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package net.sf.basedb.meludi.dao; |
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import java.lang.reflect.Field; |
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import java.util.ArrayList; |
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import java.util.Collections; |
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import java.util.List; |
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import org.json.simple.JSONObject; |
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import net.sf.basedb.core.Annotatable; |
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import net.sf.basedb.core.AnnotationSet; |
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import net.sf.basedb.core.AnnotationType; |
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import net.sf.basedb.core.DbControl; |
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import net.sf.basedb.core.Include; |
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import net.sf.basedb.core.InvalidDataException; |
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import net.sf.basedb.core.Item; |
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import net.sf.basedb.core.ItemNotFoundException; |
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import net.sf.basedb.core.ItemQuery; |
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import net.sf.basedb.core.Type; |
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import net.sf.basedb.core.query.Expression; |
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import net.sf.basedb.core.query.Expressions; |
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import net.sf.basedb.core.query.Hql; |
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import net.sf.basedb.core.query.Restrictions; |
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import net.sf.basedb.core.snapshot.AnnotationSnapshot; |
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import net.sf.basedb.core.snapshot.AnnotationTypeFilter; |
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import net.sf.basedb.core.snapshot.SnapshotManager; |
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/** |
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Used to define a annotation type items. |
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|
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@author nicklas (Reggie) |
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@since 1.0 |
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*/ |
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public class Annotationtype |
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{ |
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/** |
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The "PersonalNumber" annotation type, used |
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to store 12-digit personal number for biosources (Patient). The |
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number should be unique and is stored as a string. |
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*/ |
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public static final Annotationtype PERSONAL_NUMBER = |
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new Annotationtype("PersonalNumber", Type.STRING, true, Item.BIOSOURCE); |
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|
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/** |
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The "FamilyName" annotation type, used |
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to store the family name for biosources (Patient). It is a |
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string annotation type. |
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*/ |
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public static final Annotationtype FAMILY_NAME = |
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new Annotationtype("FamilyName", Type.STRING, true, Item.BIOSOURCE); |
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|
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/** |
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The "AllFirstNames" annotation type, used |
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to store the first names for biosources (Patient). It is a |
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string annotation type. |
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*/ |
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public static final Annotationtype ALL_FIRST_NAMES = |
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new Annotationtype("AllFirstNames", Type.STRING, true, Item.BIOSOURCE); |
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|
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/** |
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The "Gender" annotation type, used |
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to store the gender of biosources (Patient). It is an |
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enumerated string annotation type with two options: F and M. |
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*/ |
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public static final Annotationtype GENDER = |
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new Annotationtype("Gender", Type.STRING, false, Item.BIOSOURCE); |
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|
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/** |
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The "DateOfBirth" annotation type, used |
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to store the date of birth for biosources (Patient). It is a |
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date annotation type. |
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*/ |
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public static final Annotationtype DATE_OF_BIRTH = |
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new Annotationtype("DateOfBirth", Type.DATE, false, Item.BIOSOURCE); |
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|
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/** |
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The "Consent" annotation type, used |
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for samples (Case). It is an enumerated string annotation |
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type with three options: Yes, No and Not asked |
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*/ |
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public static final Annotationtype CONSENT = |
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new Annotationtype("Consent", Type.STRING, false, Item.SAMPLE); |
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|
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/** |
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The "ConsentDate" annotation type, used |
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for samples (Case). It is a date annotation. |
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*/ |
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public static final Annotationtype CONSENT_DATE = |
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new Annotationtype("ConsentDate", Type.DATE, false, Item.SAMPLE); |
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/** |
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The "DiagnosisConfirmed" annotation type, used |
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for samples (Case). It is a boolean annotation. |
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*/ |
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public static final Annotationtype DIAGNOSIS_CONFIRMED = |
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new Annotationtype("DiagnosisConfirmed", Type.BOOLEAN, false, Item.SAMPLE); |
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/** |
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The "BloodSamplingDateTime" annotation, used |
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for samples (Blood). It is a time stamp annotation. |
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*/ |
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public static final Annotationtype BLOOD_SAMPLING_DATETIME = |
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new Annotationtype("BloodSamplingDateTime", Type.TIMESTAMP, false, Item.SAMPLE); |
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|
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/** |
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The "BloodSample" annotation, used for samples (Blood). It |
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is an enumerated string annotation with options: |
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PreNeo, PreOp, FollowUp06, FollowUp12, FollowUp36 |
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*/ |
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/* |
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public static final Annotationtype BLOOD_SAMPLE = |
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new Annotationtype("BloodSample", Type.STRING, false, Item.SAMPLE); |
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*/ |
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|
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/** |
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The "TubeLabel" annotation type, used |
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for samples (Blood). It is a string annotation type. |
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*/ |
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public static final Annotationtype TUBE_LABEL = |
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new Annotationtype("TubeLabel", Type.STRING, true, Item.SAMPLE); |
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|
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/** |
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The "ReferralId" annotation type, used |
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for samples (Case). It is a string annotation type. |
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*/ |
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public static final Annotationtype REFERRAL_ID = |
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new Annotationtype("ReferralId", Type.STRING, true, Item.SAMPLE); |
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|
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/** |
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The "CaseId" annotation type, used |
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for samples (Blood, FFPE blocks). It is a string annotation type. |
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*/ |
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public static final Annotationtype CASE_ID = |
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new Annotationtype("CaseId", Type.STRING, false, Item.SAMPLE); |
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|
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/** |
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The "PLNumber" annotation type, used |
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for samples (Specimen). It is a string annotation type. |
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*/ |
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public static final Annotationtype PL_NUMBER = |
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new Annotationtype("PLNumber", Type.STRING, true, Item.SAMPLE); |
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|
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/** |
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The "PAD" annotation type, used |
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for samples (Specimen). It is a string annotation type. |
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*/ |
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public static final Annotationtype PAD = |
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new Annotationtype("PAD", Type.STRING, true, Item.SAMPLE); |
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|
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/** |
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The "MaterialNumber" annotation type, used |
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for samples (FFPE block). It is a string annotation type. |
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*/ |
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public static final Annotationtype MATERIAL_NUMBER = |
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new Annotationtype("MaterialNumber", Type.STRING, true, Item.SAMPLE); |
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|
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/** |
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The "Localisation" annotation type, used |
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for samples (FFPE block). It is a string annotation type. |
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*/ |
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public static final Annotationtype LOCALISATION = |
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new Annotationtype("Localisation", Type.STRING, false, Item.SAMPLE); |
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|
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/** |
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The "OtherPathNote" annotation type, |
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used for samples (Specimen). It is a string annotation type. |
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*/ |
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public static final Annotationtype OTHER_PATH_NOTE = |
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new Annotationtype("OtherPathNote", Type.STRING, false, Item.SAMPLE); |
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|
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/** |
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The "SamplingDate" annotation type, used |
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for samples (Specimen). It is a date annotation. |
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*/ |
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public static final Annotationtype SAMPLING_DATE = |
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new Annotationtype("SamplingDate", Type.DATE, false, Item.SAMPLE); |
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|
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/** |
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The "ArrivalDate" annotation type, used |
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for samples (Specimen). It is a time stamp annotation. |
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*/ |
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public static final Annotationtype ARRIVAL_DATE = |
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new Annotationtype("ArrivalDate", Type.DATE, false, Item.SAMPLE); |
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|
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/** |
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The "ArrivalOperator" annotation type, used |
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for samples (Blood). It is a String annotation type. |
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@since 1.6.0 |
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*/ |
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public static final Annotationtype ARRIVAL_OPERATOR = |
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new Annotationtype("ArrivalOperator", Type.STRING, false, Item.SAMPLE); |
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|
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/** |
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The "NofDeliveredTubes" annotation type, used |
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for samples (Specimen). It is an Integer annotation type. |
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*/ |
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public static final Annotationtype NOF_DELIVERED_TUBES = |
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new Annotationtype("NofDeliveredTubes", Type.INT, false, Item.SAMPLE); |
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|
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/** |
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The "OperatorDeliveryComment" annotation type, used |
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for samples (Specimen). It is a String annotation type. |
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*/ |
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public static final Annotationtype OPERATOR_DELIVERY_COMMENT = |
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new Annotationtype("OperatorDeliveryComment", Type.STRING, false, Item.SAMPLE); |
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|
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/** |
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The "MutationAnalysis" annotation type, |
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used for samples (Specimen). It is a String annotation type. |
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*/ |
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public static final Annotationtype MUTATION_ANALYSIS = |
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new Annotationtype("MutationAnalysis", Type.STRING, false, Item.SAMPLE); |
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|
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/** |
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The "Site" annotation type, used for samples (Specimen). |
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It is a String enumeration annotation. |
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*/ |
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public static final Annotationtype SITE = |
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new Annotationtype("Site", Type.STRING, false, Item.SAMPLE); |
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|
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/** |
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The "TubeContentType" annotation type, used for |
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samples. It is a String enumeration annotation. |
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*/ |
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public static final Annotationtype TUBE_CONTENT_TYPE = |
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new Annotationtype("TubeContentType", Type.STRING, false, Item.SAMPLE); |
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|
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/** |
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The "ProjectFocus" annotation type, used for samples (Specimen). |
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It is a String enumeration annotation. |
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*/ |
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public static final Annotationtype PROJECT_FOCUS = |
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new Annotationtype("ProjectFocus", Type.STRING, false, Item.SAMPLE); |
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|
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/** |
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The "MetastasisSite" annotation type, used for samples (Specimen). |
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It is a String enumeration annotation. |
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*/ |
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public static final Annotationtype METASTASIS_SITE = |
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new Annotationtype("MetastasisSite", Type.STRING, false, Item.SAMPLE); |
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|
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/** |
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The "SpecimenType" annotation type, used for |
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samples (Specimen). It is a String enumeration annotation. |
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This property describes the biological origin of the specimen, |
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e.g. "Primary tumour" or "Metastasis". |
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*/ |
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public static final Annotationtype SPECIMEN_TYPE = |
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new Annotationtype("SpecimenType", Type.STRING, false, Item.SAMPLE); |
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|
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/** |
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31 Oct 16 |
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The "SpecimenInputType" annotation type, used for |
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31 Oct 16 |
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samples (Specimen). It is a String enumeration annotation. |
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This property describes the form in which the specimen is delivered, |
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e.g. "Fresh frozen", "FFPE punch", "FFPE section", "FFPE slide", or "Cell line". |
