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

A

AsciiHexInputStream - class org.mbari.io.AsciiHexInputStream.

Used for reading ASCII hexadecimal values from a stream.

AsciiHexInputStream(InputStream) - Constructor for class org.mbari.io.AsciiHexInputStream

AsciiHexReader - class org.mbari.io.AsciiHexReader.

Convert

AsciiHexReader(Reader) - Constructor for class org.mbari.io.AsciiHexReader

accept(File, String) - Method in class org.mbari.hobilabs.HRCalFileNameFilter

accept(File, String) - Method in class org.mbari.io.GenericFilenameFilter

accept(File, String) - Method in class org.mbari.io.NcFilenameFilter

accept(File, String) - Method in class org.mbari.io.OasisExtractFilter

altitude - Variable in class org.mbari.util.SolarPosition

attributes - Variable in class org.mbari.oasis.OMSAttributeReader

axesP - Variable in class org.mbari.oasis.OMSAbstractSchemaConstructor

azimuth - Variable in class org.mbari.util.SolarPosition

B

BOTTOM - Static variable in class org.mbari.awt.layout.VerticalFlowLayout

binarySearch(Array, long, int) - Static method in class org.mbari.ma2.Ma2Util

Search a multiarray using a binary search

binarySearch(double[], double) - Static method in class org.mbari.util.MathUtil

Searches the specified array of doubles for the specified value using the binary search algorithm.

C

COLUMNS - Static variable in class org.mbari.io.OasisPco2Reader

CalibrationHistory - class org.mbari.oasis.CalibrationHistory.

Contains methods for storing and retrieving calibration history information for MBARI moorings.

CalibrationHistory() - Constructor for class org.mbari.oasis.CalibrationHistory

Default Constructor.

CalibrationHistory(String) - Constructor for class org.mbari.oasis.CalibrationHistory

Adds the isntrument type to the list.

CalibrationHistoryFactory - class org.mbari.oasis.CalibrationHistoryFactory.

Constructs a CalibrationHistory instance from a OASIS mooring configuration file.

CalibrationHistoryFactory(String) - Constructor for class org.mbari.oasis.CalibrationHistoryFactory

CalibrationHistoryFactory(File) - Constructor for class org.mbari.oasis.CalibrationHistoryFactory

calcIrradiance(long, double, double, double, double, double) - Method in class org.mbari.model.solar.FrouinIrradianceModel

This subroutine calculates the incoming clear-sky solar irradiance just above the surface at SeaWiFS wavelengths (412, 443, 490, 510, 555, 670 nm), using this equation: E = E0 * ESfactor * COS(SolZen) * TransG * TransA / (1 - (Sa * As)) where: E0 = extra-terrestrial solar irradiance (mW/cm^2/um) ESfactor = Earth-Sun distance factor SolZen = solar zenith angle (deg).

calcIrradiance(long, double, double) - Method in class org.mbari.model.solar.FrouinIrradianceModel

calcIrradiance(int, int, int, double, double, double) - Method in class org.mbari.model.solar.FrouinIrradianceModel

Haven't checked this yet

calcSurfSolIrrad(double[], int, int, int, double, double, double, double, double, double) - Static method in class org.mbari.model.solar.FrouinExtended

This subroutine calculates the incoming clear-sky solar irradiance just above the surface at SeaWiFS wavelengths (412, 443, 490, 510, 555, 670 nm), using this equation: E = E0 * ESfactor * COS(SolZen) * TransG * TransA / (1 - (Sa * As)) where: E0 = extra-terrestrial solar irradiance (mW/cm^2/um) ESfactor = Earth-Sun distance factor SolZen = solar zenith angle (deg).

