B C D E F G H I L M N O P R S T U V W Y

B

Base64 - Class in org.systemsbiology.jrap.stax

Encodes and decodes to and from Base64 notation.

Base64.InputStream - Class in org.systemsbiology.jrap.stax

A Base64#InputStream will read data from another InputStream, given in the constructor, and encode/decode to/from Base64 notation on the fly.

Base64.InputStream(InputStream) - Constructor for class org.systemsbiology.jrap.stax.Base64.InputStream

Constructs a Base64#InputStream in DECODE mode.

Base64.InputStream(InputStream, boolean) - Constructor for class org.systemsbiology.jrap.stax.Base64.InputStream

Constructs a Base64#InputStream in either ENCODE or DECODE mode.

Base64.InputStream(InputStream, boolean, boolean) - Constructor for class org.systemsbiology.jrap.stax.Base64.InputStream

Constructs a Base64#InputStream in either ENCODE or DECODE mode.

Base64.OutputStream - Class in org.systemsbiology.jrap.stax

A Base64#OutputStream will write data to another OutputStream, given in the constructor, and encode/decode to/from Base64 notation on the fly.

Base64.OutputStream(OutputStream) - Constructor for class org.systemsbiology.jrap.stax.Base64.OutputStream

Constructs a Base64#OutputStream in ENCODE mode.

Base64.OutputStream(OutputStream, boolean) - Constructor for class org.systemsbiology.jrap.stax.Base64.OutputStream

Constructs a Base64#OutputStream in either ENCODE or DECODE mode.

Base64.OutputStream(OutputStream, boolean, boolean) - Constructor for class org.systemsbiology.jrap.stax.Base64.OutputStream

Constructs a Base64#OutputStream in either ENCODE or DECODE mode.

baseLineReduced - Variable in class org.systemsbiology.jrap.stax.DataProcessingInfo

basePeakIntensity - Variable in class org.systemsbiology.jrap.stax.ScanHeader

TODO: Describe

basePeakMz - Variable in class org.systemsbiology.jrap.stax.ScanHeader

TODO: Describe

byteOrder - Variable in class org.systemsbiology.jrap.stax.ScanHeader

Peaks attribute for mzXML_3.0

C

centroided - Variable in class org.systemsbiology.jrap.stax.DataProcessingInfo

centroided - Variable in class org.systemsbiology.jrap.stax.ScanHeader

TODO: Describe

chargeDeconvoluted - Variable in class org.systemsbiology.jrap.stax.DataProcessingInfo

chargeDeconvoluted - Variable in class org.systemsbiology.jrap.stax.ScanHeader

TODO: Describe

chrogramIndex - Variable in class org.systemsbiology.jrap.stax.MSXMLParser

close() - Method in class org.systemsbiology.jrap.stax.Base64.OutputStream

Flushes and closes (I think, in the superclass) the stream.

collisionEnergy - Variable in class org.systemsbiology.jrap.stax.ScanHeader

TODO: Describe

COMPRESS - Static variable in class org.systemsbiology.jrap.stax.Base64

Specify that data should be compressed (value is true).

compressedLen - Variable in class org.systemsbiology.jrap.stax.ScanHeader

compressionType - Variable in class org.systemsbiology.jrap.stax.ScanHeader

contentType - Variable in class org.systemsbiology.jrap.stax.ScanHeader

D

dataProcessing - Variable in class org.systemsbiology.jrap.stax.MZXMLFileInfo

DataProcessingInfo - Class in org.systemsbiology.jrap.stax

DataProcessingInfo contains information about what settings and software were used to process the data contained in an mzXML file.