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*/ |
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public static final Annotationtype SPECIMEN_INPUT_TYPE = |
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new Annotationtype("SpecimenInputType", Type.STRING, false, Item.SAMPLE); |
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|
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/** |
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14 Nov 14 |
olle |
The "BiopsyType" annotation type, used for |
| 2933 |
14 Nov 14 |
olle |
samples (Specimen). It is a String enumeration annotation. |
| 2933 |
14 Nov 14 |
olle |
265 |
*/ |
| 3050 |
17 Dec 14 |
olle |
266 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype BIOPSY_TYPE = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("BiopsyType", Type.STRING, false, Item.SAMPLE); |
| 3050 |
17 Dec 14 |
olle |
269 |
*/ |
| 2933 |
14 Nov 14 |
olle |
270 |
|
| 2933 |
14 Nov 14 |
olle |
271 |
/** |
| 5031 |
16 Oct 18 |
olle |
The "YellowLabel" annotation type, used |
| 5031 |
16 Oct 18 |
olle |
for samples (Specimen). It is a String enumeration annotation type. |
| 5031 |
16 Oct 18 |
olle |
@since 4.0 |
| 5031 |
16 Oct 18 |
olle |
275 |
*/ |
| 5031 |
16 Oct 18 |
olle |
276 |
public static final Annotationtype YELLOW_LABEL = |
| 5031 |
16 Oct 18 |
olle |
277 |
new Annotationtype("YellowLabel", Type.STRING, false, Item.SAMPLE); |
| 5031 |
16 Oct 18 |
olle |
278 |
|
| 5031 |
16 Oct 18 |
olle |
279 |
/** |
| 5031 |
16 Oct 18 |
olle |
The "CompletedDate" annotation type, used |
| 5031 |
16 Oct 18 |
olle |
for samples (Specimen) that are also YellowLabel. |
| 5031 |
16 Oct 18 |
olle |
It is a date annotation that when set indicates the date the |
| 5031 |
16 Oct 18 |
olle |
processing of the specimen has been completed. |
| 5031 |
16 Oct 18 |
olle |
@since 4.3 |
| 5031 |
16 Oct 18 |
olle |
285 |
*/ |
| 5031 |
16 Oct 18 |
olle |
286 |
public static final Annotationtype COMPLETED_DATE = |
| 5031 |
16 Oct 18 |
olle |
287 |
new Annotationtype("CompletedDate", Type.DATE, false, Item.SAMPLE); |
| 5031 |
16 Oct 18 |
olle |
288 |
|
| 5031 |
16 Oct 18 |
olle |
289 |
/** |
| 5243 |
17 Jan 19 |
olle |
The "FFPEBlockOrderDate" annotation type, used |
| 5243 |
17 Jan 19 |
olle |
for samples (Case). It is a date annotation type that |
| 5243 |
17 Jan 19 |
olle |
when set indicates the date an FFPE order form is created |
| 5243 |
17 Jan 19 |
olle |
and approved. |
| 5158 |
30 Nov 18 |
olle |
@since 1.6.0 |
| 5158 |
30 Nov 18 |
olle |
295 |
*/ |
| 5243 |
17 Jan 19 |
olle |
296 |
public static final Annotationtype FFPE_BLOCK_ORDER_DATE = |
| 5243 |
17 Jan 19 |
olle |
297 |
new Annotationtype("FFPEBlockOrderDate", Type.DATE, false, Item.SAMPLE); |
| 5158 |
30 Nov 18 |
olle |
298 |
|
| 5158 |
30 Nov 18 |
olle |
299 |
/** |
| 5061 |
30 Oct 18 |
olle |
The "UsedForFFPESectionOrderForm" annotation, used |
| 5052 |
25 Oct 18 |
olle |
for samples (FFPE blocks). It is a Boolean annotation type. |
| 5061 |
30 Oct 18 |
olle |
Store a flag indicating if the item is used for FFPE section |
| 5158 |
30 Nov 18 |
olle |
order form, and therefore should not appear in these selection lists. |
| 5052 |
25 Oct 18 |
olle |
@since 1.6.0 |
| 5052 |
25 Oct 18 |
olle |
305 |
*/ |
| 5061 |
30 Oct 18 |
olle |
306 |
public static final Annotationtype USED_FOR_FFPE_SECTION_ORDER_FORM = |
| 5061 |
30 Oct 18 |
olle |
307 |
new Annotationtype("UsedForFFPESectionOrderForm", Type.BOOLEAN, false, Item.SAMPLE); |
| 5052 |
25 Oct 18 |
olle |
308 |
|
| 5052 |
25 Oct 18 |
olle |
309 |
/** |
| 5061 |
30 Oct 18 |
olle |
The "UsedForFFPESection" annotation, used |
| 5061 |
30 Oct 18 |
olle |
for samples (FFPE blocks). It is a Boolean annotation type. |
| 5061 |
30 Oct 18 |
olle |
Store a flag indicating if the item is used for FFPE section, |
| 5061 |
30 Oct 18 |
olle |
and therefore not should appear in these selection lists. |
| 5061 |
30 Oct 18 |
olle |
@since 1.6.0 |
| 5061 |
30 Oct 18 |
olle |
315 |
*/ |
| 5061 |
30 Oct 18 |
olle |
316 |
public static final Annotationtype USED_FOR_FFPE_SECTION = |
| 5061 |
30 Oct 18 |
olle |
317 |
new Annotationtype("UsedForFFPESection", Type.BOOLEAN, false, Item.SAMPLE); |
| 5061 |
30 Oct 18 |
olle |
318 |
|
| 5061 |
30 Oct 18 |
olle |
319 |
/** |
| 5060 |
29 Oct 18 |
olle |
The "ReturnedDate" annotation type, used |
| 5060 |
29 Oct 18 |
olle |
for samples (FFPE blocks). |
| 5060 |
29 Oct 18 |
olle |
It is a date annotation that when set indicates the date the |
| 5060 |
29 Oct 18 |
olle |
FFPE block was returned to another destination for storage. |
| 5060 |
29 Oct 18 |
olle |
@since 4.3 |
| 5060 |
29 Oct 18 |
olle |
325 |
*/ |
| 5060 |
29 Oct 18 |
olle |
326 |
public static final Annotationtype RETURNED_DATE = |
| 5060 |
29 Oct 18 |
olle |
327 |
new Annotationtype("ReturnedDate", Type.DATE, false, Item.SAMPLE); |
| 5060 |
29 Oct 18 |
olle |
328 |
|
| 5060 |
29 Oct 18 |
olle |
329 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "NofPieces" annotation type, used for |
| 2933 |
14 Nov 14 |
olle |
samples (Specimen). It is a Integer annotation type. |
| 2933 |
14 Nov 14 |
olle |
332 |
*/ |
| 3028 |
11 Dec 14 |
olle |
333 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype NOF_PIECES = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("NofPieces", Type.INT, false, Item.SAMPLE); |
| 3028 |
11 Dec 14 |
olle |
336 |
*/ |
| 2933 |
14 Nov 14 |
olle |
337 |
|
| 2933 |
14 Nov 14 |
olle |
338 |
/** |
| 3028 |
11 Dec 14 |
olle |
The "NofSections" annotation type, used for |
| 3028 |
11 Dec 14 |
olle |
samples (Specimen). It is a Integer annotation type. |
| 3028 |
11 Dec 14 |
olle |
341 |
*/ |
| 3028 |
11 Dec 14 |
olle |
342 |
public static final Annotationtype NOF_SECTIONS = |
| 3028 |
11 Dec 14 |
olle |
343 |
new Annotationtype("NofSections", Type.INT, false, Item.SAMPLE); |
| 3028 |
11 Dec 14 |
olle |
344 |
|
| 3028 |
11 Dec 14 |
olle |
345 |
/** |
| 3067 |
08 Jan 15 |
olle |
The "ViableTumourCellsPercent" annotation type, used for |
| 3067 |
08 Jan 15 |
olle |
samples (Specimen). It is a Integer annotation type. |
| 3067 |
08 Jan 15 |
olle |
348 |
*/ |
| 3067 |
08 Jan 15 |
olle |
349 |
public static final Annotationtype VIABLE_TUMOUR_CELLS_PERCENT = |
| 3067 |
08 Jan 15 |
olle |
350 |
new Annotationtype("ViableTumourCellsPercent", Type.INT, false, Item.SAMPLE); |
| 3067 |
08 Jan 15 |
olle |
351 |
|
| 3067 |
08 Jan 15 |
olle |
352 |
/** |
| 5111 |
20 Nov 18 |
olle |
The "TumourCellsPercent" annotation type, used for |
| 5111 |
20 Nov 18 |
olle |
samples (Stain). It is a Integer annotation type. |
| 5111 |
20 Nov 18 |
olle |
355 |
*/ |
| 5111 |
20 Nov 18 |
olle |
356 |
public static final Annotationtype TUMOUR_CELLS_PERCENT = |
| 5111 |
20 Nov 18 |
olle |
357 |
new Annotationtype("TumourCellsPercent", Type.INT, false, Item.SAMPLE); |
| 5111 |
20 Nov 18 |
olle |
358 |
|
| 5111 |
20 Nov 18 |
olle |
359 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "OtherPartitionComment" annotation type, used |
| 2933 |
14 Nov 14 |
olle |
for samples (Specimen). It s a String annotation type. |
| 2933 |
14 Nov 14 |
olle |
362 |
*/ |
| 2933 |
14 Nov 14 |
olle |
363 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype OPERATOR_PARTITION_COMMENT = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("OperatorPartitionComment", Type.STRING, false, Item.SAMPLE); |
| 2933 |
14 Nov 14 |
olle |
366 |
*/ |
| 2933 |
14 Nov 14 |
olle |
367 |
|
| 2933 |
14 Nov 14 |
olle |
368 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "Partition date" annotation type, used for |
| 2933 |
14 Nov 14 |
olle |
samples (Histology) and extracts (Lysate). It is a date annotation type. |
| 2933 |
14 Nov 14 |
olle |
371 |
*/ |
| 2933 |
14 Nov 14 |
olle |
372 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype PARTITION_DATE = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("PartitionDate", Type.DATE, false, Item.SAMPLE, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
375 |
*/ |
| 2933 |
14 Nov 14 |
olle |
376 |
|
| 2933 |
14 Nov 14 |
olle |
377 |
/** |
| 5111 |
20 Nov 18 |
olle |
The "IHC" annotation type, used for bioplates (HE glass) to indicate the |
| 5111 |
20 Nov 18 |
olle |
type of staining. It is a string enumeration annotation type. |
| 5111 |
20 Nov 18 |
olle |
@since 1.6.0 |
| 5111 |
20 Nov 18 |
olle |
381 |
*/ |
| 5111 |
20 Nov 18 |
olle |
382 |
public static final Annotationtype IHC = |
| 5111 |
20 Nov 18 |
olle |
383 |
new Annotationtype("IHC", Type.STRING, false, Item.BIOPLATE); |
| 5111 |
20 Nov 18 |
olle |
384 |
|
| 5111 |
20 Nov 18 |
olle |
385 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "MultPieces" annotation, used for samples (Lysate). It is a |
| 2933 |
14 Nov 14 |
olle |
boolean annotation type. |
| 2933 |
14 Nov 14 |
olle |
@since 2.7 |
| 2933 |
14 Nov 14 |
olle |
389 |
*/ |
| 2933 |
14 Nov 14 |
olle |
390 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype MULTIPLE_PIECES = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("MultPieces", Type.BOOLEAN, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
393 |
*/ |
| 2933 |
14 Nov 14 |
olle |
394 |
|
| 2933 |
14 Nov 14 |
olle |
395 |
/** |
| 3318 |
08 May 15 |
olle |
The "SamplingDateExtract" annotation type, used |
| 3318 |
08 May 15 |
olle |
for extracts (RNA, DNA). It is a date annotation. |
| 3318 |
08 May 15 |
olle |
398 |
*/ |
| 3318 |
08 May 15 |
olle |
399 |
public static final Annotationtype SAMPLING_DATE_EXTRACT = |
| 3318 |
08 May 15 |
olle |
400 |
new Annotationtype("SamplingDateExtract", Type.DATE, false, Item.EXTRACT); |
| 3318 |
08 May 15 |
olle |
401 |
|
| 3318 |
08 May 15 |
olle |
402 |
/** |
| 3318 |
08 May 15 |
olle |
The "ArrivalDateExtract" annotation type, used |
| 3318 |
08 May 15 |
olle |
for extracts (RNA, DNA). It is a time stamp annotation. |
| 3318 |
08 May 15 |
olle |
405 |
*/ |
| 3318 |
08 May 15 |
olle |
406 |
public static final Annotationtype ARRIVAL_DATE_EXTRACT = |
| 3318 |
08 May 15 |
olle |
407 |
new Annotationtype("ArrivalDateExtract", Type.DATE, false, Item.EXTRACT); |
| 3318 |
08 May 15 |
olle |
408 |
|
| 3318 |
08 May 15 |
olle |
409 |
/** |
| 3318 |
08 May 15 |
olle |
The "SpecimenTypeExtract" annotation type, used for |
| 3318 |
08 May 15 |
olle |
extracts (RNA, DNA). It is a String enumeration annotation. |
| 3318 |
08 May 15 |
olle |
412 |
*/ |
| 3318 |
08 May 15 |
olle |
413 |
public static final Annotationtype SPECIMEN_TYPE_EXTRACT = |
| 3318 |
08 May 15 |
olle |
414 |
new Annotationtype("SpecimenTypeExtract", Type.STRING, false, Item.EXTRACT); |
| 3318 |
08 May 15 |
olle |
415 |
|
| 3318 |
08 May 15 |
olle |
416 |
/** |
| 3318 |
08 May 15 |
olle |
The "ViableTumourCellsPercentExtract" annotation type, used for |
| 3318 |
08 May 15 |
olle |
extracts (RNA, DNA). It is a Integer annotation type. |
| 3318 |
08 May 15 |
olle |
419 |
*/ |
| 3318 |
08 May 15 |
olle |
420 |
public static final Annotationtype VIABLE_TUMOUR_CELLS_PERCENT_EXTRACT = |
| 3318 |
08 May 15 |
olle |
421 |
new Annotationtype("ViableTumourCellsPercentExtract", Type.INT, false, Item.EXTRACT); |
| 3318 |
08 May 15 |
olle |
422 |
|
| 3318 |
08 May 15 |
olle |
423 |
/** |
| 3318 |
08 May 15 |
olle |
The "OperatorDeliveryCommentExtract" annotation type, used |
| 3318 |
08 May 15 |
olle |
for extracts (RNA, DNA). It is a String annotation type. |
| 3318 |
08 May 15 |
olle |
426 |
*/ |
| 3318 |
08 May 15 |
olle |
427 |
public static final Annotationtype OPERATOR_DELIVERY_COMMENT_EXTRACT = |
| 3318 |
08 May 15 |
olle |
428 |
new Annotationtype("OperatorDeliveryCommentExtract", Type.STRING, false, Item.EXTRACT); |
| 3318 |
08 May 15 |
olle |
429 |
|
| 3318 |
08 May 15 |
olle |
430 |
/** |
| 3180 |
17 Mar 15 |
olle |
The "IsolationDate" annotation type, used for extracts (RNA, DNA). |
| 3180 |
17 Mar 15 |
olle |
It is a date annotation type. |
| 3180 |
17 Mar 15 |
olle |
@since 1.2 |
| 3180 |
17 Mar 15 |
olle |
434 |
*/ |
| 3180 |
17 Mar 15 |
olle |
435 |
public static final Annotationtype ISOLATION_DATE = |
| 3180 |
17 Mar 15 |
olle |
436 |
new Annotationtype("IsolationDate", Type.DATE, false, Item.EXTRACT); |
| 3180 |
17 Mar 15 |
olle |
437 |
|
| 3180 |
17 Mar 15 |
olle |
438 |
/** |
| 3501 |
21 Sep 15 |
olle |
The "ExtractionOperator" annotation type, used for extracts (RNA, DNA). |
| 3501 |
21 Sep 15 |
olle |
It is a string annotation type. |
| 3501 |
21 Sep 15 |
olle |
@since 1.3.2 |
| 3501 |
21 Sep 15 |
olle |
442 |
*/ |
| 3501 |
21 Sep 15 |
olle |
443 |
public static final Annotationtype EXTRACTION_OPERATOR = |
| 3501 |
21 Sep 15 |
olle |
444 |
new Annotationtype("ExtractionOperator", Type.STRING, false, Item.EXTRACT); |
| 3501 |
21 Sep 15 |
olle |
445 |
|
| 3501 |
21 Sep 15 |
olle |
446 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "QiacubeDate" annotation type, used for extracts (RNA, DNA). |
| 2933 |
14 Nov 14 |
olle |
It is a date annotation type. |
| 3176 |
06 Mar 15 |
olle |
@since 1.2 |
| 2933 |
14 Nov 14 |
olle |
450 |
*/ |
| 2933 |
14 Nov 14 |
olle |
451 |
public static final Annotationtype QIACUBE_DATE = |
| 2933 |
14 Nov 14 |
olle |
452 |
new Annotationtype("QiacubeDate", Type.DATE, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
453 |
|
| 2933 |
14 Nov 14 |
olle |
454 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "QiacubeOperator" annotation type, used for extracts (RNA, DNA). |
| 2933 |
14 Nov 14 |
olle |
It is a string annotation type. |
| 3176 |
06 Mar 15 |
olle |
@since 1.2 |
| 2933 |
14 Nov 14 |
olle |
458 |
*/ |
| 2933 |
14 Nov 14 |
olle |
459 |
public static final Annotationtype QIACUBE_OPERATOR = |
| 2933 |
14 Nov 14 |
olle |
460 |
new Annotationtype("QiacubeOperator", Type.STRING, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
461 |
|
| 2933 |
14 Nov 14 |
olle |
462 |
/** |
| 3176 |
06 Mar 15 |
olle |
The "QiacubeInstrumentPrefix" annotation type, used for extracts (RNA, DNA). |
| 3176 |
06 Mar 15 |
olle |
It is a string annotation type indicating the QIAcube instrument used. |
| 3176 |
06 Mar 15 |
olle |
@since 1.2 |
| 3176 |
06 Mar 15 |
olle |
466 |
*/ |
| 3176 |
06 Mar 15 |
olle |
467 |
public static final Annotationtype QIACUBE_INSTRUMENT_PREFIX = |
| 3176 |
06 Mar 15 |
olle |
468 |
new Annotationtype("QiacubeInstrumentPrefix", Type.STRING, false, Item.EXTRACT); |
| 3176 |
06 Mar 15 |
olle |
469 |
|
| 3176 |
06 Mar 15 |
olle |
470 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "QiacubePosition" annotation type, used for extracts (RNA, DNA). |
| 2933 |
14 Nov 14 |
olle |
It is an integer annotation type with allowed values between 1 and 12. |
| 3176 |
06 Mar 15 |
olle |
@since 1.2 |
| 2933 |
14 Nov 14 |
olle |
474 |
*/ |
| 2933 |
14 Nov 14 |
olle |
475 |
public static final Annotationtype QIACUBE_POSITION = |
| 2933 |
14 Nov 14 |
olle |
476 |
new Annotationtype("QiacubePosition", Type.INT, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
477 |
|
| 2933 |
14 Nov 14 |
olle |
478 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "QiacubeRunNo" annotation type, used for extracts (RNA, DNA). |
| 2933 |
14 Nov 14 |
olle |
It is an integer annotation type with allowed values >= 1. |
| 3176 |
06 Mar 15 |
olle |
@since 1.2 |
| 2933 |
14 Nov 14 |
olle |
482 |
*/ |
| 2933 |
14 Nov 14 |
olle |
483 |
public static final Annotationtype QIACUBE_RUN_NO = |
| 2933 |
14 Nov 14 |
olle |
484 |
new Annotationtype("QiacubeRunNo", Type.INT, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
485 |
|
| 2933 |
14 Nov 14 |
olle |
486 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "RLT_Plus" annotation type, used for extracts (Lysate). |
| 2933 |
14 Nov 14 |
olle |
@since 2.16 |
| 2933 |
14 Nov 14 |
olle |
489 |
*/ |
| 2933 |
14 Nov 14 |
olle |
490 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype RLT_PLUS = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("RLT_Plus", Type.STRING, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
493 |
*/ |
| 2933 |
14 Nov 14 |
olle |
494 |
|
| 2933 |
14 Nov 14 |
olle |
495 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "BetaMerca" annotation type, used for extracts (Lysate). |
| 2933 |
14 Nov 14 |
olle |
@since 2.16 |
| 2933 |
14 Nov 14 |
olle |
498 |
*/ |
| 2933 |
14 Nov 14 |
olle |
499 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype BETA_MERCA = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("BetaMerca", Type.STRING, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
502 |
*/ |
| 2933 |
14 Nov 14 |
olle |
503 |
|
| 2933 |
14 Nov 14 |
olle |
504 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "ReagentDX" annotation type, used for extracts (Lysate). |
| 2933 |
14 Nov 14 |
olle |
@since 2.16 |
| 2933 |
14 Nov 14 |
olle |
507 |
*/ |
| 2933 |
14 Nov 14 |
olle |
508 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype REAGENT_DX = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("ReagentDX", Type.STRING, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
511 |
*/ |
| 2933 |
14 Nov 14 |
olle |
512 |
|
| 2933 |
14 Nov 14 |
olle |
513 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "QiaShredder" annotation type, used for extracts (Lysate). |
| 2933 |
14 Nov 14 |
olle |
@since 2.16 |
| 2933 |
14 Nov 14 |
olle |
516 |
*/ |
| 2933 |
14 Nov 14 |
olle |
517 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype QIA_SHREDDER = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("QiaShredder", Type.STRING, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
520 |
*/ |
| 2933 |
14 Nov 14 |
olle |
521 |
|
| 2933 |
14 Nov 14 |
olle |
522 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "AllprepMiniKit" annotation type, used for extracts (RNA, DNA). |
| 2933 |
14 Nov 14 |
olle |
@since 2.16 |
| 2933 |
14 Nov 14 |
olle |
525 |
*/ |
| 2933 |
14 Nov 14 |
olle |
526 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype ALLPREP_MINI_KIT = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("AllprepMiniKit", Type.STRING, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
529 |
*/ |
| 2933 |
14 Nov 14 |
olle |
530 |
|
| 2933 |
14 Nov 14 |
olle |
531 |
/** |
| 3176 |
06 Mar 15 |
olle |
The "AllprepFfpeKit" annotation type, used for extracts (RNA, DNA). |
| 3176 |
06 Mar 15 |
olle |
@since 1.2 |
| 3176 |
06 Mar 15 |
olle |
534 |
*/ |
| 3176 |
06 Mar 15 |
olle |
535 |
public static final Annotationtype ALLPREP_FFPE_KIT = |
| 3176 |
06 Mar 15 |
olle |
536 |
new Annotationtype("AllprepFfpeKit", Type.STRING, false, Item.EXTRACT); |
| 3176 |
06 Mar 15 |
olle |
537 |
|
| 3176 |
06 Mar 15 |
olle |
538 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "ETOH70" annotation type, used for extracts (RNA, DNA). |
| 2933 |
14 Nov 14 |
olle |
@since 2.16 |
| 2933 |
14 Nov 14 |
olle |
541 |
*/ |
| 2933 |
14 Nov 14 |
olle |
542 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype ETOH70 = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("ETOH70", Type.STRING, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
545 |
*/ |
| 2933 |
14 Nov 14 |
olle |
546 |
|
| 2933 |
14 Nov 14 |
olle |
547 |
/** |
| 3176 |
06 Mar 15 |
olle |
The "Xylene_Specimen" annotation type, used for extracts (RNA, DNA). |
| 3176 |
06 Mar 15 |
olle |
@since 1.2 |
| 3176 |
06 Mar 15 |
olle |
550 |
*/ |
| 3176 |
06 Mar 15 |
olle |
551 |
public static final Annotationtype XYLENE_SPECIMEN = |
| 3176 |
06 Mar 15 |
olle |
552 |
new Annotationtype("Xylene_Specimen", Type.STRING, false, Item.EXTRACT); |
| 3176 |
06 Mar 15 |
olle |
553 |
|
| 3176 |
06 Mar 15 |
olle |
554 |
/** |
| 3176 |
06 Mar 15 |
olle |
The "ETOH995_Specimen" annotation type, used for extracts (RNA, DNA). |
| 3176 |
06 Mar 15 |
olle |
@since 1.2 |
| 3176 |
06 Mar 15 |
olle |
557 |
*/ |
| 3176 |
06 Mar 15 |
olle |
558 |
public static final Annotationtype ETOH995_SPECIMEN = |
| 3176 |
06 Mar 15 |
olle |
559 |
new Annotationtype("ETOH995_Specimen", Type.STRING, false, Item.EXTRACT); |
| 3176 |
06 Mar 15 |
olle |
560 |
|
| 3176 |
06 Mar 15 |
olle |
561 |
/** |
| 3176 |
06 Mar 15 |
olle |
The "BufferPKD_Specimen" annotation type, used for extracts (RNA, DNA). |
| 3176 |
06 Mar 15 |
olle |
@since 1.2 |
| 3176 |
06 Mar 15 |
olle |
564 |
*/ |
| 3176 |
06 Mar 15 |
olle |
565 |
public static final Annotationtype BUFFER_PKD_SPECIMEN = |
| 3176 |
06 Mar 15 |
olle |
566 |
new Annotationtype("BufferPKD_Specimen", Type.STRING, false, Item.EXTRACT); |
| 3176 |
06 Mar 15 |
olle |
567 |
|
| 3176 |
06 Mar 15 |
olle |
568 |
/** |
| 3176 |
06 Mar 15 |
olle |
The "BufferATL_Specimen" annotation type, used for extracts (RNA, DNA). |
| 3176 |
06 Mar 15 |
olle |
@since 1.2 |
| 3176 |
06 Mar 15 |
olle |
571 |
*/ |
| 3176 |
06 Mar 15 |
olle |
572 |
public static final Annotationtype BUFFER_ATL_SPECIMEN = |
| 3176 |
06 Mar 15 |
olle |
573 |
new Annotationtype("BufferATL_Specimen", Type.STRING, false, Item.EXTRACT); |
| 3176 |
06 Mar 15 |
olle |
574 |
|
| 3176 |
06 Mar 15 |
olle |
575 |
/** |
| 3176 |
06 Mar 15 |
olle |
The "ProteinaseK_Specimen" annotation type, used for extracts (RNA, DNA). |
| 3176 |
06 Mar 15 |
olle |
@since 1.2 |
| 3176 |
06 Mar 15 |
olle |
578 |
*/ |
| 3176 |
06 Mar 15 |
olle |
579 |
public static final Annotationtype PROTEINASE_K_SPECIMEN = |
| 3176 |
06 Mar 15 |
olle |
580 |
new Annotationtype("ProteinaseK_Specimen", Type.STRING, false, Item.EXTRACT); |
| 3176 |
06 Mar 15 |
olle |
581 |
|
| 3176 |
06 Mar 15 |
olle |
582 |
/** |
| 3176 |
06 Mar 15 |
olle |
The "RNaseA_Specimen" annotation type, used for extracts (RNA, DNA). |
| 3176 |
06 Mar 15 |
olle |
@since 1.2 |
| 3176 |
06 Mar 15 |
olle |
585 |
*/ |
| 3176 |
06 Mar 15 |
olle |
586 |
public static final Annotationtype RNASE_A_SPECIMEN = |
| 3176 |
06 Mar 15 |
olle |
587 |
new Annotationtype("RNaseA_Specimen", Type.STRING, false, Item.EXTRACT); |
| 3176 |
06 Mar 15 |
olle |
588 |
|
| 3176 |
06 Mar 15 |
olle |
589 |
/** |
| 3176 |
06 Mar 15 |
olle |
The "ETOH995" annotation type, used for extracts (RNA, DNA). |
| 3176 |
06 Mar 15 |
olle |
@since 1.2 |
| 3176 |
06 Mar 15 |
olle |
592 |
*/ |
| 3176 |
06 Mar 15 |
olle |
593 |
public static final Annotationtype ETOH995 = |
| 3176 |
06 Mar 15 |
olle |
594 |
new Annotationtype("ETOH995", Type.STRING, false, Item.EXTRACT); |
| 3176 |
06 Mar 15 |
