2837	List<AnnotationSnapshot> snapshots = manager.findAnnotations(dc, item, snapshotFilter, false);
3571	30 Oct 15	nicklas	2838	return snapshots.size() > 0 ? snapshots.get(0).getThisValues().get(0) : null;
1676	31 May 12	nicklas	2839	}
1676	31 May 12	nicklas	2840
1676	31 May 12	nicklas	2841	/**
1610	23 Apr 12	nicklas	2842	Get an array annotation value from an item. Returns an empty list if
1610	23 Apr 12	nicklas	2843	there are no annotations of the given type.
1610	23 Apr 12	nicklas	2844	*/
1610	23 Apr 12	nicklas	2845	public List<?> getAnnotationValues(DbControl dc, Annotatable item)
1610	23 Apr 12	nicklas	2846	{
1610	23 Apr 12	nicklas	2847	AnnotationType at = load(dc);
1610	23 Apr 12	nicklas	2848	if (!item.isAnnotated()) return Collections.emptyList();
1610	23 Apr 12	nicklas	2849	AnnotationSet as = item.getAnnotationSet();
3571	30 Oct 15	nicklas	2850	if (!as.hasAnnotation(at, Annotation.Source.PRIMARY)) return Collections.emptyList();
1610	23 Apr 12	nicklas	2851	return as.getAnnotation(at).getValues();
1610	23 Apr 12	nicklas	2852	}
1610	23 Apr 12	nicklas	2853
1610	23 Apr 12	nicklas	2854	/**
3166	05 Mar 15	nicklas	2855	Get the annotation value (single) for this annotation type from the
3166	05 Mar 15	nicklas	2856	annotatable item using a snapshot stored on the disk if available.
3166	05 Mar 15	nicklas	2857	@return The value, or null if the item is not annotated
3166	05 Mar 15	nicklas	2858	@since 3.2
3166	05 Mar 15	nicklas	2859	*/
3166	05 Mar 15	nicklas	2860	public List<?> getAnnotationValues(DbControl dc, SnapshotManager manager, Annotatable item)
3166	05 Mar 15	nicklas	2861	{
3166	05 Mar 15	nicklas	2862	if (manager == null) return getAnnotationValues(dc, item);
3166	05 Mar 15	nicklas	2863	if (snapshotFilter == null)
3166	05 Mar 15	nicklas	2864	{
3166	05 Mar 15	nicklas	2865	snapshotFilter = new AnnotationTypeFilter(load(dc));
3166	05 Mar 15	nicklas	2866	}
3166	05 Mar 15	nicklas	2867	List<AnnotationSnapshot> snapshots = manager.findAnnotations(dc, item, snapshotFilter, false);
3571	30 Oct 15	nicklas	2868	return snapshots.size() > 0 ? snapshots.get(0).getThisValues() : null;
3166	05 Mar 15	nicklas	2869	}
3166	05 Mar 15	nicklas	2870
3166	05 Mar 15	nicklas	2871
3166	05 Mar 15	nicklas	2872	/**
1610	23 Apr 12	nicklas	2873	Set a (single) annotation value on an item. If the value is null the annotation
1610	23 Apr 12	nicklas	2874	will be removed.
4496	10 May 17	nicklas	2875	@return TRUE if the existing annotation value was changed, FALSE if not
1610	23 Apr 12	nicklas	2876	*/
4496	10 May 17	nicklas	2877	public boolean setAnnotationValue(DbControl dc, Annotatable item, Object value)
1610	23 Apr 12	nicklas	2878	{
1610	23 Apr 12	nicklas	2879	AnnotationType at = load(dc);
4496	10 May 17	nicklas	2880	boolean changed = false;
1610	23 Apr 12	nicklas	2881	if (value == null)
1610	23 Apr 12	nicklas	2882	{
3571	30 Oct 15	nicklas	2883	if (item.isAnnotated() && item.getAnnotationSet().hasAnnotation(at, Annotation.Source.PRIMARY))
1610	23 Apr 12	nicklas	2884	{
1610	23 Apr 12	nicklas	2885	item.getAnnotationSet().removeAnnotation(at);
4496	10 May 17	nicklas	2886	changed = true;
1610	23 Apr 12	nicklas	2887	}
1610	23 Apr 12	nicklas	2888	}
1610	23 Apr 12	nicklas	2889	else
1610	23 Apr 12	nicklas	2890	{
1639	09 May 12	nicklas	2891	Type valueType = at.getValueType();
1639	09 May 12	nicklas	2892	if (valueType.isNumerical() && value instanceof Number)
1639	09 May 12	nicklas	2893	{
1639	09 May 12	nicklas	2894	value = valueType.convertNumber((Number)value);
1639	09 May 12	nicklas	2895	}
4496	10 May 17	nicklas	2896	changed = item.getAnnotationSet().getAnnotation(at).setValueIfDifferent(value, null);
1610	23 Apr 12	nicklas	2897	}
4496	10 May 17	nicklas	2898	return changed;
1610	23 Apr 12	nicklas	2899	}
2226	13 Feb 14	nicklas	2900
2226	13 Feb 14	nicklas	2901	/**
6926	02 Dec 22	nicklas	2902	Add or update an annotation value on an item, but do nothing if the new value is null.
6926	02 Dec 22	nicklas	2903	@since 4.41
6926	02 Dec 22	nicklas	2904	*/
6926	02 Dec 22	nicklas	2905	public boolean addOrUpdateAnnotationValue(DbControl dc, Annotatable item, Object value)
6926	02 Dec 22	nicklas	2906	{
6926	02 Dec 22	nicklas	2907	return value == null ? false : setAnnotationValue(dc, item, value);
6926	02 Dec 22	nicklas	2908	}
6926	02 Dec 22	nicklas	2909
6926	02 Dec 22	nicklas	2910	/**
2226	13 Feb 14	nicklas	2911	Set a multi-valued annotation on an item. If the values list is null or
2226	13 Feb 14	nicklas	2912	emtpy the annotation will be removed.
2226	13 Feb 14	nicklas	2913	@since 2.15
2226	13 Feb 14	nicklas	2914	*/
2226	13 Feb 14	nicklas	2915	public void setAnnotationValues(DbControl dc, Annotatable item, List<?> values)
2226	13 Feb 14	nicklas	2916	{
2226	13 Feb 14	nicklas	2917	AnnotationType at = load(dc);
2226	13 Feb 14	nicklas	2918	if (values == null \|\| values.isEmpty())
2226	13 Feb 14	nicklas	2919	{
3571	30 Oct 15	nicklas	2920	if (item.isAnnotated() && item.getAnnotationSet().hasAnnotation(at, Annotation.Source.PRIMARY))
2226	13 Feb 14	nicklas	2921	{
2226	13 Feb 14	nicklas	2922	item.getAnnotationSet().removeAnnotation(at);
2226	13 Feb 14	nicklas	2923	}
2226	13 Feb 14	nicklas	2924	}
2226	13 Feb 14	nicklas	2925	else
2226	13 Feb 14	nicklas	2926	{
3861	22 Apr 16	nicklas	2927	item.getAnnotationSet().getAnnotation(at).setValuesIfDifferent(values, null);
2226	13 Feb 14	nicklas	2928	}
2226	13 Feb 14	nicklas	2929	}
1610	23 Apr 12	nicklas	2930
1610	23 Apr 12	nicklas	2931	/**
1610	23 Apr 12	nicklas	2932	Append an annotation value to a multi-valued annotation type where each
1610	23 Apr 12	nicklas	2933	value should be unique.
1610	23 Apr 12	nicklas	2934	*/
1610	23 Apr 12	nicklas	2935	public void appendAnnotationValueIfUnique(DbControl dc, Annotatable item, Object value)
1610	23 Apr 12	nicklas	2936	{
1610	23 Apr 12	nicklas	2937	List<?> currentValues = getAnnotationValues(dc, item);
1610	23 Apr 12	nicklas	2938	if (!currentValues.contains(value))
1610	23 Apr 12	nicklas	2939	{
1610	23 Apr 12	nicklas	2940	AnnotationType at = load(dc);
1610	23 Apr 12	nicklas	2941	List<Object> newValues = new ArrayList<Object>(currentValues);
1610	23 Apr 12	nicklas	2942	newValues.add(value);
3861	22 Apr 16	nicklas	2943	item.getAnnotationSet().getAnnotation(at).setValuesIfDifferent(newValues, null);
1610	23 Apr 12	nicklas	2944	}
1610	23 Apr 12	nicklas	2945	}
1610	23 Apr 12	nicklas	2946
1610	23 Apr 12	nicklas	2947	/**
1610	23 Apr 12	nicklas	2948	Remove an annotation value to a multi-valued annotation type where each
1610	23 Apr 12	nicklas	2949	value should be unique.
