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

A

actionPerformed(ActionEvent) - Method in class org.systemsbiology.mzxmlviewer.MzXMLViewer
 
addFileFilter(String[], String) - Method in class org.systemsbiology.mzxmlviewer.utilities.GenericFileChooser
Add a new choosable item (description->extensions) filter.

B

Base64 - Class in org.systemsbiology.jrap
Encodes and decodes to and from Base64 notation.
Base64.InputStream - Class in org.systemsbiology.jrap
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.Base64.InputStream
Constructs a Base64#InputStream in DECODE mode.
Base64.InputStream(InputStream, boolean) - Constructor for class org.systemsbiology.jrap.Base64.InputStream
Constructs a Base64#InputStream in either ENCODE or DECODE mode.
Base64.InputStream(InputStream, boolean, boolean) - Constructor for class org.systemsbiology.jrap.Base64.InputStream
Constructs a Base64#InputStream in either ENCODE or DECODE mode.
Base64.OutputStream - Class in org.systemsbiology.jrap
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.Base64.OutputStream
Constructs a Base64#OutputStream in ENCODE mode.
Base64.OutputStream(OutputStream, boolean) - Constructor for class org.systemsbiology.jrap.Base64.OutputStream
Constructs a Base64#OutputStream in either ENCODE or DECODE mode.
Base64.OutputStream(OutputStream, boolean, boolean) - Constructor for class org.systemsbiology.jrap.Base64.OutputStream
Constructs a Base64#OutputStream in either ENCODE or DECODE mode.
basePeakIntensity - Variable in class org.systemsbiology.jrap.ScanHeader
TODO: Describe
basePeakMz - Variable in class org.systemsbiology.jrap.ScanHeader
TODO: Describe
byteOrder - Variable in class org.systemsbiology.jrap.ScanHeader
Peaks attribute for mzXML_3.0

C

centroided - Variable in class org.systemsbiology.jrap.DataProcessingInfo
 
centroided - Variable in class org.systemsbiology.jrap.ScanHeader
TODO: Describe
characters(char[], int, int) - Method in class org.systemsbiology.jrap.SAX2HeaderHandler
 
characters(char[], int, int) - Method in class org.systemsbiology.jrap.SAX2IndexHandler
Characters.
characters(char[], int, int) - Method in class org.systemsbiology.jrap.SAX2ScanHandler
Characters.
characters(char[], int, int) - Method in class org.systemsbiology.jrap.SAX2ScanHeaderHandler
Characters.
chargeDeconvoluted - Variable in class org.systemsbiology.jrap.DataProcessingInfo
 
chargeDeconvoluted - Variable in class org.systemsbiology.jrap.ScanHeader
TODO: Describe
close() - Method in class org.systemsbiology.jrap.Base64.OutputStream
Flushes and closes (I think, in the superclass) the stream.
collisionEnergy - Variable in class org.systemsbiology.jrap.ScanHeader
TODO: Describe
COMPRESS - Static variable in class org.systemsbiology.jrap.Base64
Specify that data should be compressed (value is true).
compressedLen - Variable in class org.systemsbiology.jrap.ScanHeader
 
compressionType - Variable in class org.systemsbiology.jrap.ScanHeader
 
construct() - Method in class org.systemsbiology.mzxmlviewer.utilities.SwingWorker
Compute the value to be returned by the get method.
CONT_AFTER_FATAL_ERROR_ID - Static variable in class org.systemsbiology.jrap.MSXMLParser
Continue after fatal error id.
contentType - Variable in class org.systemsbiology.jrap.ScanHeader
 
createFileProcPanel() - Method in class org.systemsbiology.mzxmlviewer.dialogs.InfoDialog
 
createInstrumentPanel() - Method in class org.systemsbiology.mzxmlviewer.dialogs.InfoDialog
 

D

dataProcessing - Variable in class org.systemsbiology.jrap.MZXMLFileInfo
 
DataProcessingInfo - Class in org.systemsbiology.jrap
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.DataProcessingInfo
 
dataProcessingMode - Variable in class org.systemsbiology.jrap.SAX2HeaderHandler
 
dataProcessingSoftware - Variable in class org.systemsbiology.jrap.SAX2HeaderHandler
 
DECODE - Static variable in class org.systemsbiology.jrap.Base64
Specify decoding (value is false).
decode(String) - Static method in class org.systemsbiology.jrap.Base64
Decodes data from Base64 notation.
decode(byte[], int, int) - Static method in class org.systemsbiology.jrap.Base64
Decodes Base64 content in byte array format and returns the decoded byte array.
decodeFromFile(String) - Static method in class org.systemsbiology.jrap.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.Base64
Simple helper method that Base64-decodes data to a file.
decodeToObject(String) - Static method in class org.systemsbiology.jrap.Base64
Attempts to decode Base64 data and deserialize a Java Object within.
decodeToString(String) - Static method in class org.systemsbiology.jrap.Base64
Decodes data from Base64 notation and returns it as a string.
DEFAULT_CONT_AFTER_FATAL_ERROR - Static variable in class org.systemsbiology.jrap.MSXMLParser
Default dynamic validation support (false).
DEFAULT_CONT_AFTER_FATAL_ERROR - Static variable in class org.systemsbiology.jrap.MSXMLParserGeneric
Default dynamic validation support (false).
DEFAULT_DYNAMIC_VALIDATION - Static variable in class org.systemsbiology.jrap.MSXMLParser
Default dynamic validation support (false).
DEFAULT_DYNAMIC_VALIDATION - Static variable in class org.systemsbiology.jrap.MSXMLParserGeneric
Default dynamic validation support (false).
DEFAULT_NAMESPACE_PREFIXES - Static variable in class org.systemsbiology.jrap.MSXMLParser
Default namespace prefixes (false).
DEFAULT_NAMESPACES - Static variable in class org.systemsbiology.jrap.MSXMLParser
Default namespaces support (false).
DEFAULT_PARSER_NAME - Static variable in class org.systemsbiology.jrap.MSXMLParser
Default parser name.
DEFAULT_SCHEMA_FULL_CHECKING - Static variable in class org.systemsbiology.jrap.MSXMLParser
Default Schema full checking support (false).
DEFAULT_SCHEMA_FULL_CHECKING - Static variable in class org.systemsbiology.jrap.MSXMLParserGeneric
Default Schema full checking support (false).
DEFAULT_SCHEMA_VALIDATION - Static variable in class org.systemsbiology.jrap.MSXMLParser
Default Schema validation support (false).
DEFAULT_SCHEMA_VALIDATION - Static variable in class org.systemsbiology.jrap.MSXMLParserGeneric
Default Schema validation support (false).
DEFAULT_VALIDATION - Static variable in class org.systemsbiology.jrap.MSXMLParser
Default validation support (false).
DEFAULT_VALIDATION - Static variable in class org.systemsbiology.jrap.MSXMLParserGeneric
Default validation support (false).
deisotoped - Variable in class org.systemsbiology.jrap.DataProcessingInfo
 