olle |
595 |
|
| 3176 |
06 Mar 15 |
olle |
596 |
/** |
| 3176 |
06 Mar 15 |
olle |
The "BufferRLT" annotation type, used for extracts (RNA, DNA). |
| 3176 |
06 Mar 15 |
olle |
@since 1.2 |
| 3176 |
06 Mar 15 |
olle |
599 |
*/ |
| 3176 |
06 Mar 15 |
olle |
600 |
public static final Annotationtype BUFFER_RLT = |
| 3176 |
06 Mar 15 |
olle |
601 |
new Annotationtype("BufferRLT", Type.STRING, false, Item.EXTRACT); |
| 3176 |
06 Mar 15 |
olle |
602 |
|
| 3176 |
06 Mar 15 |
olle |
603 |
/** |
| 3176 |
06 Mar 15 |
olle |
The "BufferFRN" annotation type, used for extracts (RNA, DNA). |
| 3176 |
06 Mar 15 |
olle |
@since 1.2 |
| 3176 |
06 Mar 15 |
olle |
606 |
*/ |
| 3176 |
06 Mar 15 |
olle |
607 |
public static final Annotationtype BUFFER_FRN = |
| 3176 |
06 Mar 15 |
olle |
608 |
new Annotationtype("BufferFRN", Type.STRING, false, Item.EXTRACT); |
| 3176 |
06 Mar 15 |
olle |
609 |
|
| 3176 |
06 Mar 15 |
olle |
610 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "BufferRW1" annotation type, used for extracts (RNA, DNA). |
| 2933 |
14 Nov 14 |
olle |
@since 2.16 |
| 2933 |
14 Nov 14 |
olle |
613 |
*/ |
| 2933 |
14 Nov 14 |
olle |
614 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype BUFFER_RW1 = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("BufferRW1", Type.STRING, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
617 |
*/ |
| 2933 |
14 Nov 14 |
olle |
618 |
|
| 2933 |
14 Nov 14 |
olle |
619 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "BufferRPE" annotation type, used for extracts (RNA, DNA). |
| 3176 |
06 Mar 15 |
olle |
@since 1.2 |
| 2933 |
14 Nov 14 |
olle |
622 |
*/ |
| 2933 |
14 Nov 14 |
olle |
623 |
public static final Annotationtype BUFFER_RPE = |
| 2933 |
14 Nov 14 |
olle |
624 |
new Annotationtype("BufferRPE", Type.STRING, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
625 |
|
| 2933 |
14 Nov 14 |
olle |
626 |
/** |
| 3176 |
06 Mar 15 |
olle |
The "BufferAL" annotation type, used for extracts (RNA, DNA). |
| 3176 |
06 Mar 15 |
olle |
@since 1.2 |
| 3176 |
06 Mar 15 |
olle |
629 |
*/ |
| 3176 |
06 Mar 15 |
olle |
630 |
public static final Annotationtype BUFFER_AL = |
| 3176 |
06 Mar 15 |
olle |
631 |
new Annotationtype("BufferAL", Type.STRING, false, Item.EXTRACT); |
| 3176 |
06 Mar 15 |
olle |
632 |
|
| 3176 |
06 Mar 15 |
olle |
633 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "BufferAW1" annotation type, used for extracts (RNA, DNA). |
| 3176 |
06 Mar 15 |
olle |
@since 1.2 |
| 2933 |
14 Nov 14 |
olle |
636 |
*/ |
| 2933 |
14 Nov 14 |
olle |
637 |
public static final Annotationtype BUFFER_AW1 = |
| 2933 |
14 Nov 14 |
olle |
638 |
new Annotationtype("BufferAW1", Type.STRING, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
639 |
|
| 2933 |
14 Nov 14 |
olle |
640 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "BufferAW2" annotation type, used for extracts (RNA, DNA). |
| 3176 |
06 Mar 15 |
olle |
@since 1.2 |
| 2933 |
14 Nov 14 |
olle |
643 |
*/ |
| 2933 |
14 Nov 14 |
olle |
644 |
public static final Annotationtype BUFFER_AW2 = |
| 2933 |
14 Nov 14 |
olle |
645 |
new Annotationtype("BufferAW2", Type.STRING, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
646 |
|
| 2933 |
14 Nov 14 |
olle |
647 |
/** |
| 3176 |
06 Mar 15 |
olle |
The "BufferATE" annotation type, used for extracts (RNA, DNA). |
| 3176 |
06 Mar 15 |
olle |
@since 1.2 |
| 3176 |
06 Mar 15 |
olle |
650 |
*/ |
| 3176 |
06 Mar 15 |
olle |
651 |
public static final Annotationtype BUFFER_ATE = |
| 3176 |
06 Mar 15 |
olle |
652 |
new Annotationtype("BufferATE", Type.STRING, false, Item.EXTRACT); |
| 3176 |
06 Mar 15 |
olle |
653 |
|
| 3176 |
06 Mar 15 |
olle |
654 |
/** |
| 3176 |
06 Mar 15 |
olle |
The "BufferRDD" annotation type, used for extracts (RNA, DNA). |
| 3176 |
06 Mar 15 |
olle |
@since 1.2 |
| 3176 |
06 Mar 15 |
olle |
657 |
*/ |
| 3176 |
06 Mar 15 |
olle |
658 |
public static final Annotationtype BUFFER_RDD = |
| 3176 |
06 Mar 15 |
olle |
659 |
new Annotationtype("BufferRDD", Type.STRING, false, Item.EXTRACT); |
| 3176 |
06 Mar 15 |
olle |
660 |
|
| 3176 |
06 Mar 15 |
olle |
661 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "BufferEB" annotation type, used for extracts (RNA, DNA). |
| 2933 |
14 Nov 14 |
olle |
@since 2.16 |
| 2933 |
14 Nov 14 |
olle |
664 |
*/ |
| 2933 |
14 Nov 14 |
olle |
665 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype BUFFER_EB = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("BufferEB", Type.STRING, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
668 |
*/ |
| 2933 |
14 Nov 14 |
olle |
669 |
|
| 2933 |
14 Nov 14 |
olle |
670 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "RNaseFreeWater" annotation type, used for extracts (RNA, DNA). |
| 3176 |
06 Mar 15 |
olle |
@since 1.2 |
| 2933 |
14 Nov 14 |
olle |
673 |
*/ |
| 2933 |
14 Nov 14 |
olle |
674 |
public static final Annotationtype RNASE_FREE_WATER = |
| 2933 |
14 Nov 14 |
olle |
675 |
new Annotationtype("RNaseFreeWater", Type.STRING, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
676 |
|
| 2933 |
14 Nov 14 |
olle |
677 |
/** |
| 3176 |
06 Mar 15 |
olle |
The "DNaseMix" annotation type, used for extracts (RNA, DNA). |
| 3176 |
06 Mar 15 |
olle |
@since 1.2 |
| 3176 |
06 Mar 15 |
olle |
680 |
*/ |
| 3176 |
06 Mar 15 |
olle |
681 |
public static final Annotationtype DNASE_MIX = |
| 3176 |
06 Mar 15 |
olle |
682 |
new Annotationtype("DNaseMix", Type.STRING, false, Item.EXTRACT); |
| 3176 |
06 Mar 15 |
olle |
683 |
|
| 3176 |
06 Mar 15 |
olle |
684 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "AllPrepDNA_col" annotation type, used for extracts (RNA, DNA). |
| 2933 |
14 Nov 14 |
olle |
@since 2.16 |
| 2933 |
14 Nov 14 |
olle |
687 |
*/ |
| 2933 |
14 Nov 14 |
olle |
688 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype ALLPREP_DNA_COL = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("AllPrepDNA_col", Type.STRING, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
691 |
*/ |
| 2933 |
14 Nov 14 |
olle |
692 |
|
| 2933 |
14 Nov 14 |
olle |
693 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "RNeasy_col" annotation type, used for extracts (RNA, DNA). |
| 2933 |
14 Nov 14 |
olle |
@since 2.16 |
| 2933 |
14 Nov 14 |
olle |
696 |
*/ |
| 2933 |
14 Nov 14 |
olle |
697 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype RNEASY_COL = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("RNeasy_col", Type.STRING, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
700 |
*/ |
| 2933 |
14 Nov 14 |
olle |
701 |
|
| 2933 |
14 Nov 14 |
olle |
702 |
/** |
| 3176 |
06 Mar 15 |
olle |
The "RNeasyMinEluteSpin_col" annotation type, used for extracts (RNA, DNA). |
| 3176 |
06 Mar 15 |
olle |
@since 1.2 |
| 3176 |
06 Mar 15 |
olle |
705 |
*/ |
| 3176 |
06 Mar 15 |
olle |
706 |
public static final Annotationtype RNEASY_MIN_ELUTE_SPIN_COL = |
| 3176 |
06 Mar 15 |
olle |
707 |
new Annotationtype("RNeasyMinEluteSpin_col", Type.STRING, false, Item.EXTRACT); |
| 3176 |
06 Mar 15 |
olle |
708 |
|
| 3176 |
06 Mar 15 |
olle |
709 |
/** |
| 3176 |
06 Mar 15 |
olle |
The "QIAampMinEluteSpin_col" annotation type, used for extracts (RNA, DNA). |
| 3176 |
06 Mar 15 |
olle |
@since 1.2 |
| 3176 |
06 Mar 15 |
olle |
712 |
*/ |
| 3176 |
06 Mar 15 |
olle |
713 |
public static final Annotationtype QIAAMP_MIN_ELUTE_SPIN_COL = |
| 3176 |
06 Mar 15 |
olle |
714 |
new Annotationtype("QIAampMinEluteSpin_col", Type.STRING, false, Item.EXTRACT); |
| 3176 |
06 Mar 15 |
olle |
715 |
|
| 3176 |
06 Mar 15 |
olle |
716 |
/** |
| 3324 |
11 May 15 |
olle |
The "KapaSybrFast" annotation type, used for extracts (RNA, DNA). |
| 3324 |
11 May 15 |
olle |
@since 1.2.4 |
| 3324 |
11 May 15 |
olle |
719 |
*/ |
| 3324 |
11 May 15 |
olle |
720 |
public static final Annotationtype KAPA_SYBR_FAST = |
| 3324 |
11 May 15 |
olle |
721 |
new Annotationtype("KapaSybrFast", Type.STRING, false, Item.EXTRACT); |
| 3324 |
11 May 15 |
olle |
722 |
|
| 3324 |
11 May 15 |
olle |
723 |
/** |
| 3324 |
11 May 15 |
olle |
The "QualityControlPrimersQcpRgt" annotation type, used for extracts (RNA, DNA). |
| 3324 |
11 May 15 |
olle |
@since 1.2.4 |
| 3324 |
11 May 15 |
olle |
726 |
*/ |
| 3324 |
11 May 15 |
olle |
727 |
public static final Annotationtype QUALITY_CONTROL_PRIMERS_QCP_RGT = |
| 3324 |
11 May 15 |
olle |
728 |
new Annotationtype("QualityControlPrimersQcpRgt", Type.STRING, false, Item.EXTRACT); |
| 3324 |
11 May 15 |
olle |
729 |
|
| 3324 |
11 May 15 |
olle |
730 |
/** |
| 3438 |
03 Jul 15 |
olle |
The "QualityControlTemplateQct" annotation type, used for extracts (RNA, DNA). |
| 3438 |
03 Jul 15 |
olle |
@since 1.3 |
| 3438 |
03 Jul 15 |
olle |
733 |
*/ |
| 3438 |
03 Jul 15 |
olle |
734 |
public static final Annotationtype QUALITY_CONTROL_TEMPLATE_QCT = |
| 3438 |
03 Jul 15 |
olle |
735 |
new Annotationtype("QualityControlTemplateQct", Type.STRING, false, Item.EXTRACT); |
| 3438 |
03 Jul 15 |
olle |
736 |
|
| 3438 |
03 Jul 15 |
olle |
737 |
/** |
| 3324 |
11 May 15 |
olle |
The "QubitDnaHighSens" annotation type, used for extracts (RNA, DNA). |
| 3324 |
11 May 15 |
olle |
@since 1.2.4 |
| 3324 |
11 May 15 |
olle |
740 |
*/ |
| 3324 |
11 May 15 |
olle |
741 |
public static final Annotationtype QUBIT_DNA_HIGH_SENS = |
| 3324 |
11 May 15 |
olle |
742 |
new Annotationtype("QubitDnaHighSens", Type.STRING, false, Item.EXTRACT); |
| 3324 |
11 May 15 |
olle |
743 |
|
| 3324 |
11 May 15 |
olle |
744 |
/** |
| 3324 |
11 May 15 |
olle |
The "QubitDnaBroadRange" annotation type, used for extracts (RNA, DNA). |
| 3324 |
11 May 15 |
olle |
@since 1.2.4 |
| 3324 |
11 May 15 |
olle |
747 |
*/ |
| 3324 |
11 May 15 |
olle |
748 |
public static final Annotationtype QUBIT_DNA_BROAD_RANGE = |
| 3324 |
11 May 15 |
olle |
749 |
new Annotationtype("QubitDnaBroadRange", Type.STRING, false, Item.EXTRACT); |
| 3324 |
11 May 15 |
olle |
750 |
|
| 3324 |
11 May 15 |
olle |
751 |
/** |
| 3233 |
09 Apr 15 |
olle |
The "SourceItemNamesListString" annotation which, if set, indicates names |
| 3233 |
09 Apr 15 |
olle |
of source items for bioplates. It is a text annotation type. It is expected |
| 3233 |
09 Apr 15 |
olle |
to be used to store a comma-separated list of extract source item names, |
| 3233 |
09 Apr 15 |
olle |
and can therefore be used, when it is important that the order of the items |
| 3233 |
09 Apr 15 |
olle |
is retained. |
| 3233 |
09 Apr 15 |
olle |
@since 1.2.1 |
| 3233 |
09 Apr 15 |
olle |
758 |
*/ |
| 3233 |
09 Apr 15 |
olle |
759 |
public static final Annotationtype SOURCE_ITEM_NAMES_LIST_STRING = |
| 3233 |
09 Apr 15 |
olle |
760 |
new Annotationtype("SourceItemNamesListString", Type.TEXT, false, Item.BIOPLATE); |
| 3233 |
09 Apr 15 |
olle |
761 |
|
| 3233 |
09 Apr 15 |
olle |
762 |
/** |
| 3180 |
17 Mar 15 |
olle |
The "BatchNumberExtraQiacubeItems" annotation type, used for bioplates (RNA/DNA). |
| 3180 |
17 Mar 15 |
olle |
It is an integer annotation type with allowed values >= 0. |
| 3180 |
17 Mar 15 |
olle |
@since 1.2 |
| 3180 |
17 Mar 15 |
olle |
766 |
*/ |
| 3180 |
17 Mar 15 |
olle |
767 |
public static final Annotationtype BATCH_NUMBER_EXTRA_QIACUBE_ITEMS = |
| 3180 |
17 Mar 15 |
olle |
768 |
new Annotationtype("BatchNumberExtraQiacubeItems", Type.INT, false, Item.BIOPLATE); |
| 3180 |
17 Mar 15 |
olle |
769 |
|
| 3180 |
17 Mar 15 |
olle |
770 |
/** |
| 3245 |
14 Apr 15 |
olle |
The "ExtraQiacubeItemNamesListString" annotation which, if set, indicates names |
| 3245 |
14 Apr 15 |
olle |
of extra QIAcube items for bioplates. It is a text annotation type. It is expected |
| 3245 |
14 Apr 15 |
olle |
to be used to store a comma-separated list of extra QIAcube item names, |
| 3245 |
14 Apr 15 |
olle |
and can therefore be used, when it is important that the order of the items |
| 3245 |
14 Apr 15 |
olle |
is retained. |
| 3245 |
14 Apr 15 |
olle |
@since 1.2.2 |
| 3245 |
14 Apr 15 |
olle |
777 |
*/ |
| 3245 |
14 Apr 15 |
olle |
778 |
public static final Annotationtype EXTRA_QIACUBE_ITEM_NAMES_LIST_STRING = |
| 3245 |
14 Apr 15 |
olle |
779 |
new Annotationtype("ExtraQiacubeItemNamesListString", Type.TEXT, false, Item.BIOPLATE); |
| 3245 |
14 Apr 15 |
olle |
780 |
|
| 3245 |
14 Apr 15 |
olle |
781 |
/** |
| 3180 |
17 Mar 15 |
olle |
The "BatchIsolationDate" annotation, used |
| 3180 |
17 Mar 15 |
olle |
for bioplates (RNA/DNA). It is a date annotation type. |
| 3180 |
17 Mar 15 |
olle |
@since 1.2 |
| 3180 |
17 Mar 15 |
olle |
785 |
*/ |
| 3180 |
17 Mar 15 |
olle |
786 |
public static final Annotationtype BATCH_ISOLATION_DATE = |
| 3180 |
17 Mar 15 |
olle |
787 |
new Annotationtype("BatchIsolationDate", Type.DATE, false, Item.BIOPLATE); |
| 3180 |
17 Mar 15 |
olle |
788 |
|
| 3180 |
17 Mar 15 |
olle |
789 |
/** |
| 3180 |
17 Mar 15 |
olle |
The "BatchExtractionProtocolId" annotation, used |
| 3180 |
17 Mar 15 |
olle |
for bioplates (RNA/DNA). It is an integer annotation type. |
| 3180 |
17 Mar 15 |
olle |
@since 1.2 |
| 3180 |
17 Mar 15 |
olle |
793 |
*/ |
| 3180 |
17 Mar 15 |
olle |
794 |
public static final Annotationtype BATCH_EXTRACTION_PROTOCOL_ID = |
| 3180 |
17 Mar 15 |
olle |
795 |
new Annotationtype("BatchExtractionProtocolId", Type.INT, false, Item.BIOPLATE); |
| 3180 |
17 Mar 15 |
olle |
796 |
|
| 3180 |
17 Mar 15 |
olle |
797 |
/** |
| 3180 |
17 Mar 15 |
olle |
The "BatchExtractionProtocolName" annotation, used |
| 3180 |
17 Mar 15 |
olle |
for bioplates (RNA/DNA). It is a string annotation type. |
| 3180 |
17 Mar 15 |
olle |
@since 1.2 |
| 3180 |
17 Mar 15 |
olle |
801 |
*/ |
| 3180 |
17 Mar 15 |
olle |
802 |
public static final Annotationtype BATCH_EXTRACTION_PROTOCOL_NAME = |
| 3180 |
17 Mar 15 |
olle |
803 |
new Annotationtype("BatchExtractionProtocolName", Type.STRING, false, Item.BIOPLATE); |
| 3180 |
17 Mar 15 |
olle |
804 |
|
| 3180 |
17 Mar 15 |
olle |
805 |
/** |
| 3180 |
17 Mar 15 |
olle |
The "BatchRnaDefaultVolumeInMicroLitre" annotation, used |
| 3180 |
17 Mar 15 |
olle |
for bioplates (RNA/DNA). It is a float annotation type. |
| 3180 |
17 Mar 15 |
olle |
@since 1.2 |
| 3180 |
17 Mar 15 |
olle |
809 |
*/ |
| 3180 |
17 Mar 15 |
olle |
810 |
public static final Annotationtype BATCH_RNA_DEFAULT_VOLUME_IN_MICROLITRE = |
| 3180 |
17 Mar 15 |
olle |
811 |
new Annotationtype("BatchRnaDefaultVolumeInMicroLitre", Type.FLOAT, false, Item.BIOPLATE); |
| 3180 |
17 Mar 15 |
olle |
812 |
|
| 3180 |
17 Mar 15 |
olle |
813 |
/** |
| 3180 |
17 Mar 15 |
olle |
The "BatchDnaDefaultVolumeInMicroLitre" annotation, used |
| 3180 |
17 Mar 15 |
olle |
for bioplates (RNA/DNA). It is a float annotation type. |
| 3180 |
17 Mar 15 |
olle |
@since 1.2 |
| 3180 |
17 Mar 15 |
olle |
817 |
*/ |
| 3180 |
17 Mar 15 |
olle |
818 |
public static final Annotationtype BATCH_DNA_DEFAULT_VOLUME_IN_MICROLITRE = |
| 3180 |
17 Mar 15 |
olle |
819 |
new Annotationtype("BatchDnaDefaultVolumeInMicroLitre", Type.FLOAT, false, Item.BIOPLATE); |
| 3180 |
17 Mar 15 |
olle |
820 |
|
| 3180 |
17 Mar 15 |
olle |
821 |
/** |
| 3180 |
17 Mar 15 |
olle |
The "BatchQiacubeDate" annotation type, used |
| 3180 |
17 Mar 15 |
olle |
for bioplates (RNA/DNA). It is a date annotation type. |
| 3180 |
17 Mar 15 |
olle |
@since 1.2 |
| 3180 |
17 Mar 15 |
olle |
825 |
*/ |
| 3180 |
17 Mar 15 |
olle |
826 |
public static final Annotationtype BATCH_QIACUBE_DATE = |
| 3180 |
17 Mar 15 |
olle |
827 |
new Annotationtype("BatchQiacubeDate", Type.DATE, false, Item.BIOPLATE); |
| 3180 |
17 Mar 15 |
olle |
828 |
|
| 3180 |
17 Mar 15 |
olle |
829 |
/** |
| 3180 |
17 Mar 15 |
olle |
The "BatchQiacubePrimaryPrefix" annotation, used |
| 3180 |
17 Mar 15 |
olle |
for bioplates (RNA/DNA). It is a string annotation type. |
| 3180 |
17 Mar 15 |
olle |
@since 1.2 |
| 3180 |
17 Mar 15 |
olle |
833 |
*/ |
| 3180 |
17 Mar 15 |
olle |
834 |
public static final Annotationtype BATCH_QIACUBE_PRIMARY_PREFIX = |
| 3180 |
17 Mar 15 |
olle |
835 |
new Annotationtype("BatchQiacubePrimaryPrefix", Type.STRING, false, Item.BIOPLATE); |
| 3180 |
17 Mar 15 |
olle |
836 |
|
| 3180 |
17 Mar 15 |
olle |
837 |
/** |
| 3180 |
17 Mar 15 |
olle |
The "BatchQiacubeSecondaryPrefix" annotation, used |
| 3180 |
17 Mar 15 |
olle |
for bioplates (RNA/DNA). It is a string annotation type. |
| 3180 |
17 Mar 15 |
olle |
@since 1.2 |
| 3180 |
17 Mar 15 |
olle |
841 |
*/ |
| 3180 |
17 Mar 15 |
olle |
842 |
public static final Annotationtype BATCH_QIACUBE_SECONDARY_PREFIX = |
| 3180 |
17 Mar 15 |
olle |
843 |
new Annotationtype("BatchQiacubeSecondaryPrefix", Type.STRING, false, Item.BIOPLATE); |
| 3180 |
17 Mar 15 |
olle |
844 |
|
| 3180 |
17 Mar 15 |
olle |
845 |
/** |
| 3180 |
17 Mar 15 |
olle |
The "BatchQiacubeRunNo" annotation type, used for bioplates (RNA/DNA). |
| 3180 |
17 Mar 15 |
olle |
It is an integer annotation type with allowed values >= 1. |
| 3180 |
17 Mar 15 |
olle |
@since 1.2 |
| 3180 |
17 Mar 15 |
olle |
849 |
*/ |
| 3180 |
17 Mar 15 |
olle |
850 |
public static final Annotationtype BATCH_QIACUBE_RUN_NO = |
| 3180 |
17 Mar 15 |
olle |
851 |
new Annotationtype("BatchQiacubeRunNo", Type.INT, false, Item.BIOPLATE); |
| 3180 |
17 Mar 15 |
olle |
852 |
|
| 3180 |
17 Mar 15 |
olle |
853 |
/** |
| 3180 |
17 Mar 15 |
olle |
The "BatchQiacubeOperator" annotation, used |
| 3180 |
17 Mar 15 |
olle |
for bioplates (RNA/DNA). It is a string annotation type. |
| 3180 |
17 Mar 15 |
olle |
@since 1.2 |
| 3180 |
17 Mar 15 |
olle |
857 |
*/ |
| 3180 |
17 Mar 15 |
olle |
858 |
public static final Annotationtype BATCH_QIACUBE_OPERATOR = |
| 3180 |
17 Mar 15 |
olle |
859 |
new Annotationtype("BatchQiacubeOperator", Type.STRING, false, Item.BIOPLATE); |
| 3180 |
17 Mar 15 |
olle |
860 |
|
| 3180 |
17 Mar 15 |
olle |
861 |
/** |
| 3180 |
17 Mar 15 |
olle |
The "BatchAllprepFfpeKit" annotation type, used |
| 3180 |
17 Mar 15 |
olle |
for bioplates (RNA/DNA). It is a string annotation type. |
| 3180 |
17 Mar 15 |
olle |
@since 1.2 |
| 3180 |
17 Mar 15 |
olle |
865 |
*/ |
| 3180 |
17 Mar 15 |
olle |
866 |
public static final Annotationtype BATCH_ALLPREP_FFPE_KIT = |
| 3180 |
17 Mar 15 |
olle |
867 |
new Annotationtype("BatchAllprepFfpeKit", Type.STRING, false, Item.BIOPLATE); |
| 3180 |
17 Mar 15 |
olle |
868 |
|
| 3180 |
17 Mar 15 |
olle |
869 |
/** |
| 3430 |
29 Jun 15 |
olle |
The "SamplePrepListIsProcessed" annotation, used for item lists. |
| 3430 |
29 Jun 15 |
olle |
Store a flag indicating if the item list is processed, and the items |
| 3430 |
29 Jun 15 |
olle |
therefore not should appear in selection lists. |
| 3430 |
29 Jun 15 |
olle |
@since 1.3 |
| 3430 |
29 Jun 15 |
olle |
874 |
*/ |
| 3430 |
29 Jun 15 |
olle |
875 |
public static final Annotationtype SAMPLE_PREP_LIST_IS_PROCESSED = |
| 3430 |
29 Jun 15 |
olle |
876 |
new Annotationtype("SamplePrepListIsProcessed", Type.BOOLEAN, false, Item.ITEMLIST); |
| 3430 |
29 Jun 15 |
olle |
877 |
|
| 3430 |
29 Jun 15 |
olle |
878 |
/** |
| 3430 |
29 Jun 15 |
olle |
The "ListIsolationDate" annotation, used |
| 3430 |
29 Jun 15 |
olle |
for item lists. It is a date annotation type. |
| 3430 |
29 Jun 15 |
olle |
@since 1.3 |
| 3430 |
29 Jun 15 |
olle |
882 |
*/ |
| 3430 |
29 Jun 15 |
olle |
883 |
public static final Annotationtype LIST_ISOLATION_DATE = |
| 3430 |
29 Jun 15 |
olle |
884 |
new Annotationtype("ListIsolationDate", Type.DATE, false, Item.ITEMLIST); |
| 3430 |
29 Jun 15 |
olle |
885 |
|
| 3430 |
29 Jun 15 |
olle |
886 |
/** |
| 3501 |
21 Sep 15 |
olle |
The "ListExtractionOperator" annotation, used |
| 3501 |
21 Sep 15 |
olle |
for item lists. It is a string annotation type. |
| 3501 |
21 Sep 15 |
olle |
@since 1.3.2 |
| 3501 |
21 Sep 15 |
olle |
890 |
*/ |
| 3501 |
21 Sep 15 |
olle |
891 |
public static final Annotationtype LIST_EXTRACTION_OPERATOR = |
| 3501 |
21 Sep 15 |
olle |
892 |
new Annotationtype("ListExtractionOperator", Type.STRING, false, Item.ITEMLIST); |
| 3501 |
21 Sep 15 |
olle |
893 |
|
| 3501 |
21 Sep 15 |
olle |
894 |
/** |
| 3430 |
29 Jun 15 |
olle |
The "ListExtractionDate" annotation, used |
| 3430 |
29 Jun 15 |
olle |
for item lists. It is a date annotation type. |
| 3430 |
29 Jun 15 |
olle |
@since 1.3 |
| 3430 |
29 Jun 15 |
olle |
898 |
*/ |
| 3430 |
29 Jun 15 |
olle |
899 |
public static final Annotationtype LIST_EXTRACTION_DATE = |
| 3430 |
29 Jun 15 |
olle |
900 |
new Annotationtype("ListExtractionDate", Type.DATE, false, Item.ITEMLIST); |
| 3430 |
29 Jun 15 |
olle |
901 |
|
| 3430 |
29 Jun 15 |
olle |
902 |
/** |
| 3430 |
29 Jun 15 |
olle |
The "ListExtractionProtocolId" annotation, used |
| 3430 |
29 Jun 15 |
olle |
for item lists. It is an integer annotation type. |
| 3430 |
29 Jun 15 |
olle |
@since 1.3 |
| 3430 |
29 Jun 15 |
olle |
906 |
*/ |
| 3430 |
29 Jun 15 |
olle |
907 |
public static final Annotationtype LIST_EXTRACTION_PROTOCOL_ID = |
| 3430 |
29 Jun 15 |
olle |
908 |
new Annotationtype("ListExtractionProtocolId", Type.INT, false, Item.ITEMLIST); |
| 3430 |
29 Jun 15 |
olle |
909 |
|
| 3430 |
29 Jun 15 |
olle |
910 |
/** |
| 3430 |
29 Jun 15 |
olle |
The "ListExtractionProtocolName" annotation, used |
| 3430 |
29 Jun 15 |
olle |
for item lists. It is a string annotation type. |
| 3430 |
29 Jun 15 |
olle |
@since 1.3 |
| 3430 |
29 Jun 15 |
olle |
914 |
*/ |
| 3430 |
29 Jun 15 |
olle |
915 |
public static final Annotationtype LIST_EXTRACTION_PROTOCOL_NAME = |
| 3430 |
29 Jun 15 |
olle |
916 |
new Annotationtype("ListExtractionProtocolName", Type.STRING, false, Item.ITEMLIST); |
| 3430 |
29 Jun 15 |
olle |
917 |
|
| 3430 |
29 Jun 15 |
olle |
918 |
/** |
| 3430 |
29 Jun 15 |
olle |
The "ListRnaDefaultVolumeInMicroLitre" annotation, used |
| 3430 |
29 Jun 15 |
olle |
for item lists. It is a float annotation type. |
| 3430 |
29 Jun 15 |
olle |
@since 1.3 |
| 3430 |
29 Jun 15 |
olle |
922 |
*/ |
| 3430 |
29 Jun 15 |
olle |
923 |
public static final Annotationtype LIST_RNA_DEFAULT_VOLUME_IN_MICROLITRE = |
| 3430 |
29 Jun 15 |
olle |
924 |
new Annotationtype("ListRnaDefaultVolumeInMicroLitre", Type.FLOAT, false, Item.ITEMLIST); |
| 3430 |
29 Jun 15 |
olle |
925 |
|
| 3430 |
29 Jun 15 |
olle |
926 |
/** |
| 3430 |
29 Jun 15 |
olle |
The "ListDnaDefaultVolumeInMicroLitre" annotation, used |
| 3430 |
29 Jun 15 |
olle |
