-
Notifications
You must be signed in to change notification settings - Fork 18
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Add basic metadata for MALDI-TOF MS spectra
- Loading branch information
1 parent
82a5d7f
commit 3d00709
Showing
5 changed files
with
259 additions
and
15 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
89 changes: 89 additions & 0 deletions
89
...model/src/org/eclipse/chemclipse/msd/model/core/AbstractVendorStandaloneMassSpectrum.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,89 @@ | ||
| /******************************************************************************* | ||
| * Copyright (c) 2022 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.msd.model.core; | ||
|
|
||
| import java.util.Date; | ||
|
|
||
| public abstract class AbstractVendorStandaloneMassSpectrum extends AbstractVendorMassSpectrum implements IVendorStandaloneMassSpectrum { | ||
|
|
||
| /** | ||
| * Renew the serialVersionUID any time you have changed some fields or | ||
| * methods. | ||
| */ | ||
| private static final long serialVersionUID = 7180911179209208597L; | ||
| // | ||
| private String sample; | ||
| private String description; | ||
| private String operator; | ||
| private Date acquisitionDate; | ||
| private String instrument; | ||
|
|
||
| @Override | ||
| public String getSampleName() { | ||
|
|
||
| return sample; | ||
| } | ||
|
|
||
| @Override | ||
| public void setSampleName(String name) { | ||
|
|
||
| this.sample = name; | ||
| } | ||
|
|
||
| @Override | ||
| public String getOperator() { | ||
|
|
||
| return operator; | ||
| } | ||
|
|
||
| @Override | ||
| public void setOperator(String operator) { | ||
|
|
||
| this.operator = operator; | ||
| } | ||
|
|
||
| @Override | ||
| public Date getDate() { | ||
|
|
||
| return acquisitionDate; | ||
| } | ||
|
|
||
| @Override | ||
| public void setDate(Date acquisitionDate) { | ||
|
|
||
| this.acquisitionDate = acquisitionDate; | ||
| } | ||
|
|
||
| @Override | ||
| public String getInstrument() { | ||
|
|
||
| return instrument; | ||
| } | ||
|
|
||
| @Override | ||
| public void setInstrument(String instrument) { | ||
|
|
||
| this.instrument = instrument; | ||
| } | ||
|
|
||
| @Override | ||
| public String getDescription() { | ||
|
|
||
| return description; | ||
| } | ||
|
|
||
| @Override | ||
| public void setDescription(String description) { | ||
|
|
||
| this.description = description; | ||
| } | ||
| } |
42 changes: 42 additions & 0 deletions
42
...se.msd.model/src/org/eclipse/chemclipse/msd/model/core/IVendorStandaloneMassSpectrum.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,42 @@ | ||
| /******************************************************************************* | ||
| * Copyright (c) 2022 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.msd.model.core; | ||
|
|
||
| import java.util.Date; | ||
|
|
||
| /** | ||
| * An interface for single MALDI-TOF MS spectra which contain additional metadata. | ||
| * | ||
| * @author Matthias Mailänder | ||
| */ | ||
| public interface IVendorStandaloneMassSpectrum extends IVendorMassSpectrum { | ||
|
|
||
| String getSampleName(); | ||
|
|
||
| void setSampleName(String name); | ||
|
|
||
| String getDescription(); | ||
|
|
||
| void setDescription(String description); | ||
|
|
||
| String getOperator(); | ||
|
|
||
| void setOperator(String operator); | ||
|
|
||
| Date getDate(); | ||
|
|
||
| void setDate(Date date); | ||
|
|
||
| String getInstrument(); | ||
|
|
||
| void setInstrument(String instrument); | ||
| } |
92 changes: 92 additions & 0 deletions
92
...del/src/org/eclipse/chemclipse/msd/model/implementation/VendorStandaloneMassSpectrum.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,92 @@ | ||
| /******************************************************************************* | ||
| * Copyright (c) 2008, 2022 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: | ||
| * Dr. Philip Wenig - initial API and implementation | ||
| *******************************************************************************/ | ||
| package org.eclipse.chemclipse.msd.model.implementation; | ||
|
|
||
| import org.eclipse.chemclipse.logging.core.Logger; | ||
| import org.eclipse.chemclipse.model.exceptions.AbundanceLimitExceededException; | ||
| import org.eclipse.chemclipse.msd.model.core.AbstractVendorStandaloneMassSpectrum; | ||
| import org.eclipse.chemclipse.msd.model.core.IIon; | ||
| import org.eclipse.chemclipse.msd.model.core.IScanIon; | ||
| import org.eclipse.chemclipse.msd.model.core.IVendorMassSpectrum; | ||
| import org.eclipse.chemclipse.msd.model.core.IVendorStandaloneMassSpectrum; | ||
| import org.eclipse.chemclipse.msd.model.exceptions.IonLimitExceededException; | ||
|
|
||
| public class VendorStandaloneMassSpectrum extends AbstractVendorStandaloneMassSpectrum implements IVendorStandaloneMassSpectrum { | ||
|
|
||
| /** | ||
| * Renew the serialVersionUID any time you have changed some fields or | ||
| * methods. | ||
| */ | ||
| private static final long serialVersionUID = 7540947309609765366L; | ||
| private static final Logger logger = Logger.getLogger(VendorStandaloneMassSpectrum.class); | ||
| public static final int MAX_IONS = Integer.MAX_VALUE; | ||
|
|
||
| @Override | ||
| public int getMaxPossibleIons() { | ||
|
|
||
| return MAX_IONS; | ||
| } | ||
|
|
||
| @Override | ||
| public int getMaxPossibleRetentionTime() { | ||
|
|
||
| return 0; // TODO: this should move away | ||
| } | ||
|
|
||
| @Override | ||
| public int getMinPossibleRetentionTime() { | ||
|
|
||
| return 0; // TODO: this should move away | ||
| } | ||
|
|
||
| /** | ||
| * Keep in mind, it is a covariant return.<br/> | ||
| * IMassSpectrum is needed. ISupplierMassSpectrum is a subtype of | ||
| * IMassSpectrum. | ||
| */ | ||
| @Override | ||
| public IVendorMassSpectrum makeDeepCopy() throws CloneNotSupportedException { | ||
|
|
||
| /* | ||
| * The method super.clone() is not used here to avoid removing the mass | ||
| * fragments from the mass spectrum and to add freshly created ones | ||
| * again. | ||
| */ | ||
| IVendorMassSpectrum massSpectrum = (IVendorMassSpectrum)super.clone(); | ||
| IScanIon defaultIon; | ||
| /* | ||
| * The instance variables have been copied by super.clone();.<br/> The | ||
| * ions in the ion list need not to be removed via | ||
| * removeAllIons as the method super.clone() has created a new | ||
| * list.<br/> It is necessary to fill the list again, as the abstract | ||
| * super class does not know each available type of ion.<br/> | ||
| * Make a deep copy of all ions. | ||
| */ | ||
| for(IIon ion : getIons()) { | ||
| try { | ||
| defaultIon = new ScanIon(ion.getIon(), ion.getAbundance()); | ||
| massSpectrum.addIon(defaultIon); | ||
| } catch(AbundanceLimitExceededException e) { | ||
| logger.warn(e); | ||
| } catch(IonLimitExceededException e) { | ||
| logger.warn(e); | ||
| } | ||
| } | ||
| return massSpectrum; | ||
| } | ||
|
|
||
| @Override | ||
| protected Object clone() throws CloneNotSupportedException { | ||
|
|
||
| return makeDeepCopy(); | ||
| } | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters