Index (msdk-io-mzml 0.0.27 API)

A B C D E F G I L M N O P R S T V Z
All Classes All Packages

A

ACC_NUMPRESS_LINEAR - Static variable in class io.github.msdk.io.mzml.util.MSNumpress: Constant ACC_NUMPRESS_LINEAR="MS:1002312"
ACC_NUMPRESS_PIC - Static variable in class io.github.msdk.io.mzml.util.MSNumpress: Constant ACC_NUMPRESS_PIC="MS:1002313"
ACC_NUMPRESS_SLOF - Static variable in class io.github.msdk.io.mzml.util.MSNumpress: Constant ACC_NUMPRESS_SLOF="MS:1002314"
addCVParam(MzMLCVParam) - Method in class io.github.msdk.io.mzml.data.MzMLCVGroup: Adds a CV Parameter to the MzMLCVGroup
addPrecursor(MzMLPrecursorElement) - Method in class io.github.msdk.io.mzml.data.MzMLPrecursorList: addPrecursor.
addProduct(MzMLProduct) - Method in class io.github.msdk.io.mzml.data.MzMLProductList: addProduct.
addScan(MzMLScan) - Method in class io.github.msdk.io.mzml.data.MzMLScanList: addScan.
addScanWindow(MzMLScanWindow) - Method in class io.github.msdk.io.mzml.data.MzMLScanWindowList: addScanWindow.
addSelectedIon(MzMLPrecursorSelectedIon) - Method in class io.github.msdk.io.mzml.data.MzMLPrecursorSelectedIonList: addSelectedIon.
ATTR_ACCESSION - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant ATTR_ACCESSION="accession"
ATTR_COUNT - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant ATTR_COUNT="count"
ATTR_CV_REF - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant ATTR_CV_REF="cvRef"
ATTR_DEFAULT_ARRAY_LENGTH - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant ATTR_DEFAULT_ARRAY_LENGTH="defaultArrayLength"
ATTR_DEFAULT_DATA_PROCESSING_REF - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant ATTR_DEFAULT_INSTRUMENT_CONFIGURATION_REF="defaultInstrumentConfigurationRef"
ATTR_DEFAULT_INSTRUMENT_CONFIGURATION_REF - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant ATTR_DEFAULT_INSTRUMENT_CONFIGURATION_REF="defaultInstrumentConfigurationRef"
ATTR_ENCODED_LENGTH - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant ATTR_ENCODED_LENGTH="encodedLength"
ATTR_ID - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant ATTR_ID="id"
ATTR_ID_REF - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant ATTR_ID_REF="idRef"
ATTR_INDEX - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant ATTR_INDEX="index"
ATTR_NAME - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant ATTR_NAME="name"
ATTR_ORDER - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant ATTR_ORDER="order"
ATTR_SCHEME_LOCATION - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant ATTR_SCHEME_LOCATION="schemeLocation"
ATTR_SOFTWARE_REF - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant ATTR_SOFTWARE_REF="softwareRef"
ATTR_SPECTRUM_REF - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant ATTR_SPECTRUM_REF="spectrumRef"
ATTR_UNIT_ACCESSION - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant ATTR_UNIT_ACCESSION="unitAccession"
ATTR_VALUE - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant ATTR_VALUE="value"
ATTR_VERSION - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant ATTR_VERSION="version"
ATTR_XSI - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant ATTR_XSI="xsi"
available() - Method in class io.github.msdk.io.mzml.util.ByteBufferInputStream: available.

B

ByteBufferInputStream - Class in io.github.msdk.io.mzml.util: A bridge between byte buffers and input streams.
ByteBufferInputStream(ByteBuffer) - Constructor for class io.github.msdk.io.mzml.util.ByteBufferInputStream: Creates a new byte-buffer input stream from a single ByteBuffer.
ByteBufferInputStream(ByteBuffer[], long, int, boolean[]) - Constructor for class io.github.msdk.io.mzml.util.ByteBufferInputStream: Creates a new byte-buffer input stream.