for item lists. It is a float annotation type. |
| 3430 |
29 Jun 15 |
olle |
@since 1.3 |
| 3430 |
29 Jun 15 |
olle |
930 |
*/ |
| 3430 |
29 Jun 15 |
olle |
931 |
public static final Annotationtype LIST_DNA_DEFAULT_VOLUME_IN_MICROLITRE = |
| 3430 |
29 Jun 15 |
olle |
932 |
new Annotationtype("ListDnaDefaultVolumeInMicroLitre", Type.FLOAT, false, Item.ITEMLIST); |
| 3430 |
29 Jun 15 |
olle |
933 |
|
| 3430 |
29 Jun 15 |
olle |
934 |
/** |
| 3430 |
29 Jun 15 |
olle |
The "ListQiacubeDate" annotation type, used |
| 3430 |
29 Jun 15 |
olle |
for item lists. It is a date annotation type. |
| 3430 |
29 Jun 15 |
olle |
@since 1.3 |
| 3430 |
29 Jun 15 |
olle |
938 |
*/ |
| 3430 |
29 Jun 15 |
olle |
939 |
public static final Annotationtype LIST_QIACUBE_DATE = |
| 3430 |
29 Jun 15 |
olle |
940 |
new Annotationtype("ListQiacubeDate", Type.DATE, false, Item.ITEMLIST); |
| 3430 |
29 Jun 15 |
olle |
941 |
|
| 3430 |
29 Jun 15 |
olle |
942 |
/** |
| 3430 |
29 Jun 15 |
olle |
The "ListQiacubePrimaryPrefix" annotation, used |
| 3430 |
29 Jun 15 |
olle |
for item lists. It is a string annotation type. |
| 3430 |
29 Jun 15 |
olle |
@since 1.3 |
| 3430 |
29 Jun 15 |
olle |
946 |
*/ |
| 3430 |
29 Jun 15 |
olle |
947 |
public static final Annotationtype LIST_QIACUBE_PRIMARY_PREFIX = |
| 3430 |
29 Jun 15 |
olle |
948 |
new Annotationtype("ListQiacubePrimaryPrefix", Type.STRING, false, Item.ITEMLIST); |
| 3430 |
29 Jun 15 |
olle |
949 |
|
| 3430 |
29 Jun 15 |
olle |
950 |
/** |
| 3430 |
29 Jun 15 |
olle |
The "ListQiacubeSecondaryPrefix" annotation, used |
| 3430 |
29 Jun 15 |
olle |
for item lists. It is a string annotation type. |
| 3430 |
29 Jun 15 |
olle |
@since 1.3 |
| 3430 |
29 Jun 15 |
olle |
954 |
*/ |
| 3430 |
29 Jun 15 |
olle |
955 |
public static final Annotationtype LIST_QIACUBE_SECONDARY_PREFIX = |
| 3430 |
29 Jun 15 |
olle |
956 |
new Annotationtype("ListQiacubeSecondaryPrefix", Type.STRING, false, Item.ITEMLIST); |
| 3430 |
29 Jun 15 |
olle |
957 |
|
| 3430 |
29 Jun 15 |
olle |
958 |
/** |
| 3430 |
29 Jun 15 |
olle |
The "ListQiacubeRunNo" annotation type, used for item lists. |
| 3430 |
29 Jun 15 |
olle |
It is an integer annotation type with allowed values >= 1. |
| 3430 |
29 Jun 15 |
olle |
@since 1.3 |
| 3430 |
29 Jun 15 |
olle |
962 |
*/ |
| 3430 |
29 Jun 15 |
olle |
963 |
public static final Annotationtype LIST_QIACUBE_RUN_NO = |
| 3430 |
29 Jun 15 |
olle |
964 |
new Annotationtype("ListQiacubeRunNo", Type.INT, false, Item.ITEMLIST); |
| 3430 |
29 Jun 15 |
olle |
965 |
|
| 3430 |
29 Jun 15 |
olle |
966 |
/** |
| 3430 |
29 Jun 15 |
olle |
The "ListQiacubeOperator" annotation, used |
| 3430 |
29 Jun 15 |
olle |
for item lists. It is a string annotation type. |
| 3430 |
29 Jun 15 |
olle |
@since 1.3 |
| 3430 |
29 Jun 15 |
olle |
970 |
*/ |
| 3430 |
29 Jun 15 |
olle |
971 |
public static final Annotationtype LIST_QIACUBE_OPERATOR = |
| 3430 |
29 Jun 15 |
olle |
972 |
new Annotationtype("ListQiacubeOperator", Type.STRING, false, Item.ITEMLIST); |
| 3430 |
29 Jun 15 |
olle |
973 |
|
| 3430 |
29 Jun 15 |
olle |
974 |
/** |
| 3430 |
29 Jun 15 |
olle |
The "ListAllprepFfpeKit" annotation type, used |
| 3430 |
29 Jun 15 |
olle |
for item lists. It is a string annotation type. |
| 3430 |
29 Jun 15 |
olle |
@since 1.3 |
| 3430 |
29 Jun 15 |
olle |
978 |
*/ |
| 3430 |
29 Jun 15 |
olle |
979 |
public static final Annotationtype LIST_ALLPREP_FFPE_KIT = |
| 3430 |
29 Jun 15 |
olle |
980 |
new Annotationtype("ListAllprepFfpeKit", Type.STRING, false, Item.ITEMLIST); |
| 3430 |
29 Jun 15 |
olle |
981 |
|
| 3430 |
29 Jun 15 |
olle |
982 |
/** |
| 3501 |
21 Sep 15 |
olle |
The "ListXylene_Specimen" annotation type, used |
| 3501 |
21 Sep 15 |
olle |
for item lists. It is a string annotation type. |
| 3501 |
21 Sep 15 |
olle |
@since 1.3.2 |
| 3501 |
21 Sep 15 |
olle |
986 |
*/ |
| 3501 |
21 Sep 15 |
olle |
987 |
public static final Annotationtype LIST_XYLENE_SPECIMEN = |
| 3501 |
21 Sep 15 |
olle |
988 |
new Annotationtype("ListXylene_Specimen", Type.STRING, false, Item.ITEMLIST); |
| 3501 |
21 Sep 15 |
olle |
989 |
|
| 3501 |
21 Sep 15 |
olle |
990 |
/** |
| 3501 |
21 Sep 15 |
olle |
The "ListETOH995_Specimen" annotation type, used |
| 3501 |
21 Sep 15 |
olle |
for item lists. It is a string annotation type. |
| 3501 |
21 Sep 15 |
olle |
@since 1.3.2 |
| 3501 |
21 Sep 15 |
olle |
994 |
*/ |
| 3501 |
21 Sep 15 |
olle |
995 |
public static final Annotationtype LIST_ETOH995_SPECIMEN = |
| 3501 |
21 Sep 15 |
olle |
996 |
new Annotationtype("ListETOH995_Specimen", Type.STRING, false, Item.ITEMLIST); |
| 3501 |
21 Sep 15 |
olle |
997 |
|
| 3501 |
21 Sep 15 |
olle |
998 |
/** |
| 3501 |
21 Sep 15 |
olle |
The "ListBufferPKD_Specimen" annotation type, used |
| 3501 |
21 Sep 15 |
olle |
for item lists. It is a string annotation type. |
| 3501 |
21 Sep 15 |
olle |
@since 1.3.2 |
| 3501 |
21 Sep 15 |
olle |
1002 |
*/ |
| 3501 |
21 Sep 15 |
olle |
1003 |
public static final Annotationtype LIST_BUFFER_PKD_SPECIMEN = |
| 3501 |
21 Sep 15 |
olle |
1004 |
new Annotationtype("ListBufferPKD_Specimen", Type.STRING, false, Item.ITEMLIST); |
| 3501 |
21 Sep 15 |
olle |
1005 |
|
| 3501 |
21 Sep 15 |
olle |
1006 |
/** |
| 3501 |
21 Sep 15 |
olle |
The "ListBufferATL_Specimen" annotation type, used |
| 3501 |
21 Sep 15 |
olle |
for item lists. It is a string annotation type. |
| 3501 |
21 Sep 15 |
olle |
@since 1.3.2 |
| 3501 |
21 Sep 15 |
olle |
1010 |
*/ |
| 3501 |
21 Sep 15 |
olle |
1011 |
public static final Annotationtype LIST_BUFFER_ATL_SPECIMEN = |
| 3501 |
21 Sep 15 |
olle |
1012 |
new Annotationtype("ListBufferATL_Specimen", Type.STRING, false, Item.ITEMLIST); |
| 3501 |
21 Sep 15 |
olle |
1013 |
|
| 3501 |
21 Sep 15 |
olle |
1014 |
/** |
| 3501 |
21 Sep 15 |
olle |
The "ListProteinaseK_Specimen" annotation type, used |
| 3501 |
21 Sep 15 |
olle |
for item lists. It is a string annotation type. |
| 3501 |
21 Sep 15 |
olle |
@since 1.3.2 |
| 3501 |
21 Sep 15 |
olle |
1018 |
*/ |
| 3501 |
21 Sep 15 |
olle |
1019 |
public static final Annotationtype LIST_PROTEINASE_K_SPECIMEN = |
| 3501 |
21 Sep 15 |
olle |
1020 |
new Annotationtype("ListProteinaseK_Specimen", Type.STRING, false, Item.ITEMLIST); |
| 3501 |
21 Sep 15 |
olle |
1021 |
|
| 3501 |
21 Sep 15 |
olle |
1022 |
/** |
| 3501 |
21 Sep 15 |
olle |
The "ListRNaseA_Specimen" annotation type, used |
| 3501 |
21 Sep 15 |
olle |
for item lists. It is a string annotation type. |
| 3501 |
21 Sep 15 |
olle |
@since 1.3.2 |
| 3501 |
21 Sep 15 |
olle |
1026 |
*/ |
| 3501 |
21 Sep 15 |
olle |
1027 |
public static final Annotationtype LIST_RNASE_A_SPECIMEN = |
| 3501 |
21 Sep 15 |
olle |
1028 |
new Annotationtype("ListRNaseA_Specimen", Type.STRING, false, Item.ITEMLIST); |
| 3501 |
21 Sep 15 |
olle |
1029 |
|
| 3501 |
21 Sep 15 |
olle |
1030 |
/** |
| 3501 |
21 Sep 15 |
olle |
The "ListETOH995" annotation type, used |
| 3501 |
21 Sep 15 |
olle |
for item lists. It is a string annotation type. |
| 3501 |
21 Sep 15 |
olle |
@since 1.3.2 |
| 3501 |
21 Sep 15 |
olle |
1034 |
*/ |
| 3501 |
21 Sep 15 |
olle |
1035 |
public static final Annotationtype LIST_ETOH995 = |
| 3501 |
21 Sep 15 |
olle |
1036 |
new Annotationtype("ListETOH995", Type.STRING, false, Item.ITEMLIST); |
| 3501 |
21 Sep 15 |
olle |
1037 |
|
| 3501 |
21 Sep 15 |
olle |
1038 |
/** |
| 3501 |
21 Sep 15 |
olle |
The "ListBufferRLT" annotation type, used |
| 3501 |
21 Sep 15 |
olle |
for item lists. It is a string annotation type. |
| 3501 |
21 Sep 15 |
olle |
@since 1.3.2 |
| 3501 |
21 Sep 15 |
olle |
1042 |
*/ |
| 3501 |
21 Sep 15 |
olle |
1043 |
public static final Annotationtype LIST_BUFFER_RLT = |
| 3501 |
21 Sep 15 |
olle |
1044 |
new Annotationtype("ListBufferRLT", Type.STRING, false, Item.ITEMLIST); |
| 3501 |
21 Sep 15 |
olle |
1045 |
|
| 3501 |
21 Sep 15 |
olle |
1046 |
/** |
| 3501 |
21 Sep 15 |
olle |
The "ListBufferFRN" annotation type, used |
| 3501 |
21 Sep 15 |
olle |
for item lists. It is a string annotation type. |
| 3501 |
21 Sep 15 |
olle |
@since 1.3.2 |
| 3501 |
21 Sep 15 |
olle |
1050 |
*/ |
| 3501 |
21 Sep 15 |
olle |
1051 |
public static final Annotationtype LIST_BUFFER_FRN = |
| 3501 |
21 Sep 15 |
olle |
1052 |
new Annotationtype("ListBufferFRN", Type.STRING, false, Item.ITEMLIST); |
| 3501 |
21 Sep 15 |
olle |
1053 |
|
| 3501 |
21 Sep 15 |
olle |
1054 |
/** |
| 3501 |
21 Sep 15 |
olle |
The "ListBufferRPE" annotation type, used |
| 3501 |
21 Sep 15 |
olle |
for item lists. It is a string annotation type. |
| 3501 |
21 Sep 15 |
olle |
@since 1.3.2 |
| 3501 |
21 Sep 15 |
olle |
1058 |
*/ |
| 3501 |
21 Sep 15 |
olle |
1059 |
public static final Annotationtype LIST_BUFFER_RPE = |
| 3501 |
21 Sep 15 |
olle |
1060 |
new Annotationtype("ListBufferRPE", Type.STRING, false, Item.ITEMLIST); |
| 3501 |
21 Sep 15 |
olle |
1061 |
|
| 3501 |
21 Sep 15 |
olle |
1062 |
/** |
| 3501 |
21 Sep 15 |
olle |
The "ListBufferAL" annotation type, used |
| 3501 |
21 Sep 15 |
olle |
for item lists. It is a string annotation type. |
| 3501 |
21 Sep 15 |
olle |
@since 1.3.2 |
| 3501 |
21 Sep 15 |
olle |
1066 |
*/ |
| 3501 |
21 Sep 15 |
olle |
1067 |
public static final Annotationtype LIST_BUFFER_AL = |
| 3501 |
21 Sep 15 |
olle |
1068 |
new Annotationtype("ListBufferAL", Type.STRING, false, Item.ITEMLIST); |
| 3501 |
21 Sep 15 |
olle |
1069 |
|
| 3501 |
21 Sep 15 |
olle |
1070 |
/** |
| 3501 |
21 Sep 15 |
olle |
The "ListBufferAW1" annotation type, used |
| 3501 |
21 Sep 15 |
olle |
for item lists. It is a string annotation type. |
| 3501 |
21 Sep 15 |
olle |
@since 1.3.2 |
| 3501 |
21 Sep 15 |
olle |
1074 |
*/ |
| 3501 |
21 Sep 15 |
olle |
1075 |
public static final Annotationtype LIST_BUFFER_AW1 = |
| 3501 |
21 Sep 15 |
olle |
1076 |
new Annotationtype("ListBufferAW1", Type.STRING, false, Item.ITEMLIST); |
| 3501 |
21 Sep 15 |
olle |
1077 |
|
| 3501 |
21 Sep 15 |
olle |
1078 |
/** |
| 3501 |
21 Sep 15 |
olle |
The "ListBufferAW2" annotation type, used |
| 3501 |
21 Sep 15 |
olle |
for item lists. It is a string annotation type. |
| 3501 |
21 Sep 15 |
olle |
@since 1.3.2 |
| 3501 |
21 Sep 15 |
olle |
1082 |
*/ |
| 3501 |
21 Sep 15 |
olle |
1083 |
public static final Annotationtype LIST_BUFFER_AW2 = |
| 3501 |
21 Sep 15 |
olle |
1084 |
new Annotationtype("ListBufferAW2", Type.STRING, false, Item.ITEMLIST); |
| 3501 |
21 Sep 15 |
olle |
1085 |
|
| 3501 |
21 Sep 15 |
olle |
1086 |
/** |
| 3501 |
21 Sep 15 |
olle |
The "ListBufferATE" annotation type, used |
| 3501 |
21 Sep 15 |
olle |
for item lists. It is a string annotation type. |
| 3501 |
21 Sep 15 |
olle |
@since 1.3.2 |
| 3501 |
21 Sep 15 |
olle |
1090 |
*/ |
| 3501 |
21 Sep 15 |
olle |
1091 |
public static final Annotationtype LIST_BUFFER_ATE = |
| 3501 |
21 Sep 15 |
olle |
1092 |
new Annotationtype("ListBufferATE", Type.STRING, false, Item.ITEMLIST); |
| 3501 |
21 Sep 15 |
olle |
1093 |
|
| 3501 |
21 Sep 15 |
olle |
1094 |
/** |
| 3501 |
21 Sep 15 |
olle |
The "ListBufferRDD" annotation type, used |
| 3501 |
21 Sep 15 |
olle |
for item lists. It is a string annotation type. |
| 3501 |
21 Sep 15 |
olle |
@since 1.3.2 |
| 3501 |
21 Sep 15 |
olle |
1098 |
*/ |
| 3501 |
21 Sep 15 |
olle |
1099 |
public static final Annotationtype LIST_BUFFER_RDD = |
| 3501 |
21 Sep 15 |
olle |
1100 |
new Annotationtype("ListBufferRDD", Type.STRING, false, Item.ITEMLIST); |
| 3501 |
21 Sep 15 |
olle |
1101 |
|
| 3501 |
21 Sep 15 |
olle |
1102 |
/** |
| 3501 |
21 Sep 15 |
olle |
The "ListRNaseFreeWater" annotation type, used |
| 3501 |
21 Sep 15 |
olle |
for item lists. It is a string annotation type. |
| 3501 |
21 Sep 15 |
olle |
@since 1.3.2 |
| 3501 |
21 Sep 15 |
olle |
1106 |
*/ |
| 3501 |
21 Sep 15 |
olle |
1107 |
public static final Annotationtype LIST_RNASE_FREE_WATER = |
| 3501 |
21 Sep 15 |
olle |
1108 |
new Annotationtype("ListRNaseFreeWater", Type.STRING, false, Item.ITEMLIST); |
| 3501 |
21 Sep 15 |
olle |
1109 |
|
| 3501 |
21 Sep 15 |
olle |
1110 |
/** |
| 3501 |
21 Sep 15 |
olle |
The "ListDNaseMix" annotation type, used |
| 3501 |
21 Sep 15 |
olle |
for item lists. It is a string annotation type. |
| 3501 |
21 Sep 15 |
olle |
@since 1.3.2 |
| 3501 |
21 Sep 15 |
olle |
1114 |
*/ |
| 3501 |
21 Sep 15 |
olle |
1115 |
public static final Annotationtype LIST_DNASE_MIX = |
| 3501 |
21 Sep 15 |
olle |
1116 |
new Annotationtype("ListDNaseMix", Type.STRING, false, Item.ITEMLIST); |
| 3501 |
21 Sep 15 |
olle |
1117 |
|
| 3501 |
21 Sep 15 |
olle |
1118 |
/** |
| 3501 |
21 Sep 15 |
olle |
The "ListRNeasyMinEluteSpin_col" annotation type, used |
| 3501 |
21 Sep 15 |
olle |
for item lists. It is a string annotation type. |
| 3501 |
21 Sep 15 |
olle |
@since 1.3.2 |
| 3501 |
21 Sep 15 |
olle |
1122 |
*/ |
| 3501 |
21 Sep 15 |
olle |
1123 |
public static final Annotationtype LIST_RNEASY_MIN_ELUTE_SPIN_COL = |
| 3501 |
21 Sep 15 |
olle |
1124 |
new Annotationtype("ListRNeasyMinEluteSpin_col", Type.STRING, false, Item.ITEMLIST); |
| 3501 |
21 Sep 15 |
olle |
1125 |
|
| 3501 |
21 Sep 15 |
olle |
1126 |
/** |
| 3501 |
21 Sep 15 |
olle |
The "ListQIAampMinEluteSpin_col" annotation type, used |
| 3501 |
21 Sep 15 |
olle |
for item lists. It is a string annotation type. |
| 3501 |
21 Sep 15 |
olle |
@since 1.3.2 |
| 3501 |
21 Sep 15 |
olle |
1130 |
*/ |
| 3501 |
21 Sep 15 |
olle |
1131 |
public static final Annotationtype LIST_QIAAMP_MIN_ELUTE_SPIN_COL = |
| 3501 |
21 Sep 15 |
olle |
1132 |
new Annotationtype("ListQIAampMinEluteSpin_col", Type.STRING, false, Item.ITEMLIST); |
| 3501 |
21 Sep 15 |
olle |
1133 |
|
| 3501 |
21 Sep 15 |
olle |
1134 |
/** |
| 3501 |
21 Sep 15 |
olle |
The "ListKapaSybrFast" annotation type, used |
| 3501 |
21 Sep 15 |
olle |
for item lists. It is a string annotation type. |
| 3501 |
21 Sep 15 |
olle |
@since 1.3.2 |
| 3501 |
21 Sep 15 |
olle |
1138 |
*/ |
| 3501 |
21 Sep 15 |
olle |
1139 |
public static final Annotationtype LIST_KAPA_SYBR_FAST = |
| 3501 |
21 Sep 15 |
olle |
1140 |
new Annotationtype("ListKapaSybrFast", Type.STRING, false, Item.ITEMLIST); |
| 3501 |
21 Sep 15 |
olle |
1141 |
|
| 3501 |
21 Sep 15 |
olle |
1142 |
/** |
| 3501 |
21 Sep 15 |
olle |
The "ListQualityControlPrimersQcpRgt" annotation type, used |
| 3501 |
21 Sep 15 |
olle |
for item lists. It is a string annotation type. |
| 3501 |
21 Sep 15 |
olle |
@since 1.3.2 |
| 3501 |
21 Sep 15 |
olle |
1146 |
*/ |
| 3501 |
21 Sep 15 |
olle |
1147 |
public static final Annotationtype LIST_QUALITY_CONTROL_PRIMERS_QCP_RGT = |
| 3501 |
21 Sep 15 |
olle |
1148 |
new Annotationtype("ListQualityControlPrimersQcpRgt", Type.STRING, false, Item.ITEMLIST); |
| 3501 |
21 Sep 15 |
olle |
1149 |
|
| 3501 |
21 Sep 15 |
olle |
1150 |
/** |
| 3501 |
21 Sep 15 |
olle |
The "ListQualityControlTemplateQct" annotation type, used |
| 3501 |
21 Sep 15 |
olle |
for item lists. It is a string annotation type. |
| 3501 |
21 Sep 15 |
olle |
@since 1.3.2 |
| 3501 |
21 Sep 15 |
olle |
1154 |
*/ |
| 3501 |
21 Sep 15 |
olle |
1155 |
public static final Annotationtype LIST_QUALITY_CONTROL_TEMPLATE_QCT = |
| 3501 |
21 Sep 15 |
olle |
1156 |
new Annotationtype("ListQualityControlTemplateQct", Type.STRING, false, Item.ITEMLIST); |
| 3501 |
21 Sep 15 |
olle |
1157 |
|
| 3501 |
21 Sep 15 |
olle |
1158 |
/** |
| 3501 |
21 Sep 15 |
olle |
The "ListQubitDnaHighSens" annotation type, used |
| 3501 |
21 Sep 15 |
olle |
for item lists. It is a string annotation type. |
| 3501 |
21 Sep 15 |
olle |
@since 1.3.2 |
| 3501 |
21 Sep 15 |
olle |
1162 |
*/ |
| 3501 |
21 Sep 15 |
olle |
1163 |
public static final Annotationtype LIST_QUBIT_DNA_HIGH_SENS = |
| 3501 |
21 Sep 15 |
olle |
1164 |
new Annotationtype("ListQubitDnaHighSens", Type.STRING, false, Item.ITEMLIST); |
| 3501 |
21 Sep 15 |
olle |
1165 |
|
| 3501 |
21 Sep 15 |
olle |
1166 |
/** |
| 3501 |
21 Sep 15 |
olle |
The "ListQubitDnaBroadRange" annotation type, used |
| 3501 |
21 Sep 15 |
olle |
for item lists. It is a string annotation type. |
| 3501 |
21 Sep 15 |
olle |
@since 1.3.2 |
| 3501 |
21 Sep 15 |
olle |
1170 |
*/ |
| 3501 |
21 Sep 15 |
olle |
1171 |
public static final Annotationtype LIST_QUBIT_DNA_BROAD_RANGE = |
| 3501 |
21 Sep 15 |
olle |
1172 |
new Annotationtype("ListQubitDnaBroadRange", Type.STRING, false, Item.ITEMLIST); |
| 3501 |
21 Sep 15 |
olle |
1173 |
|
| 3501 |
21 Sep 15 |
olle |
1174 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitLibPrepBox1" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1178 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1179 |
public static final Annotationtype LIBPREPKIT_LIB_PREP_BOX1 = |
| 3610 |
20 Nov 15 |
olle |
1180 |
new Annotationtype("LibPrepKitLibPrepBox1", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1181 |
|
| 3610 |
20 Nov 15 |
olle |
1182 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitIndexKit" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1186 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1187 |
public static final Annotationtype LIBPREPKIT_LIB_INDEX_KIT = |
| 3610 |
20 Nov 15 |
olle |
1188 |
new Annotationtype("LibPrepKitIndexKit", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1189 |
|
| 3610 |
20 Nov 15 |
olle |
1190 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitContentSetBox3" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1194 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1195 |
public static final Annotationtype LIBPREPKIT_CONTENT_SET_BOX3 = |
| 3610 |
20 Nov 15 |
olle |
1196 |
new Annotationtype("LibPrepKitContentSetBox3", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1197 |
|
| 3610 |
20 Nov 15 |
olle |
1198 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitOligoPoolAFpa" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1202 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1203 |
public static final Annotationtype LIBPREPKIT_OLIGO_POOL_A_FPA = |
| 3610 |
20 Nov 15 |
olle |
1204 |
new Annotationtype("LibPrepKitOligoPoolAFpa", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1205 |
|
| 3610 |
20 Nov 15 |
olle |
1206 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitOligoPoolBFpb" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1210 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1211 |
public static final Annotationtype LIBPREPKIT_OLIGO_POOL_B_FPB = |
| 3610 |
20 Nov 15 |
olle |
1212 |
new Annotationtype("LibPrepKitOligoPoolBFpb", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1213 |
|
| 3610 |
20 Nov 15 |
olle |
1214 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitOligoHybrSeqReagent3Ohs3" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1218 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1219 |
public static final Annotationtype LIBPREPKIT_OLIGO_HYBR_SEQ_REAGENT3_OHS3 = |
| 3610 |
20 Nov 15 |
olle |
1220 |
new Annotationtype("LibPrepKitOligoHybrSeqReagent3Ohs3", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1221 |
|
| 3610 |
20 Nov 15 |
olle |
1222 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitStringentWash1Sw1" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1226 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1227 |
public static final Annotationtype LIBPREPKIT_STRINGENT_WASH1_SW1 = |
| 3610 |
20 Nov 15 |
olle |
1228 |
new Annotationtype("LibPrepKitStringentWash1Sw1", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1229 |
|
| 3610 |
20 Nov 15 |
olle |
1230 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitExtensionLigationMix3Elm3" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1234 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1235 |
public static final Annotationtype LIBPREPKIT_EXTENSION_LIGATION_MIX3_ELM3 = |
| 3610 |
20 Nov 15 |
olle |
1236 |
new Annotationtype("LibPrepKitExtensionLigationMix3Elm3", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1237 |
|
| 3610 |
20 Nov 15 |
olle |
1238 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitPcrMasterMix2Pmm2" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1242 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1243 |
public static final Annotationtype LIBPREPKIT_PCR_MASTER_MIX2_PMM2 = |
| 3610 |
20 Nov 15 |
olle |
1244 |
new Annotationtype("LibPrepKitPcrMasterMix2Pmm2", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1245 |
|
| 3610 |
20 Nov 15 |
olle |
1246 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitUb1" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1250 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1251 |
public static final Annotationtype LIBPREPKIT_UB1 = |
| 3610 |
20 Nov 15 |
olle |
1252 |
new Annotationtype("LibPrepKitUb1", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1253 |
|
| 3610 |
20 Nov 15 |
olle |
1254 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitTdp" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1258 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1259 |
public static final Annotationtype LIBPREPKIT_TDP = |
| 3610 |
20 Nov 15 |
olle |
1260 |
new Annotationtype("LibPrepKitTdp", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1261 |
|
| 3610 |
20 Nov 15 |
olle |
1262 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitFilterPlate" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1266 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1267 |
public static final Annotationtype LIBPREPKIT_FILTER_PLATE = |
| 3610 |
20 Nov 15 |
olle |
1268 |
new Annotationtype("LibPrepKitFilterPlate", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1269 |
|
| 3610 |
20 Nov 15 |
olle |
1270 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitA701" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1274 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1275 |
public static final Annotationtype LIBPREPKIT_A701 = |
| 3610 |
20 Nov 15 |
olle |
1276 |
new Annotationtype("LibPrepKitA701", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1277 |
|
| 3610 |
20 Nov 15 |
olle |
1278 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitA702" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1282 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1283 |
public static final Annotationtype LIBPREPKIT_A702 = |
| 3610 |
20 Nov 15 |
olle |
1284 |
