Added read support for older RDML versions

chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/META-INF/MANIFEST.MF

@@ -14,7 +14,8 @@ Require-Bundle: org.eclipse.core.runtime,
  org.eclipse.chemclipse.logging;bundle-version="0.8.0",
  org.eclipse.chemclipse.processing;bundle-version="0.8.0",
  org.eclipse.chemclipse.support;bundle-version="0.8.0",
- jakarta.xml.bind-api;bundle-version="4.0.0"
+ jakarta.xml.bind-api;bundle-version="4.0.0",
+ org.eclipse.chemclipse.xxd.converter.supplier.chemclipse;bundle-version="0.9.0"
 Bundle-RequiredExecutionEnvironment: JavaSE-17
 Bundle-ActivationPolicy: lazy
 Import-Package: jakarta.xml.bind,

chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/CdnaSynthesisMethodType.java

@@ -0,0 +1,71 @@
+/*******************************************************************************
+ * Copyright (c) 2023 Lablicate GmbH.
+ *
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ * 
+ * Contributors:
+ * Matthias Mailänder - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model;
+
+import jakarta.xml.bind.annotation.XmlAccessType;
+import jakarta.xml.bind.annotation.XmlAccessorType;
+import jakarta.xml.bind.annotation.XmlSchemaType;
+import jakarta.xml.bind.annotation.XmlType;
+
+/**
+ * Description of the cDNA synthesis method.
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "cdnaSynthesisMethodType", propOrder = {"enzyme", "primingMethod", "dnaseTreatment", "thermalCyclingConditions"})
+public class CdnaSynthesisMethodType {
+
+ protected String enzyme;
+ @XmlSchemaType(name = "string")
+ protected PrimingMethodType primingMethod;
+ protected Boolean dnaseTreatment;
+ protected IdReferencesType thermalCyclingConditions;
+
+ public String getEnzyme() {
+
+ return enzyme;
+ }
+
+ public void setEnzyme(String value) {
+
+ this.enzyme = value;
+ }
+
+ public PrimingMethodType getPrimingMethod() {
+
+ return primingMethod;
+ }
+
+ public void setPrimingMethod(PrimingMethodType value) {
+
+ this.primingMethod = value;
+ }
+
+ public Boolean isDnaseTreatment() {
+
+ return dnaseTreatment;
+ }
+
+ public void setDnaseTreatment(Boolean value) {
+
+ this.dnaseTreatment = value;
+ }
+
+ public IdReferencesType getThermalCyclingConditions() {
+
+ return thermalCyclingConditions;
+ }
+
+ public void setThermalCyclingConditions(IdReferencesType value) {
+
+ this.thermalCyclingConditions = value;
+ }
+}

chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/CommercialAssayType.java

@@ -0,0 +1,51 @@
+/*******************************************************************************
+ * Copyright (c) 2023 Lablicate GmbH.
+ *
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ * 
+ * Contributors:
+ * Matthias Mailänder - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model;
+
+import jakarta.xml.bind.annotation.XmlAccessType;
+import jakarta.xml.bind.annotation.XmlAccessorType;
+import jakarta.xml.bind.annotation.XmlElement;
+import jakarta.xml.bind.annotation.XmlType;
+
+/**
+ * For some commercial assays the primer sequences may be unknown. This element
+ * allows to describe commercial assays.
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "commercialAssayType", propOrder = {"company", "orderNumber"})
+public class CommercialAssayType {
+
+ @XmlElement(required = true)
+ protected String company;
+ @XmlElement(required = true)
+ protected String orderNumber;
+
+ public String getCompany() {
+
+ return company;
+ }
+
+ public void setCompany(String value) {
+
+ this.company = value;
+ }
+
+ public String getOrderNumber() {
+
+ return orderNumber;
+ }
+
+ public void setOrderNumber(String value) {
+
+ this.orderNumber = value;
+ }
+}

chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/CqDetectionMethodType.java