deisotoped - Variable in class org.systemsbiology.jrap.ScanHeader
TODO: Describe
detector - Variable in class org.systemsbiology.jrap.MSInstrumentInfo
 
DONT_COMPRESS - Static variable in class org.systemsbiology.jrap.Base64
Specify that data should not be compressed (value is false).
doubleMassIntensityList - Variable in class org.systemsbiology.jrap.Scan
 
DYNAMIC_VALIDATION_FEATURE_ID - Static variable in class org.systemsbiology.jrap.MSXMLParser
Dynamic validation feature id (http://apache.org/xml/features/validation/dynamic).

E

email - Variable in class org.systemsbiology.jrap.MSOperator
 
ENCODE - Static variable in class org.systemsbiology.jrap.Base64
Specify encoding (value is true).
encodeBytes(byte[]) - Static method in class org.systemsbiology.jrap.Base64
Encodes a byte array into Base64 notation.
encodeBytes(byte[], boolean) - Static method in class org.systemsbiology.jrap.Base64
Encodes a byte array into Base64 notation.
encodeBytes(byte[], int, int) - Static method in class org.systemsbiology.jrap.Base64
Encodes a byte array into Base64 notation.
encodeBytes(byte[], int, int, boolean) - Static method in class org.systemsbiology.jrap.Base64
Encodes a byte array into Base64 notation.
encodeFromFile(String) - Static method in class org.systemsbiology.jrap.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.Base64
Serializes an object and returns the Base64-encoded version of that serialized object.
encodeObject(Serializable, boolean) - Static method in class org.systemsbiology.jrap.Base64
Serializes an object and returns the Base64-encoded version of that serialized object.
encodeString(String) - Static method in class org.systemsbiology.jrap.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.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.Base64
Simple helper method that Base64-encodes data to a file.
endElement(String, String, String) - Method in class org.systemsbiology.jrap.SAX2HeaderHandler
 
endElement(String, String, String) - Method in class org.systemsbiology.jrap.SAX2IndexHandler
 
endElement(String, String, String) - Method in class org.systemsbiology.jrap.SAX2ScanHandler
 
endElement(String, String, String) - Method in class org.systemsbiology.jrap.SAX2ScanHeaderHandler
 
endMz - Variable in class org.systemsbiology.jrap.ScanHeader
TODO: Describe
error(SAXParseException) - Method in class org.systemsbiology.jrap.SAX2IndexHandler
Error.
error(SAXParseException) - Method in class org.systemsbiology.jrap.SAX2ScanHandler
Error.
error(SAXParseException) - Method in class org.systemsbiology.jrap.SAX2ScanHeaderHandler
Error.

F

fatalError(SAXParseException) - Method in class org.systemsbiology.jrap.SAX2IndexHandler
Fatal error.
fatalError(SAXParseException) - Method in class org.systemsbiology.jrap.SAX2ScanHandler
Fatal error.
fatalError(SAXParseException) - Method in class org.systemsbiology.jrap.SAX2ScanHeaderHandler
Fatal error.
fileMD5 - Variable in class org.systemsbiology.jrap.MSXMLParser
The MD5 signature found the last time we read the index
fileMD5 - Variable in class org.systemsbiology.jrap.MSXMLParserGeneric
The MD5 signature found the last time we read the index
FileMenu - Class in org.systemsbiology.mzxmlviewer.menus
 
fileName - Variable in class org.systemsbiology.jrap.MSXMLParser
The file we are in charge of reading
fileName - Variable in class org.systemsbiology.jrap.MSXMLParserGeneric
The file we are in charge of reading
finish() - Method in class org.systemsbiology.jrap.SAX2HeaderHandler
 
finished() - Method in class org.systemsbiology.mzxmlviewer.utilities.SwingWorker
Called on the event dispatching thread (not on the worker thread) after the construct method has returned.
firstName - Variable in class org.systemsbiology.jrap.MSOperator
 
floatMassIntensityList - Variable in class org.systemsbiology.jrap.Scan
A 2-dimensional array, element 0 contains a list of masses of peaks, element 1 contains a list of intensities of peaks.
flush() - Method in class org.systemsbiology.jrap.Base64.OutputStream
Appropriately pads Base64 notation when encoding or throws an exception if Base64 input is not properly padded when decoding.
foundIdxOffset - Variable in class org.systemsbiology.jrap.SAX2IndexHandler
Flag to indicate if there is an index in this file
foundOffset() - Method in class org.systemsbiology.jrap.SAX2IndexHandler
Status of index offset
foundScanOffset - Variable in class org.systemsbiology.jrap.SAX2IndexHandler
True if we are sitting on an offset line

G

GenericFileChooser - Class in org.systemsbiology.mzxmlviewer.utilities
A generic file chooser that contains 1..* description/extension combinations.
get() - Method in class org.systemsbiology.mzxmlviewer.utilities.SwingWorker
Return the value created by the construct method.
getBasePeakIntensity() - Method in class org.systemsbiology.jrap.Scan
 
getBasePeakIntensity() - Method in class org.systemsbiology.jrap.ScanHeader
 
getBasePeakMz() - Method in class org.systemsbiology.jrap.Scan
 
getBasePeakMz() - Method in class org.systemsbiology.jrap.ScanHeader
 
getBPIComponent(ScanHeader[], SpectrumComponent.ClickListener) - Static method in class org.systemsbiology.mzxmlviewer.utilities.SpectrumComponent
 
getByteOrder() - Method in class org.systemsbiology.jrap.Scan
 
getByteOrder() - Method in class org.systemsbiology.jrap.ScanHeader
 
getCentroided() - Method in class org.systemsbiology.jrap.DataProcessingInfo
Was the data centroided?
getCentroided() - Method in class org.systemsbiology.jrap.Scan
 
getCentroided() - Method in class org.systemsbiology.jrap.ScanHeader
 
getChargeDeconvoluted() - Method in class org.systemsbiology.jrap.DataProcessingInfo
Was the data charge deconvoluted?
getChargeDeconvoluted() - Method in class org.systemsbiology.jrap.Scan
 
getChargeDeconvoluted() - Method in class org.systemsbiology.jrap.ScanHeader
 
getCollisionEnergy() - Method in class org.systemsbiology.jrap.Scan
 
getCollisionEnergy() - Method in class org.systemsbiology.jrap.ScanHeader
 
getColumnCount() - Method in class org.systemsbiology.mzxmlviewer.tables.MzTableModel
 
getColumnName(int) - Method in class org.systemsbiology.mzxmlviewer.tables.MzTableModel
 
getCompressedLen() - Method in class org.systemsbiology.jrap.Scan
 
getCompressedLen() - Method in class org.systemsbiology.jrap.ScanHeader
 
getCompressionType() - Method in class org.systemsbiology.jrap.Scan
 
getCompressionType() - Method in class org.systemsbiology.jrap.ScanHeader
 
getContentType() - Method in class org.systemsbiology.jrap.Scan
 
getContentType() - Method in class org.systemsbiology.jrap.ScanHeader
 
getDataProcessing() - Method in class org.systemsbiology.jrap.MZXMLFileInfo
Get data about how the data was processed.
getDeisotoped() - Method in class org.systemsbiology.jrap.DataProcessingInfo
Was the data charge deisotoped?
getDeisotoped() - Method in class org.systemsbiology.jrap.Scan
 
getDeisotoped() - Method in class org.systemsbiology.jrap.ScanHeader
 
getDetector() - Method in class org.systemsbiology.jrap.MSInstrumentInfo
 
getDoubleMassIntensityList() - Method in class org.systemsbiology.jrap.Scan
 
getDoubleRetentionTime() - Method in class org.systemsbiology.jrap.Scan
 
getDoubleRetentionTime() - Method in class org.systemsbiology.jrap.ScanHeader
 
getEndMz() - Method in class org.systemsbiology.jrap.Scan
 
getEndMz() - Method in class org.systemsbiology.jrap.ScanHeader
 
getFloatMassIntensityList() - Method in class org.systemsbiology.jrap.Scan
Return the peaks in this scan as two lists: one of mass values and one of intensity values.
getHeader() - Method in class org.systemsbiology.jrap.Scan
 
getHeaderInfo() - Method in class org.systemsbiology.jrap.MSXMLParser
Get the header information contained in the mzXML file, which is constant for every scan.
getHeaderInfo() - Method in class org.systemsbiology.jrap.MSXMLParserGeneric
Get the header information contained in the mzXML file, which is constant for every scan.
getHighMz() - Method in class org.systemsbiology.jrap.Scan
 
getHighMz() - Method in class org.systemsbiology.jrap.ScanHeader
 
getIndexPosition() - Method in class org.systemsbiology.jrap.SAX2IndexHandler
Get byte position of the index in the file
getInfo() - Method in class org.systemsbiology.jrap.SAX2HeaderHandler
 
getInstance() - Static method in class org.systemsbiology.mzxmlviewer.menus.FileMenu
 
getInstance() - Static method in class org.systemsbiology.mzxmlviewer.menus.HelpMenu
 
getInstance() - Static method in class org.systemsbiology.mzxmlviewer.menus.RootMenuBar
 
getInstance() - Static method in class org.systemsbiology.mzxmlviewer.utilities.GenericFileChooser
 
getInstrumentInfo() - Method in class org.systemsbiology.jrap.MZXMLFileInfo
Get information about the MS instrument used to extract data.
getIntensityCutoff() - Method in class org.systemsbiology.jrap.DataProcessingInfo
Return the intensity cutoff that was used to eliminate low-signal peaks.
getIonisationEnergy() - Method in class org.systemsbiology.jrap.Scan
 
getIonisationEnergy() - Method in class org.systemsbiology.jrap.ScanHeader
 
getIonization() - Method in class org.systemsbiology.jrap.MSInstrumentInfo
 
getLowMz() - Method in class org.systemsbiology.jrap.Scan
 
getLowMz() - Method in class org.systemsbiology.jrap.ScanHeader
 
getManufacturer() - Method in class org.systemsbiology.jrap.MSInstrumentInfo
 
getMassAnalyzer() - Method in class org.systemsbiology.jrap.MSInstrumentInfo
 
getMinimumSize() - Method in class org.systemsbiology.mzxmlviewer.utilities.SpectrumComponent
 
