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Fixed mzML EncodedLength according to specification #844

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merged 2 commits into from
Dec 8, 2021
Merged

Fixed mzML EncodedLength according to specification #844

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90a774b
Save the base64 character instead of the compressed data length.
Mailaender Dec 8, 2021
734cbfd
Set the chromatogram count as it is a required parameter.
Mailaender Dec 8, 2021
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10 changes: 6 additions & 4 deletions ...c/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/converter/BinaryWriter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,8 @@
import java.nio.FloatBuffer;
import java.util.zip.Deflater;

import javax.xml.bind.DatatypeConverter;

import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.BinaryDataArrayType;
import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.CVParamType;
import org.eclipse.chemclipse.msd.converter.supplier.mzml.preferences.PreferenceSupplier;
Expand Down Expand Up @@ -69,16 +71,16 @@ private static BinaryDataArrayType createBinaryDataArray(ByteBuffer byteBuffer)
compresser.finish();
ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
byte[] readBuffer = new byte[1024];
int compressedDataLength = 0;
while(!compresser.finished()) {
int compressCount = compresser.deflate(readBuffer);
if(compressCount > 0) {
compressedDataLength += compressCount;
outputStream.write(readBuffer, 0, compressCount);
}
}
binaryDataArrayType.setEncodedLength(BigInteger.valueOf(compressedDataLength));
binaryDataArrayType.setBinary(outputStream.toByteArray());
byte[] outputByteArray = outputStream.toByteArray();
String characters = DatatypeConverter.printBase64Binary(outputByteArray);
binaryDataArrayType.setEncodedLength(BigInteger.valueOf(characters.length()));
binaryDataArrayType.setBinary(outputByteArray);
compresser.end();
} else {
binaryDataArrayType.setBinary(byteBuffer.array());
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2 changes: 2 additions & 0 deletions ...ipse/chemclipse/msd/converter/supplier/mzml/internal/io/ChromatogramWriterVersion110.java
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Expand Up @@ -14,6 +14,7 @@
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.math.BigInteger;
import java.util.Date;
import java.util.GregorianCalendar;
import java.util.List;
Expand Down Expand Up @@ -62,6 +63,7 @@ public void writeChromatogram(File file, IChromatogramMSD chromatogram, IProgres
RunType run = new RunType();
SpectrumListType spectrumList = new SpectrumListType();
ChromatogramListType chromatogramList = new ChromatogramListType();
chromatogramList.setCount(BigInteger.valueOf(1));
//
int scans = chromatogram.getNumberOfScans();
float[] totalSignals = new float[scans];
Expand Down