@@ -0,0 +1,52 @@
+/*******************************************************************************
+ * Copyright (c) 2023 Lablicate GmbH.
+ *
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ * 
+ * Contributors:
+ * Matthias Mailänder - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model;
+
+import jakarta.xml.bind.annotation.XmlEnum;
+import jakarta.xml.bind.annotation.XmlEnumValue;
+import jakarta.xml.bind.annotation.XmlType;
+
+@XmlType(name = "cqDetectionMethodType")
+@XmlEnum
+public enum CqDetectionMethodType {
+
+ @XmlEnumValue("automated threshold and baseline settings")
+ AUTOMATED_THRESHOLD_AND_BASELINE_SETTINGS("automated threshold and baseline settings"), //
+ @XmlEnumValue("manual threshold and baseline settings")
+ MANUAL_THRESHOLD_AND_BASELINE_SETTINGS("manual threshold and baseline settings"), //
+ @XmlEnumValue("second derivative maximum")
+ SECOND_DERIVATIVE_MAXIMUM("second derivative maximum"), //
+ @XmlEnumValue("other")
+ OTHER("other");
+
+ private final String value;
+
+ CqDetectionMethodType(String v) {
+
+ value = v;
+ }
+
+ public String value() {
+
+ return value;
+ }
+
+ public static CqDetectionMethodType fromValue(String v) {
+
+ for(CqDetectionMethodType c : CqDetectionMethodType.values()) {
+ if(c.value.equals(v)) {
+ return c;
+ }
+ }
+ throw new IllegalArgumentException(v);
+ }
+}

chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/DataCollectionSoftwareType.java

@@ -0,0 +1,50 @@
+/*******************************************************************************
+ * Copyright (c) 2023 Lablicate GmbH.
+ *
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ * 
+ * Contributors:
+ * Matthias Mailänder - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model;
+
+import jakarta.xml.bind.annotation.XmlAccessType;
+import jakarta.xml.bind.annotation.XmlAccessorType;
+import jakarta.xml.bind.annotation.XmlElement;
+import jakarta.xml.bind.annotation.XmlType;
+
+/**
+ * Software name and version used to collect the data.
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "dataCollectionSoftwareType", propOrder = {"name", "version"})
+public class DataCollectionSoftwareType {
+
+ @XmlElement(required = true)
+ protected String name;
+ @XmlElement(required = true)
+ protected String version;
+
+ public String getName() {
+
+ return name;
+ }
+
+ public void setName(String value) {
+
+ this.name = value;
+ }
+
+ public String getVersion() {
+
+ return version;
+ }
+
+ public void setVersion(String value) {
+
+ this.version = value;
+ }
+}

chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/DataType.java

@@ -0,0 +1,125 @@
+/*******************************************************************************
+ * Copyright (c) 2023 Lablicate GmbH.
+ *
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ * 
+ * Contributors:
+ * Matthias Mailänder - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import jakarta.xml.bind.annotation.XmlAccessType;
+import jakarta.xml.bind.annotation.XmlAccessorType;
+import jakarta.xml.bind.annotation.XmlElement;
+import jakarta.xml.bind.annotation.XmlType;
+
+/**
+ * Due to the high numbers of this elements names are kept short.
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "dataType", propOrder = {"tar", "cq", "quantity", "excl", "adp", "mdp", "endPt", "bgFluor", "quantFluor"})
+public class DataType {
+
+ @XmlElement(required = true)
+ protected IdReferencesType tar;
+ protected Float cq;
+ protected QuantityType quantity;
+ protected String excl;
+ protected List<DpAmpCurveType> adp;
+ protected List<DpMeltingCurveType> mdp;
+ protected Float endPt;
+ protected Float bgFluor;
+ protected Float quantFluor;
+
+ public IdReferencesType getTar() {
+
+ return tar;
+ }
+
+ public void setTar(IdReferencesType value) {
+
+ this.tar = value;
+ }
+
+ public Float getCq() {
+
+ return cq;
+ }
+
+ public void setCq(Float value) {
+
+ this.cq = value;
+ }
+
+ public QuantityType getQuantity() {
+
+ return quantity;
+ }
+
+ public void setQuantity(QuantityType value) {
+
+ this.quantity = value;
+ }
+
+ public String getExcl() {
+
+ return excl;
+ }
+
+ public void setExcl(String value) {
+
+ this.excl = value;
+ }
+
+ public List<DpAmpCurveType> getAdp() {
+
+ if(adp == null) {
+ adp = new ArrayList<>();
+ }
+ return this.adp;
+ }
+
+ public List<DpMeltingCurveType> getMdp() {
+
+ if(mdp == null) {
+ mdp = new ArrayList<>();
+ }
+ return this.mdp;
+ }
+
+ public Float getEndPt() {
+
+ return endPt;
+ }
+
+ public void setEndPt(Float value) {
+
+ this.endPt = value;
+ }
+
+ public Float getBgFluor() {
+
+ return bgFluor;
+ }
+
+ public void setBgFluor(Float value) {
+
+ this.bgFluor = value;
+ }
+
+ public Float getQuantFluor() {
+
+ return quantFluor;
+ }
+
+ public void setQuantFluor(Float value) {
+
+ this.quantFluor = value;
+ }
+}