DataProcessingInfo() - Constructor for class org.systemsbiology.jrap.stax.DataProcessingInfo

DECODE - Static variable in class org.systemsbiology.jrap.stax.Base64

Specify decoding (value is false).

decode(String) - Static method in class org.systemsbiology.jrap.stax.Base64

Decodes data from Base64 notation.

decode(byte[], int, int) - Static method in class org.systemsbiology.jrap.stax.Base64

Decodes Base64 content in byte array format and returns the decoded byte array.

decode(byte[], int, int, byte[]) - Static method in class org.systemsbiology.jrap.stax.Base64

decodeFromFile(String) - Static method in class org.systemsbiology.jrap.stax.Base64

Simple helper method that Base64-decodes a file and returns the decoded data or null if there was an error.

decodeToFile(byte[], String) - Static method in class org.systemsbiology.jrap.stax.Base64

Simple helper method that Base64-decodes data to a file.

decodeToObject(String) - Static method in class org.systemsbiology.jrap.stax.Base64

Attempts to decode Base64 data and deserialize a Java Object within.

decodeToString(String) - Static method in class org.systemsbiology.jrap.stax.Base64

Decodes data from Base64 notation and returns it as a string.

deisotoped - Variable in class org.systemsbiology.jrap.stax.DataProcessingInfo

deisotoped - Variable in class org.systemsbiology.jrap.stax.ScanHeader

TODO: Describe

detector - Variable in class org.systemsbiology.jrap.stax.MSInstrumentInfo

DONT_COMPRESS - Static variable in class org.systemsbiology.jrap.stax.Base64

Specify that data should not be compressed (value is false).

doubleIntensityList - Variable in class org.systemsbiology.jrap.stax.Scan

doubleMassList - Variable in class org.systemsbiology.jrap.stax.Scan

No matter 32-bit m/z or 64 bit m/z return as a double list Support for mzML

E

email - Variable in class org.systemsbiology.jrap.stax.MSOperator

ENCODE - Static variable in class org.systemsbiology.jrap.stax.Base64

Specify encoding (value is true).

encodeBytes(byte[]) - Static method in class org.systemsbiology.jrap.stax.Base64

Encodes a byte array into Base64 notation.

encodeBytes(byte[], boolean) - Static method in class org.systemsbiology.jrap.stax.Base64

Encodes a byte array into Base64 notation.

encodeBytes(byte[], int, int) - Static method in class org.systemsbiology.jrap.stax.Base64

Encodes a byte array into Base64 notation.

encodeBytes(byte[], int, int, boolean) - Static method in class org.systemsbiology.jrap.stax.Base64

Encodes a byte array into Base64 notation.

encodeFromFile(String) - Static method in class org.systemsbiology.jrap.stax.Base64

Simple helper method that Base64-encodes a file and returns the encoded string or null if there was an error.

encodeObject(Serializable) - Static method in class org.systemsbiology.jrap.stax.Base64

Serializes an object and returns the Base64-encoded version of that serialized object.

encodeObject(Serializable, boolean) - Static method in class org.systemsbiology.jrap.stax.Base64

Serializes an object and returns the Base64-encoded version of that serialized object.

encodeString(String) - Static method in class org.systemsbiology.jrap.stax.Base64

Encodes a string in Base64 notation with line breaks after every 75 Base64 characters.

encodeString(String, boolean) - Static method in class org.systemsbiology.jrap.stax.Base64

Encodes a string in Base64 notation with line breaks after every 75 Base64 characters.

encodeToFile(byte[], String) - Static method in class org.systemsbiology.jrap.stax.Base64

Simple helper method that Base64-encodes data to a file.

endMz - Variable in class org.systemsbiology.jrap.stax.ScanHeader

TODO: Describe

F

FileHeaderParser - Class in org.systemsbiology.jrap.stax

fileName - Variable in class org.systemsbiology.jrap.stax.MSXMLParser

The file we are in charge of reading

filterLine - Variable in class org.systemsbiology.jrap.stax.ScanHeader

for S(M)RM

firstName - Variable in class org.systemsbiology.jrap.stax.MSOperator

flush() - Method in class org.systemsbiology.jrap.stax.Base64.OutputStream

Appropriately pads Base64 notation when encoding or throws an exception if Base64 input is not properly padded when decoding.