calcSurfSolIrrad(double[], long, double, double) - Static method in class org.mbari.model.solar.FrouinExtended

calcSurfSolIrrad(double[], int, int, int, double, double, double) - Static method in class org.mbari.model.solar.FrouinExtended

calcWavelength(HRPacket, double[]) - Static method in class org.mbari.util.HRUtil

calcWavelength(double, double, double, double[]) - Static method in class org.mbari.util.HRUtil

cfgfile - Variable in class org.mbari.oasis.OMSAbstractSchema

cfgfile - Variable in class org.mbari.oasis.OMSAbstractSchemaConstructor

coallate(File, File) - Static method in class org.mbari.oasis.OasisFileCoallator

Combine files created by extract.

coallate(File) - Static method in class org.mbari.oasis.OasisFileCoallator

Combine files created by extract.

coallate(String) - Static method in class org.mbari.oasis.OasisFileCoallator

Combine files created by extract.

coallate(String, String) - Static method in class org.mbari.oasis.OasisFileCoallator

Combine files created by extract.

columnNames - Variable in class org.mbari.io.DelimitedFile

convert() - Method in class org.mbari.hobilabs.HRBinaryConverter

countAttributes() - Method in class org.mbari.oasis.OMSAttributeReader

Count the number of attributes in the file

countBanks() - Method in class org.mbari.oasis.OMSConfigReader

countChannels() - Method in class org.mbari.oasis.OMSConfigReader

countColumns() - Method in class org.mbari.io.FlatFileReader

Method to get the number of columns in the data array

countRows() - Method in class org.mbari.io.FlatFileReader

Method to get the number of rows in the data array

countVariables() - Method in class org.mbari.oasis.OMSVariableReader

Count the number of variables in the file

cumSum(double[]) - Static method in class org.mbari.util.MathUtil

Cumulatively sum a vector Example: cumSum([1 1 1 1 2]) = [1 2 3 4 6]

D

DateConverter - class org.mbari.util.DateConverter.

Utilities for converting between diferent types of commonly used scientific date formats

DateConverter() - Constructor for class org.mbari.util.DateConverter

DelimitedFile - class org.mbari.io.DelimitedFile.

Read a delimited text file into a double array.

DelimitedFile(String) - Constructor for class org.mbari.io.DelimitedFile

Create a DelimitedFileReader.

DelimitedFile(File) - Constructor for class org.mbari.io.DelimitedFile

Create a DelimitedFileReader and intialize memory.

Depth - Variable in class org.mbari.hobilabs.HRPacket

DirNode - class org.mbari.swing.tree.DirNode.

Represents a directory node in a tree

DirNode(File) - Constructor for class org.mbari.swing.tree.DirNode

DirectoryTree1 - class org.mbari.swing.DirectoryTree1.

Creates a directory tree (folders only) of all roots and allows the user to open and drill down through these directories

DirectoryTree1() - Constructor for class org.mbari.swing.DirectoryTree1

Defualt constructor.

Do - Variable in class org.mbari.hobilabs.HRPacket

Drazen - class org.mbari.gis.Drazen.

Drazen() - Constructor for class org.mbari.gis.Drazen

Dt - Variable in class org.mbari.hobilabs.HRPacket

DuplicateRemover - class org.mbari.oasis.DuplicateRemover.

Removes duplicate data lines and sorts the data from OASIS data files.

If the file does not contain duplicate or unsorted daa it will not be rewritten.

DuplicateRemover(String) - Constructor for class org.mbari.oasis.DuplicateRemover

DuplicateRemover(File) - Constructor for class org.mbari.oasis.DuplicateRemover

data - Variable in class org.mbari.io.DelimitedFile

data - Variable in class org.mbari.io.FlatFileReader

Description of the Field

dateToDayOfYear(Date) - Static method in class org.mbari.util.DateConverter

dateToDayOfYear(long) - Static method in class org.mbari.util.DateConverter

dateToDayOfYear(Date) - Static method in class org.mbari.util.TimeUtil

dateToDayOfYear(long) - Static method in class org.mbari.util.TimeUtil

dayNumber(int, int, int) - Static method in class org.mbari.model.solar.FrouinExtended

subroutine day_number(jday,month,ia,j)

dayOfYearToDate(double, double) - Static method in class org.mbari.util.TimeUtil

Convert the Day of a Year to a Date object.