C

cancel() - Method in class io.github.msdk.io.mzml.MzMLFileExportMethod
cancel() - Method in class io.github.msdk.io.mzml.MzMLFileImportMethod
centroidCvParam - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant centroidCvParam
CHUNK_SIZE - Static variable in class io.github.msdk.io.mzml.util.ByteBufferInputStream: The size of a chunk created by ByteBufferInputStream.map(FileChannel, FileChannel.MapMode).
constrain(long, long) - Method in class io.github.msdk.io.mzml.util.ByteBufferInputStream: constrain.
copy() - Method in class io.github.msdk.io.mzml.util.ByteBufferInputStream: copy.
current() - Method in class io.github.msdk.io.mzml.util.TagTracker: current.
cvActivationCID - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvActivationCID="MS:1000133"
cvActivationEnergy - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvActivationEnergy="MS:1000045"
cvCentroidSpectrum - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvCentroidSpectrum="MS:1000127"
cvChargeState - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvChargeState="MS:1000041"
cvChromatogramBPC - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvChromatogramBPC="MS:1000628"
cvChromatogramMRM_SRM - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvChromatogramMRM_SRM="MS:1001473"
cvChromatogramSIC - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvChromatogramSIC="MS:1000627"
cvChromatogramTIC - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvChromatogramTIC="MS:1000235"
cvHighestMz - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvHighestMz="MS:1000527"
cvIntensityArray - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvIntensityArray="MS:1000515"
cvIsolationWindowLowerOffset - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvIsolationWindowLowerOffset="MS:1000828"
cvIsolationWindowTarget - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvIsolationWindowTarget="MS:1000827"
cvIsolationWindowUpperOffset - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvIsolationWindowUpperOffset="MS:1000829"
cvLowestMz - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvLowestMz="MS:1000528"
cvMS1Spectrum - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvMS1Spectrum="MS:1000579"
cvMSLevel - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvMSLevel="MS:1000511"
cvMz - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvMz="MS:1000040"
cvMzArray - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvMzArray="MS:1000514"
cvPolarityNegative - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvPolarityNegative="MS:1000129"
cvPolarityPositive - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvPolarityPositive="MS:1000130"
cvPrecursorMz - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvPrecursorMz="MS:1000744"
cvProfileSpectrum - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvProfileSpectrum="MS:1000128"
cvRetentionTimeArray - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvRetentionTimeArray="MS:1000595"
cvScanFilterString - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvScanFilterString="MS:1000512"
cvScanWindowLowerLimit - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvScanWindowLowerLimit="MS:1000501"
cvScanWindowUpperLimit - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvScanWindowUpperLimit="MS:1000500"
cvTIC - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvTIC="MS:1000285"
cvUnitsIntensity1 - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvUnitsIntensity1="MS:1000131"
cvUnitsMin1 - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvUnitsMin1="MS:1000038"
cvUnitsMin2 - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvUnitsMin2="UO:0000031"
cvUnitsSec - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvUnitsSec="UO:0000010"
cvUVSpectrum - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant cvUVSpectrum="MS:1000804"

D

decode(String, byte[], int) - Static method in class io.github.msdk.io.mzml.util.MSNumpress: Convenience function for decoding binary data encoded by MSNumpress.
decodeFixedPoint(byte[]) - Static method in class io.github.msdk.io.mzml.util.MSNumpress: decodeFixedPoint.
decodeLinear(byte[], int, double[]) - Static method in class io.github.msdk.io.mzml.util.MSNumpress: Decodes data encoded by encodeLinear.
decodeLinear(byte[], int, float[]) - Static method in class io.github.msdk.io.mzml.util.MSNumpress: Decodes data encoded by encodeLinear.
decodePic(byte[], int, double[]) - Static method in class io.github.msdk.io.mzml.util.MSNumpress: Decodes data encoded by encodePic
decodePic(byte[], int, float[]) - Static method in class io.github.msdk.io.mzml.util.MSNumpress: Decodes data encoded by encodePic
decodeSlof(byte[], int, double[]) - Static method in class io.github.msdk.io.mzml.util.MSNumpress: Decodes data encoded by encodeSlof
decodeSlof(byte[], int, float[]) - Static method in class io.github.msdk.io.mzml.util.MSNumpress: Decodes data encoded by encodeSlof
decodeToDouble(InputStream, MzMLBinaryDataInfo, double[]) - Static method in class io.github.msdk.io.mzml.data.MzMLPeaksDecoder: Converts a base64 encoded mz or intensity string used in mzML files to an array of doubles.
decodeToFloat(InputStream, MzMLBinaryDataInfo, float[]) - Static method in class io.github.msdk.io.mzml.data.MzMLPeaksDecoder: Converts a base64 encoded mz or intensity string used in mzML files to an array of floats.
DEFAULT_CHAR_ARR_SIZE - Static variable in class io.github.msdk.io.mzml.util.TagTracker: Constant DEFAULT_CHAR_ARR_SIZE=64
DEFAULT_MAX_DEPTH - Static variable in class io.github.msdk.io.mzml.util.TagTracker: Constant DEFAULT_MAX_DEPTH=128
dispose() - Method in class io.github.msdk.io.mzml.data.MzMLRawDataFile