G

getBaseLineReduced() - Method in class org.systemsbiology.jrap.stax.DataProcessingInfo

Were chromatogram base line reduced?

getBasePeakIntensity() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getBasePeakMz() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getByteOrder() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getCentroided() - Method in class org.systemsbiology.jrap.stax.DataProcessingInfo

Was the data centroided?

getCentroided() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getChargeDeconvoluted() - Method in class org.systemsbiology.jrap.stax.DataProcessingInfo

Was the data charge deconvoluted?

getChargeDeconvoluted() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getChrogramIndex() - Method in class org.systemsbiology.jrap.stax.IndexParser

getCollisionEnergy() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getCompressedLen() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getCompressionType() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getContentType() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getDataProcessing() - Method in class org.systemsbiology.jrap.stax.MZXMLFileInfo

Get data about how the data was processed.

getDeisotoped() - Method in class org.systemsbiology.jrap.stax.DataProcessingInfo

Was the data charge deisotoped?

getDeisotoped() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getDetector() - Method in class org.systemsbiology.jrap.stax.MSInstrumentInfo

getDoubleIntensityList() - Method in class org.systemsbiology.jrap.stax.Scan

getDoubleMassList() - Method in class org.systemsbiology.jrap.stax.Scan

getDoubleRetentionTime() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getEndMz() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getFilterLine() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getFloatValue(XMLStreamReader, String) - Method in class org.systemsbiology.jrap.stax.MLScanAndHeaderParser

getFloatValue(XMLStreamReader, String) - Method in class org.systemsbiology.jrap.stax.ScanAndHeaderParser

getHeader() - Method in class org.systemsbiology.jrap.stax.MLScanAndHeaderParser

getHeader() - Method in class org.systemsbiology.jrap.stax.Scan

getHeader() - Method in class org.systemsbiology.jrap.stax.ScanAndHeaderParser

getHighMz() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getInfo() - Method in class org.systemsbiology.jrap.stax.FileHeaderParser

getInstrumentInfo() - Method in class org.systemsbiology.jrap.stax.MZXMLFileInfo

Get information about the MS instrument used to extract data.

getIntenCompressedLen() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getIntenCompressionType() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getIntenPrecision() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getIntensityCutoff() - Method in class org.systemsbiology.jrap.stax.DataProcessingInfo

Return the intensity cutoff that was used to eliminate low-signal peaks.

getIntValue(XMLStreamReader, String) - Method in class org.systemsbiology.jrap.stax.MLScanAndHeaderParser

getIntValue(XMLStreamReader, String) - Method in class org.systemsbiology.jrap.stax.ScanAndHeaderParser

getIonisationEnergy() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getIonization() - Method in class org.systemsbiology.jrap.stax.MSInstrumentInfo

getLowIntensityDataRemoved() - Method in class org.systemsbiology.jrap.stax.DataProcessingInfo

Were chromatogram remove low intensity data

getLowMz() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getManufacturer() - Method in class org.systemsbiology.jrap.stax.MSInstrumentInfo

getMassAnalyzer() - Method in class org.systemsbiology.jrap.stax.MSInstrumentInfo

getMassCompressedLen() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getMassCompressionType() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getMassIntensityList() - Method in class org.systemsbiology.jrap.stax.Scan

getMassPrecision() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getMaxScan() - Method in class org.systemsbiology.jrap.stax.IndexParser

getMaxScanNumber() - Method in class org.systemsbiology.jrap.stax.MSXMLParser

getModel() - Method in class org.systemsbiology.jrap.stax.MSInstrumentInfo

getMsLevel() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getNum() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getOffsetMap() - Method in class org.systemsbiology.jrap.stax.IndexParser

getOperator() - Method in class org.systemsbiology.jrap.stax.MSInstrumentInfo

getParentFiles() - Method in class org.systemsbiology.jrap.stax.MZXMLFileInfo

Get information about parent files, chronologically ordered.

getPeakPicked() - Method in class org.systemsbiology.jrap.stax.DataProcessingInfo

Were peaks extracted?

getPeaks(String, int) - Method in class org.systemsbiology.jrap.stax.MLScanAndHeaderParser

getPeaks(String) - Method in class org.systemsbiology.jrap.stax.ScanAndHeaderParser

getPeaksCount() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getPolarity() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getPrecision() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getPrecursorCharge() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getPrecursorIntensity() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getPrecursorMz() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getPrecursorScanNum() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getRetentionTime() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getRT() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getScan() - Method in class org.systemsbiology.jrap.stax.MLScanAndHeaderParser

getScan() - Method in class org.systemsbiology.jrap.stax.ScanAndHeaderParser

getScanCount() - Method in class org.systemsbiology.jrap.stax.MSXMLParser

Get the total number of scans in the mzXMLfile handled by this parser.