new Annotationtype("LibPrepKitA702", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1285 |
|
| 3610 |
20 Nov 15 |
olle |
1286 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitA703" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1290 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1291 |
public static final Annotationtype LIBPREPKIT_A703 = |
| 3610 |
20 Nov 15 |
olle |
1292 |
new Annotationtype("LibPrepKitA703", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1293 |
|
| 3610 |
20 Nov 15 |
olle |
1294 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitA704" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1298 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1299 |
public static final Annotationtype LIBPREPKIT_A704 = |
| 3610 |
20 Nov 15 |
olle |
1300 |
new Annotationtype("LibPrepKitA704", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1301 |
|
| 3610 |
20 Nov 15 |
olle |
1302 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitA705" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1306 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1307 |
public static final Annotationtype LIBPREPKIT_A705 = |
| 3610 |
20 Nov 15 |
olle |
1308 |
new Annotationtype("LibPrepKitA705", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1309 |
|
| 3610 |
20 Nov 15 |
olle |
1310 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitA706" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1314 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1315 |
public static final Annotationtype LIBPREPKIT_A706 = |
| 3610 |
20 Nov 15 |
olle |
1316 |
new Annotationtype("LibPrepKitA706", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1317 |
|
| 3610 |
20 Nov 15 |
olle |
1318 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitA707" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1322 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1323 |
public static final Annotationtype LIBPREPKIT_A707 = |
| 3610 |
20 Nov 15 |
olle |
1324 |
new Annotationtype("LibPrepKitA707", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1325 |
|
| 3610 |
20 Nov 15 |
olle |
1326 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitA708" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1330 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1331 |
public static final Annotationtype LIBPREPKIT_A708 = |
| 3610 |
20 Nov 15 |
olle |
1332 |
new Annotationtype("LibPrepKitA708", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1333 |
|
| 3610 |
20 Nov 15 |
olle |
1334 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitA709" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1338 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1339 |
public static final Annotationtype LIBPREPKIT_A709 = |
| 3610 |
20 Nov 15 |
olle |
1340 |
new Annotationtype("LibPrepKitA709", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1341 |
|
| 3610 |
20 Nov 15 |
olle |
1342 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitA710" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1346 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1347 |
public static final Annotationtype LIBPREPKIT_A710 = |
| 3610 |
20 Nov 15 |
olle |
1348 |
new Annotationtype("LibPrepKitA710", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1349 |
|
| 3610 |
20 Nov 15 |
olle |
1350 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitA711" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1354 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1355 |
public static final Annotationtype LIBPREPKIT_A711 = |
| 3610 |
20 Nov 15 |
olle |
1356 |
new Annotationtype("LibPrepKitA711", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1357 |
|
| 3610 |
20 Nov 15 |
olle |
1358 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitA712" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1362 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1363 |
public static final Annotationtype LIBPREPKIT_A712 = |
| 3610 |
20 Nov 15 |
olle |
1364 |
new Annotationtype("LibPrepKitA712", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1365 |
|
| 3610 |
20 Nov 15 |
olle |
1366 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitA501" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1370 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1371 |
public static final Annotationtype LIBPREPKIT_A501 = |
| 3610 |
20 Nov 15 |
olle |
1372 |
new Annotationtype("LibPrepKitA501", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1373 |
|
| 3610 |
20 Nov 15 |
olle |
1374 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitA502" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1378 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1379 |
public static final Annotationtype LIBPREPKIT_A502 = |
| 3610 |
20 Nov 15 |
olle |
1380 |
new Annotationtype("LibPrepKitA502", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1381 |
|
| 3610 |
20 Nov 15 |
olle |
1382 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitA503" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1386 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1387 |
public static final Annotationtype LIBPREPKIT_A503 = |
| 3610 |
20 Nov 15 |
olle |
1388 |
new Annotationtype("LibPrepKitA503", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1389 |
|
| 3610 |
20 Nov 15 |
olle |
1390 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitA504" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1394 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1395 |
public static final Annotationtype LIBPREPKIT_A504 = |
| 3610 |
20 Nov 15 |
olle |
1396 |
new Annotationtype("LibPrepKitA504", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1397 |
|
| 3610 |
20 Nov 15 |
olle |
1398 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitA505" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1402 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1403 |
public static final Annotationtype LIBPREPKIT_A505 = |
| 3610 |
20 Nov 15 |
olle |
1404 |
new Annotationtype("LibPrepKitA505", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1405 |
|
| 3610 |
20 Nov 15 |
olle |
1406 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitA506" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1410 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1411 |
public static final Annotationtype LIBPREPKIT_A506 = |
| 3610 |
20 Nov 15 |
olle |
1412 |
new Annotationtype("LibPrepKitA506", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1413 |
|
| 3610 |
20 Nov 15 |
olle |
1414 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitA507" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1418 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1419 |
public static final Annotationtype LIBPREPKIT_A507 = |
| 3610 |
20 Nov 15 |
olle |
1420 |
new Annotationtype("LibPrepKitA507", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1421 |
|
| 3610 |
20 Nov 15 |
olle |
1422 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitA508" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1426 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1427 |
public static final Annotationtype LIBPREPKIT_A508 = |
| 3610 |
20 Nov 15 |
olle |
1428 |
new Annotationtype("LibPrepKitA508", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1429 |
|
| 3610 |
20 Nov 15 |
olle |
1430 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitLastUpdated" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a date annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1434 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1435 |
public static final Annotationtype LIBPREPKIT_LAST_UPDATED = |
| 3610 |
20 Nov 15 |
olle |
1436 |
new Annotationtype("LibPrepKitLastUpdated", Type.DATE, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1437 |
|
| 3610 |
20 Nov 15 |
olle |
1438 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitNumberTimesUsed" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is an integer annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1442 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1443 |
public static final Annotationtype LIBPREPKIT_NUMBER_TIMES_USED = |
| 3610 |
20 Nov 15 |
olle |
1444 |
new Annotationtype("LibPrepKitNumberTimesUsed", Type.INT, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1445 |
|
| 3610 |
20 Nov 15 |
olle |
1446 |
/** |
| 3610 |
20 Nov 15 |
olle |
The "LibPrepKitUnusedFpaWells" annotation type, used for kits (Library Preparation). |
| 3610 |
20 Nov 15 |
olle |
It is a string annotation type. |
| 3610 |
20 Nov 15 |
olle |
@since 1.3.4 |
| 3610 |
20 Nov 15 |
olle |
1450 |
*/ |
| 3610 |
20 Nov 15 |
olle |
1451 |
public static final Annotationtype LIBPREPKIT_UNUSED_FPA_WELLS = |
| 3610 |
20 Nov 15 |
olle |
1452 |
new Annotationtype("LibPrepKitUnusedFpaWells", Type.STRING, false, Item.KIT); |
| 3610 |
20 Nov 15 |
olle |
1453 |
|
| 3610 |
20 Nov 15 |
olle |
1454 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "QCRunDate" annotation, used |
| 2933 |
14 Nov 14 |
olle |
for bioplates (RNA). It is a date annotation type. |
| 2933 |
14 Nov 14 |
olle |
1457 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1458 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype QC_RUN_DATE = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("QCRunDate", Type.DATE, false, Item.BIOPLATE); |
| 2933 |
14 Nov 14 |
olle |
1461 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1462 |
|
| 2933 |
14 Nov 14 |
olle |
1463 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "QCOperator" annotation, used |
| 2933 |
14 Nov 14 |
olle |
for bioplates (RNA). It is a string annotation type. |
| 2933 |
14 Nov 14 |
olle |
1466 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1467 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype QC_OPERATOR = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("QCOperator", Type.STRING, false, Item.BIOPLATE); |
| 2933 |
14 Nov 14 |
olle |
1470 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1471 |
|
| 2933 |
14 Nov 14 |
olle |
1472 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "BA_RIN" annotation, used |
| 2933 |
14 Nov 14 |
olle |
for extract (RNAQC). It is a float annotation type |
| 2933 |
14 Nov 14 |
olle |
1475 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1476 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype BA_RIN = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("BA_RIN", Type.FLOAT, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
1479 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1480 |
|
| 2933 |
14 Nov 14 |
olle |
1481 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "CA_RQS" annotation, used |
| 2933 |
14 Nov 14 |
olle |
for extract (RNAQC). It is a float annotation type |
| 2933 |
14 Nov 14 |
olle |
1484 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1485 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype CA_RQS = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("CA_RQS", Type.FLOAT, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
1488 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1489 |
|
| 2933 |
14 Nov 14 |
olle |
1490 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "NDConc" annotation, used for extract (DNA/RNA). |
| 3176 |
06 Mar 15 |
olle |
@since 1.2 |
| 2933 |
14 Nov 14 |
olle |
1493 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1494 |
public static final Annotationtype ND_CONC = |
| 2933 |
14 Nov 14 |
olle |
1495 |
new Annotationtype("NDConc", Type.FLOAT, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
1496 |
|
| 2933 |
14 Nov 14 |
olle |
1497 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "ND260by280" annotation, used for extract (DNA/RNA). |
| 2933 |
14 Nov 14 |
olle |
It is a float annotation type. |
| 3176 |
06 Mar 15 |
olle |
@since 1.2 |
| 2933 |
14 Nov 14 |
olle |
1501 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1502 |
public static final Annotationtype ND_260_BY_280 = |
| 2933 |
14 Nov 14 |
olle |
1503 |
new Annotationtype("ND260by280", Type.FLOAT, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
1504 |
|
| 2933 |
14 Nov 14 |
olle |
1505 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "ND260by230" annotation, used for extract (DNA/RNA). |
| 2933 |
14 Nov 14 |
olle |
It is a float annotation type. |
| 3176 |
06 Mar 15 |
olle |
@since 1.2 |
| 2933 |
14 Nov 14 |
olle |
1509 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1510 |
public static final Annotationtype ND_260_BY_230 = |
| 2933 |
14 Nov 14 |
olle |
1511 |
new Annotationtype("ND260by230", Type.FLOAT, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
1512 |
|
| 2933 |
14 Nov 14 |
olle |
1513 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "QCHiSense" annotation, used for |
| 2933 |
14 Nov 14 |
olle |
extract (RNAQC). It is a boolean annotation type. |
| 2933 |
14 Nov 14 |
olle |
1516 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1517 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype QC_HISENSE = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("QCHiSense", Type.BOOLEAN, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
1520 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1521 |
|
| 2933 |
14 Nov 14 |
olle |
1522 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "AutoProcessing" annotation which, if set, is a |
| 2933 |
14 Nov 14 |
olle |
flag to indicate how the item should be handled by |
| 2933 |
14 Nov 14 |
olle |
auto-processing wizards. No value indicates normal |
| 2933 |
14 Nov 14 |
olle |
processing in the regular flow. Other values may mean |
| 2933 |
14 Nov 14 |
olle |
either disabled auto-processing (eg. "Disable") or |
| 2933 |
14 Nov 14 |
olle |
forced (re)-auto-processing (eg. "ReProcess"). The |
| 2933 |
14 Nov 14 |
olle |
support and meaning is up to each wizard. |
| 2933 |
14 Nov 14 |
olle |
@since 2.12 |
| 2933 |
14 Nov 14 |
olle |
1531 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1532 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype AUTO_PROCESSING = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("AutoProcessing", Type.STRING, false, Item.EXTRACT, Item.DERIVEDBIOASSAY, Item.SAMPLE); |
| 2933 |
14 Nov 14 |
olle |
1535 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1536 |
|
| 2933 |
14 Nov 14 |
olle |
1537 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "PlateProcessResult" annotation which is set after a reaction |
| 3449 |
28 Jul 15 |
olle |
plate has been processed to indicate the outcome of the plate as |
| 2933 |
14 Nov 14 |
olle |
a whole. A value of "Successful" typically means that the next step |
| 2933 |
14 Nov 14 |
olle |
in the process can be taken, but a value of "Failed" indicates a |
| 2933 |
14 Nov 14 |
olle |
complete failure and everything should be restarted at a previous level. |
| 2933 |
14 Nov 14 |
olle |
Can also be used on a flow cell (physical bioassay). |
| 2933 |
14 Nov 14 |
olle |
@since 2.12 |
| 2933 |
14 Nov 14 |
olle |
1545 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1546 |
public static final Annotationtype PLATE_PROCESS_RESULT = |
| 2933 |
14 Nov 14 |
olle |
1547 |
new Annotationtype("PlateProcessResult", Type.STRING, false, Item.BIOPLATE, Item.PHYSICALBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
1548 |
|
| 2933 |
14 Nov 14 |
olle |
1549 |
/** |
| 3449 |
28 Jul 15 |
olle |
Expected concentration after diluting RNA to be processed |
| 3449 |
28 Jul 15 |
olle |
to libraries. Used on "DNA" and "Library" items. |
| 3449 |
28 Jul 15 |
olle |
@since 1.3 |
| 2933 |
14 Nov 14 |
olle |
1553 |
*/ |
| 3449 |
28 Jul 15 |
olle |
1554 |
public static final Annotationtype DILUTION_CONC = |
| 3449 |
28 Jul 15 |
olle |
1555 |
new Annotationtype("DilutionConc", Type.FLOAT, false, Item.EXTRACT); |
| 3449 |
28 Jul 15 |
olle |
1556 |
|
| 3449 |
28 Jul 15 |
olle |
1557 |
/** |
| 3449 |
28 Jul 15 |
olle |
Annotation for DNA dilution date. |
| 3449 |
28 Jul 15 |
olle |
@since 1.3 |
| 3449 |
28 Jul 15 |
olle |
1560 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1561 |
public static final Annotationtype DILUTION_DATE = |
| 2933 |
14 Nov 14 |
olle |
1562 |
new Annotationtype("DilutionDate", Type.DATE, false, Item.BIOPLATE); |
| 2933 |
14 Nov 14 |
olle |
1563 |
|
| 2933 |
14 Nov 14 |
olle |
1564 |
/** |
| 2933 |
14 Nov 14 |
olle |
Annotation for mRNA dilution operator. |
| 3449 |
28 Jul 15 |
olle |
@since 1.3 |
| 2933 |
14 Nov 14 |
olle |
1567 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1568 |
public static final Annotationtype DILUTION_OPERATOR = |
| 2933 |
14 Nov 14 |
olle |
1569 |
new Annotationtype("DilutionOperator", Type.STRING, false, Item.BIOPLATE); |
| 2933 |
14 Nov 14 |
olle |
1570 |
|
| 2933 |
14 Nov 14 |
olle |
1571 |
|
| 2933 |
14 Nov 14 |
olle |
1572 |
/** |
| 2933 |
14 Nov 14 |
olle |
Annotation for mRNA purification date. |
| 2933 |
14 Nov 14 |
olle |
@since 2.12 |
| 2933 |
14 Nov 14 |
olle |
1575 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1576 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype PURIFICATION_DATE = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("PurificationDate", Type.DATE, false, Item.BIOPLATE); |
| 2933 |
14 Nov 14 |
olle |
1579 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1580 |
|
| 2933 |
14 Nov 14 |
olle |
1581 |
/** |
| 2933 |
14 Nov 14 |
olle |
Annotation for mRNA purification operator. |
| 2933 |
14 Nov 14 |
olle |
@since 2.12 |
| 2933 |
14 Nov 14 |
olle |
1584 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1585 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype PURIFICATION_OPERATOR = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("PurificationOperator", Type.STRING, false, Item.BIOPLATE); |
| 2933 |
14 Nov 14 |
olle |
1588 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1589 |
|
| 2933 |
14 Nov 14 |
olle |
1590 |
/** |
| 2933 |
14 Nov 14 |
olle |
Annotation for mRNA fragmentation date. |
| 2933 |
14 Nov 14 |
olle |
@since 2.12 |
| 2933 |
14 Nov 14 |
olle |
1593 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1594 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype FRAGMENTATION_DATE = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("FragmentationDate", Type.DATE, false, Item.BIOPLATE); |
| 2933 |
14 Nov 14 |
olle |
1597 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1598 |
|
| 2933 |
14 Nov 14 |
olle |
1599 |
/** |
| 2933 |
14 Nov 14 |
olle |
Annotation for mRNA fragmentation operator. |
| 2933 |
14 Nov 14 |
olle |
@since 2.12 |
| 2933 |
14 Nov 14 |
olle |
1602 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1603 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype FRAGMENTATION_OPERATOR = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("FragmentationOperator", Type.STRING, false, Item.BIOPLATE); |
| 2933 |
14 Nov 14 |
olle |
1606 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1607 |
|
| 2933 |
14 Nov 14 |
olle |
1608 |
/** |
| 2933 |
14 Nov 14 |
olle |
Annotation for mRNA cleanup date. |
| 2933 |
14 Nov 14 |
olle |
@since 2.12 |
| 2933 |
14 Nov 14 |
olle |
1611 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1612 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype CLEANUP_DATE = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("CleanupDate", Type.DATE, false, Item.BIOPLATE); |
| 2933 |
14 Nov 14 |
olle |
1615 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1616 |
|
| 2933 |
14 Nov 14 |
olle |
1617 |
/** |
| 2933 |
14 Nov 14 |
olle |
Annotation for mRNA cleanup operator. |
| 2933 |
14 Nov 14 |
olle |
@since 2.12 |
| 2933 |
14 Nov 14 |
olle |
1620 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1621 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype CLEANUP_OPERATOR = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("CleanupOperator", Type.STRING, false, Item.BIOPLATE); |
| 2933 |
14 Nov 14 |
olle |
1624 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1625 |
|
| 2933 |
14 Nov 14 |
olle |
1626 |
/** |
| 2933 |
14 Nov 14 |
olle |
Annotation for cDNA synthesis date. |
| 2933 |
14 Nov 14 |
olle |
@since 2.12 |
| 2933 |
14 Nov 14 |
olle |
1629 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1630 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype SYNTHESIS_DATE = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("SynthesisDate", Type.DATE, false, Item.BIOPLATE); |
| 2933 |
14 Nov 14 |
olle |
1633 |
*/ |
| 3449 |
28 Jul 15 |
olle |
1634 |
|
| 2933 |
14 Nov 14 |
olle |
1635 |
/** |
| 2933 |
14 Nov 14 |
olle |
Annotation for cDNA synthesis operator. |
| 2933 |
14 Nov 14 |
olle |
@since 2.12 |
| 2933 |
14 Nov 14 |
olle |
1638 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1639 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype SYNTHESIS_OPERATOR = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("SynthesisOperator", Type.STRING, false, Item.BIOPLATE); |
| 2933 |
14 Nov 14 |
olle |
1642 |
*/ |
| 3449 |
28 Jul 15 |
olle |
1643 |
|
| 2933 |
14 Nov 14 |
olle |
1644 |
/** |
| 2933 |
14 Nov 14 |
olle |
Annotation for Lib amplification date. |
| 2933 |
14 Nov 14 |
olle |
@since 2.12 |
| 2933 |
14 Nov 14 |
olle |
1647 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1648 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype AMPLIFICATION_DATE = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("AmplificationDate", Type.DATE, false, Item.BIOPLATE); |
| 2933 |
14 Nov 14 |
olle |
1651 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1652 |
|
| 2933 |
14 Nov 14 |
olle |
1653 |
/** |
| 2933 |
14 Nov 14 |
olle |
Annotation for Lib amplification operator. |
| 2933 |
14 Nov 14 |
olle |
@since 2.12 |
| 2933 |
14 Nov 14 |
olle |
1656 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1657 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype AMPLIFICATION_OPERATOR = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("AmplificationOperator", Type.STRING, false, Item.BIOPLATE); |
| 2933 |
14 Nov 14 |
olle |
1660 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1661 |
|
| 2933 |
14 Nov 14 |
olle |
1662 |
|
| 2933 |
14 Nov 14 |
olle |
1663 |
/** |
| 2933 |
14 Nov 14 |
olle |
Annotation for pooling operator |
| 2933 |
14 Nov 14 |