E

encodeDouble(double[], MzMLCompressionType) - Static method in class io.github.msdk.io.mzml.data.MzMLPeaksEncoder: encodeDouble.
encodeFixedPoint(double, byte[]) - Static method in class io.github.msdk.io.mzml.util.MSNumpress: encodeFixedPoint.
encodeFloat(float[], MzMLCompressionType) - Static method in class io.github.msdk.io.mzml.data.MzMLPeaksEncoder: encodeFloat.
encodeInt(long, byte[], int) - Static method in class io.github.msdk.io.mzml.util.MSNumpress: This encoding works on a 4 byte integer, by truncating initial zeros or ones.
encodeLinear(double[], int, byte[], double) - Static method in class io.github.msdk.io.mzml.util.MSNumpress: Encodes the doubles in data by first using a - lossy conversion to a 4 byte 5 decimal fixed point repressentation - storing the residuals from a linear prediction after first to values - encoding by encodeInt (see above)
encodePic(double[], int, byte[]) - Static method in class io.github.msdk.io.mzml.util.MSNumpress: Encodes ion counts by simply rounding to the nearest 4 byte integer, and compressing each integer with encodeInt.
encodeSlof(double[], int, byte[], double) - Static method in class io.github.msdk.io.mzml.util.MSNumpress: Encodes ion counts by taking the natural logarithm, and storing a fixed point representation of this.
enter(CharArray) - Method in class io.github.msdk.io.mzml.util.TagTracker: enter.
execute() - Method in class io.github.msdk.io.mzml.MzMLFileExportMethod
execute() - Method in class io.github.msdk.io.mzml.MzMLFileImportMethod
exit(CharArray) - Method in class io.github.msdk.io.mzml.util.TagTracker: exit.

F

FileMemoryMapper - Class in io.github.msdk.io.mzml.util: Used to load a File onto a ByteBufferInputStream
FileMemoryMapper() - Constructor for class io.github.msdk.io.mzml.util.FileMemoryMapper

G

getAccession() - Method in enum io.github.msdk.io.mzml.data.MzMLArrayType: Getter for the field accession.
getAccession() - Method in enum io.github.msdk.io.mzml.data.MzMLCompressionType: Getter for the field accession.
getAccession() - Method in class io.github.msdk.io.mzml.data.MzMLCVParam: Getter for the field accession.
getActivation() - Method in class io.github.msdk.io.mzml.data.MzMLPrecursorElement: Getter for the field activation.
getArrayLength() - Method in class io.github.msdk.io.mzml.data.MzMLBinaryDataInfo: Getter for the field arrayLength.
getArrayType() - Method in class io.github.msdk.io.mzml.data.MzMLBinaryDataInfo: Getter for the field arrayType.
getArrayType(String) - Method in class io.github.msdk.io.mzml.data.MzMLBinaryDataInfo: Gets the binary data array type for the given accession
getBitLength() - Method in class io.github.msdk.io.mzml.data.MzMLBinaryDataInfo: Getter for the field bitLength.
getBitLength(String) - Method in class io.github.msdk.io.mzml.data.MzMLBinaryDataInfo: Gets the bit length for the given accession
getChromatogramPredicate() - Method in class io.github.msdk.io.mzml.MzMLFileImportMethod: Getter for the field chromatogramPredicate.
getChromatograms() - Method in class io.github.msdk.io.mzml.data.MzMLRawDataFile
getCompressionType() - Method in class io.github.msdk.io.mzml.data.MzMLBinaryDataInfo: Getter for the field compressionType.
getCompressionType(String) - Method in class io.github.msdk.io.mzml.data.MzMLBinaryDataInfo: Gets the compression type for the given accession
getCVParams() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan: getCVParams.
getCVParamsList() - Method in class io.github.msdk.io.mzml.data.MzMLCVGroup: getCVParamsList.
getCVValue(MzMLCVGroup, String) - Method in class io.github.msdk.io.mzml.data.MzMLMsScan: Search for the CV Parameter value for the given accession in the given MzMLCVGroup
getCVValue(String) - Method in class io.github.msdk.io.mzml.data.MzMLMsScan: Search for the CV Parameter value for the given accession in the MsScan's CV Parameters
getDefaultDataProcessingChromatogram() - Method in class io.github.msdk.io.mzml.data.MzMLRawDataFile
getDefaultDataProcessingScan() - Method in class io.github.msdk.io.mzml.data.MzMLRawDataFile
getDefaultInstrumentConfiguration() - Method in class io.github.msdk.io.mzml.data.MzMLRawDataFile
getEncodedLength() - Method in class io.github.msdk.io.mzml.data.MzMLBinaryDataInfo: Getter for the field encodedLength.
getFinishedPercentage() - Method in class io.github.msdk.io.mzml.MzMLFileExportMethod
getFinishedPercentage() - Method in class io.github.msdk.io.mzml.MzMLFileImportMethod
getId() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan: Getter for the field id.
getInputStream() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan: getInputStream.
getIntensityBinaryDataInfo() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan: Getter for the field intensityBinaryDataInfo.
getIntensityValues(float[]) - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