dayOfYearToDate(int, int) - Static method in class org.mbari.util.TimeUtil

Convert the Day of a Year to a Date object

dayOfYearToDate(float, int) - Static method in class org.mbari.util.TimeUtil

Convert the Day of a Year to a Date object

dayOfYearToDate(double, int) - Static method in class org.mbari.util.TimeUtil

Convert the Day of a Year to a Date object

decode() - Method in class org.mbari.hobilabs.HRBinaryDecoder

Method to process the binary file.

distance - Variable in class org.mbari.util.SolarPosition

doyToDate(double, double) - Static method in class org.mbari.util.DateConverter

Convert the Day of a Year to a Date object.

doyToDate(int, int) - Static method in class org.mbari.util.DateConverter

Convert the Day of a Year to a Date object

doyToDate(float, int) - Static method in class org.mbari.util.DateConverter

Convert the Day of a Year to a Date object

doyToDate(double, int) - Static method in class org.mbari.util.DateConverter

Convert the Day of a Year to a Date object

E

EARTH_ORBIT_ECCENTRICITY - Static variable in class org.mbari.util.SolarUtil

estimDobson(int, double) - Static method in class org.mbari.model.solar.FrouinExtended

Estimate Dobson units from climatology, given the month and latitude.

estimDobson(int, double) - Static method in class org.mbari.util.SolarUtil

Estimate Dobson units from climatology, given the month and latitude.

explore() - Method in class org.mbari.swing.tree.DirNode

explore() - Method in class org.mbari.swing.tree.FileNode

explore() - Method in class org.mbari.swing.tree.FileSystemNode

F

FileChoicePanelOpen1 - class org.mbari.swing.FileChoicePanelOpen1.

A standard widget used for browsing for a file to open.

FileChoicePanelOpen1() - Constructor for class org.mbari.swing.FileChoicePanelOpen1

FileChoicePanelSave1 - class org.mbari.swing.FileChoicePanelSave1.

A standard widget used for browsing for a file to save to.

FileChoicePanelSave1() - Constructor for class org.mbari.swing.FileChoicePanelSave1

FileListPanel1 - class org.mbari.swing.FileListPanel1.

A standard widget for selecting multiple files.

FileListPanel1() - Constructor for class org.mbari.swing.FileListPanel1

FileNode - class org.mbari.swing.tree.FileNode.

Represents a file node in a tree.

FileNode(File) - Constructor for class org.mbari.swing.tree.FileNode

FileOpenPanel1 - class org.mbari.swing.FileOpenPanel1.

A standard widget used for browsing for files to open.

FileOpenPanel1() - Constructor for class org.mbari.swing.FileOpenPanel1

FileProgressFrame - class org.mbari.swing.FileProgressFrame.

A frame containing a progress bar.

FileProgressFrame() - Constructor for class org.mbari.swing.FileProgressFrame

FileSavePanel1 - class org.mbari.swing.FileSavePanel1.

A standard widget used for browsing for files to save.

FileSavePanel1() - Constructor for class org.mbari.swing.FileSavePanel1

FileSystemNode - class org.mbari.swing.tree.FileSystemNode.

Reprents a File or directory node in a tree.

FileSystemNode(File) - Constructor for class org.mbari.swing.tree.FileSystemNode

FileUtil - class org.mbari.util.FileUtil.

Utilities for working with files.

FirstPix - Variable in class org.mbari.hobilabs.HRPacket

FlatFileReader - class org.mbari.io.FlatFileReader.

Constructors initialize memory only, to actually read the data file call the readFile method.

FlatFileReader(String) - Constructor for class org.mbari.io.FlatFileReader

Create a FlatFileReader and intialize memory.

FlatFileReader(File) - Constructor for class org.mbari.io.FlatFileReader

Create a FlatFileReader and intialize memory.

FlatFileReader(String, int) - Constructor for class org.mbari.io.FlatFileReader

Create a FlatFileReader and intialize memory.

