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60 changes: 60 additions & 0 deletions
60
...pse/chemclipse/msd/converter/supplier/mzxml/converter/ChromatogramMagicNumberMatcher.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,60 @@ | ||
| /******************************************************************************* | ||
| * Copyright (c) 2016, 2021 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 | ||
| * Matthias Mailänder - auto detection for chromatography files | ||
| *******************************************************************************/ | ||
| package org.eclipse.chemclipse.msd.converter.supplier.mzxml.converter; | ||
|
|
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| import java.io.File; | ||
|
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| import javax.xml.bind.JAXBContext; | ||
| import javax.xml.bind.Unmarshaller; | ||
| import javax.xml.parsers.DocumentBuilder; | ||
| import javax.xml.parsers.DocumentBuilderFactory; | ||
|
|
||
| import org.eclipse.chemclipse.converter.core.AbstractMagicNumberMatcher; | ||
| import org.eclipse.chemclipse.converter.core.IMagicNumberMatcher; | ||
| import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.io.IConstants; | ||
| import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.io.IFormat; | ||
| import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.io.SpecificationValidator; | ||
| import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v32.model.MsRun; | ||
| import org.w3c.dom.Document; | ||
| import org.w3c.dom.NodeList; | ||
|
|
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| public class ChromatogramMagicNumberMatcher extends AbstractMagicNumberMatcher implements IMagicNumberMatcher { | ||
|
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| @Override | ||
| public boolean checkFileFormat(File file) { | ||
|
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| boolean isValidFormat = false; | ||
| try { | ||
| file = SpecificationValidator.validateSpecification(file); | ||
| if(!file.exists()) { | ||
| return isValidFormat; | ||
| } | ||
| if(!checkFileExtension(file, ".mzXML")) { | ||
| return isValidFormat; | ||
| } | ||
| DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance(); | ||
| DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder(); | ||
| Document document = documentBuilder.parse(file); | ||
| NodeList nodeList = document.getElementsByTagName(IConstants.NODE_MS_RUN); | ||
| // | ||
| JAXBContext jaxbContext = JAXBContext.newInstance(IFormat.CONTEXT_PATH_V_320); | ||
| Unmarshaller unmarshaller = jaxbContext.createUnmarshaller(); | ||
| MsRun msRun = (MsRun)unmarshaller.unmarshal(nodeList.item(0)); | ||
| if(msRun.getScan().size() > 1) | ||
| isValidFormat = true; | ||
| } catch(Exception e) { | ||
| e.printStackTrace(); | ||
| } | ||
| return isValidFormat; | ||
| } | ||
| } |
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...src/org/eclipse/chemclipse/msd/converter/supplier/mzxml/converter/MagicNumberMatcher.java
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60 changes: 60 additions & 0 deletions
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...pse/chemclipse/msd/converter/supplier/mzxml/converter/MassSpectrumMagicNumberMatcher.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,60 @@ | ||
| /******************************************************************************* | ||
| * Copyright (c) 2016, 2021 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 | ||
| * Matthias Mailänder - auto detection for MALDI files | ||
| *******************************************************************************/ | ||
| package org.eclipse.chemclipse.msd.converter.supplier.mzxml.converter; | ||
|
|
||
| import java.io.File; | ||
|
|
||
| import javax.xml.bind.JAXBContext; | ||
| import javax.xml.bind.Unmarshaller; | ||
| import javax.xml.parsers.DocumentBuilder; | ||
| import javax.xml.parsers.DocumentBuilderFactory; | ||
|
|
||
| import org.eclipse.chemclipse.converter.core.AbstractMagicNumberMatcher; | ||
| import org.eclipse.chemclipse.converter.core.IMagicNumberMatcher; | ||
| import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.io.IConstants; | ||
| import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.io.IFormat; | ||
| import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.io.SpecificationValidator; | ||
| import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v32.model.MsRun; | ||
| import org.w3c.dom.Document; | ||
| import org.w3c.dom.NodeList; | ||
|
|
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| public class MassSpectrumMagicNumberMatcher extends AbstractMagicNumberMatcher implements IMagicNumberMatcher { | ||
|
|
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| @Override | ||
| public boolean checkFileFormat(File file) { | ||
|
|
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| boolean isValidFormat = false; | ||
| try { | ||
| file = SpecificationValidator.validateSpecification(file); | ||
| if(!file.exists()) { | ||
| return isValidFormat; | ||
| } | ||
| if(!checkFileExtension(file, ".mzXML")) { | ||
| return isValidFormat; | ||
| } | ||
| DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance(); | ||
| DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder(); | ||
| Document document = documentBuilder.parse(file); | ||
| NodeList nodeList = document.getElementsByTagName(IConstants.NODE_MS_RUN); | ||
| // | ||
| JAXBContext jaxbContext = JAXBContext.newInstance(IFormat.CONTEXT_PATH_V_320); | ||
| Unmarshaller unmarshaller = jaxbContext.createUnmarshaller(); | ||
| MsRun msRun = (MsRun)unmarshaller.unmarshal(nodeList.item(0)); | ||
| if(msRun.getScan().size() == 1) | ||
| isValidFormat = true; | ||
| } catch(Exception e) { | ||
| e.printStackTrace(); | ||
| } | ||
| return isValidFormat; | ||
| } | ||
| } |