getModel() - Method in class org.systemsbiology.jrap.MSInstrumentInfo
 
getMsLevel() - Method in class org.systemsbiology.jrap.Scan
 
getMsLevel() - Method in class org.systemsbiology.jrap.ScanHeader
 
getNum() - Method in class org.systemsbiology.jrap.Scan
 
getNum() - Method in class org.systemsbiology.jrap.ScanHeader
 
getOperator() - Method in class org.systemsbiology.jrap.MSInstrumentInfo
 
getParentFiles() - Method in class org.systemsbiology.jrap.MZXMLFileInfo
Get information about parent files, chronologically ordered.
getPeakList() - Method in class org.systemsbiology.jrap.Scan
 
getPeaksCount() - Method in class org.systemsbiology.jrap.Scan
 
getPeaksCount() - Method in class org.systemsbiology.jrap.ScanHeader
 
getPolarity() - Method in class org.systemsbiology.jrap.Scan
 
getPolarity() - Method in class org.systemsbiology.jrap.ScanHeader
 
getPrecision() - Method in class org.systemsbiology.jrap.Scan
 
getPrecision() - Method in class org.systemsbiology.jrap.ScanHeader
 
getPrecursorCharge() - Method in class org.systemsbiology.jrap.Scan
 
getPrecursorCharge() - Method in class org.systemsbiology.jrap.ScanHeader
 
getPrecursorMz() - Method in class org.systemsbiology.jrap.Scan
 
getPrecursorMz() - Method in class org.systemsbiology.jrap.ScanHeader
 
getPrecursorScanNum() - Method in class org.systemsbiology.jrap.Scan
 
getPrecursorScanNum() - Method in class org.systemsbiology.jrap.ScanHeader
 
getPreferredSize() - Method in class org.systemsbiology.mzxmlviewer.utilities.SpectrumComponent
 
getRetentionTime() - Method in class org.systemsbiology.jrap.Scan
 
getRetentionTime() - Method in class org.systemsbiology.jrap.ScanHeader
 
getRowCount() - Method in class org.systemsbiology.mzxmlviewer.tables.MzTableModel
 
getScan() - Method in class org.systemsbiology.jrap.SAX2ScanHandler
 
getScanCount() - Method in class org.systemsbiology.jrap.MSXMLParser
Get the total number of scans in the mzXMLfile handled by this parser.
getScanCount() - Method in class org.systemsbiology.jrap.MSXMLParserGeneric
Get the total number of scans in the mzXMLfile handled by this parser.
getScanHeader() - Method in class org.systemsbiology.jrap.SAX2ScanHeaderHandler
 
getScanOffset(int) - Method in class org.systemsbiology.jrap.MSXMLParser
get scan offset, scan number is 1 based.
getScanOffset(int) - Method in class org.systemsbiology.jrap.MSXMLParserGeneric
get scan offset, scan number is 1 based.
getScanOffset(int) - Method in class org.systemsbiology.jrap.SAX2IndexHandler
Get scan offset
getScanType() - Method in class org.systemsbiology.jrap.Scan
 
getScanType() - Method in class org.systemsbiology.jrap.ScanHeader
 
getSha1() - Method in class org.systemsbiology.jrap.ParentFile
Get the sha1-sum of this file.
getSoftwareInfo() - Method in class org.systemsbiology.jrap.MSInstrumentInfo
 
getSoftwareUsed() - Method in class org.systemsbiology.jrap.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.DataProcessingInfo
Were spots integrated?
getStartMz() - Method in class org.systemsbiology.jrap.Scan
 
getStartMz() - Method in class org.systemsbiology.jrap.ScanHeader
 
getTICComponent(ScanHeader[], SpectrumComponent.ClickListener) - Static method in class org.systemsbiology.mzxmlviewer.utilities.SpectrumComponent
 
getTotIonCurrent() - Method in class org.systemsbiology.jrap.Scan
 
getTotIonCurrent() - Method in class org.systemsbiology.jrap.ScanHeader
 
getType() - Method in class org.systemsbiology.jrap.ParentFile
Return the type of parent file.
getURI() - Method in class org.systemsbiology.jrap.ParentFile
Get the URI of this file.
getValue() - Method in class org.systemsbiology.mzxmlviewer.utilities.SwingWorker
Get the value produced by the worker thread, or null if it hasn't been constructed yet.
getValueAt(int, int) - Method in class org.systemsbiology.mzxmlviewer.tables.MzTableModel
 

H

header - Variable in class org.systemsbiology.jrap.Scan
 
HelpMenu - Class in org.systemsbiology.mzxmlviewer.menus
 
highMz - Variable in class org.systemsbiology.jrap.ScanHeader
TODO: Describe

I

idxOffset - Variable in class org.systemsbiology.jrap.SAX2IndexHandler
If an index exists this is the byte position where it occurs
ignorableWhitespace(char[], int, int) - Method in class org.systemsbiology.jrap.SAX2IndexHandler
Ignorable whitespace.
ignorableWhitespace(char[], int, int) - Method in class org.systemsbiology.jrap.SAX2ScanHandler
Ignorable whitespace.
ignorableWhitespace(char[], int, int) - Method in class org.systemsbiology.jrap.SAX2ScanHeaderHandler
Ignorable whitespace.
indexes - Variable in class org.systemsbiology.jrap.MSXMLParser
The indexes
indexes - Variable in class org.systemsbiology.jrap.MSXMLParserGeneric
The indexes
info - Variable in class org.systemsbiology.jrap.MSXMLParser
The information contained in the header of the mzXML file.
info - Variable in class org.systemsbiology.jrap.MSXMLParserGeneric
The information contained in the header of the mzXML file.
info - Variable in class org.systemsbiology.jrap.SAX2HeaderHandler
 
info - Variable in class org.systemsbiology.mzxmlviewer.dialogs.InfoDialog
 
InfoDialog - Class in org.systemsbiology.mzxmlviewer.dialogs
InfoDialog gives information about the header information contained in an mzXML document.
InfoDialog(JFrame, String, MZXMLFileInfo) - Constructor for class org.systemsbiology.mzxmlviewer.dialogs.InfoDialog
 