FlatFileReader(File, int) - Constructor for class org.mbari.io.FlatFileReader

Create a FlatFileReader and intialize memory.

FrouinExtended - class org.mbari.model.solar.FrouinExtended.

Test program for subroutine to calculate clear-sky solar irradiance at the surface at the SeaWiFS wavelengths (412, 443, 490, 510, 555, 670 nm).

FrouinExtended() - Constructor for class org.mbari.model.solar.FrouinExtended

FrouinIrradianceModel - class org.mbari.model.solar.FrouinIrradianceModel.

FrouinIrradianceModel(double[]) - Constructor for class org.mbari.model.solar.FrouinIrradianceModel

file - Variable in class org.mbari.io.FlatFileReader

Description of the Field

find(double[], double) - Static method in class org.mbari.util.MathUtil

fix(double) - Static method in class org.mbari.util.MathUtil

G

GenericFilenameFilter - class org.mbari.io.GenericFilenameFilter.

GenericFilenameFilter() - Constructor for class org.mbari.io.GenericFilenameFilter

GenericFilenameFilter(String, String) - Constructor for class org.mbari.io.GenericFilenameFilter

GisUtil - class org.mbari.gis.util.GisUtil.

Static methods useful for GIS Applications

GmtCalendar - class org.mbari.util.GmtCalendar.

GmtCalendar is a useful class for working with times that are based using GMT time.

GmtCalendar(int, int, int) - Constructor for class org.mbari.util.GmtCalendar

Constructs a GmtCalendar with the given date set in the GMT time zone with the default locale.

GmtCalendar(int, int, int, int, int) - Constructor for class org.mbari.util.GmtCalendar

Constructs a GregorianCalendar with the given date and time set for the GMT time zone with the default locale.

GmtCalendar(int, int, int, int, int, int) - Constructor for class org.mbari.util.GmtCalendar

Constructs a GregorianCalendar with the given date and time set for the GMT time zone with the default locale.

GmtCalendar(Date) - Constructor for class org.mbari.util.GmtCalendar

Constructor for the GmtCalendar object

GmtCalendar(long) - Constructor for class org.mbari.util.GmtCalendar

Constructor for the GmtCalendar object

geoToUtm(double, double, int) - Static method in class org.mbari.gis.util.GisUtil

Converts a set of Longitude and Latitude co-ordinates to UTM for the WGS84 ellipsoid

get() - Method in class org.mbari.hobilabs.HRParser

This method is used to get the data after it's been parsed

get(String) - Method in class org.mbari.io.OasisPco2Reader

Return the data

get(Date) - Method in class org.mbari.oasis.CalibrationHistory

Returns the name of the correct calibration file to use based on date

get(long) - Method in class org.mbari.oasis.CalibrationHistory

Returns the name of the correct calibration file to use based on date

get(String) - Method in class org.mbari.oasis.Pco2Reader

Return the data

getAWave() - Method in class org.mbari.hobilabs.HRCalibrationFileReader

getAllowsChildren() - Method in class org.mbari.swing.tree.FileSystemNode

getAttribute(int) - Method in class org.mbari.oasis.OMSAttributeReader

Get a single attribute

getAttributes() - Method in class org.mbari.oasis.OMSAttributeReader

Get all attributes

getAxes() - Method in class org.mbari.oasis.OMSAbstractSchemaConstructor

getBWave() - Method in class org.mbari.hobilabs.HRCalibrationFileReader

getBank() - Method in class org.mbari.oasis.OMSSensor

getCWave() - Method in class org.mbari.hobilabs.HRCalibrationFileReader

getCalData() - Method in class org.mbari.io.OasisPco2Reader2

getCalTime() - Method in class org.mbari.io.OasisPco2Reader2

getChannel() - Method in class org.mbari.oasis.OMSSensor

getChannelNumber() - Method in class org.mbari.hobilabs.HRBinaryDecoder

getChannelsInBank(int) - Method in class org.mbari.oasis.OMSConfigReader

getChooser() - Method in class org.mbari.swing.FileChoicePanelOpen1

Return the chooser used for this component.