olle |
@since 2.14 |
| 2933 |
14 Nov 14 |
olle |
1666 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1667 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype POOL_OPERATOR = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("PoolOperator", Type.STRING, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
1670 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1671 |
|
| 2933 |
14 Nov 14 |
olle |
1672 |
|
| 2933 |
14 Nov 14 |
olle |
1673 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "Flag" annotation which, if set, is a |
| 2933 |
14 Nov 14 |
olle |
flag to indicate a special condition that happened |
| 2933 |
14 Nov 14 |
olle |
during the processing of an item. This annotation is |
| 2933 |
14 Nov 14 |
olle |
usually set in combination with adding the item to |
| 2933 |
14 Nov 14 |
olle |
a biomaterial list (eg. {@link BiomaterialList#FLAGGED_RNA}). |
| 2933 |
14 Nov 14 |
olle |
@since 2.12 |
| 2933 |
14 Nov 14 |
olle |
1680 |
*/ |
| 3050 |
17 Dec 14 |
olle |
1681 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype FLAG = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("Flag", Type.STRING, false, Item.SAMPLE, Item.EXTRACT); |
| 3050 |
17 Dec 14 |
olle |
1684 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1685 |
|
| 2933 |
14 Nov 14 |
olle |
1686 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "PoolSchema" annotation which, if set, indicates the default |
| 2933 |
14 Nov 14 |
olle |
pooling schema to use when working with mRNA, cDNA and Library |
| 2933 |
14 Nov 14 |
olle |
plates. It an enumerated string annotation type. |
| 2933 |
14 Nov 14 |
olle |
@since 2.12 |
| 2933 |
14 Nov 14 |
olle |
1691 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1692 |
public static final Annotationtype POOL_SCHEMA = |
| 2933 |
14 Nov 14 |
olle |
1693 |
new Annotationtype("PoolSchema", Type.STRING, false, Item.BIOPLATE); |
| 2933 |
14 Nov 14 |
olle |
1694 |
|
| 2933 |
14 Nov 14 |
olle |
1695 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "BarcodeVariant" annotation which, if set, indicates the default |
| 2933 |
14 Nov 14 |
olle |
barcode variant to use when working with mRNA, cDNA and Library |
| 2933 |
14 Nov 14 |
olle |
plates. It a string annotation type. |
| 2933 |
14 Nov 14 |
olle |
@since 2.12 |
| 2933 |
14 Nov 14 |
olle |
1700 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1701 |
public static final Annotationtype BARCODE_VARIANT = |
| 2933 |
14 Nov 14 |
olle |
1702 |
new Annotationtype("BarcodeVariant", Type.STRING, false, Item.BIOPLATE); |
| 2933 |
14 Nov 14 |
olle |
1703 |
|
| 2933 |
14 Nov 14 |
olle |
1704 |
/** |
| 3176 |
06 Mar 15 |
olle |
The "QubitConc" annotation, used for extract (DNA/RNAA). |
| 3176 |
06 Mar 15 |
olle |
@since 1.2 |
| 2933 |
14 Nov 14 |
olle |
1707 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1708 |
public static final Annotationtype QUBIT_CONC = |
| 2933 |
14 Nov 14 |
olle |
1709 |
new Annotationtype("QubitConc", Type.FLOAT, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
1710 |
|
| 2933 |
14 Nov 14 |
olle |
1711 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "QubitConcAfterSpeedVac" annotation, used for extract (Library). |
| 2933 |
14 Nov 14 |
olle |
@since 2.12 |
| 2933 |
14 Nov 14 |
olle |
1714 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1715 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype QUBIT_CONC_AFTER_SPEEDVAC = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("QubitConcAfterSpeedVac", Type.FLOAT, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
1718 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1719 |
|
| 2933 |
14 Nov 14 |
olle |
1720 |
/** |
| 3176 |
06 Mar 15 |
olle |
The "deltaCt" annotation, used for extract (DNA/RNA). |
| 3176 |
06 Mar 15 |
olle |
@since 1.2 |
| 3176 |
06 Mar 15 |
olle |
1723 |
*/ |
| 3176 |
06 Mar 15 |
olle |
1724 |
public static final Annotationtype DELTA_CT = |
| 3176 |
06 Mar 15 |
olle |
1725 |
new Annotationtype("deltaCt", Type.FLOAT, false, Item.EXTRACT); |
| 3176 |
06 Mar 15 |
olle |
1726 |
|
| 3176 |
06 Mar 15 |
olle |
1727 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "CA_Size" annotation, used for extract (Library). |
| 2933 |
14 Nov 14 |
olle |
Read from Caliper well table CSV, Region[180-600] Size [BP] |
| 2933 |
14 Nov 14 |
olle |
@since 2.12 |
| 2933 |
14 Nov 14 |
olle |
1731 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1732 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype CA_SIZE = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("CA_Size", Type.FLOAT, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
1735 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1736 |
|
| 2933 |
14 Nov 14 |
olle |
1737 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "CA_Molarity" annotation, used for extract (Library). |
| 2933 |
14 Nov 14 |
olle |
Read from Caliper well table CSV, Region[180-600] Molarity (nmol/l) |
| 2933 |
14 Nov 14 |
olle |
multiplied by 10. Used to store calculated values, but since 2.15.2 |
| 2933 |
14 Nov 14 |
olle |
these have move to {@link LIBRARY_MOLARITY_EST} |
| 2933 |
14 Nov 14 |
olle |
@since 2.12, 2.15.2 |
| 2933 |
14 Nov 14 |
olle |
1743 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1744 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype CA_MOLARITY = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("CA_Molarity", Type.FLOAT, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
1747 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1748 |
|
| 2933 |
14 Nov 14 |
olle |
1749 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "CA_Size_Adpt" annotation, used for extract (Library). |
| 2933 |
14 Nov 14 |
olle |
Read from Caliper well table CSV, Region[120-140] Size [BP] |
| 2933 |
14 Nov 14 |
olle |
@since 2.15.2 |
| 2933 |
14 Nov 14 |
olle |
1753 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1754 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype CA_SIZE_ADPT = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("CA_Size_Adpt", Type.FLOAT, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
1757 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1758 |
|
| 2933 |
14 Nov 14 |
olle |
1759 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "CA_Molarity_Adpt" annotation, used for extract (Library). |
| 2933 |
14 Nov 14 |
olle |
Read from Caliper well table CSV, Region[120-140] Molarity (nmol/l) |
| 2933 |
14 Nov 14 |
olle |
multiplied by 10. |
| 2933 |
14 Nov 14 |
olle |
@since 2.15.2 |
| 2933 |
14 Nov 14 |
olle |
1764 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1765 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype CA_MOLARITY_ADPT = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("CA_Molarity_Adpt", Type.FLOAT, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
1768 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1769 |
|
| 2933 |
14 Nov 14 |
olle |
1770 |
/** |
| 2933 |
14 Nov 14 |
olle |
Calculated value for library molarity. |
| 2933 |
14 Nov 14 |
olle |
@since 2.15.2 |
| 2933 |
14 Nov 14 |
olle |
1773 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1774 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype LIBRARY_MOLARITY_EST = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("Library_Molarity_Est", Type.FLOAT, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
1777 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1778 |
|
| 2933 |
14 Nov 14 |
olle |
1779 |
/** |
| 2933 |
14 Nov 14 |
olle |
Calculated value for library size. Weighted average of |
| 2933 |
14 Nov 14 |
olle |
{@link #CA_SIZE} and {@link #CA_SIZE_ADPT}. |
| 2933 |
14 Nov 14 |
olle |
@since 2.15.2 |
| 2933 |
14 Nov 14 |
olle |
1783 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1784 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype LIBRARY_SIZE_EST = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("Library_Size_Est", Type.FLOAT, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
1787 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1788 |
|
| 2933 |
14 Nov 14 |
olle |
1789 |
/** |
| 2933 |
14 Nov 14 |
olle |
Calculated value for adapter fraction (in percent). Calculated |
| 2933 |
14 Nov 14 |
olle |
from {@link #CA_MOLARITY} and {@link #CA_MOLARITY_ADPT}. |
| 2933 |
14 Nov 14 |
olle |
@since 2.15.2 |
| 2933 |
14 Nov 14 |
olle |
1793 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1794 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype LIBRARY_FRAC_ADPT = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("Library_Frac_Adpt", Type.INT, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
1797 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1798 |
|
| 2933 |
14 Nov 14 |
olle |
1799 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "PoolConc" annotation, used for extracts (PooledLibrary). |
| 2933 |
14 Nov 14 |
olle |
Automatically calculated from the quantities used from the |
| 2933 |
14 Nov 14 |
olle |
libraries mixed in the pool. |
| 2933 |
14 Nov 14 |
olle |
@since 2.12 |
| 2933 |
14 Nov 14 |
olle |
1804 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1805 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype POOL_CONC = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("PoolConc", Type.FLOAT, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
1808 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1809 |
|
| 2933 |
14 Nov 14 |
olle |
1810 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "PoolMolarity" annotation, used for extracts (PooledLibrary). |
| 2933 |
14 Nov 14 |
olle |
Automatically calculated using the molarity from from the |
| 2933 |
14 Nov 14 |
olle |
libraries mixed in the pool. |
| 2933 |
14 Nov 14 |
olle |
@since 2.12 |
| 2933 |
14 Nov 14 |
olle |
1815 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1816 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype POOL_MOLARITY = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("PoolMolarity", Type.FLOAT, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
1819 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1820 |
|
| 2933 |
14 Nov 14 |
olle |
1821 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "PoolTargetVolumePerLib" annotation, used for extracts (PooledLibrary). |
| 2933 |
14 Nov 14 |
olle |
Store the admin-defined setting for target volume per library in a |
| 2933 |
14 Nov 14 |
olle |
pool. The actual volume may be different due to limitations implied by |
| 2933 |
14 Nov 14 |
olle |
library concentration and rounding. |
| 2933 |
14 Nov 14 |
olle |
@since 2.13 |
| 2933 |
14 Nov 14 |
olle |
1827 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1828 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype POOL_TARGET_VOLUME_PER_LIB = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("PoolTargetVolumePerLib", Type.FLOAT, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
1831 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1832 |
|
| 2933 |
14 Nov 14 |
olle |
1833 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "PoolTargetMolarity" annotation, used for extracts (PooledLibrary). |
| 2933 |
14 Nov 14 |
olle |
Store the admin-defined setting for target molarity used when designing |
| 2933 |
14 Nov 14 |
olle |
the pool. The actual molarity may different due to limitations implied by |
| 2933 |
14 Nov 14 |
olle |
library concentration and rounding. |
| 2933 |
14 Nov 14 |
olle |
@since 2.14 |
| 2933 |
14 Nov 14 |
olle |
1839 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1840 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype POOL_TARGET_MOLARITY = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("PoolTargetMolarity", Type.FLOAT, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
1843 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1844 |
|
| 2933 |
14 Nov 14 |
olle |
1845 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "PoolIsManual" annotation, used for extracts (PooledLibrary). |
| 2933 |
14 Nov 14 |
olle |
Store a flag indicating if the pool is manaually created. If not set, |
| 2933 |
14 Nov 14 |
olle |
it is asssumed that the pool is created from an entire library working plate. |
| 2933 |
14 Nov 14 |
olle |
@since 2.14 |
| 2933 |
14 Nov 14 |
olle |
1850 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1851 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype POOL_IS_MANUAL = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("PoolIsManual", Type.BOOLEAN, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
1854 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1855 |
|
| 2933 |
14 Nov 14 |
olle |
1856 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "PoolDate" annotation, used for extracts (PooledLibrary). |
| 2933 |
14 Nov 14 |
olle |
The date the pool was created. |
| 2933 |
14 Nov 14 |
olle |
@since 2.13 |
| 2933 |
14 Nov 14 |
olle |
1860 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1861 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype POOL_DATE = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("PoolDate", Type.DATE, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
1864 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1865 |
|
| 2933 |
14 Nov 14 |
olle |
1866 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "PoolMixingStrategy" annotation, used for extracts (PooledLibrary). |
| 2933 |
14 Nov 14 |
olle |
Store the admin-defined setting for the strategy to use when mixing the pool. |
| 2933 |
14 Nov 14 |
olle |
Enumeration: fixed, dynamic. Default is fixed. |
| 2933 |
14 Nov 14 |
olle |
@since 2.13 |
| 2933 |
14 Nov 14 |
olle |
1871 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1872 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype POOL_MIXING_STRATEGY = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("PoolMixingStrategy", Type.STRING, false, Item.EXTRACT); |
| 2933 |
14 Nov 14 |
olle |
1875 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1876 |
|
| 2933 |
14 Nov 14 |
olle |
1877 |
/** |
| 3630 |
27 Nov 15 |
olle |
The "ControlLotNo" annotation, used for extract (DNA/RNA). |
| 3630 |
27 Nov 15 |
olle |
It is a string annotation. |
| 3630 |
27 Nov 15 |
olle |
@since 1.3.4 |
| 3630 |
27 Nov 15 |
olle |
1881 |
*/ |
| 3630 |
27 Nov 15 |
olle |
1882 |
public static final Annotationtype CONTROL_LOT_NO = |
| 3630 |
27 Nov 15 |
olle |
1883 |
new Annotationtype("ControlLotNo", Type.STRING, false, Item.EXTRACT); |
| 3630 |
27 Nov 15 |
olle |
1884 |
|
| 3630 |
27 Nov 15 |
olle |
1885 |
/** |
| 3719 |
22 Jan 16 |
olle |
The "QpcrBranch" annotation, used for extracts (DNA). |
| 3719 |
22 Jan 16 |
olle |
Store a flag indicating if the DNA is to be processed by qPCR. If not set, |
| 3719 |
22 Jan 16 |
olle |
it is assumed that the DNA is to be put on a start DNA plate. |
| 3719 |
22 Jan 16 |
olle |
@since 1.4.2 |
| 3719 |
22 Jan 16 |
olle |
1890 |
*/ |
| 3719 |
22 Jan 16 |
olle |
1891 |
public static final Annotationtype QPCR_BRANCH = |
| 3719 |
22 Jan 16 |
olle |
1892 |
new Annotationtype("QpcrBranch", Type.BOOLEAN, false, Item.EXTRACT); |
| 3719 |
22 Jan 16 |
olle |
1893 |
|
| 3719 |
22 Jan 16 |
olle |
1894 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "FlowCellID" annotation, used for physical bioassays (FlowCell). |
| 2933 |
14 Nov 14 |
olle |
@since 2.13 |
| 2933 |
14 Nov 14 |
olle |
1897 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1898 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype FLOWCELL_ID = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("FlowCellID", Type.STRING, false, Item.PHYSICALBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
1901 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1902 |
|
| 2933 |
14 Nov 14 |
olle |
1903 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "FlowCellType" annotation, used for physical bioassays (FlowCell). |
| 2933 |
14 Nov 14 |
olle |
@since 2.15.1 |
| 2933 |
14 Nov 14 |
olle |
1906 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1907 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype FLOWCELL_TYPE = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("FlowCellType", Type.STRING, false, Item.PHYSICALBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
1910 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1911 |
|
| 2933 |
14 Nov 14 |
olle |
1912 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "ClusterStart" annotation, used for physical bioassays (FlowCell). |
| 2933 |
14 Nov 14 |
olle |
The date the flow cell was clustered. |
| 2933 |
14 Nov 14 |
olle |
@since 2.13 |
| 2933 |
14 Nov 14 |
olle |
1916 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1917 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype CLUSTER_START = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("ClusterStart", Type.DATE, false, Item.PHYSICALBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
1920 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1921 |
|
| 2933 |
14 Nov 14 |
olle |
1922 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "ClusterOperator" annotation, used for physical bioassays (FlowCell). |
| 2933 |
14 Nov 14 |
olle |
The operator that is responsible for clustering. |
| 2933 |
14 Nov 14 |
olle |
@since 2.13 |
| 2933 |
14 Nov 14 |
olle |
1926 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1927 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype CLUSTER_OPERATOR = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("ClusterOperator", Type.STRING, false, Item.PHYSICALBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
1930 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1931 |
|
| 2933 |
14 Nov 14 |
olle |
1932 |
|
| 2933 |
14 Nov 14 |
olle |
1933 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "SequencingCycles" annotation, used for physical bioassays and |
| 2933 |
14 Nov 14 |
olle |
(FlowCell) derived bioassays (SequencingRun). |
| 2933 |
14 Nov 14 |
olle |
@since 2.13 |
| 2933 |
14 Nov 14 |
olle |
1937 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1938 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype SEQUENCING_CYCLES = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("SequencingCycles", Type.STRING, false, Item.PHYSICALBIOASSAY, Item.DERIVEDBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
1941 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1942 |
|
| 2933 |
14 Nov 14 |
olle |
1943 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "FailedLanes" annotation, used for physical bioassays (FlowCell). |
| 2933 |
14 Nov 14 |
olle |
It is a multi-valued annotation type representing the index numbers |
| 2933 |
14 Nov 14 |
olle |
of lanes that failed during sequencing of a flow cell. The index numbers |
| 2933 |
14 Nov 14 |
olle |
go from 1 to the size of the flow cell (eg. 1-8). |
| 2933 |
14 Nov 14 |
olle |
@since 2.15 |
| 2933 |
14 Nov 14 |
olle |
1949 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1950 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype FAILED_LANES = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("FailedLanes", Type.INT, false, Item.PHYSICALBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
1953 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1954 |
|
| 2933 |
14 Nov 14 |
olle |
1955 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "HiSeqPosition" annotation, used for derived bioassays (SequencingRun). |
| 2933 |
14 Nov 14 |
olle |
It is an enumerated string annotation type with two options: A and B |
| 2933 |
14 Nov 14 |
olle |
@since 2.13 |
| 2933 |
14 Nov 14 |
olle |
1959 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1960 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype HISEQ_POSITION = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("HiSeqPosition", Type.STRING, false, Item.DERIVEDBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
1963 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1964 |
|
| 2933 |
14 Nov 14 |
olle |
1965 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "SequencingStart" annotation, used for derived bioassays (SequencingRun). |
| 2933 |
14 Nov 14 |
olle |
@since 2.13 |
| 2933 |
14 Nov 14 |
olle |
1968 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1969 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype SEQUENCING_START = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("SequencingStart", Type.DATE, false, Item.DERIVEDBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
1972 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1973 |
|
| 2933 |
14 Nov 14 |
olle |
1974 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "SequencingTurnAround" annotation, used for derived bioassays (SequencingRun). |
| 2933 |
14 Nov 14 |
olle |
@since 2.14 |
| 2933 |
14 Nov 14 |
olle |
1977 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1978 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype SEQUENCING_TURN_AROUND = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("SequencingTurnAround", Type.TIMESTAMP, false, Item.DERIVEDBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
1981 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1982 |
|
| 2933 |
14 Nov 14 |
olle |
1983 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "SequencingEnd" annotation, used for derived bioassays (SequencingRun). |
| 2933 |
14 Nov 14 |
olle |
@since 2.14 |
| 2933 |
14 Nov 14 |
olle |
1986 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1987 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype SEQUENCING_END = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("SequencingEnd", Type.TIMESTAMP, false, Item.DERIVEDBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
1990 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1991 |
|
| 2933 |
14 Nov 14 |
olle |
1992 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "SequencingRunNumber" annotation, used for derived bioassays (SequencingRun). |
| 2933 |
14 Nov 14 |
olle |
@since 2.15 |
| 2933 |
14 Nov 14 |
olle |
1995 |
*/ |
| 2933 |
14 Nov 14 |
olle |
1996 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype SEQUENCING_RUN_NUMBER = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("SequencingRunNumber", Type.INT, false, Item.DERIVEDBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
1999 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2000 |
|
| 2933 |
14 Nov 14 |
olle |
2001 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "SequencingOperator" annotation, used for derived bioassays (SequencingRun). |
| 2933 |
14 Nov 14 |
olle |
@since 2.13 |
| 2933 |
14 Nov 14 |
olle |
2004 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2005 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype SEQUENCING_OPERATOR = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("SequencingOperator", Type.STRING, false, Item.DERIVEDBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
2008 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2009 |
|
| 2933 |
14 Nov 14 |
olle |
2010 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "DataFilesFolder" annotation, used for derived bioassays that |
| 2933 |
14 Nov 14 |
olle |
are linked with data files on the server. |
| 2933 |
14 Nov 14 |
olle |
@since 2.15 |
| 2933 |
14 Nov 14 |
olle |
2014 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2015 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype DATA_FILES_FOLDER = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("DataFilesFolder", Type.STRING, false, Item.DERIVEDBIOASSAY, Item.RAWBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
2018 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2019 |
|
| 2933 |
14 Nov 14 |
olle |
2020 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "SequencingResult" annotation, used for derived bioassays (SequencingRun). |
| 2933 |
14 Nov 14 |
olle |
A value of "Successful" typically means that the process can continue with |
| 2933 |
14 Nov 14 |
olle |
next step (demux and merge). A value of "Failed" indicates a complete |
| 2933 |
14 Nov 14 |
olle |
failure that require a new flow cell to be clustered. The pooled |
| 2933 |
14 Nov 14 |
olle |
libraries on the current flow cell are flagged with "SequencingFailed". |
| 2933 |
14 Nov 14 |
olle |
A value of "FirstBaseReportFailed" indicates that the first sequencing attempt |
| 2933 |
14 Nov 14 |
olle |
failed but that it is possible to re-start with the same flow cell. The |
| 2933 |
14 Nov 14 |
olle |
annotation is also copied to the flow cell. |
| 2933 |
14 Nov 14 |
olle |
@since 2.15 |
| 2933 |
14 Nov 14 |
olle |
2030 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2031 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype SEQUENCING_RESULT = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("SequencingResult", Type.STRING, false, Item.PHYSICALBIOASSAY, Item.DERIVEDBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
2034 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2035 |
|
| 2933 |
14 Nov 14 |
olle |
2036 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "SequencingConfirmed" annotation, used for derived bioassays (SequencingRun). |
| 2933 |
14 Nov 14 |
olle |
Store a flag indicating that the sequencing result has been confirmed by a |
| 2933 |
14 Nov 14 |
olle |
user with {@link RegggieRole#SECONDARY_ANALYSIS} role. |
| 2933 |
14 Nov 14 |
olle |
@since 2.15 |
| 2933 |
14 Nov 14 |
olle |
2041 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2042 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype SEQUENCING_CONFIRMED = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("SequencingConfirmed", Type.BOOLEAN, false, Item.DERIVEDBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
2045 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2046 |
|
| 2933 |
14 Nov 14 |
olle |
2047 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "ReadString" annotation, used for derived bioassays (DemuxedSequences). |
| 2933 |
14 Nov 14 |
olle |
@since 2.13 |
| 2933 |
14 Nov 14 |
olle |
2050 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2051 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype READ_STRING = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("ReadString", Type.STRING, false, Item.DERIVEDBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
2054 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2055 |
|
| 2933 |
14 Nov 14 |
olle |
2056 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "OmitLanes" annotation, used for derived bioassays (DemuxedSequences). |
| 2933 |
14 Nov 14 |
olle |
It is a multi-valued annotation type representing the index numbers |
| 2933 |
14 Nov 14 |
olle |
of lanes that was omitted during demulitplexing of the sequenced data. |
| 2933 |
14 Nov 14 |
olle |
The index numbers go from 1 to the size of the flow cell (eg. 1-8). |
| 2933 |
14 Nov 14 |
olle |
@since 2.16 |
| 2933 |
14 Nov 14 |
olle |
2062 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2063 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype OMIT_LANES = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("OmitLanes", Type.INT, false, Item.DERIVEDBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
2066 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2067 |
|
| 2933 |
14 Nov 14 |
olle |
2068 |
/** |
| 3449 |
28 Jul 15 |
olle |
The "BarcodeSequence" annotation, used for tags (Barcode). |
| 2933 |
14 Nov 14 |
olle |
It is a string annotation containing the sequence for |
| 2933 |
14 Nov 14 |
olle |
the barcode. Typically 7 characters from ACGT. |
| 3449 |
28 Jul 15 |
olle |
@since 1.3 |
| 2933 |
14 Nov 14 |
olle |
2073 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2074 |
public static final Annotationtype BARCODE_SEQUENCE = |
| 2933 |
14 Nov 14 |
olle |
2075 |
new Annotationtype("BarcodeSequence", Type.STRING, false, Item.TAG); |
| 2933 |
14 Nov 14 |
olle |
2076 |
|
| 2933 |
14 Nov 14 |
olle |
2077 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "AnalysisResult" annotation, used for derived bioassays. |
| 2933 |
14 Nov 14 |
olle |
A value of "Successful" typically means that the process can continue with |
| 2933 |
14 Nov 14 |
olle |
next step in the analysis pipeline. A value of "Failed" indicates a |
| 2933 |
14 Nov 14 |
olle |
failure that require analysis and/or sequencing to be re-done at a |
| 2933 |
14 Nov 14 |
olle |
higher level. The current pipeline is not continued. |
| 2933 |
14 Nov 14 |
olle |
@since 2.16 |
| 2933 |
14 Nov 14 |
olle |
2084 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2085 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype ANALYSIS_RESULT = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("AnalysisResult", Type.STRING, false, Item.DERIVEDBIOASSAY, Item.RAWBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
2088 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2089 |
|
| 2933 |
14 Nov 14 |
olle |
2090 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "READS" annotation, used for derived bioassays (MergedSequences). |
| 2933 |
14 Nov 14 |
olle |
The annotation is the number of sequences that has been assigned to |
| 2933 |
14 Nov 14 |
olle |
the library before any masking or filtering. |
| 2933 |
14 Nov 14 |
olle |
@since 2.16 |
| 2933 |
14 Nov 14 |
olle |
2095 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2096 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype READS = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("READS", Type.LONG, false, Item.DERIVEDBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
2099 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2100 |
|
| 2933 |
14 Nov 14 |
olle |
2101 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "PF_READS" annotation, used for derived bioassays (MergedSequences). |
| 2933 |
14 Nov 14 |
olle |
The annotation is the number of sequences that has been assigned to |
| 2933 |
14 Nov 14 |
olle |
the library after filtering. |
| 2933 |
14 Nov 14 |
olle |
@since 2.16 |
| 2933 |
14 Nov 14 |
olle |
2106 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2107 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype PF_READS = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("PF_READS", Type.LONG, false, Item.DERIVEDBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
2110 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2111 |
|
| 2933 |
14 Nov 14 |
olle |
2112 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "ADAPTER_READS" annotation, used for derived bioassays (MergedSequences). |
| 2933 |
14 Nov 14 |
olle |
The annotation is the number of sequences that was removed due to matching |
| 2933 |
14 Nov 14 |
olle |
an Illumina adpter sequence. |
| 2933 |
14 Nov 14 |
olle |
@since 2.16 |
| 2933 |
14 Nov 14 |
olle |
2117 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2118 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype ADAPTER_READS = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("ADAPTER_READS", Type.LONG, false, Item.DERIVEDBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
2121 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2122 |
|
| 2933 |
14 Nov 14 |
olle |
2123 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "PT_READS" annotation, used for derived bioassays (MergedSequences). |
| 2933 |
14 Nov 14 |
olle |
The annotation is the number of sequences that remains for a library after |
| 2933 |
14 Nov 14 |
olle |
running trimmomatic. |
| 2933 |
14 Nov 14 |
olle |
@since 2.16 |
| 2933 |
14 Nov 14 |
olle |
2128 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2129 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype PT_READS = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("PT_READS", Type.LONG, false, Item.DERIVEDBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
2132 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2133 |
|
| 2933 |
14 Nov 14 |
olle |
2134 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "FragmentSizeAvg" annotation, used for derived bioassays (MergedSequences). |
| 2933 |
14 Nov 14 |
olle |
The annotation is the average size of fragments in the library |
| 2933 |
14 Nov 14 |
olle |
as estimated after alignment. |
| 2933 |
14 Nov 14 |
olle |
@since 2.16 |
| 2933 |
14 Nov 14 |
olle |
2139 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2140 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype FRAGMENT_SIZE_AVG = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("FragmentSizeAvg", Type.INT, false, Item.DERIVEDBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
2143 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2144 |
|
| 2933 |
14 Nov 14 |
olle |
2145 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "FragmentSizeStdev" annotation, used for derived bioassays (MergedSequences). |
| 2933 |
14 Nov 14 |
olle |
The annotation is the standard deviation of the size of fragments in the library |
| 2933 |
14 Nov 14 |
olle |
as estimated after alignment. |
| 2933 |
14 Nov 14 |
olle |
@since 2.16 |
| 2933 |
14 Nov 14 |
olle |
2150 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2151 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype FRAGMENT_SIZE_STDEV = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("FragmentSizeStdev", Type.INT, false, Item.DERIVEDBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
2154 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2155 |
|
| 2933 |
14 Nov 14 |
olle |
2156 |
|
| 2933 |
14 Nov 14 |
olle |
2157 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "PF_NNNN_PCT" annotation, used for derived bioassays (DemuxedSequences). |
| 2933 |
14 Nov 14 |
olle |
The annotation is the percentage of sequences that has could not be assigned |
| 2933 |
14 Nov 14 |
olle |
to any barcode when demultiplexing. |
| 2933 |
14 Nov 14 |
olle |
@since 2.16 |
| 2933 |
14 Nov 14 |
olle |
2162 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2163 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype PF_NNNN_PCT = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("PF_NNNN_PCT", Type.FLOAT, false, Item.DERIVEDBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
2166 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2167 |
|
| 2933 |
14 Nov 14 |
olle |
2168 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "PF_UNUSED_PCT" annotation, used for derived bioassays (DemuxedSequences). |
| 2933 |
14 Nov 14 |
olle |
The annotation is the percentage of sequences that was assigned to a barcode |
| 2933 |
14 Nov 14 |
olle |
that has not been used in the pool (used to detect misatakes when pooling or |
| 2933 |
14 Nov 14 |
olle |
loading the sequencer). |
| 2933 |
14 Nov 14 |
olle |
@since 2.16 |
| 2933 |
14 Nov 14 |
olle |
2174 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2175 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype PF_UNUSED_PCT = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("PF_UNUSED_PCT", Type.FLOAT, false, Item.DERIVEDBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
2178 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2179 |
|
| 2933 |
14 Nov 14 |
olle |
2180 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "DemuxWarnings" annotation, used for derived bioassays (DemuxedSequences). |
| 2933 |
14 Nov 14 |
olle |
Use to register warnings about things that seem strange during the demultiplexing. |
| 2933 |
14 Nov 14 |
olle |
Eg. high percentage of unused barcodes. |
| 2933 |
14 Nov 14 |
olle |
@since 2.16 |
| 2933 |
14 Nov 14 |
olle |
2185 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2186 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype DEMUX_WARNINGS = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("DemuxWarnings", Type.STRING, false, Item.DERIVEDBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
2189 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2190 |
|
| 2933 |
14 Nov 14 |
olle |
2191 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "PM_READS" annotation, used for derived bioassays (MaskedSequences). |
| 2933 |
14 Nov 14 |
olle |
The annotation is the number of sequences that has been assigned to |
| 2933 |
14 Nov 14 |
olle |
the library after masking. |
| 2933 |
14 Nov 14 |
olle |
@since 2.16 |
| 2933 |
14 Nov 14 |
olle |
2196 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2197 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype PM_READS = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("PM_READS", Type.LONG, false, Item.DERIVEDBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
2200 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2201 |
|
| 2933 |
14 Nov 14 |
olle |
2202 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "ALIGNED_PAIRS" annotation, used for derived bioassays (AlignedSequences). |
| 2933 |
14 Nov 14 |
olle |
The annotation is the number of sequences that has been assigned to |
| 2933 |
14 Nov 14 |
olle |
the library after aligning. |
| 2933 |
14 Nov 14 |
olle |
@since 2.16 |
| 2933 |
14 Nov 14 |
olle |
2207 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2208 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype ALIGNED_PAIRS = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("ALIGNED_PAIRS", Type.LONG, false, Item.DERIVEDBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
2211 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2212 |
|
| 2933 |
14 Nov 14 |
olle |
2213 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "READ_PAIRS_EXAMINED" annotation, used for derived bioassays (AlignedSequences). |
| 2933 |
14 Nov 14 |
olle |
The annotation is the number of sequences that has been examined by picard MarkDuplicates. |
| 2933 |
14 Nov 14 |
olle |
@since 2.16 |
| 2933 |
14 Nov 14 |
olle |
2217 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2218 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype READ_PAIRS_EXAMINED = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("READ_PAIRS_EXAMINED", Type.LONG, false, Item.DERIVEDBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
2221 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2222 |
|
| 2933 |
14 Nov 14 |
olle |
2223 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "READ_PAIR_DUPLICATES" annotation, used for derived bioassays (AlignedSequences). |
| 2933 |
14 Nov 14 |
olle |
The annotation is the number of sequences that has been found as duplicates |
| 2933 |
14 Nov 14 |
olle |
by picard MarkDuplicates. |
| 2933 |
14 Nov 14 |
olle |
@since 2.16 |
| 2933 |
14 Nov 14 |
olle |
2228 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2229 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype READ_PAIR_DUPLICATES = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("READ_PAIR_DUPLICATES", Type.LONG, false, Item.DERIVEDBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
2232 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2233 |
|
| 2933 |
14 Nov 14 |
olle |
2234 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "FRACTION_DUPLICATION" annotation, used for derived bioassays (AlignedSequences). |
| 2933 |
14 Nov 14 |
olle |
The annotation is the fraction of sequences that has been found as duplicates |
| 2933 |
14 Nov 14 |
olle |
by picard MarkDuplicates (PERCENT_DUPLICATION field). |
| 2933 |
14 Nov 14 |
olle |
@since 2.16 |
| 2933 |
14 Nov 14 |
olle |
2239 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2240 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype FRACTION_DUPLICATION = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("FRACTION_DUPLICATION", Type.FLOAT, false, Item.DERIVEDBIOASSAY); |
| 2933 |
14 Nov 14 |
olle |
2243 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2244 |
|
| 2933 |
14 Nov 14 |
olle |
2245 |
/** |
| 2933 |
14 Nov 14 |
olle |
The "SerialNumber" annotation, used for hardware items. |
| 2933 |
14 Nov 14 |
olle |
It is a string annotation containing a typically unique |
| 2933 |
14 Nov 14 |
olle |
value for each hardware item. |
| 2933 |
14 Nov 14 |
olle |
@since 2.16 |
| 2933 |
14 Nov 14 |
olle |
2250 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2251 |
/* |
| 2933 |
14 Nov 14 |
olle |
public static final Annotationtype SERIAL_NUMBER = |
| 2933 |
14 Nov 14 |
olle |
new Annotationtype("SerialNumber", Type.STRING, false, Item.HARDWARE); |
| 2933 |
14 Nov 14 |
olle |
2254 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2255 |
|
| 2933 |
14 Nov 14 |
olle |
2256 |
/** |
| 2933 |
14 Nov 14 |
olle |
Get the annotation type by name of the static constant defined in this class. |
| 2933 |
14 Nov 14 |
olle |
2258 |
|
| 2933 |
14 Nov 14 |
olle |
@param name The name of the static constant |
| 2933 |
14 Nov 14 |
olle |
@return An annotationtype object or null if not found |
| 2933 |
14 Nov 14 |
olle |
2261 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2262 |
public static Annotationtype getByCName(String cName) |
| 2933 |
14 Nov 14 |
olle |
2263 |
{ |
| 2933 |
14 Nov 14 |
olle |
2264 |
if (cName == null) return null; |
| 2933 |
14 Nov 14 |
olle |
2265 |
Annotationtype type = null; |
| 2933 |
14 Nov 14 |
olle |
2266 |
try |
| 2933 |
14 Nov 14 |
olle |
2267 |
{ |
| 2933 |
14 Nov 14 |
olle |
2268 |
Field f = Annotationtype.class.getDeclaredField(cName); |
| 2933 |
14 Nov 14 |
olle |
2269 |
type = (Annotationtype)f.get(null); |
| 2933 |
14 Nov 14 |
olle |
2270 |
} |
| 2933 |
14 Nov 14 |
olle |
2271 |
catch (NoSuchFieldException ex) |
| 2933 |
14 Nov 14 |
olle |
2272 |
{} |
| 2933 |
14 Nov 14 |
olle |
2273 |
catch (IllegalAccessException ex) |
| 2933 |
14 Nov 14 |
olle |
2274 |
{} |
| 2933 |
14 Nov 14 |
olle |
2275 |
catch (ClassCastException ex) |
| 2933 |
14 Nov 14 |
olle |
2276 |
{} |
| 2933 |
14 Nov 14 |
olle |
2277 |
return type; |
| 2933 |
14 Nov 14 |
olle |
2278 |
} |
| 2933 |
14 Nov 14 |
olle |
2279 |
|
| 2933 |
14 Nov 14 |
olle |
2280 |
private final String name; |
| 2933 |
14 Nov 14 |
olle |
2281 |
private final boolean disableLog; |
| 2933 |
14 Nov 14 |
olle |
2282 |
private final Item[] mainType; |
| 2933 |
14 Nov 14 |
olle |
2283 |
private final Type valueType; |
| 2933 |
14 Nov 14 |
olle |
2284 |
|
| 2933 |
14 Nov 14 |
olle |
2285 |
private int id; |
| 2933 |
14 Nov 14 |
olle |
2286 |
private AnnotationTypeFilter snapshotFilter; |
| 2933 |
14 Nov 14 |
olle |
2287 |
private JSONObject json; |
| 2933 |
14 Nov 14 |
olle |
2288 |
|
| 2933 |
14 Nov 14 |
olle |
2289 |
|
| 2933 |
14 Nov 14 |
olle |
2290 |
/** |
| 2933 |
14 Nov 14 |
olle |
Create a new definition of an annotation type. |
| 2933 |
14 Nov 14 |
olle |
2292 |
|
| 2933 |
14 Nov 14 |
olle |
@param name The name of the subtype |
| 2933 |
14 Nov 14 |
olle |
@param valueType The date type of values that can be stored |
| 2933 |
14 Nov 14 |
olle |
@param disableLog TRUE if change history logging of annotation values should be disabled |
| 2933 |
14 Nov 14 |
olle |
@param mainType The main item type(s) of the annotation type |
| 2933 |
14 Nov 14 |
olle |
2297 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2298 |
private Annotationtype(String name, Type valueType, boolean disableLog, Item... mainType) |
| 2933 |
14 Nov 14 |
olle |
2299 |
{ |
| 2933 |
14 Nov 14 |
olle |
2300 |
this.name = name; |
| 2933 |
14 Nov 14 |
olle |
2301 |
this.valueType = valueType; |
| 2933 |
14 Nov 14 |
olle |
2302 |
this.disableLog = disableLog; |
| 2933 |
14 Nov 14 |
olle |
2303 |
this.mainType = mainType; |
| 2933 |
14 Nov 14 |
olle |
2304 |
} |
| 2933 |
14 Nov 14 |
olle |
2305 |
|
| 2933 |
14 Nov 14 |
olle |
2306 |
/** |
| 2933 |
14 Nov 14 |
olle |
Get the name of the subtype. |
| 2933 |
14 Nov 14 |
olle |
2308 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2309 |
public String getName() |
| 2933 |
14 Nov 14 |
olle |
2310 |
{ |
| 2933 |
14 Nov 14 |
olle |
2311 |
return name; |
| 2933 |
14 Nov 14 |
olle |
2312 |
} |
| 2933 |
14 Nov 14 |
olle |
2313 |
|
| 2933 |
14 Nov 14 |
olle |
2314 |
/** |
| 2933 |
14 Nov 14 |
olle |
Get the data type of the values that can be stored. |
| 2933 |
14 Nov 14 |
olle |
2316 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2317 |
public Type getValueType() |
| 2933 |
14 Nov 14 |
olle |
2318 |
{ |
| 2933 |
14 Nov 14 |
olle |
2319 |
return valueType; |
| 2933 |
14 Nov 14 |
olle |
2320 |
} |
| 2933 |
14 Nov 14 |
olle |
2321 |
|
| 2933 |
14 Nov 14 |
olle |
2322 |
/** |
| 2933 |
14 Nov 14 |
olle |
Should change history logging be disabled or not for annotation values. |
| 2933 |
14 Nov 14 |
olle |
@since 2.16 |
| 2933 |
14 Nov 14 |
olle |