getScanOffset(int) - Method in class org.systemsbiology.jrap.stax.MSXMLParser

get scan offset, scan number is 1 based.

getScanType() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getSha1() - Method in class org.systemsbiology.jrap.stax.ParentFile

Get the sha1-sum of this file.

getSmoothed() - Method in class org.systemsbiology.jrap.stax.DataProcessingInfo

Were Chromatogram smoothed?

getSoftwareInfo() - Method in class org.systemsbiology.jrap.stax.MSInstrumentInfo

getSoftwareUsed() - Method in class org.systemsbiology.jrap.stax.DataProcessingInfo

Return an array of information about all software that was used to process the data, in chronological order.

getSpotIntegration() - Method in class org.systemsbiology.jrap.stax.DataProcessingInfo

Were spots integrated?

getStartMz() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getStringValue(XMLStreamReader, String) - Method in class org.systemsbiology.jrap.stax.MLScanAndHeaderParser

getStringValue(XMLStreamReader, String) - Method in class org.systemsbiology.jrap.stax.ScanAndHeaderParser

getTotIonCurrent() - Method in class org.systemsbiology.jrap.stax.ScanHeader

getType() - Method in class org.systemsbiology.jrap.stax.ParentFile

Return the type of parent file.

getURI() - Method in class org.systemsbiology.jrap.stax.ParentFile

Get the URI of this file.

H

header - Variable in class org.systemsbiology.jrap.stax.Scan

highMz - Variable in class org.systemsbiology.jrap.stax.ScanHeader

TODO: Describe

I

IndexParser - Class in org.systemsbiology.jrap.stax

IndexParser(String) - Constructor for class org.systemsbiology.jrap.stax.IndexParser

instrumentInfo - Variable in class org.systemsbiology.jrap.stax.MZXMLFileInfo

intenCompressedLen - Variable in class org.systemsbiology.jrap.stax.ScanHeader

intenCompressionType - Variable in class org.systemsbiology.jrap.stax.ScanHeader

intenPrecision - Variable in class org.systemsbiology.jrap.stax.ScanHeader

intensityCutoff - Variable in class org.systemsbiology.jrap.stax.DataProcessingInfo

ionisationEnergy - Variable in class org.systemsbiology.jrap.stax.ScanHeader

TODO: Describe

ionization - Variable in class org.systemsbiology.jrap.stax.MSInstrumentInfo

isML - Variable in class org.systemsbiology.jrap.stax.MSXMLParser

isXML - Variable in class org.systemsbiology.jrap.stax.MSXMLParser

L

lastName - Variable in class org.systemsbiology.jrap.stax.MSOperator

lowIntensityDataRemoved - Variable in class org.systemsbiology.jrap.stax.DataProcessingInfo

lowMz - Variable in class org.systemsbiology.jrap.stax.ScanHeader

TODO: Describe

M

main(String[]) - Static method in class org.systemsbiology.jrap.stax.Base64

Testing.

main(String[]) - Static method in class org.systemsbiology.jrap.stax.TestParser

manufacturer - Variable in class org.systemsbiology.jrap.stax.MSInstrumentInfo

massAnalyzer - Variable in class org.systemsbiology.jrap.stax.MSInstrumentInfo

massCompressedLen - Variable in class org.systemsbiology.jrap.stax.ScanHeader

massCompressionType - Variable in class org.systemsbiology.jrap.stax.ScanHeader

massIntensityList - Variable in class org.systemsbiology.jrap.stax.Scan

No matter 32-bit or 64-bit peak pair, return as double list.

massPrecision - Variable in class org.systemsbiology.jrap.stax.ScanHeader

for mzML

maxScan - Variable in class org.systemsbiology.jrap.stax.MSXMLParser

MLScanAndHeaderParser - Class in org.systemsbiology.jrap.stax

MLScanAndHeaderParser() - Constructor for class org.systemsbiology.jrap.stax.MLScanAndHeaderParser

model - Variable in class org.systemsbiology.jrap.stax.MSInstrumentInfo

MSInstrumentInfo - Class in org.systemsbiology.jrap.stax

The MSInstrumentInfo class contains information about the MS instrument used for a certain MzXML file.