getChooser() - Method in class org.mbari.swing.FileChoicePanelSave1

Return the chooser used for this component.

getChooser() - Method in class org.mbari.swing.FileListPanel1

Return the chooser used for this component.

getChooser() - Method in class org.mbari.swing.FileOpenPanel1

Return the chooser used for this component.

getChooser() - Method in class org.mbari.swing.FileSavePanel1

Return the chooser used for this component.

getCoef() - Method in class org.mbari.oasis.OMSSensor

getColumn(int) - Method in class org.mbari.io.FlatFileReader

Return a specific column of data.

getColumnNames() - Method in class org.mbari.io.DelimitedFile

getColumnNames() - Method in class org.mbari.oasis.Pco2FileFormat

getCommentTag() - Method in class org.mbari.io.DelimitedFile

getCompleteConfiguration() - Method in class org.mbari.oasis.OMSConfigReader

Returns the complete configuration as listed in the config files.

getCompleteConfiguration(int) - Method in class org.mbari.oasis.OMSConfigReader

getConfiguration() - Method in class org.mbari.oasis.OMSConfigReader

Get the configuration information out of the files.

getConfiguration(int) - Method in class org.mbari.oasis.OMSConfigReader

Return the configuration parameters from a single sensor

getCorrectedETIrradiance(double[], int) - Static method in class org.mbari.util.SolarUtil

getDWave() - Method in class org.mbari.hobilabs.HRCalibrationFileReader

getData() - Method in class org.mbari.hobilabs.HRBinaryDecoder

getData() - Method in class org.mbari.io.DelimitedFile

Accesor method to access the data in the flat file

getData() - Method in class org.mbari.io.FlatFileReader

Accesor method to access the data in the flat file

getData(int, int) - Method in class org.mbari.io.FlatFileReader

Accesor method to access a single data point in the flat file

getData() - Method in class org.mbari.io.OasisPco2Reader2

Return the data

getDataDescription() - Method in class org.mbari.hobilabs.HRBinaryDecoder

Returns a string of the channel description.

getDataSymbol(OMSSensor) - Static method in class org.mbari.oasis.OMSUtil

Returns a short symbol used to represent the data in equations.

getDataType() - Method in class org.mbari.hobilabs.HRBinaryDecoder

getDateFromName(String) - Static method in class org.mbari.oasis.OMSUtil

Converts a file name like '99123' or '1999123' to a Date object

getDatum(int, int) - Method in class org.mbari.io.DelimitedFile

getDay(String) - Static method in class org.mbari.oasis.OMSUtil

Extract the day from filenames of types 'yyddd' or 'yyyyddd'.

getDefault() - Method in class org.mbari.oasis.CalibrationHistory

returns the default calibration.

getDefaultListModel() - Method in class org.mbari.swing.MultiFileSelectPanel1

getDefaultTreeModel() - Static method in class org.mbari.swing.DirectoryTree1

Evidently I can't just override JTree's getDefaultTreeModel.

getDelimiter() - Method in class org.mbari.io.DelimitedFile

getDepth() - Method in class org.mbari.hobilabs.HSDPacket

getDirRoots() - Static method in class org.mbari.util.FileUtil

List the available root directories.

getE0(double[]) - Static method in class org.mbari.model.solar.FrouinExtended

getEarthSunDistanceLP(int) - Static method in class org.mbari.util.SolarUtil

Low Precision Distance in astronomical units

getEarthSunIrradianceCorrectionLP(int) - Static method in class org.mbari.util.SolarUtil