getIsolations() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
getIsolationWindow() - Method in class io.github.msdk.io.mzml.data.MzMLPrecursorElement: Getter for the field isolationWindow.
getIsolationWindow() - Method in class io.github.msdk.io.mzml.data.MzMLProduct: Getter for the field isolationWindow.
getMsFunction() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
getMsFunctions() - Method in class io.github.msdk.io.mzml.data.MzMLRawDataFile
getMsLevel() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
getMsScanPredicate() - Method in class io.github.msdk.io.mzml.MzMLFileImportMethod: Getter for the field msScanPredicate.
getMsScanType() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
getMzBinaryDataInfo() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan: Getter for the field mzBinaryDataInfo.
getMzMLFile() - Method in class io.github.msdk.io.mzml.MzMLFileImportMethod: Getter for the field mzMLFile.
getMzMLRawFile() - Method in class io.github.msdk.io.mzml.data.MzMLParser: getMzMLRawFile.
getMzRange() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
getMzTolerance() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
getMzValues(double[]) - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
getName() - Method in enum io.github.msdk.io.mzml.data.MzMLCompressionType: Getter for the field name.
getName() - Method in class io.github.msdk.io.mzml.data.MzMLCVParam: Getter for the field name.
getName() - Method in class io.github.msdk.io.mzml.data.MzMLRawDataFile
getNumberOfDataPoints() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
getOriginalFile() - Method in class io.github.msdk.io.mzml.data.MzMLRawDataFile
getParamGroupName() - Method in class io.github.msdk.io.mzml.data.MzMLReferenceableParamGroup: Getter for the field paramGroupName.
getPolarity() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
getPosition() - Method in class io.github.msdk.io.mzml.data.MzMLBinaryDataInfo: Getter for the field position.
getPrecursorElements() - Method in class io.github.msdk.io.mzml.data.MzMLPrecursorList: Getter for the field precursorElements.
getPrecursorList() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan: getPrecursorList.
getProductList() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan: getProductList.
getProducts() - Method in class io.github.msdk.io.mzml.data.MzMLProductList: Getter for the field products.
getRawDataFile() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
getRawDataFileType() - Method in class io.github.msdk.io.mzml.data.MzMLRawDataFile
getRequiredAttribute(XMLStreamReader, String) - Method in class io.github.msdk.io.mzml.data.MzMLParser: Gets the required attribute from xmlStreamReader, throws an exception if the attribute is not found
getResult() - Method in class io.github.msdk.io.mzml.MzMLFileExportMethod
getResult() - Method in class io.github.msdk.io.mzml.MzMLFileImportMethod
getRetentionTime() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
getScanDefinition() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
getScanList() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan: getScanList.
getScanningRange() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
getScanNumber() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
getScanNumber(String) - Method in class io.github.msdk.io.mzml.data.MzMLMsScan: getScanNumber.
getScanNumber(String) - Method in class io.github.msdk.io.mzml.data.MzMLParser: getScanNumber.
getScans() - Method in class io.github.msdk.io.mzml.data.MzMLRawDataFile
getScans() - Method in class io.github.msdk.io.mzml.data.MzMLScanList: Getter for the field scans.
getScanWindowList() - Method in class io.github.msdk.io.mzml.data.MzMLScan: Getter for the field scanWindowList.
getScanWindows() - Method in class io.github.msdk.io.mzml.data.MzMLScanWindowList: Getter for the field scanWindows.
getSelectedIonList() - Method in class io.github.msdk.io.mzml.data.MzMLPrecursorElement: Getter for the field selectedIonList.
getSelectedIonList() - Method in class io.github.msdk.io.mzml.data.MzMLPrecursorSelectedIonList: Getter for the field selectedIonList.
getSourceInducedFragmentation() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
getSpectrumRef() - Method in class io.github.msdk.io.mzml.data.MzMLPrecursorElement: Getter for the field spectrumRef.
getSpectrumType() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
getTIC() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
getUnitAccession() - Method in class io.github.msdk.io.mzml.data.MzMLCVParam: Getter for the field unitAccession.
getValue() - Method in enum io.github.msdk.io.mzml.data.MzMLBitLength: getValue.
getValue() - Method in class io.github.msdk.io.mzml.data.MzMLCVParam: Getter for the field value.