MSInstrumentInfo() - Constructor for class org.systemsbiology.jrap.stax.MSInstrumentInfo

msLevel - Variable in class org.systemsbiology.jrap.stax.ScanHeader

MS Scan Level

MSOperator - Class in org.systemsbiology.jrap.stax

MSOperator provides information on who operated the hardware used to acquire data.

MSOperator() - Constructor for class org.systemsbiology.jrap.stax.MSOperator

MSXMLParser - Class in org.systemsbiology.jrap.stax

A generic utility class for reading an MSXML file in a random access fashion and utilizing a stored scan index for fast reads.

MSXMLParser(String) - Constructor for class org.systemsbiology.jrap.stax.MSXMLParser

MZXMLFileInfo - Class in org.systemsbiology.jrap.stax

MZXMLFileInfo is a class that contains all information from the header of an MzXML file that is constant for the entire file.

MZXMLFileInfo() - Constructor for class org.systemsbiology.jrap.stax.MZXMLFileInfo

N

name - Variable in class org.systemsbiology.jrap.stax.SoftwareInfo

NO - Static variable in class org.systemsbiology.jrap.stax.DataProcessingInfo

num - Variable in class org.systemsbiology.jrap.stax.ScanHeader

Scan Number

O

offsets - Variable in class org.systemsbiology.jrap.stax.MSXMLParser

The indexes

operator - Variable in class org.systemsbiology.jrap.stax.MSInstrumentInfo

org.systemsbiology.jrap.stax - package org.systemsbiology.jrap.stax

P

ParentFile - Class in org.systemsbiology.jrap.stax

The ParentFile class contains information about parent files of an mzXML file.

ParentFile(String, String, String) - Constructor for class org.systemsbiology.jrap.stax.ParentFile

parseFileHeader() - Method in class org.systemsbiology.jrap.stax.FileHeaderParser

parseIndexes() - Method in class org.systemsbiology.jrap.stax.IndexParser

parseMLScanAndHeader() - Method in class org.systemsbiology.jrap.stax.MLScanAndHeaderParser

parseScanAndHeader() - Method in class org.systemsbiology.jrap.stax.ScanAndHeaderParser

peakPicked - Variable in class org.systemsbiology.jrap.stax.DataProcessingInfo

peaksCount - Variable in class org.systemsbiology.jrap.stax.ScanHeader

Number of peaks in scan

phoneNumber - Variable in class org.systemsbiology.jrap.stax.MSOperator

polarity - Variable in class org.systemsbiology.jrap.stax.ScanHeader

TODO: Describe

precision - Variable in class org.systemsbiology.jrap.stax.ScanHeader

TODO: Describe

precursorCharge - Variable in class org.systemsbiology.jrap.stax.ScanHeader

TODO: Describe

precursorIntensity - Variable in class org.systemsbiology.jrap.stax.ScanHeader

precursorMz - Variable in class org.systemsbiology.jrap.stax.ScanHeader

TODO: Describe

precursorScanNum - Variable in class org.systemsbiology.jrap.stax.ScanHeader

TODO: Describe

R

rap(int) - Method in class org.systemsbiology.jrap.stax.MSXMLParser

Read a particular scan from a MSXML file and return a generic Scan object with it's data.

rapFileHeader() - Method in class org.systemsbiology.jrap.stax.MSXMLParser

this gives back the file header (info before scan)

rapHeader(int) - Method in class org.systemsbiology.jrap.stax.MSXMLParser

read() - Method in class org.systemsbiology.jrap.stax.Base64.InputStream

Reads enough of the input stream to convert to/from Base64 and returns the next byte.

read(byte[], int, int) - Method in class org.systemsbiology.jrap.stax.Base64.InputStream

Calls Base64.InputStream.read() repeatedly until the end of stream is reached or len bytes are read.

readFile(String, boolean) - Static method in class org.systemsbiology.jrap.stax.Base64

Reads a file and either encodes or decodes it.

readFile(File, boolean) - Static method in class org.systemsbiology.jrap.stax.Base64

Reads a file and either encodes or decodes it.

retentionTime - Variable in class org.systemsbiology.jrap.stax.ScanHeader

TODO: Describe

rt - Variable in class org.systemsbiology.jrap.stax.ScanHeader

for mzML

S

Scan - Class in org.systemsbiology.jrap.stax

A simple class to hold the contents of a scan from a MSXML file.