Low Precision This is equal to 1/earthSunDistance

getFile() - Method in class org.mbari.io.DelimitedFile

Accesor method to get the file read by the FlatFileReader

getFile() - Method in class org.mbari.swing.FileChoicePanelOpen1

getFile() - Method in class org.mbari.swing.FileChoicePanelSave1

getFile() - Method in class org.mbari.swing.FileOpenPanel1

getFile() - Method in class org.mbari.swing.FileSavePanel1

getFile() - Method in class org.mbari.swing.tree.FileSystemNode

getFile(String) - Static method in class org.mbari.util.SystemUtil

getFilename() - Method in class org.mbari.io.DelimitedFile

Deprecated. 07 Feb 2002; use getFile() instead

getFilename() - Method in class org.mbari.io.FlatFileReader

Accesor method to get the filename of read by the FlatFileReader

getFilename() - Method in class org.mbari.oasis.OMSAttributeReader

getFilename() - Method in class org.mbari.oasis.OMSConfigReader

getFilename() - Method in class org.mbari.oasis.OMSVariableReader

getFormat() - Method in class org.mbari.oasis.Pco2Reader

getGain() - Method in class org.mbari.hobilabs.HSDPacket

getGain(int) - Method in class org.mbari.hobilabs.HSDPacket

getHasColumnNames() - Method in class org.mbari.io.DelimitedFile

getHgap() - Method in class org.mbari.awt.layout.VerticalFlowLayout

Gets the horizontal gap between components.

getHistory(String) - Method in class org.mbari.oasis.CalibrationHistoryFactory

getHorizontalFill() - Method in class org.mbari.awt.layout.VerticalFlowLayout

getID() - Method in class org.mbari.hobilabs.HRCalibrationFileReader

getInstrumentType() - Method in class org.mbari.hobilabs.HRBinaryDecoder

getInstrumentType() - Method in class org.mbari.oasis.CalibrationHistory

Returns the type of instrument calibrations stored in this object

getJProgressBar() - Method in class org.mbari.swing.FileProgressFrame

getJulianDate(Date) - Static method in class org.mbari.util.TimeUtil

getJulianDate(long[]) - Static method in class org.mbari.util.TimeUtil

getJulianDate(long) - Static method in class org.mbari.util.TimeUtil

Julian Date (not Day of Year).

getKO3(double[]) - Static method in class org.mbari.model.solar.FrouinExtended

getLongName(String) - Static method in class org.mbari.oasis.OMSUtil

Assign a long descriptive name based on the short name found in the calibration files.

getLongName() - Method in class org.mbari.oasis.Pco2FileFormat

getMaxNumColumns() - Method in class org.mbari.oasis.Pco2FileFormat

getMillivolts() - Method in class org.mbari.io.OasisPco2Reader

getMillivolts(String) - Method in class org.mbari.io.OasisPco2Reader

getMinMax() - Method in class org.mbari.oasis.OMSSensor

getMinNumColumns() - Method in class org.mbari.oasis.Pco2FileFormat

getName() - Method in class org.mbari.oasis.OMSSensor

getNeckelLabIrradiance(double[]) - Static method in class org.mbari.util.SolarUtil

getNeckelLabIrradiance() - Static method in class org.mbari.util.SolarUtil

getNeckelLabWavelengths() - Static method in class org.mbari.util.SolarUtil

getNumOfColumns() - Method in class org.mbari.io.DelimitedFile

Method to get the number of columns in the data array

getNumOfRows() - Method in class org.mbari.io.DelimitedFile

Method to get the number of rows in the data array

getNumberOfBanks() - Method in class org.mbari.oasis.OMSConfigReader

Deprecated. Use countBanks

getNumberOfChannels() - Method in class org.mbari.oasis.OMSConfigReader

getOzoneAbsorption() - Static method in class org.mbari.util.SolarUtil

getOzoneAbsorption(double[]) - Static method in class org.mbari.util.SolarUtil

getOzoneWavelengths() - Static method in class org.mbari.util.SolarUtil

getPco2() - Method in class org.mbari.io.OasisPco2Reader

getPco2(String) - Method in class org.mbari.io.OasisPco2Reader

getPco2() - Method in class org.mbari.oasis.Pco2Reader

getPco2(String) - Method in class org.mbari.oasis.Pco2Reader

getPressure() - Method in class org.mbari.io.OasisPco2Reader

getPressure(String) - Method in class org.mbari.io.OasisPco2Reader

getProperties() - Method in class org.mbari.hobilabs.HS2CalibrationFileReader

Returns a Properties object for the values found in the calibration file.