I

inside(CharSequence) - Method in class io.github.msdk.io.mzml.util.TagTracker: inside.
INTENSITY - io.github.msdk.io.mzml.data.MzMLArrayType
io.github.msdk.io.mzml - package io.github.msdk.io.mzml
io.github.msdk.io.mzml.data - package io.github.msdk.io.mzml.data
io.github.msdk.io.mzml.util - package io.github.msdk.io.mzml.util
isArrayTypeAccession(String) - Method in class io.github.msdk.io.mzml.data.MzMLBinaryDataInfo: Check if the given CV Parameter accession is that of a binary data array type
isBitLengthAccession(String) - Method in class io.github.msdk.io.mzml.data.MzMLBinaryDataInfo: Check if the given CV Parameter accession is that of bit length
isCompressionTypeAccession(String) - Method in class io.github.msdk.io.mzml.data.MzMLBinaryDataInfo: Check if the given CV Parameter accession is that of a compression method

L

length() - Method in class io.github.msdk.io.mzml.util.ByteBufferInputStream: length.

M

manageCompression(MzMLBinaryDataInfo, String) - Method in class io.github.msdk.io.mzml.data.MzMLParser: manageCompression.
map(FileChannel, FileChannel.MapMode) - Static method in class io.github.msdk.io.mzml.util.ByteBufferInputStream: Creates a new byte-buffer input stream by mapping a given file channel.
mapToMemory(File) - Static method in class io.github.msdk.io.mzml.util.FileMemoryMapper: Used to load a File onto a ByteBufferInputStream *
mark(int) - Method in class io.github.msdk.io.mzml.util.ByteBufferInputStream
markSupported() - Method in class io.github.msdk.io.mzml.util.ByteBufferInputStream
MS_RT_RETENTION_TIME - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant MS_RT_RETENTION_TIME="MS:1000894"
MS_RT_RETENTION_TIME_LOCAL - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant MS_RT_RETENTION_TIME_LOCAL="MS:1000895"
MS_RT_RETENTION_TIME_NORMALIZED - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant MS_RT_RETENTION_TIME_NORMALIZED="MS:1000896"
MS_RT_SCAN_START - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant MS_RT_SCAN_START="MS:1000016"
MSNumpress - Class in io.github.msdk.io.mzml.util: MSNumpressDouble class.
MSNumpress() - Constructor for class io.github.msdk.io.mzml.util.MSNumpress
MZ - io.github.msdk.io.mzml.data.MzMLArrayType
MzMLArrayType - Enum in io.github.msdk.io.mzml.data: Enumeration of different types of arrays which are parsed by the MzML Parser
MzMLBinaryDataInfo - Class in io.github.msdk.io.mzml.data: MzMLBinaryDataInfo class.
MzMLBinaryDataInfo(int, int) - Constructor for class io.github.msdk.io.mzml.data.MzMLBinaryDataInfo: Constructor for MzMLBinaryDataInfo
MzMLBitLength - Enum in io.github.msdk.io.mzml.data: Enumeration of different types of precision bit lengths which are parsed by the MzML Parser
MzMLCompressionType - Enum in io.github.msdk.io.mzml.data: Enumeration of different compression types which are parsed by the MzML Parser
MzMLCV - Class in io.github.msdk.io.mzml.data: Controlled vocabulary (CV) values for mzML files.
MzMLCV() - Constructor for class io.github.msdk.io.mzml.data.MzMLCV
MzMLCVGroup - Class in io.github.msdk.io.mzml.data: A group (or list) of CV Parameters
MzMLCVGroup() - Constructor for class io.github.msdk.io.mzml.data.MzMLCVGroup: Constructor for MzMLCVGroup.
MzMLCVParam - Class in io.github.msdk.io.mzml.data: A CV Parameter object which contains the CV Parameter's accession and value, name & unitAccession if available
MzMLCVParam(String, String, String, String) - Constructor for class io.github.msdk.io.mzml.data.MzMLCVParam: Constructor for MzMLCVParam
MzMLFileExportMethod - Class in io.github.msdk.io.mzml: This class contains methods which can be used to write data contained in a RawDataFile to a file, in mzML format
MzMLFileExportMethod(RawDataFile, File, MzMLCompressionType, MzMLCompressionType) - Constructor for class io.github.msdk.io.mzml.MzMLFileExportMethod: Constructor for MzMLFileExportMethod.
MzMLFileImportMethod - Class in io.github.msdk.io.mzml: This class contains methods which parse data in MzML format from File, Path or InputStream
Scans and Chromatograms will be parsed, and the values pre-loaded when the Predicate is passed.
MzMLFileImportMethod(File) - Constructor for class io.github.msdk.io.mzml.MzMLFileImportMethod: Constructor for MzMLFileImportMethod.
MzMLFileImportMethod(File, Predicate<MsScan>, Predicate<Chromatogram>) - Constructor for class io.github.msdk.io.mzml.MzMLFileImportMethod: Constructor for MzMLFileImportMethod.
MzMLFileImportMethod(InputStream) - Constructor for class io.github.msdk.io.mzml.MzMLFileImportMethod: Constructor for MzMLFileImportMethod.