Scan() - Constructor for class org.systemsbiology.jrap.stax.Scan

ScanAndHeaderParser - Class in org.systemsbiology.jrap.stax

ScanAndHeaderParser() - Constructor for class org.systemsbiology.jrap.stax.ScanAndHeaderParser

ScanHeader - Class in org.systemsbiology.jrap.stax

ScanHeader is a class that contains all information associated with a Scan, except for the actual peakList.

ScanHeader() - Constructor for class org.systemsbiology.jrap.stax.ScanHeader

scanType - Variable in class org.systemsbiology.jrap.stax.ScanHeader

TODO: Describe

setBaseLineReduced(int) - Method in class org.systemsbiology.jrap.stax.DataProcessingInfo

setBasePeakIntensity(float) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setBasePeakMz(float) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setByteOrder(String) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setCentroided(int) - Method in class org.systemsbiology.jrap.stax.DataProcessingInfo

Set centroided to one of UNKNOWN, YES or NO.

setCentroided(int) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setChargeDeconvoluted(int) - Method in class org.systemsbiology.jrap.stax.DataProcessingInfo

Set charge deconvoluted to one of UNKNOWN, YES or NO.

setChargeDeconvoluted(int) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setCollisionEnergy(float) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setCompressedLen(int) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setCompressionType(String) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setContentType(String) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setDeisotoped(int) - Method in class org.systemsbiology.jrap.stax.DataProcessingInfo

Set deisotoped to one of UNKNOWN, YES or NO.

setDeisotoped(int) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setDoubleIntensityList(double[]) - Method in class org.systemsbiology.jrap.stax.Scan

setDoubleMassList(double[]) - Method in class org.systemsbiology.jrap.stax.Scan

setEndMz(float) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setFileInputStream(FileInputStream) - Method in class org.systemsbiology.jrap.stax.MLScanAndHeaderParser

setFileInputStream(FileInputStream) - Method in class org.systemsbiology.jrap.stax.ScanAndHeaderParser

setFilterLine(String) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setHeader(ScanHeader) - Method in class org.systemsbiology.jrap.stax.Scan

setHighMz(float) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setIntenCompressedLen(int) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setIntenCompressionType(String) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setIntenPrecision(int) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setIntensityCutoff(double) - Method in class org.systemsbiology.jrap.stax.DataProcessingInfo

Set the intensity cutoff that was used to eliminate low-signal peaks.

setIonisationEnergy(float) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setIsScan(boolean) - Method in class org.systemsbiology.jrap.stax.MLScanAndHeaderParser

setIsScan(boolean) - Method in class org.systemsbiology.jrap.stax.ScanAndHeaderParser

setLowIntensityDataRemoved(int) - Method in class org.systemsbiology.jrap.stax.DataProcessingInfo

setLowMz(float) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setMassCompressedLen(int) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setMassCompressionType(String) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setMassIntensityList(double[][]) - Method in class org.systemsbiology.jrap.stax.Scan

setMassPrecision(int) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setMsLevel(int) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setName(String) - Method in class org.systemsbiology.jrap.stax.SoftwareInfo

setNum(int) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setPeakPicked(int) - Method in class org.systemsbiology.jrap.stax.DataProcessingInfo

set value of peakPicked to one of UNKNOWN, YES or NO

setPeaksCount(int) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setPolarity(String) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setPrecision(int) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setPrecursorCharge(int) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setPrecursorIntensity(float) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setPrecursorMz(float) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setPrecursorScanNum(int) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setRetentionTime(String) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setRT(double) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setScanType(String) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setSmoothed(int) - Method in class org.systemsbiology.jrap.stax.DataProcessingInfo

setSoftwareUsed(ArrayList<SoftwareInfo>) - Method in class org.systemsbiology.jrap.stax.DataProcessingInfo

Set the chronological array of used software for data processing.