2325 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2326 |
public boolean getDisableChangeHistoryLog() |
| 2933 |
14 Nov 14 |
olle |
2327 |
{ |
| 2933 |
14 Nov 14 |
olle |
2328 |
return disableLog; |
| 2933 |
14 Nov 14 |
olle |
2329 |
} |
| 2933 |
14 Nov 14 |
olle |
2330 |
|
| 2933 |
14 Nov 14 |
olle |
2331 |
/** |
| 2933 |
14 Nov 14 |
olle |
Get the item type on which this annotation type can be used. |
| 2933 |
14 Nov 14 |
olle |
2333 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2334 |
public Item[] getMainType() |
| 2933 |
14 Nov 14 |
olle |
2335 |
{ |
| 2933 |
14 Nov 14 |
olle |
2336 |
return mainType; |
| 2933 |
14 Nov 14 |
olle |
2337 |
} |
| 2933 |
14 Nov 14 |
olle |
2338 |
|
| 2933 |
14 Nov 14 |
olle |
2339 |
/** |
| 2933 |
14 Nov 14 |
olle |
Get the annotation type information as a JSON object ready to be sent as an AJAX response. |
| 2933 |
14 Nov 14 |
olle |
2341 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2342 |
@SuppressWarnings("unchecked") |
| 2933 |
14 Nov 14 |
olle |
2343 |
public JSONObject asJSONObject(DbControl dc) |
| 2933 |
14 Nov 14 |
olle |
2344 |
{ |
| 2933 |
14 Nov 14 |
olle |
2345 |
if (json == null) |
| 2933 |
14 Nov 14 |
olle |
2346 |
{ |
| 2933 |
14 Nov 14 |
olle |
2347 |
if (id==0) load(dc); // Ensure that the annotationtype has been loaded |
| 2933 |
14 Nov 14 |
olle |
2348 |
json = new JSONObject(); |
| 2933 |
14 Nov 14 |
olle |
2349 |
json.put("id", id); |
| 2933 |
14 Nov 14 |
olle |
2350 |
json.put("name", getName()); |
| 2933 |
14 Nov 14 |
olle |
2351 |
} |
| 2933 |
14 Nov 14 |
olle |
2352 |
return json; |
| 2933 |
14 Nov 14 |
olle |
2353 |
} |
| 2933 |
14 Nov 14 |
olle |
2354 |
|
| 2933 |
14 Nov 14 |
olle |
2355 |
/** |
| 2933 |
14 Nov 14 |
olle |
Load the underlying annotation type. If it doesn't exists and exception is thrown. |
| 2933 |
14 Nov 14 |
olle |
2357 |
|
| 2933 |
14 Nov 14 |
olle |
@param dc The DbControl to use for database access |
| 2933 |
14 Nov 14 |
olle |
@return An AnnotationType object |
| 2933 |
14 Nov 14 |
olle |
2360 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2361 |
public AnnotationType load(DbControl dc) |
| 2933 |
14 Nov 14 |
olle |
2362 |
{ |
| 2933 |
14 Nov 14 |
olle |
2363 |
AnnotationType type = null; |
| 2933 |
14 Nov 14 |
olle |
2364 |
if (id == 0) |
| 2933 |
14 Nov 14 |
olle |
2365 |
{ |
| 2933 |
14 Nov 14 |
olle |
2366 |
List<AnnotationType> result = list(dc); |
| 2933 |
14 Nov 14 |
olle |
2367 |
if (result.size() == 0) |
| 2933 |
14 Nov 14 |
olle |
2368 |
{ |
| 2933 |
14 Nov 14 |
olle |
2369 |
throw new ItemNotFoundException("AnnotationType["+name+"]"); |
| 2933 |
14 Nov 14 |
olle |
2370 |
} |
| 2933 |
14 Nov 14 |
olle |
2371 |
else if (result.size() > 1) |
| 2933 |
14 Nov 14 |
olle |
2372 |
{ |
| 2933 |
14 Nov 14 |
olle |
2373 |
throw new InvalidDataException("Found > 1 AnnotationType["+name+"]"); |
| 2933 |
14 Nov 14 |
olle |
2374 |
} |
| 2933 |
14 Nov 14 |
olle |
2375 |
type = result.get(0); |
| 2933 |
14 Nov 14 |
olle |
2376 |
id = type.getId(); |
| 2933 |
14 Nov 14 |
olle |
2377 |
} |
| 2933 |
14 Nov 14 |
olle |
2378 |
else |
| 2933 |
14 Nov 14 |
olle |
2379 |
{ |
| 2933 |
14 Nov 14 |
olle |
2380 |
type = AnnotationType.getById(dc, id); |
| 2933 |
14 Nov 14 |
olle |
2381 |
} |
| 2933 |
14 Nov 14 |
olle |
2382 |
return type; |
| 2933 |
14 Nov 14 |
olle |
2383 |
} |
| 2933 |
14 Nov 14 |
olle |
2384 |
|
| 2933 |
14 Nov 14 |
olle |
2385 |
/** |
| 2933 |
14 Nov 14 |
olle |
Load the annotation type as a BASE item. Same as {@link #load(DbControl)} but return null |
| 2933 |
14 Nov 14 |
olle |
if no BASE item is found instead of throwing an exception. |
| 2933 |
14 Nov 14 |
olle |
@param dc The DbControl to use for database access |
| 2933 |
14 Nov 14 |
olle |
@return An ItemSubtype object |
| 2933 |
14 Nov 14 |
olle |
@since 2.16 |
| 2933 |
14 Nov 14 |
olle |
2391 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2392 |
public AnnotationType get(DbControl dc) |
| 2933 |
14 Nov 14 |
olle |
2393 |
{ |
| 2933 |
14 Nov 14 |
olle |
2394 |
AnnotationType type = null; |
| 2933 |
14 Nov 14 |
olle |
2395 |
if (id == 0) |
| 2933 |
14 Nov 14 |
olle |
2396 |
{ |
| 2933 |
14 Nov 14 |
olle |
2397 |
List<AnnotationType> result = list(dc); |
| 2933 |
14 Nov 14 |
olle |
2398 |
if (result.size() == 1) |
| 2933 |
14 Nov 14 |
olle |
2399 |
{ |
| 2933 |
14 Nov 14 |
olle |
2400 |
type = result.get(0); |
| 2933 |
14 Nov 14 |
olle |
2401 |
id = type.getId(); |
| 2933 |
14 Nov 14 |
olle |
2402 |
} |
| 2933 |
14 Nov 14 |
olle |
2403 |
} |
| 2933 |
14 Nov 14 |
olle |
2404 |
else |
| 2933 |
14 Nov 14 |
olle |
2405 |
{ |
| 2933 |
14 Nov 14 |
olle |
2406 |
type = AnnotationType.getById(dc, id); |
| 2933 |
14 Nov 14 |
olle |
2407 |
} |
| 2933 |
14 Nov 14 |
olle |
2408 |
return type; |
| 2933 |
14 Nov 14 |
olle |
2409 |
} |
| 2933 |
14 Nov 14 |
olle |
2410 |
|
| 2933 |
14 Nov 14 |
olle |
2411 |
/** |
| 2933 |
14 Nov 14 |
olle |
List all annotation types registered in BASE with a name and main item type |
| 2933 |
14 Nov 14 |
olle |
matching this annotation type definition. Normally, only a single annotation |
| 2933 |
14 Nov 14 |
olle |
type should be returned. |
| 2933 |
14 Nov 14 |
olle |
2415 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2416 |
public List<AnnotationType> list(DbControl dc) |
| 2933 |
14 Nov 14 |
olle |
2417 |
{ |
| 2933 |
14 Nov 14 |
olle |
2418 |
ItemQuery<AnnotationType> query = AnnotationType.getQuery(null); |
| 2933 |
14 Nov 14 |
olle |
2419 |
query.restrict(Restrictions.eq(Hql.property("name"), Expressions.parameter("name", name, Type.STRING))); |
| 2933 |
14 Nov 14 |
olle |
2420 |
|
| 2933 |
14 Nov 14 |
olle |
2421 |
Item[] mt = getMainType(); |
| 2933 |
14 Nov 14 |
olle |
2422 |
Expression[] mainTypes = new Expression[mt.length]; |
| 2933 |
14 Nov 14 |
olle |
2423 |
for (int i = 0; i < mainTypes.length; ++i) |
| 2933 |
14 Nov 14 |
olle |
2424 |
{ |
| 2933 |
14 Nov 14 |
olle |
2425 |
mainTypes[i] = Expressions.integer(mt[i].getValue()); |
| 2933 |
14 Nov 14 |
olle |
2426 |
} |
| 2933 |
14 Nov 14 |
olle |
2427 |
if (mainTypes.length > 0) |
| 2933 |
14 Nov 14 |
olle |
2428 |
{ |
| 2933 |
14 Nov 14 |
olle |
2429 |
query.joinPermanent(Hql.innerJoin("itemTypes", "it")); |
| 2933 |
14 Nov 14 |
olle |
2430 |
query.restrictPermanent(Restrictions.in(Hql.alias("it"), mainTypes)); |
| 2933 |
14 Nov 14 |
olle |
2431 |
} |
| 2933 |
14 Nov 14 |
olle |
2432 |
|
| 2933 |
14 Nov 14 |
olle |
2433 |
query.include(Include.ALL); |
| 2933 |
14 Nov 14 |
olle |
2434 |
query.setDistinct(true); |
| 2933 |
14 Nov 14 |
olle |
2435 |
return query.list(dc); |
| 2933 |
14 Nov 14 |
olle |
2436 |
} |
| 2933 |
14 Nov 14 |
olle |
2437 |
|
| 2933 |
14 Nov 14 |
olle |
2438 |
/** |
| 2933 |
14 Nov 14 |
olle |
Get the annotation value (single) for this annotation type from the |
| 2933 |
14 Nov 14 |
olle |
annotatable item. |
| 2933 |
14 Nov 14 |
olle |
@return The value, or null if the item is not annotated |
| 2933 |
14 Nov 14 |
olle |
2442 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2443 |
public Object getAnnotationValue(DbControl dc, Annotatable item) |
| 2933 |
14 Nov 14 |
olle |
2444 |
{ |
| 2933 |
14 Nov 14 |
olle |
2445 |
if (item == null) return null; |
| 2933 |
14 Nov 14 |
olle |
2446 |
AnnotationType at = load(dc); |
| 2933 |
14 Nov 14 |
olle |
2447 |
if (!item.isAnnotated()) return null; |
| 2933 |
14 Nov 14 |
olle |
2448 |
AnnotationSet as = item.getAnnotationSet(); |
| 5468 |
04 Jun 19 |
olle |
//if (!as.hasAnnotation(at)) return null; |
| 5468 |
04 Jun 19 |
olle |
2450 |
if (!as.hasAnnotation(at, null)) return null; |
| 2933 |
14 Nov 14 |
olle |
2451 |
return as.getAnnotation(at).getValues().get(0); |
| 2933 |
14 Nov 14 |
olle |
2452 |
} |
| 2933 |
14 Nov 14 |
olle |
2453 |
|
| 2933 |
14 Nov 14 |
olle |
2454 |
/** |
| 2933 |
14 Nov 14 |
olle |
Get the annotation value (single) for this annotation type from the |
| 2933 |
14 Nov 14 |
olle |
annotatable item using a snapshot stored on the disk if available. |
| 2933 |
14 Nov 14 |
olle |
@return The value, or null if the item is not annotated |
| 2933 |
14 Nov 14 |
olle |
@since 2.7 |
| 2933 |
14 Nov 14 |
olle |
2459 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2460 |
public Object getAnnotationValue(DbControl dc, SnapshotManager manager, Annotatable item) |
| 2933 |
14 Nov 14 |
olle |
2461 |
{ |
| 2933 |
14 Nov 14 |
olle |
2462 |
if (snapshotFilter == null) |
| 2933 |
14 Nov 14 |
olle |
2463 |
{ |
| 2933 |
14 Nov 14 |
olle |
2464 |
snapshotFilter = new AnnotationTypeFilter(load(dc)); |
| 2933 |
14 Nov 14 |
olle |
2465 |
} |
| 2933 |
14 Nov 14 |
olle |
2466 |
List<AnnotationSnapshot> snapshots = manager.findAnnotations(dc, item, snapshotFilter, false); |
| 5468 |
04 Jun 19 |
olle |
//return snapshots.size() > 0 ? snapshots.get(0).getValues().get(0) : null; |
| 5468 |
04 Jun 19 |
olle |
2468 |
return snapshots.size() > 0 ? snapshots.get(0).getThisValues().get(0) : null; |
| 2933 |
14 Nov 14 |
olle |
2469 |
} |
| 2933 |
14 Nov 14 |
olle |
2470 |
|
| 2933 |
14 Nov 14 |
olle |
2471 |
/** |
| 2933 |
14 Nov 14 |
olle |
Get an array annotation value from an item. Returns an empty list if |
| 2933 |
14 Nov 14 |
olle |
there are no annotations of the given type. |
| 2933 |
14 Nov 14 |
olle |
2474 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2475 |
public List<?> getAnnotationValues(DbControl dc, Annotatable item) |
| 2933 |
14 Nov 14 |
olle |
2476 |
{ |
| 2933 |
14 Nov 14 |
olle |
2477 |
AnnotationType at = load(dc); |
| 2933 |
14 Nov 14 |
olle |
2478 |
if (!item.isAnnotated()) return Collections.emptyList(); |
| 2933 |
14 Nov 14 |
olle |
2479 |
AnnotationSet as = item.getAnnotationSet(); |
| 5468 |
04 Jun 19 |
olle |
//if (!as.hasAnnotation(at)) return Collections.emptyList(); |
| 5468 |
04 Jun 19 |
olle |
2481 |
if (!as.hasAnnotation(at, null)) return Collections.emptyList(); |
| 2933 |
14 Nov 14 |
olle |
2482 |
return as.getAnnotation(at).getValues(); |
| 2933 |
14 Nov 14 |
olle |
2483 |
} |
| 2933 |
14 Nov 14 |
olle |
2484 |
|
| 2933 |
14 Nov 14 |
olle |
2485 |
/** |
| 3233 |
09 Apr 15 |
olle |
Get an array annotation value from an item. Returns an empty list if |
| 3233 |
09 Apr 15 |
olle |
there are no annotations of the given type. If flag 'fromListString' |
| 3233 |
09 Apr 15 |
olle |
is set to 'true', the list is expected to be stored as a string with |
| 3233 |
09 Apr 15 |
olle |
comma-separated values. |
| 3233 |
09 Apr 15 |
olle |
2490 |
*/ |
| 3233 |
09 Apr 15 |
olle |
2491 |
public List<?> getAnnotationValues(DbControl dc, Annotatable item, Boolean fromListString) |
| 3233 |
09 Apr 15 |
olle |
2492 |
{ |
| 3233 |
09 Apr 15 |
olle |
2493 |
return getAnnotationValues(dc, item, fromListString, false); |
| 3233 |
09 Apr 15 |
olle |
2494 |
} |
| 3233 |
09 Apr 15 |
olle |
2495 |
|
| 3233 |
09 Apr 15 |
olle |
2496 |
/** |
| 3233 |
09 Apr 15 |
olle |
Get an array annotation value from an item. Returns an empty list if |
| 3233 |
09 Apr 15 |
olle |
there are no annotations of the given type. If flag 'fromListString' |
| 3233 |
09 Apr 15 |
olle |
is set to 'true', the list is expected to be stored as a string with |
| 3233 |
09 Apr 15 |
olle |
comma-separated values. |
| 3233 |
09 Apr 15 |
olle |
2501 |
*/ |
| 3233 |
09 Apr 15 |
olle |
2502 |
public List<?> getAnnotationValues(DbControl dc, Annotatable item, Boolean fromListString, Boolean trim) |
| 3233 |
09 Apr 15 |
olle |
2503 |
{ |
| 3233 |
09 Apr 15 |
olle |
2504 |
AnnotationType at = load(dc); |
| 3233 |
09 Apr 15 |
olle |
2505 |
if (!item.isAnnotated()) return Collections.emptyList(); |
| 3233 |
09 Apr 15 |
olle |
2506 |
if (fromListString == null || !fromListString) |
| 3233 |
09 Apr 15 |
olle |
2507 |
{ |
| 3233 |
09 Apr 15 |
olle |
2508 |
AnnotationSet as = item.getAnnotationSet(); |
| 5468 |
04 Jun 19 |
olle |
//if (!as.hasAnnotation(at)) return Collections.emptyList(); |
| 5468 |
04 Jun 19 |
olle |
2510 |
if (!as.hasAnnotation(at, null)) return Collections.emptyList(); |
| 3233 |
09 Apr 15 |
olle |
2511 |
return as.getAnnotation(at).getValues(); |
| 3233 |
09 Apr 15 |
olle |
2512 |
} |
| 3233 |
09 Apr 15 |
olle |
2513 |
else |
| 3233 |
09 Apr 15 |
olle |
2514 |
{ |
| 3233 |
09 Apr 15 |
olle |
2515 |
List<String> list = new ArrayList<String>(); |
| 3233 |
09 Apr 15 |
olle |
2516 |
String listStr = (String) getAnnotationValue(dc, item); |
| 3233 |
09 Apr 15 |
olle |
2517 |
if (listStr != null && !listStr.equals("")) |
| 3233 |
09 Apr 15 |
olle |
2518 |
{ |
| 3233 |
09 Apr 15 |
olle |
2519 |
String[] itemNames = listStr.split(","); |
| 3233 |
09 Apr 15 |
olle |
2520 |
for (int i = 0; i < itemNames.length; i++) |
| 3233 |
09 Apr 15 |
olle |
2521 |
{ |
| 3233 |
09 Apr 15 |
olle |
2522 |
String itemName = itemNames[i]; |
| 3233 |
09 Apr 15 |
olle |
// Optional removal of leading and trailing white space |
| 3233 |
09 Apr 15 |
olle |
2524 |
if (itemName != null && trim != null && trim) |
| 3233 |
09 Apr 15 |
olle |
2525 |
{ |
| 3233 |
09 Apr 15 |
olle |
2526 |
itemName = itemName.trim(); |
| 3233 |
09 Apr 15 |
olle |
2527 |
} |
| 3233 |
09 Apr 15 |
olle |
2528 |
list.add(itemName); |
| 3233 |
09 Apr 15 |
olle |
2529 |
} |
| 3233 |
09 Apr 15 |
olle |
2530 |
} |
| 3233 |
09 Apr 15 |
olle |
2531 |
return list; |
| 3233 |
09 Apr 15 |
olle |
2532 |
} |
| 3233 |
09 Apr 15 |
olle |
2533 |
} |
| 3233 |
09 Apr 15 |
olle |
2534 |
|
| 3233 |
09 Apr 15 |
olle |
2535 |
/** |
| 2933 |
14 Nov 14 |
olle |
Set a (single) annotation value on an item. If the value is null the annotation |
| 2933 |
14 Nov 14 |
olle |
will be removed. |
| 2933 |
14 Nov 14 |
olle |
2538 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2539 |
public void setAnnotationValue(DbControl dc, Annotatable item, Object value) |
| 2933 |
14 Nov 14 |
olle |
2540 |
{ |
| 2933 |
14 Nov 14 |
olle |
2541 |
AnnotationType at = load(dc); |
| 2933 |
14 Nov 14 |
olle |
2542 |
if (value == null) |
| 2933 |
14 Nov 14 |
olle |
2543 |
{ |
| 5468 |
04 Jun 19 |
olle |
//if (item.isAnnotated() && item.getAnnotationSet().hasAnnotation(at)) |
| 5468 |
04 Jun 19 |
olle |
2545 |
if (item.isAnnotated() && item.getAnnotationSet().hasAnnotation(at, null)) |
| 2933 |
14 Nov 14 |
olle |
2546 |
{ |
| 2933 |
14 Nov 14 |
olle |
2547 |
item.getAnnotationSet().removeAnnotation(at); |
| 2933 |
14 Nov 14 |
olle |
2548 |
} |
| 2933 |
14 Nov 14 |
olle |
2549 |
} |
| 2933 |
14 Nov 14 |
olle |
2550 |
else |
| 2933 |
14 Nov 14 |
olle |
2551 |
{ |
| 2933 |
14 Nov 14 |
olle |
2552 |
Type valueType = at.getValueType(); |
| 2933 |
14 Nov 14 |
olle |
2553 |
if (valueType.isNumerical() && value instanceof Number) |
| 2933 |
14 Nov 14 |
olle |
2554 |
{ |
| 2933 |
14 Nov 14 |
olle |
2555 |
value = valueType.convertNumber((Number)value); |
| 2933 |
14 Nov 14 |
olle |
2556 |
} |
| 5468 |
04 Jun 19 |
olle |
//item.getAnnotationSet().getAnnotation(at).setValue(value); |
| 5468 |
04 Jun 19 |
olle |
2558 |
item.getAnnotationSet().getAnnotation(at).setValueIfDifferent(value, null); |
| 2933 |
14 Nov 14 |
olle |
2559 |
} |
| 2933 |
14 Nov 14 |
olle |
2560 |
} |
| 2933 |
14 Nov 14 |
olle |
2561 |
|
| 2933 |
14 Nov 14 |
olle |
2562 |
/** |
| 2933 |
14 Nov 14 |
olle |
Set a multi-valued annotation on an item. If the values list is null or |
| 2933 |
14 Nov 14 |
olle |
emtpy the annotation will be removed. |
| 2933 |
14 Nov 14 |
olle |
@since 2.15 |
| 2933 |
14 Nov 14 |
olle |
2566 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2567 |
public void setAnnotationValues(DbControl dc, Annotatable item, List<?> values) |
| 2933 |
14 Nov 14 |
olle |
2568 |
{ |
| 2933 |
14 Nov 14 |
olle |
2569 |
AnnotationType at = load(dc); |
| 2933 |
14 Nov 14 |
olle |
2570 |
if (values == null || values.isEmpty()) |
| 2933 |
14 Nov 14 |
olle |
2571 |
{ |
| 5468 |
04 Jun 19 |
olle |
//if (item.isAnnotated() && item.getAnnotationSet().hasAnnotation(at)) |
| 5468 |
04 Jun 19 |
olle |
2573 |
if (item.isAnnotated() && item.getAnnotationSet().hasAnnotation(at, null)) |
| 2933 |
14 Nov 14 |
olle |
2574 |
{ |
| 2933 |
14 Nov 14 |
olle |
2575 |
item.getAnnotationSet().removeAnnotation(at); |
| 2933 |
14 Nov 14 |
olle |
2576 |
} |
| 2933 |
14 Nov 14 |
olle |
2577 |
} |
| 2933 |
14 Nov 14 |
olle |
2578 |
else |
| 2933 |
14 Nov 14 |
olle |
2579 |
{ |
| 3233 |
09 Apr 15 |
olle |
2580 |
if (at.getMultiplicity() == 1) |
| 3233 |
09 Apr 15 |
olle |
2581 |
{ |
| 3233 |
09 Apr 15 |
olle |
2582 |
String listStr = ""; |
| 3233 |
09 Apr 15 |
olle |
2583 |
for (int i = 0; i < values.size(); i++) |
| 3233 |
09 Apr 15 |
olle |
2584 |
{ |
| 3233 |
09 Apr 15 |
olle |
2585 |
String value = (String) values.get(i); |
| 3233 |
09 Apr 15 |
olle |
2586 |
if (i > 0) |
| 3233 |
09 Apr 15 |
olle |
2587 |
{ |
| 3233 |
09 Apr 15 |
olle |
2588 |
listStr += ","; |
| 3233 |
09 Apr 15 |
olle |
2589 |
} |
| 3233 |
09 Apr 15 |
olle |
2590 |
listStr += value; |
| 3233 |
09 Apr 15 |
olle |
2591 |
} |
| 5468 |
04 Jun 19 |
olle |
//item.getAnnotationSet().getAnnotation(at).setValue(listStr); |
| 5468 |
04 Jun 19 |
olle |
2593 |
item.getAnnotationSet().getAnnotation(at).setValueIfDifferent(listStr, null); |
| 3233 |
09 Apr 15 |
olle |
2594 |
} |
| 3233 |
09 Apr 15 |
olle |
2595 |
else |
| 3233 |
09 Apr 15 |
olle |
2596 |
{ |
| 5468 |
04 Jun 19 |
olle |
//item.getAnnotationSet().getAnnotation(at).setValues(values); |
| 5468 |
04 Jun 19 |
olle |
2598 |
item.getAnnotationSet().getAnnotation(at).setValuesIfDifferent(values, null); |
| 3233 |
09 Apr 15 |
olle |
2599 |
} |
| 2933 |
14 Nov 14 |
olle |
2600 |
} |
| 2933 |
14 Nov 14 |
olle |
2601 |
} |
| 2933 |
14 Nov 14 |
olle |
2602 |
|
| 2933 |
14 Nov 14 |
olle |
2603 |
/** |
| 2933 |
14 Nov 14 |
olle |
Append an annotation value to a multi-valued annotation type where each |
| 2933 |
14 Nov 14 |
olle |
value should be unique. |
| 2933 |
14 Nov 14 |
olle |
2606 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2607 |
public void appendAnnotationValueIfUnique(DbControl dc, Annotatable item, Object value) |
| 2933 |
14 Nov 14 |
olle |
2608 |
{ |
| 2933 |
14 Nov 14 |
olle |
2609 |
List<?> currentValues = getAnnotationValues(dc, item); |
| 2933 |
14 Nov 14 |
olle |
2610 |
if (!currentValues.contains(value)) |
| 2933 |
14 Nov 14 |
olle |
2611 |
{ |
| 2933 |
14 Nov 14 |
olle |
2612 |
AnnotationType at = load(dc); |
| 2933 |
14 Nov 14 |
olle |
2613 |
List<Object> newValues = new ArrayList<Object>(currentValues); |
| 2933 |
14 Nov 14 |
olle |
2614 |
newValues.add(value); |
| 5468 |
04 Jun 19 |
olle |
//item.getAnnotationSet().getAnnotation(at).setValues(newValues); |
| 5468 |
04 Jun 19 |
olle |
2616 |
item.getAnnotationSet().getAnnotation(at).setValuesIfDifferent(newValues, null); |
| 2933 |
14 Nov 14 |
olle |
2617 |
} |
| 2933 |
14 Nov 14 |
olle |
2618 |
} |
| 2933 |
14 Nov 14 |
olle |
2619 |
|
| 2933 |
14 Nov 14 |
olle |
2620 |
/** |
| 2933 |
14 Nov 14 |
olle |
Remove an annotation value to a multi-valued annotation type where each |
| 2933 |
14 Nov 14 |
olle |
value should be unique. |
| 2933 |
14 Nov 14 |
olle |
2623 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2624 |
public void removeAnnotationValue(DbControl dc, Annotatable item, Object value) |
| 2933 |
14 Nov 14 |
olle |
2625 |
{ |
| 2933 |
14 Nov 14 |
olle |
2626 |
List<?> currentValues = getAnnotationValues(dc, item); |
| 2933 |
14 Nov 14 |
olle |
2627 |
if (currentValues.contains(value)) |
| 2933 |
14 Nov 14 |
olle |
2628 |
{ |
| 2933 |
14 Nov 14 |
olle |
2629 |
AnnotationType at = load(dc); |
| 2933 |
14 Nov 14 |
olle |
2630 |
List<Object> newValues = new ArrayList<Object>(currentValues); |
| 2933 |
14 Nov 14 |
olle |
2631 |
newValues.remove(value); |
| 5468 |
04 Jun 19 |
olle |
//item.getAnnotationSet().getAnnotation(at).setValues(newValues); |
| 5468 |
04 Jun 19 |
olle |
2633 |
item.getAnnotationSet().getAnnotation(at).setValuesIfDifferent(newValues, null); |
| 2933 |
14 Nov 14 |
olle |
2634 |
} |
| 2933 |
14 Nov 14 |
olle |
2635 |
} |
| 2933 |
14 Nov 14 |
olle |
2636 |
|
| 2933 |
14 Nov 14 |
olle |
2637 |
/** |
| 2933 |
14 Nov 14 |
olle |
Copy annotation values between two items. |
| 2933 |
14 Nov 14 |
olle |
2639 |
|
| 2933 |
14 Nov 14 |
olle |
@param from The item to copy from. If this item is not annotated with |
| 2933 |
14 Nov 14 |
olle |
the given annotation type, nothing is copied |
| 2933 |
14 Nov 14 |
olle |
@param to The item to copy to. If this item already has been annotated with |
| 2933 |
14 Nov 14 |
olle |
the given annotation type, the 'force' paremter decides if the annotation is |
| 2933 |
14 Nov 14 |
olle |
overwritten or not |
| 2933 |
14 Nov 14 |
olle |
@param force TRUE to overwrite existing annotations, FALSE to not |
| 2933 |
14 Nov 14 |
olle |
@return TRUE if this method copied annotations, FALSE if not |
| 2933 |
14 Nov 14 |
olle |
2647 |
*/ |
| 2933 |
14 Nov 14 |
olle |
2648 |
public boolean copyAnnotationValues(DbControl dc, Annotatable from, Annotatable to, boolean force) |
| 2933 |
14 Nov 14 |
olle |
2649 |
{ |
| 2933 |
14 Nov 14 |
olle |
2650 |
List<?> annotations = getAnnotationValues(dc, from); |
| 2933 |
14 Nov 14 |
olle |
2651 |
if (annotations == null || annotations.size() == 0) return false; |
| 2933 |
14 Nov 14 |
olle |
2652 |
|
| 2933 |
14 Nov 14 |
olle |
2653 |
AnnotationType at = load(dc); |
| 2933 |
14 Nov 14 |
olle |
2654 |
if (!force) |
| 2933 |
14 Nov 14 |
olle |
2655 |
{ |
| 2933 |
14 Nov 14 |
olle |
// We need to check if the 'to' item already has the annotation |
| 5468 |
04 Jun 19 |
olle |
//if (to.isAnnotated() && to.getAnnotationSet().hasAnnotation(at)) return false; |
| 5468 |
04 Jun 19 |
olle |
2658 |
if (to.isAnnotated() && to.getAnnotationSet().hasAnnotation(at, null)) return false; |
| 2933 |
14 Nov 14 |
olle |
2659 |
} |
| 2933 |
14 Nov 14 |
olle |
2660 |
|
| 2933 |
14 Nov 14 |
olle |
// Copy the values |
| 5468 |
04 Jun 19 |
olle |
//to.getAnnotationSet().getAnnotation(at).setValues(annotations); |
| 5468 |
04 Jun 19 |
olle |
2663 |
to.getAnnotationSet().getAnnotation(at).setValuesIfDifferent(annotations, null); |
| 2933 |
14 Nov 14 |
olle |
2664 |
return true; |
| 2933 |
14 Nov 14 |
olle |
2665 |
} |
| 2933 |
14 Nov 14 |
olle |
2666 |
|
| 2933 |
14 Nov 14 |
olle |
2667 |
|
| 2933 |
14 Nov 14 |
olle |
2668 |
} |