inPeak - Variable in class org.systemsbiology.jrap.SAX2ScanHandler
Flag to indicate we are reading a peak tag
inPrecursorMZ - Variable in class org.systemsbiology.jrap.SAX2ScanHandler
Flag to indicate if we are reading the precursor MZ value
inPrecursorMZ - Variable in class org.systemsbiology.jrap.SAX2ScanHeaderHandler
Flag to indicate if we are reading the precursor MZ value
instrumentInfo - Variable in class org.systemsbiology.jrap.MZXMLFileInfo
 
intensityCutoff - Variable in class org.systemsbiology.jrap.DataProcessingInfo
 
interrupt() - Method in class org.systemsbiology.mzxmlviewer.utilities.SwingWorker
A new method that interrupts the worker thread.
ionisationEnergy - Variable in class org.systemsbiology.jrap.ScanHeader
TODO: Describe
ionization - Variable in class org.systemsbiology.jrap.MSInstrumentInfo
 

L

lastName - Variable in class org.systemsbiology.jrap.MSOperator
 
LoadDataDialog - Class in org.systemsbiology.mzxmlviewer.utilities
 
LoadDataDialog(MzXMLViewer) - Constructor for class org.systemsbiology.mzxmlviewer.utilities.LoadDataDialog
 
lowMz - Variable in class org.systemsbiology.jrap.ScanHeader
TODO: Describe

M

main(String[]) - Static method in class org.systemsbiology.jrap.Base64
Testing.
main(String[]) - Static method in class org.systemsbiology.mzxmlviewer.Viewer
 
manufacturer - Variable in class org.systemsbiology.jrap.MSInstrumentInfo
 
massAnalyzer - Variable in class org.systemsbiology.jrap.MSInstrumentInfo
 
model - Variable in class org.systemsbiology.jrap.MSInstrumentInfo
 
MSInstrumentInfo - Class in org.systemsbiology.jrap
The MSInstrumentInfo class contains information about the MS instrument used for a certain MzXML file.
MSInstrumentInfo() - Constructor for class org.systemsbiology.jrap.MSInstrumentInfo
 
msInstrumentMode - Variable in class org.systemsbiology.jrap.SAX2HeaderHandler
 
msLevel - Variable in class org.systemsbiology.jrap.ScanHeader
MS Scan Level
MSOperator - Class in org.systemsbiology.jrap
MSOperator provides information on who operated the hardware used to acquire data.
MSOperator() - Constructor for class org.systemsbiology.jrap.MSOperator
 
MSXMLParser - Class in org.systemsbiology.jrap
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.MSXMLParser
 
MSXMLParserGeneric - Class in org.systemsbiology.jrap
A generic utility class for reading an MSXML file in a random access fashion and utilizing a stored scan index for fast reads.
MSXMLParserGeneric(String) - Constructor for class org.systemsbiology.jrap.MSXMLParserGeneric
 
MzTableModel - Class in org.systemsbiology.mzxmlviewer.tables
MzTableModel is a concrete implementation of AbstractTableModel to make a table showing scans.
MzTableModel(ScanHeader[]) - Constructor for class org.systemsbiology.mzxmlviewer.tables.MzTableModel
 
MZXMLFileInfo - Class in org.systemsbiology.jrap
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.MZXMLFileInfo
 
MzXMLViewer - Class in org.systemsbiology.mzxmlviewer
MzXMLViewer is a simple viewer for mzXML files.
MzXMLViewer(File) - Constructor for class org.systemsbiology.mzxmlviewer.MzXMLViewer
Construct the base MzXMLViewer Frame.

N

name - Variable in class org.systemsbiology.jrap.SoftwareInfo
 
NAMESPACE_PREFIXES_FEATURE_ID - Static variable in class org.systemsbiology.jrap.MSXMLParser
Namespace prefixes feature id (http://xml.org/sax/features/namespace-prefixes).
NAMESPACE_PREFIXES_FEATURE_ID - Static variable in class org.systemsbiology.jrap.MSXMLParserGeneric
Namespace prefixes feature id (http://xml.org/sax/features/namespace-prefixes).
NAMESPACES_FEATURE_ID - Static variable in class org.systemsbiology.jrap.MSXMLParser
Namespaces feature id (http://xml.org/sax/features/namespaces).
NAMESPACES_FEATURE_ID - Static variable in class org.systemsbiology.jrap.MSXMLParserGeneric
Namespaces feature id (http://xml.org/sax/features/namespaces).
NO - Static variable in class org.systemsbiology.jrap.DataProcessingInfo
 
num - Variable in class org.systemsbiology.jrap.ScanHeader
Scan Number

O

operator - Variable in class org.systemsbiology.jrap.MSInstrumentInfo
 
org.systemsbiology.jrap - package org.systemsbiology.jrap
 
org.systemsbiology.mzxmlviewer - package org.systemsbiology.mzxmlviewer
 
org.systemsbiology.mzxmlviewer.dialogs - package org.systemsbiology.mzxmlviewer.dialogs
 
org.systemsbiology.mzxmlviewer.menus - package org.systemsbiology.mzxmlviewer.menus
 
org.systemsbiology.mzxmlviewer.tables - package org.systemsbiology.mzxmlviewer.tables
 
org.systemsbiology.mzxmlviewer.utilities - package org.systemsbiology.mzxmlviewer.utilities
 