setSpotIntegration(int) - Method in class org.systemsbiology.jrap.stax.DataProcessingInfo

Set spot integration to one of UNKNOWN, YES or NO.

setStartMz(float) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setTotIonCurrent(float) - Method in class org.systemsbiology.jrap.stax.ScanHeader

setType(String) - Method in class org.systemsbiology.jrap.stax.SoftwareInfo

setVersion(String) - Method in class org.systemsbiology.jrap.stax.SoftwareInfo

sha1 - Variable in class org.systemsbiology.jrap.stax.ParentFile

smoothed - Variable in class org.systemsbiology.jrap.stax.DataProcessingInfo

softwareInfo - Variable in class org.systemsbiology.jrap.stax.MSInstrumentInfo

SoftwareInfo - Class in org.systemsbiology.jrap.stax

SoftwareInfo represents data that is available on software that has processed a mzXML file.

SoftwareInfo(String, String, String) - Constructor for class org.systemsbiology.jrap.stax.SoftwareInfo

spotIntegration - Variable in class org.systemsbiology.jrap.stax.DataProcessingInfo

startMz - Variable in class org.systemsbiology.jrap.stax.ScanHeader

TODO: Describe

T

TestParser - Class in org.systemsbiology.jrap.stax

A demo program which uses the MSXMLParser to read in scans from a file you specify on the command line.

TestParser() - Constructor for class org.systemsbiology.jrap.stax.TestParser

tmpScan - Variable in class org.systemsbiology.jrap.stax.MLScanAndHeaderParser

tmpScan - Variable in class org.systemsbiology.jrap.stax.ScanAndHeaderParser

tmpScanHeader - Variable in class org.systemsbiology.jrap.stax.MLScanAndHeaderParser

tmpScanHeader - Variable in class org.systemsbiology.jrap.stax.ScanAndHeaderParser

toString() - Method in class org.systemsbiology.jrap.stax.DataProcessingInfo

toString() - Method in class org.systemsbiology.jrap.stax.MSInstrumentInfo

toString() - Method in class org.systemsbiology.jrap.stax.MSOperator

toString() - Method in class org.systemsbiology.jrap.stax.MZXMLFileInfo

toString() - Method in class org.systemsbiology.jrap.stax.ParentFile

toString() - Method in class org.systemsbiology.jrap.stax.Scan

String respresentation of a Scan object.

toString() - Method in class org.systemsbiology.jrap.stax.ScanHeader

String respresentation of a ScanHeader object.

toString() - Method in class org.systemsbiology.jrap.stax.SoftwareInfo

totIonCurrent - Variable in class org.systemsbiology.jrap.stax.ScanHeader

TODO: Describe

type - Variable in class org.systemsbiology.jrap.stax.ParentFile

type - Variable in class org.systemsbiology.jrap.stax.SoftwareInfo

U

UNKNOWN - Static variable in class org.systemsbiology.jrap.stax.DataProcessingInfo

URI - Variable in class org.systemsbiology.jrap.stax.MSOperator

URI - Variable in class org.systemsbiology.jrap.stax.ParentFile

V

version - Variable in class org.systemsbiology.jrap.stax.SoftwareInfo

W

write(int) - Method in class org.systemsbiology.jrap.stax.Base64.OutputStream

Writes the byte to the output stream after converting to/from Base64 notation.

write(byte[], int, int) - Method in class org.systemsbiology.jrap.stax.Base64.OutputStream

Calls Base64.OutputStream.write(int) repeatedly until len bytes are written.

writeFile(byte[], String, boolean) - Static method in class org.systemsbiology.jrap.stax.Base64

Writes a byte array to a file either encoding it or decoding it as specified.

writeFile(byte[], File, boolean) - Static method in class org.systemsbiology.jrap.stax.Base64

Writes a byte array to a file either encoding it or decoding it as specified.

writeFile(byte[], int, int, File, boolean) - Static method in class org.systemsbiology.jrap.stax.Base64

Writes a byte array to a file either encoding it or decoding it as specified.

Y

YES - Static variable in class org.systemsbiology.jrap.stax.DataProcessingInfo

B C D E F G H I L M N O P R S T U V W Y