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Add read support for older RDML versions.
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71 changes: 71 additions & 0 deletions
71
...se/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/CdnaSynthesisMethodType.java
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/******************************************************************************* | ||
* 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; | ||
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import jakarta.xml.bind.annotation.XmlAccessType; | ||
import jakarta.xml.bind.annotation.XmlAccessorType; | ||
import jakarta.xml.bind.annotation.XmlSchemaType; | ||
import jakarta.xml.bind.annotation.XmlType; | ||
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/** | ||
* Description of the cDNA synthesis method. | ||
*/ | ||
@XmlAccessorType(XmlAccessType.FIELD) | ||
@XmlType(name = "cdnaSynthesisMethodType", propOrder = {"enzyme", "primingMethod", "dnaseTreatment", "thermalCyclingConditions"}) | ||
public class CdnaSynthesisMethodType { | ||
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protected String enzyme; | ||
@XmlSchemaType(name = "string") | ||
protected PrimingMethodType primingMethod; | ||
protected Boolean dnaseTreatment; | ||
protected IdReferencesType thermalCyclingConditions; | ||
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public String getEnzyme() { | ||
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return enzyme; | ||
} | ||
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public void setEnzyme(String value) { | ||
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this.enzyme = value; | ||
} | ||
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public PrimingMethodType getPrimingMethod() { | ||
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return primingMethod; | ||
} | ||
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public void setPrimingMethod(PrimingMethodType value) { | ||
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this.primingMethod = value; | ||
} | ||
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public Boolean isDnaseTreatment() { | ||
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return dnaseTreatment; | ||
} | ||
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public void setDnaseTreatment(Boolean value) { | ||
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this.dnaseTreatment = value; | ||
} | ||
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public IdReferencesType getThermalCyclingConditions() { | ||
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return thermalCyclingConditions; | ||
} | ||
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public void setThermalCyclingConditions(IdReferencesType value) { | ||
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this.thermalCyclingConditions = value; | ||
} | ||
} |
51 changes: 51 additions & 0 deletions
51
...clipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/CommercialAssayType.java
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/******************************************************************************* | ||
* 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; | ||
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import jakarta.xml.bind.annotation.XmlAccessType; | ||
import jakarta.xml.bind.annotation.XmlAccessorType; | ||
import jakarta.xml.bind.annotation.XmlElement; | ||
import jakarta.xml.bind.annotation.XmlType; | ||
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/** | ||
* 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 { | ||
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@XmlElement(required = true) | ||
protected String company; | ||
@XmlElement(required = true) | ||
protected String orderNumber; | ||
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public String getCompany() { | ||
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return company; | ||
} | ||
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public void setCompany(String value) { | ||
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this.company = value; | ||
} | ||
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public String getOrderNumber() { | ||
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return orderNumber; | ||
} | ||
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public void setOrderNumber(String value) { | ||
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this.orderNumber = value; | ||
} | ||
} |
52 changes: 52 additions & 0 deletions
52
...ipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/CqDetectionMethodType.java
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/******************************************************************************* | ||
* 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; | ||
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import jakarta.xml.bind.annotation.XmlEnum; | ||
import jakarta.xml.bind.annotation.XmlEnumValue; | ||
import jakarta.xml.bind.annotation.XmlType; | ||
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@XmlType(name = "cqDetectionMethodType") | ||
@XmlEnum | ||
public enum CqDetectionMethodType { | ||
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@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"); | ||
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private final String value; | ||
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CqDetectionMethodType(String v) { | ||
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value = v; | ||
} | ||
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public String value() { | ||
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return value; | ||
} | ||
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public static CqDetectionMethodType fromValue(String v) { | ||
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for(CqDetectionMethodType c : CqDetectionMethodType.values()) { | ||
if(c.value.equals(v)) { | ||
return c; | ||
} | ||
} | ||
throw new IllegalArgumentException(v); | ||
} | ||
} |
50 changes: 50 additions & 0 deletions
50
...chemclipse/pcr/converter/supplier/rdml/internal/v10/model/DataCollectionSoftwareType.java
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/******************************************************************************* | ||
* 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; | ||
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import jakarta.xml.bind.annotation.XmlAccessType; | ||
import jakarta.xml.bind.annotation.XmlAccessorType; | ||
import jakarta.xml.bind.annotation.XmlElement; | ||
import jakarta.xml.bind.annotation.XmlType; | ||
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/** | ||
* Software name and version used to collect the data. | ||
*/ | ||
@XmlAccessorType(XmlAccessType.FIELD) | ||
@XmlType(name = "dataCollectionSoftwareType", propOrder = {"name", "version"}) | ||
public class DataCollectionSoftwareType { | ||
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@XmlElement(required = true) | ||
protected String name; | ||
@XmlElement(required = true) | ||
protected String version; | ||
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public String getName() { | ||
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return name; | ||
} | ||
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public void setName(String value) { | ||
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this.name = value; | ||
} | ||
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public String getVersion() { | ||
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return version; | ||
} | ||
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public void setVersion(String value) { | ||
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this.version = value; | ||
} | ||
} |
125 changes: 125 additions & 0 deletions
125
...l/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/DataType.java
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/******************************************************************************* | ||
* 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; | ||
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import java.util.ArrayList; | ||
import java.util.List; | ||
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import jakarta.xml.bind.annotation.XmlAccessType; | ||
import jakarta.xml.bind.annotation.XmlAccessorType; | ||
import jakarta.xml.bind.annotation.XmlElement; | ||
import jakarta.xml.bind.annotation.XmlType; | ||
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/** | ||
* 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 { | ||
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@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; | ||
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public IdReferencesType getTar() { | ||
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return tar; | ||
} | ||
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public void setTar(IdReferencesType value) { | ||
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this.tar = value; | ||
} | ||
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public Float getCq() { | ||
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return cq; | ||
} | ||
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public void setCq(Float value) { | ||
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this.cq = value; | ||
} | ||
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public QuantityType getQuantity() { | ||
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return quantity; | ||
} | ||
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public void setQuantity(QuantityType value) { | ||
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this.quantity = value; | ||
} | ||
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public String getExcl() { | ||
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return excl; | ||
} | ||
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public void setExcl(String value) { | ||
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this.excl = value; | ||
} | ||
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public List<DpAmpCurveType> getAdp() { | ||
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if(adp == null) { | ||
adp = new ArrayList<>(); | ||
} | ||
return this.adp; | ||
} | ||
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public List<DpMeltingCurveType> getMdp() { | ||
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if(mdp == null) { | ||
mdp = new ArrayList<>(); | ||
} | ||
return this.mdp; | ||
} | ||
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public Float getEndPt() { | ||
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return endPt; | ||
} | ||
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public void setEndPt(Float value) { | ||
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this.endPt = value; | ||
} | ||
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public Float getBgFluor() { | ||
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return bgFluor; | ||
} | ||
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public void setBgFluor(Float value) { | ||
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this.bgFluor = value; | ||
} | ||
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public Float getQuantFluor() { | ||
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return quantFluor; | ||
} | ||
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public void setQuantFluor(Float value) { | ||
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this.quantFluor = value; | ||
} | ||
} |
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