1610	23 Apr 12	nicklas	2950	*/
1610	23 Apr 12	nicklas	2951	public void removeAnnotationValue(DbControl dc, Annotatable item, Object value)
1610	23 Apr 12	nicklas	2952	{
1610	23 Apr 12	nicklas	2953	List<?> currentValues = getAnnotationValues(dc, item);
1610	23 Apr 12	nicklas	2954	if (currentValues.contains(value))
1610	23 Apr 12	nicklas	2955	{
1610	23 Apr 12	nicklas	2956	AnnotationType at = load(dc);
1610	23 Apr 12	nicklas	2957	List<Object> newValues = new ArrayList<Object>(currentValues);
1610	23 Apr 12	nicklas	2958	newValues.remove(value);
3861	22 Apr 16	nicklas	2959	item.getAnnotationSet().getAnnotation(at).setValuesIfDifferent(newValues, null);
1610	23 Apr 12	nicklas	2960	}
1610	23 Apr 12	nicklas	2961	}
1610	23 Apr 12	nicklas	2962
1610	23 Apr 12	nicklas	2963	/**
1610	23 Apr 12	nicklas	2964	Copy annotation values between two items.
1610	23 Apr 12	nicklas	2965
1610	23 Apr 12	nicklas	2966	@param from The item to copy from. If this item is not annotated with
1610	23 Apr 12	nicklas	2967	the given annotation type, nothing is copied
1610	23 Apr 12	nicklas	2968	@param to The item to copy to. If this item already has been annotated with
1610	23 Apr 12	nicklas	2969	the given annotation type, the 'force' paremter decides if the annotation is
1610	23 Apr 12	nicklas	2970	overwritten or not
1610	23 Apr 12	nicklas	2971	@param force TRUE to overwrite existing annotations, FALSE to not
1610	23 Apr 12	nicklas	2972	@return TRUE if this method copied annotations, FALSE if not
1610	23 Apr 12	nicklas	2973	*/
1610	23 Apr 12	nicklas	2974	public boolean copyAnnotationValues(DbControl dc, Annotatable from, Annotatable to, boolean force)
1610	23 Apr 12	nicklas	2975	{
1610	23 Apr 12	nicklas	2976	List<?> annotations = getAnnotationValues(dc, from);
1610	23 Apr 12	nicklas	2977	if (annotations == null \|\| annotations.size() == 0) return false;
1610	23 Apr 12	nicklas	2978
1610	23 Apr 12	nicklas	2979	AnnotationType at = load(dc);
1610	23 Apr 12	nicklas	2980	if (!force)
1610	23 Apr 12	nicklas	2981	{
1610	23 Apr 12	nicklas	2982	// We need to check if the 'to' item already has the annotation
3571	30 Oct 15	nicklas	2983	if (to.isAnnotated() && to.getAnnotationSet().hasAnnotation(at, Annotation.Source.PRIMARY)) return false;
1610	23 Apr 12	nicklas	2984	}
1610	23 Apr 12	nicklas	2985
1610	23 Apr 12	nicklas	2986	// Copy the values
5789	13 Dec 19	nicklas	2987	return to.getAnnotationSet().getAnnotation(at).setValuesIfDifferent(annotations, null);
1610	23 Apr 12	nicklas	2988	}
1610	23 Apr 12	nicklas	2989
3618	23 Nov 15	nicklas	2990	/**
3618	23 Nov 15	nicklas	2991	Create a filter object that matches items that has been annotated
3618	23 Nov 15	nicklas	2992	with the given value.
3618	23 Nov 15	nicklas	2993	@since 4.0
3618	23 Nov 15	nicklas	2994	*/
3618	23 Nov 15	nicklas	2995	public Filter<Annotatable> createFilter(final Object value)
3618	23 Nov 15	nicklas	2996	{
5491	13 Jun 19	nicklas	2997	if (value == null) return null;
3618	23 Nov 15	nicklas	2998	return new Filter<Annotatable>()
3618	23 Nov 15	nicklas	2999	{
3618	23 Nov 15	nicklas	3000	@Override
3618	23 Nov 15	nicklas	3001	public boolean evaluate(Annotatable item)
3618	23 Nov 15	nicklas	3002	{
3618	23 Nov 15	nicklas	3003	return value.equals(getAnnotationValue(((BasicItem)item).getDbControl(), item));
3618	23 Nov 15	nicklas	3004	}
3618	23 Nov 15	nicklas	3005	};
3618	23 Nov 15	nicklas	3006	}
3618	23 Nov 15	nicklas	3007
1610	23 Apr 12	nicklas	3008
1610	23 Apr 12	nicklas	3009	}