P

ParentFile - Class in org.systemsbiology.jrap
The ParentFile class contains information about parent files of an mzXML file.
ParentFile(String, String, int) - Constructor for class org.systemsbiology.jrap.ParentFile
 
parentFiles - Variable in class org.systemsbiology.jrap.MZXMLFileInfo
 
parentFiles - Variable in class org.systemsbiology.jrap.SAX2HeaderHandler
 
parseDataProcessing(Attributes) - Method in class org.systemsbiology.jrap.SAX2HeaderHandler
 
parseMSOperator(Attributes) - Method in class org.systemsbiology.jrap.SAX2HeaderHandler
 
parser - Variable in class org.systemsbiology.jrap.MSXMLParser
A handle to the XML parser
parser - Variable in class org.systemsbiology.jrap.MSXMLParserGeneric
A handle to the XML parser
parseSoftware(Attributes) - Method in class org.systemsbiology.jrap.SAX2HeaderHandler
 
peakData - Variable in class org.systemsbiology.jrap.SAX2ScanHandler
A string to hold the Base64 peak data
peaksCount - Variable in class org.systemsbiology.jrap.ScanHeader
Number of peaks in scan
phoneNumber - Variable in class org.systemsbiology.jrap.MSOperator
 
polarity - Variable in class org.systemsbiology.jrap.ScanHeader
TODO: Describe
precision - Variable in class org.systemsbiology.jrap.ScanHeader
TODO: Describe
precursorBuffer - Variable in class org.systemsbiology.jrap.SAX2ScanHandler
Buffer to hold characters while getting precursorMZ value
precursorBuffer - Variable in class org.systemsbiology.jrap.SAX2ScanHeaderHandler
Buffer to hold characters while getting precursorMZ value
precursorCharge - Variable in class org.systemsbiology.jrap.ScanHeader
TODO: Describe
precursorMz - Variable in class org.systemsbiology.jrap.ScanHeader
TODO: Describe
precursorScanNum - Variable in class org.systemsbiology.jrap.ScanHeader
TODO: Describe
printError(String, SAXParseException) - Method in class org.systemsbiology.jrap.SAX2IndexHandler
Prints the error message.
printError(String, SAXParseException) - Method in class org.systemsbiology.jrap.SAX2ScanHandler
Prints the error message.
printError(String, SAXParseException) - Method in class org.systemsbiology.jrap.SAX2ScanHeaderHandler
Prints the error message.
processingInstruction(String, String) - Method in class org.systemsbiology.jrap.SAX2IndexHandler
Processing instruction.
processingInstruction(String, String) - Method in class org.systemsbiology.jrap.SAX2ScanHandler
Processing instruction.
processingInstruction(String, String) - Method in class org.systemsbiology.jrap.SAX2ScanHeaderHandler
Processing instruction.

R

rap(int) - Method in class org.systemsbiology.jrap.MSXMLParser
Read a particular scan from a MSXML file and return a generic Scan object with it's data.
rap(int) - Method in class org.systemsbiology.jrap.MSXMLParserGeneric
Read a particular scan from a MSXML file and return a generic Scan object with it's data.
rapHeader(int) - Method in class org.systemsbiology.jrap.MSXMLParser
 
rapHeader(int) - Method in class org.systemsbiology.jrap.MSXMLParserGeneric
 
read() - Method in class org.systemsbiology.jrap.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.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.Base64
Reads a file and either encodes or decodes it.
readFile(File, boolean) - Static method in class org.systemsbiology.jrap.Base64
Reads a file and either encodes or decodes it.
retentionTime - Variable in class org.systemsbiology.jrap.ScanHeader
TODO: Describe
RootMenuBar - Class in org.systemsbiology.mzxmlviewer.menus
 

S

SAX2HeaderHandler - Class in org.systemsbiology.jrap
SAX2HeaderHandler is a SAX2 XML handler that parses the first part of an mzXML file to extract information that comes before the scans.
SAX2HeaderHandler() - Constructor for class org.systemsbiology.jrap.SAX2HeaderHandler
 
SAX2IndexHandler - Class in org.systemsbiology.jrap
 
SAX2IndexHandler() - Constructor for class org.systemsbiology.jrap.SAX2IndexHandler
 
SAX2ScanHandler - Class in org.systemsbiology.jrap
 
SAX2ScanHandler() - Constructor for class org.systemsbiology.jrap.SAX2ScanHandler
 
SAX2ScanHeaderHandler - Class in org.systemsbiology.jrap
 
SAX2ScanHeaderHandler() - Constructor for class org.systemsbiology.jrap.SAX2ScanHeaderHandler
 
Scan - Class in org.systemsbiology.jrap
A simple class to hold the contents of a scan from a MSXML file.
Scan() - Constructor for class org.systemsbiology.jrap.Scan
Default constructor, initializes an empty Scan.
scanClicked(int) - Method in class org.systemsbiology.mzxmlviewer.MzXMLViewer
 
scanClicked(int) - Method in interface org.systemsbiology.mzxmlviewer.utilities.SpectrumComponent.ClickListener
 
ScanHeader - Class in org.systemsbiology.jrap
ScanHeader is a class that contains all information associated with a Scan, except for the actual peakList.
ScanHeader() - Constructor for class org.systemsbiology.jrap.ScanHeader
 
scanType - Variable in class org.systemsbiology.jrap.ScanHeader
TODO: Describe
SCHEMA_FULL_CHECKING_FEATURE_ID - Static variable in class org.systemsbiology.jrap.MSXMLParser
Schema full checking feature id (http://apache.org/xml/features/validation/schema-full-checking).
SCHEMA_VALIDATION_FEATURE_ID - Static variable in class org.systemsbiology.jrap.MSXMLParser
Schema validation feature id (http://apache.org/xml/features/validation/schema).
selectScan(int) - Method in class org.systemsbiology.mzxmlviewer.MzXMLViewer
Display the currently selected scan.
setBasePeakIntensity(float) - Method in class org.systemsbiology.jrap.Scan
Set the intensity of the base peak
setBasePeakIntensity(float) - Method in class org.systemsbiology.jrap.ScanHeader
 