MzMLFileImportMethod(InputStream, Predicate<MsScan>, Predicate<Chromatogram>) - Constructor for class io.github.msdk.io.mzml.MzMLFileImportMethod: Constructor for MzMLFileImportMethod.
MzMLFileImportMethod(String) - Constructor for class io.github.msdk.io.mzml.MzMLFileImportMethod: Constructor for MzMLFileImportMethod.
MzMLFileImportMethod(String, Predicate<MsScan>, Predicate<Chromatogram>) - Constructor for class io.github.msdk.io.mzml.MzMLFileImportMethod: Constructor for MzMLFileImportMethod.
MzMLFileImportMethod(Path) - Constructor for class io.github.msdk.io.mzml.MzMLFileImportMethod: Constructor for MzMLFileImportMethod.
MzMLFileImportMethod(Path, Predicate<MsScan>, Predicate<Chromatogram>) - Constructor for class io.github.msdk.io.mzml.MzMLFileImportMethod: Constructor for MzMLFileImportMethod.
MzMLIsolationWindow - Class in io.github.msdk.io.mzml.data: MzMLIsolationWindow class.
MzMLIsolationWindow() - Constructor for class io.github.msdk.io.mzml.data.MzMLIsolationWindow
MzMLMsScan - Class in io.github.msdk.io.mzml.data: MzMLMsScan class.
MzMLMsScan(MzMLRawDataFile, InputStream, String, Integer, int) - Constructor for class io.github.msdk.io.mzml.data.MzMLMsScan: Constructor for MzMLMsScan
MzMLParser - Class in io.github.msdk.io.mzml.data: Used to parse mzML meta-data and initialize MzMLBinaryDataInfo
MzMLParser(MzMLFileImportMethod) - Constructor for class io.github.msdk.io.mzml.data.MzMLParser: Constructor for MzMLParser
MzMLPeaksDecoder - Class in io.github.msdk.io.mzml.data: MzMLIntensityPeaksDecoder class.
MzMLPeaksDecoder() - Constructor for class io.github.msdk.io.mzml.data.MzMLPeaksDecoder
MzMLPeaksEncoder - Class in io.github.msdk.io.mzml.data: Abstract MzMLPeaksEncoder class.
MzMLPeaksEncoder() - Constructor for class io.github.msdk.io.mzml.data.MzMLPeaksEncoder
MzMLPrecursorActivation - Class in io.github.msdk.io.mzml.data: MzMLPrecursorActivation class.
MzMLPrecursorActivation() - Constructor for class io.github.msdk.io.mzml.data.MzMLPrecursorActivation
MzMLPrecursorElement - Class in io.github.msdk.io.mzml.data: MzMLPrecursorElement class.
MzMLPrecursorElement(String) - Constructor for class io.github.msdk.io.mzml.data.MzMLPrecursorElement: Constructor for MzMLPrecursorElement.
MzMLPrecursorList - Class in io.github.msdk.io.mzml.data: MzMLPrecursorList class.
MzMLPrecursorList() - Constructor for class io.github.msdk.io.mzml.data.MzMLPrecursorList: Constructor for MzMLPrecursorList.
MzMLPrecursorSelectedIon - Class in io.github.msdk.io.mzml.data: MzMLPrecursorSelectedIon class.
MzMLPrecursorSelectedIon() - Constructor for class io.github.msdk.io.mzml.data.MzMLPrecursorSelectedIon
MzMLPrecursorSelectedIonList - Class in io.github.msdk.io.mzml.data: MzMLPrecursorSelectedIonList class.
MzMLPrecursorSelectedIonList() - Constructor for class io.github.msdk.io.mzml.data.MzMLPrecursorSelectedIonList: Constructor for MzMLPrecursorSelectedIonList.
MzMLProduct - Class in io.github.msdk.io.mzml.data: MzMLProduct class.
MzMLProduct() - Constructor for class io.github.msdk.io.mzml.data.MzMLProduct: Constructor for MzMLProduct.
MzMLProductList - Class in io.github.msdk.io.mzml.data: MzMLProductList class.
MzMLProductList() - Constructor for class io.github.msdk.io.mzml.data.MzMLProductList: Constructor for MzMLProductList.
MzMLRawDataFile - Class in io.github.msdk.io.mzml.data: MzMLRawDataFile class.
MzMLRawDataFile(File, List<String>, List<MsScan>, List<Chromatogram>) - Constructor for class io.github.msdk.io.mzml.data.MzMLRawDataFile: Constructor for MzMLRawDataFile.
MzMLReferenceableParamGroup - Class in io.github.msdk.io.mzml.data: MzMLReferenceableParamGroup class.
MzMLReferenceableParamGroup(String) - Constructor for class io.github.msdk.io.mzml.data.MzMLReferenceableParamGroup: Constructor for MzMLReferenceableParamGroup.
MzMLScan - Class in io.github.msdk.io.mzml.data: MzMLScan class.
MzMLScan() - Constructor for class io.github.msdk.io.mzml.data.MzMLScan: Constructor for MzMLScan.
MzMLScanList - Class in io.github.msdk.io.mzml.data: MzMLScanList class.
MzMLScanList() - Constructor for class io.github.msdk.io.mzml.data.MzMLScanList: Constructor for MzMLScanList.
MzMLScanWindow - Class in io.github.msdk.io.mzml.data: MzMLScanWindow class.
MzMLScanWindow() - Constructor for class io.github.msdk.io.mzml.data.MzMLScanWindow
MzMLScanWindowList - Class in io.github.msdk.io.mzml.data: MzMLScanWindowList class.
MzMLScanWindowList() - Constructor for class io.github.msdk.io.mzml.data.MzMLScanWindowList: Constructor for MzMLScanWindowList.
MzMLTags - Class in io.github.msdk.io.mzml.data: Class containing String constants of various XML tags and attributes found in the mzML format
MzMLTags() - Constructor for class io.github.msdk.io.mzml.data.MzMLTags

N

NO_COMPRESSION - io.github.msdk.io.mzml.data.MzMLCompressionType
NUMPRESS_LINPRED - io.github.msdk.io.mzml.data.MzMLCompressionType
NUMPRESS_LINPRED_ZLIB - io.github.msdk.io.mzml.data.MzMLCompressionType
NUMPRESS_POSINT - io.github.msdk.io.mzml.data.MzMLCompressionType
NUMPRESS_POSINT_ZLIB - io.github.msdk.io.mzml.data.MzMLCompressionType
NUMPRESS_SHLOGF - io.github.msdk.io.mzml.data.MzMLCompressionType
NUMPRESS_SHLOGF_ZLIB - io.github.msdk.io.mzml.data.MzMLCompressionType

O

optimalLinearFixedPoint(double[], int) - Static method in class io.github.msdk.io.mzml.util.MSNumpress: optimalLinearFixedPoint.
optimalSlofFixedPoint(double[], int) - Static method in class io.github.msdk.io.mzml.util.MSNumpress: optimalSlofFixedPoint.

P

polarityNegativeCvParam - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant polarityNegativeCvParam
polarityPositiveCvParam - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant polarityPositiveCvParam
position() - Method in class io.github.msdk.io.mzml.util.ByteBufferInputStream: position.
position(long) - Method in class io.github.msdk.io.mzml.util.ByteBufferInputStream: position.
processCharacters(XMLStreamReaderImpl) - Method in class io.github.msdk.io.mzml.data.MzMLParser: Carry out the required parsing of the mzML data when the XMLStreamReaderImpl when CHARACTERS are found
processClosingTag(XMLStreamReaderImpl, CharArray) - Method in class io.github.msdk.io.mzml.data.MzMLParser: Carry out the required parsing of the mzML data when the XMLStreamReaderImpl exits the given tag
processOpeningTag(XMLStreamReaderImpl, InputStream, CharArray) - Method in class io.github.msdk.io.mzml.data.MzMLParser: Carry out the required parsing of the mzML data when the XMLStreamReaderImpl enters the given tag
profileCvParam - Static variable in class io.github.msdk.io.mzml.data.MzMLCV: Constant profileCvParam

R

read() - Method in class io.github.msdk.io.mzml.util.ByteBufferInputStream
read(byte[], int, int) - Method in class io.github.msdk.io.mzml.util.ByteBufferInputStream
reset() - Method in class io.github.msdk.io.mzml.util.ByteBufferInputStream

S

setActivation(MzMLPrecursorActivation) - Method in class io.github.msdk.io.mzml.data.MzMLPrecursorElement: Setter for the field activation.
setArrayType(MzMLArrayType) - Method in class io.github.msdk.io.mzml.data.MzMLBinaryDataInfo: Sets the bit length of the binary data array
setArrayType(String) - Method in class io.github.msdk.io.mzml.data.MzMLBinaryDataInfo: Sets the array type of the binary data array
setBitLength(MzMLBitLength) - Method in class io.github.msdk.io.mzml.data.MzMLBinaryDataInfo: Sets the precision bit length of the binary data array
setBitLength(String) - Method in class io.github.msdk.io.mzml.data.MzMLBinaryDataInfo: Sets the precision bit length of the binary data array
setCompressionType(MzMLCompressionType) - Method in class io.github.msdk.io.mzml.data.MzMLBinaryDataInfo: Sets the compression type of the binary data array
setCompressionType(String) - Method in class io.github.msdk.io.mzml.data.MzMLBinaryDataInfo: Sets the compression type of the binary data array
setDefaultDataProcessingChromatogram(String) - Method in class io.github.msdk.io.mzml.data.MzMLRawDataFile
setDefaultDataProcessingScan(String) - Method in class io.github.msdk.io.mzml.data.MzMLRawDataFile
setDefaultInstrumentConfiguration(String) - Method in class io.github.msdk.io.mzml.data.MzMLRawDataFile
setInputStream(InputStream) - Method in class io.github.msdk.io.mzml.data.MzMLMsScan: setInputStream.
setIntensityBinaryDataInfo(MzMLBinaryDataInfo) - Method in class io.github.msdk.io.mzml.data.MzMLMsScan: Setter for the field intensityBinaryDataInfo.
setIsolationWindow(MzMLIsolationWindow) - Method in class io.github.msdk.io.mzml.data.MzMLPrecursorElement: Setter for the field isolationWindow.
setIsolationWindow(MzMLIsolationWindow) - Method in class io.github.msdk.io.mzml.data.MzMLProduct: Setter for the field isolationWindow.
setMzBinaryDataInfo(MzMLBinaryDataInfo) - Method in class io.github.msdk.io.mzml.data.MzMLMsScan: Setter for the field mzBinaryDataInfo.
setParamGroupName(String) - Method in class io.github.msdk.io.mzml.data.MzMLReferenceableParamGroup: Setter for the field paramGroupName.
setPosition(long) - Method in class io.github.msdk.io.mzml.data.MzMLBinaryDataInfo: Set the position of the binary array in the InputStream corresponding to the MzML format data
setScanWindowList(MzMLScanWindowList) - Method in class io.github.msdk.io.mzml.data.MzMLScan: Setter for the field scanWindowList.
setSelectedIonList(MzMLPrecursorSelectedIonList) - Method in class io.github.msdk.io.mzml.data.MzMLPrecursorElement: Setter for the field selectedIonList.
SIXTEEN_BIT_FLOAT - io.github.msdk.io.mzml.data.MzMLBitLength
SIXTY_FOUR_BIT_FLOAT - io.github.msdk.io.mzml.data.MzMLBitLength
SIXTY_FOUR_BIT_INTEGER - io.github.msdk.io.mzml.data.MzMLBitLength
skip(long) - Method in class io.github.msdk.io.mzml.util.ByteBufferInputStream