setBasePeakMz(float) - Method in class org.systemsbiology.jrap.Scan
Set the base peak m/z value for this scan
setBasePeakMz(float) - Method in class org.systemsbiology.jrap.ScanHeader
 
setByteOrder(String) - Method in class org.systemsbiology.jrap.Scan
 
setByteOrder(String) - Method in class org.systemsbiology.jrap.ScanHeader
 
setCentroided(int) - Method in class org.systemsbiology.jrap.DataProcessingInfo
Set centroided to one of UNKNOWN, YES or NO.
setCentroided(int) - Method in class org.systemsbiology.jrap.Scan
Set if this scan was centroided or not
setCentroided(int) - Method in class org.systemsbiology.jrap.ScanHeader
 
setChargeDeconvoluted(int) - Method in class org.systemsbiology.jrap.DataProcessingInfo
Set charge deconvoluted to one of UNKNOWN, YES or NO.
setChargeDeconvoluted(int) - Method in class org.systemsbiology.jrap.Scan
Set if this scan was charge deconvoluted or not
setChargeDeconvoluted(int) - Method in class org.systemsbiology.jrap.ScanHeader
 
setCollisionEnergy(float) - Method in class org.systemsbiology.jrap.Scan
Set the collision energy used in this scan.
setCollisionEnergy(float) - Method in class org.systemsbiology.jrap.ScanHeader
 
setCompressedLen(int) - Method in class org.systemsbiology.jrap.Scan
 
setCompressedLen(int) - Method in class org.systemsbiology.jrap.ScanHeader
 
setCompressionType(String) - Method in class org.systemsbiology.jrap.Scan
 
setCompressionType(String) - Method in class org.systemsbiology.jrap.ScanHeader
 
setContentType(String) - Method in class org.systemsbiology.jrap.Scan
 
setContentType(String) - Method in class org.systemsbiology.jrap.ScanHeader
 
setDeisotoped(int) - Method in class org.systemsbiology.jrap.DataProcessingInfo
Set deisotoped to one of UNKNOWN, YES or NO.
setDeisotoped(int) - Method in class org.systemsbiology.jrap.Scan
Set if this scan was deisotoped or not
setDeisotoped(int) - Method in class org.systemsbiology.jrap.ScanHeader
 
setDoubleMassIntensityList(double[][]) - Method in class org.systemsbiology.jrap.Scan
 
setEndMz(float) - Method in class org.systemsbiology.jrap.Scan
 
setEndMz(float) - Method in class org.systemsbiology.jrap.ScanHeader
 
setFloatMassIntensityList(float[][]) - Method in class org.systemsbiology.jrap.Scan
 
setHeader(ScanHeader) - Method in class org.systemsbiology.jrap.Scan
 
setHighMz(float) - Method in class org.systemsbiology.jrap.Scan
 
setHighMz(float) - Method in class org.systemsbiology.jrap.ScanHeader
 
setIntensityCutoff(double) - Method in class org.systemsbiology.jrap.DataProcessingInfo
Set the intensity cutoff that was used to eliminate low-signal peaks.
setIonisationEnergy(float) - Method in class org.systemsbiology.jrap.Scan
Set the ionisation energy used in this scan.
setIonisationEnergy(float) - Method in class org.systemsbiology.jrap.ScanHeader
 
setLowMz(float) - Method in class org.systemsbiology.jrap.Scan
 
setLowMz(float) - Method in class org.systemsbiology.jrap.ScanHeader
 
setMsLevel(int) - Method in class org.systemsbiology.jrap.Scan
Set the MS level of this scan
setMsLevel(int) - Method in class org.systemsbiology.jrap.ScanHeader
 
setNum(int) - Method in class org.systemsbiology.jrap.Scan
Set the number of this scan in the file.
setNum(int) - Method in class org.systemsbiology.jrap.ScanHeader
 
setPeakList(float[][]) - Method in class org.systemsbiology.jrap.Scan
 
setPeaksCount(int) - Method in class org.systemsbiology.jrap.Scan
Set the number of peaks in this scan.
setPeaksCount(int) - Method in class org.systemsbiology.jrap.ScanHeader
 
setPolarity(String) - Method in class org.systemsbiology.jrap.Scan
Set the polarity of this scan
setPolarity(String) - Method in class org.systemsbiology.jrap.ScanHeader
 
setPrecision(int) - Method in class org.systemsbiology.jrap.Scan
 
setPrecision(int) - Method in class org.systemsbiology.jrap.ScanHeader
 
setPrecursorCharge(int) - Method in class org.systemsbiology.jrap.Scan
Set the charge of the precursor of this scan
setPrecursorCharge(int) - Method in class org.systemsbiology.jrap.ScanHeader
 
setPrecursorMz(float) - Method in class org.systemsbiology.jrap.Scan
Set the precursor m/z value for this scan
setPrecursorMz(float) - Method in class org.systemsbiology.jrap.ScanHeader
 
setPrecursorScanNum(int) - Method in class org.systemsbiology.jrap.Scan
Set the scan number in which the precursor of this scan was acquired
setPrecursorScanNum(int) - Method in class org.systemsbiology.jrap.ScanHeader
 
setRetentionTime(String) - Method in class org.systemsbiology.jrap.Scan
Set the retention time at which this scan was acquired
setRetentionTime(String) - Method in class org.systemsbiology.jrap.ScanHeader
 
setScan(Scan) - Method in class org.systemsbiology.mzxmlviewer.utilities.SpectrumComponent
 
setScanType(String) - Method in class org.systemsbiology.jrap.Scan
Set the type of this scan
setScanType(String) - Method in class org.systemsbiology.jrap.ScanHeader
 