T

TAG_ACTIVATION - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_ACTIVATION="activation"
TAG_BINARY - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_BINARY="binary"
TAG_BINARY_DATA_ARRAY - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_BINARY_DATA_ARRAY="binaryDataArray"
TAG_BINARY_DATA_ARRAY_LIST - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_BINARY_DATA_ARRAY_LIST="binaryDataArrayList"
TAG_CHROMATOGRAM - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_CHROMATOGRAM="chromatogram"
TAG_CHROMATOGRAM_LIST - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_CHROMATOGRAM_LIST="chromatogramList"
TAG_CV_LIST - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_CV_LIST="cvList"
TAG_CV_PARAM - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_CV_PARAM="cvParam"
TAG_DATA_PROCESSING - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_DATA_PROCESSING="dataProcessing"
TAG_DATA_PROCESSING_LIST - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_DATA_PROCESSING_LIST="dataProcessingList"
TAG_FILE_CHECKSUM - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_FILE_CHECKSUM="fileChecksum"
TAG_INDEX - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_INDEX="index"
TAG_INDEX_LIST - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_INDEX_LIST="indexList"
TAG_INDEX_LIST_OFFSET - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_INDEX_LIST_OFFSET="indexListOffset"
TAG_INDEXED_MZML - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_INDEXED_MZML="indexedmzML"
TAG_ISOLATION_WINDOW - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_ISOLATION_WINDOW="isolationWindow"
TAG_MZML - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_MZML="mzML"
TAG_OFFSET - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_OFFSET="offset"
TAG_PRECURSOR - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_PRECURSOR="precursor"
TAG_PRECURSOR_LIST - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_PRECURSOR_LIST="precursorList"
TAG_PROCESSING_METHOD - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_PROCESSING_METHOD="processingMethod"
TAG_PRODUCT - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_PRODUCT="product"
TAG_PRODUCT_LIST - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_PRODUCT_LIST="productList"
TAG_REF_PARAM_GROUP - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_REF_PARAM_GROUP="referenceableParamGroup"
TAG_REF_PARAM_GROUP_LIST - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_REF_PARAM_GROUP_LIST="referenceableParamGroupList"
TAG_REF_PARAM_GROUP_REF - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_REF_PARAM_GROUP_REF="referenceableParamGroupRef"
TAG_RUN - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_RUN="run"
TAG_SCAN - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_SCAN="scan"
TAG_SCAN_LIST - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_SCAN_LIST="scanList"
TAG_SCAN_WINDOW - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_SCAN_WINDOW="scanWindow"
TAG_SCAN_WINDOW_LIST - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_SCAN_WINDOW_LIST="scanWindowList"
TAG_SELECTED_ION - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_SELECTED_ION="selectedIon"
TAG_SELECTED_ION_LIST - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_SELECTED_ION_LIST="selectedIonList"
TAG_SPECTRUM - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_SPECTRUM="spectrum"
TAG_SPECTRUM_LIST - Static variable in class io.github.msdk.io.mzml.data.MzMLTags: Constant TAG_SPECTRUM_LIST="spectrumList"
TagTracker - Class in io.github.msdk.io.mzml.util: This class is not thread safe.
TagTracker() - Constructor for class io.github.msdk.io.mzml.util.TagTracker: Creates a tracker with default max depth TagTracker.DEFAULT_MAX_DEPTH.
TagTracker(int) - Constructor for class io.github.msdk.io.mzml.util.TagTracker: Constructor for TagTracker.
THIRTY_TWO_BIT_FLOAT - io.github.msdk.io.mzml.data.MzMLBitLength
THIRTY_TWO_BIT_INTEGER - io.github.msdk.io.mzml.data.MzMLBitLength
TIME - io.github.msdk.io.mzml.data.MzMLArrayType

V

valueOf(String) - Static method in enum io.github.msdk.io.mzml.data.MzMLArrayType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum io.github.msdk.io.mzml.data.MzMLBitLength: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum io.github.msdk.io.mzml.data.MzMLCompressionType: Returns the enum constant of this type with the specified name.
values() - Static method in enum io.github.msdk.io.mzml.data.MzMLArrayType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum io.github.msdk.io.mzml.data.MzMLBitLength: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum io.github.msdk.io.mzml.data.MzMLCompressionType: Returns an array containing the constants of this enum type, in the order they are declared.

Z

ZLIB - io.github.msdk.io.mzml.data.MzMLCompressionType

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