setSoftwareUsed(SoftwareInfo[]) - Method in class org.systemsbiology.jrap.DataProcessingInfo
Set the chronological array of used software for data processing.
setSpotIntegration(int) - Method in class org.systemsbiology.jrap.DataProcessingInfo
Set spot integration to one of UNKNOWN, YES or NO.
setStartMz(float) - Method in class org.systemsbiology.jrap.Scan
 
setStartMz(float) - Method in class org.systemsbiology.jrap.ScanHeader
 
setTotIonCurrent(float) - Method in class org.systemsbiology.jrap.Scan
Set the total ion current of this scan
setTotIonCurrent(float) - Method in class org.systemsbiology.jrap.ScanHeader
 
sha1 - Variable in class org.systemsbiology.jrap.ParentFile
 
showAboutBox() - Method in class org.systemsbiology.mzxmlviewer.MzXMLViewer
 
showInfoDialog() - Method in class org.systemsbiology.mzxmlviewer.MzXMLViewer
 
softwareInfo - Variable in class org.systemsbiology.jrap.MSInstrumentInfo
 
SoftwareInfo - Class in org.systemsbiology.jrap
SoftwareInfo represents data that is available on software that has processed a mzXML file.
SoftwareInfo() - Constructor for class org.systemsbiology.jrap.SoftwareInfo
 
softwareUsed - Variable in class org.systemsbiology.jrap.DataProcessingInfo
 
SpectrumComponent - Class in org.systemsbiology.mzxmlviewer.utilities
SpectrumComponent provides a view of a spectrum using JFreeChart.
SpectrumComponent() - Constructor for class org.systemsbiology.mzxmlviewer.utilities.SpectrumComponent
 
SpectrumComponent.ClickListener - Interface in org.systemsbiology.mzxmlviewer.utilities
 
spotIntegration - Variable in class org.systemsbiology.jrap.DataProcessingInfo
 
start() - Method in class org.systemsbiology.mzxmlviewer.utilities.SwingWorker
Start the worker thread.
startDocument() - Method in class org.systemsbiology.jrap.SAX2IndexHandler
Start document.
startDocument() - Method in class org.systemsbiology.jrap.SAX2ScanHandler
Start document.
startDocument() - Method in class org.systemsbiology.jrap.SAX2ScanHeaderHandler
Start document.
startElement(String, String, String, Attributes) - Method in class org.systemsbiology.jrap.SAX2HeaderHandler
 
startElement(String, String, String, Attributes) - Method in class org.systemsbiology.jrap.SAX2IndexHandler
Start element.
startElement(String, String, String, Attributes) - Method in class org.systemsbiology.jrap.SAX2ScanHandler
Start element.
startElement(String, String, String, Attributes) - Method in class org.systemsbiology.jrap.SAX2ScanHeaderHandler
Start element.
startMz - Variable in class org.systemsbiology.jrap.ScanHeader
TODO: Describe
SUCCESSFUL_COMPLETION_MESSAGE - Static variable in class org.systemsbiology.jrap.SAX2HeaderHandler
 
SwingWorker - Class in org.systemsbiology.mzxmlviewer.utilities
Copyright 2003 Sun Microsystems, Inc.
SwingWorker() - Constructor for class org.systemsbiology.mzxmlviewer.utilities.SwingWorker
Start a thread that will call the construct method and then exit.

T

tabbedPane - Variable in class org.systemsbiology.mzxmlviewer.dialogs.InfoDialog
 
tmpScan - Variable in class org.systemsbiology.jrap.SAX2ScanHandler
A new Scan Object
tmpScanHeader - Variable in class org.systemsbiology.jrap.SAX2ScanHeaderHandler
A new ScanHeader Object
toString() - Method in class org.systemsbiology.jrap.Scan
String respresentation of a Scan object.
toString() - Method in class org.systemsbiology.jrap.ScanHeader
String respresentation of a ScanHeader object.
totIonCurrent - Variable in class org.systemsbiology.jrap.ScanHeader
TODO: Describe
type - Variable in class org.systemsbiology.jrap.ParentFile
 
type - Variable in class org.systemsbiology.jrap.SoftwareInfo
 
TYPE_PROCESSED - Static variable in class org.systemsbiology.jrap.ParentFile
 
TYPE_RAW - Static variable in class org.systemsbiology.jrap.ParentFile
 

U

UNKNOWN - Static variable in class org.systemsbiology.jrap.DataProcessingInfo
 
URI - Variable in class org.systemsbiology.jrap.MSOperator
 
URI - Variable in class org.systemsbiology.jrap.ParentFile
 

V

VALIDATION_FEATURE_ID - Static variable in class org.systemsbiology.jrap.MSXMLParser
Validation feature id (http://xml.org/sax/features/validation).
VALIDATION_FEATURE_ID - Static variable in class org.systemsbiology.jrap.MSXMLParserGeneric
Validation feature id (http://xml.org/sax/features/validation).
valueToString(int) - Method in class org.systemsbiology.mzxmlviewer.dialogs.InfoDialog
 
version - Variable in class org.systemsbiology.jrap.SoftwareInfo
 
VERSION_STRING - Static variable in class org.systemsbiology.mzxmlviewer.MzXMLViewer
 
Viewer - Class in org.systemsbiology.mzxmlviewer
 
Viewer() - Constructor for class org.systemsbiology.mzxmlviewer.Viewer
 

W

warning(SAXParseException) - Method in class org.systemsbiology.jrap.SAX2IndexHandler
Warning.
warning(SAXParseException) - Method in class org.systemsbiology.jrap.SAX2ScanHandler
Warning.
warning(SAXParseException) - Method in class org.systemsbiology.jrap.SAX2ScanHeaderHandler
Warning.
write(int) - Method in class org.systemsbiology.jrap.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.Base64.OutputStream
Calls Base64.OutputStream.write(int) repeatedly until len bytes are written.
writeFile(byte[], String, boolean) - Static method in class org.systemsbiology.jrap.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.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.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.DataProcessingInfo
 

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