getSchema() - Method in class org.mbari.oasis.OMSAbstractSchema

Return the schema for use in creating a netCDF file

getSchema() - Method in class org.mbari.oasis.OMSAbstractSchemaConstructor

Return the schema for use in creating a netCDF file

getSensors() - Method in class org.mbari.oasis.OMSAbstractSchema

getSensors() - Method in class org.mbari.oasis.OMSAbstractSchemaConstructor

getSensors() - Method in class org.mbari.oasis.OMSSchemaConstructor

getSerialNumbers() - Method in class org.mbari.hobilabs.HRBinaryDecoder

getSnorm() - Method in class org.mbari.hobilabs.HSDPacket

getSnorm(int) - Method in class org.mbari.hobilabs.HSDPacket

getSolarPosition(long, double, double) - Static method in class org.mbari.util.SolarUtil

Adapted from PLOTephem.HPL and Internal parameter names (P10-P20) are identical to those in the HPL program, PLOTephem, from which this was extracted.

getSortableName(OMSSensor) - Static method in class org.mbari.oasis.OMSUtil

Assign each variable in an OMSSensor array a unique name that that can be used for sorting

getTemperature() - Method in class org.mbari.hobilabs.HSDPacket

getTemperature() - Method in class org.mbari.io.OasisPco2Reader

getTemperature(String) - Method in class org.mbari.io.OasisPco2Reader

getTime() - Method in class org.mbari.hobilabs.HSDPacket

getTime() - Method in class org.mbari.io.OasisFileReader

Accessor method to get the time stamp for each line of data in the data array

getTime() - Method in class org.mbari.io.OasisPco2Reader

getTime(String) - Method in class org.mbari.io.OasisPco2Reader

getTime() - Method in class org.mbari.io.OasisPco2Reader2

getTime() - Method in class org.mbari.oasis.Pco2Reader

getTime(String) - Method in class org.mbari.oasis.Pco2Reader

getToken(String, int, String) - Static method in class org.mbari.util.StringUtil

Return the token specified by position in a string using the specified delimiter.

getToken(String, int) - Static method in class org.mbari.util.StringUtil

Return the token specified by position in a string using white space delimiters (\t\r\n\f and space).

getType() - Method in class org.mbari.hobilabs.HSPacket

getType() - Method in class org.mbari.oasis.OMSSensor

getTypes() - Method in class org.mbari.io.OasisPco2Reader

getTypes() - Method in class org.mbari.oasis.Pco2Reader

getURL(String) - Static method in class org.mbari.util.SystemUtil

getUniqueName(String, int, int) - Static method in class org.mbari.oasis.OMSUtil

Assign each variable in an OMSSensor array a unique name

getUniqueName(OMSSensor) - Static method in class org.mbari.oasis.OMSUtil

Assign each variable in an OMSSensor array a unique name

getUnits() - Method in class org.mbari.hobilabs.HRBinaryDecoder

getUnits() - Method in class org.mbari.oasis.OMSSensor

getUnits() - Method in class org.mbari.oasis.Pco2FileFormat

getVariable(int) - Method in class org.mbari.oasis.OMSVariableReader

Get a single variable in the file

getVariables() - Method in class org.mbari.oasis.OMSVariableReader

Get all the variables in the file

getVerticalFill() - Method in class org.mbari.awt.layout.VerticalFlowLayout

getVgap() - Method in class org.mbari.awt.layout.VerticalFlowLayout

Gets the vertical gap between components.

getWave(int) - Method in class org.mbari.hobilabs.HRCalibrationFileReader

getWave(String) - Method in class org.mbari.hobilabs.HRCalibrationFileReader

getWavelength() - Method in class org.mbari.model.solar.FrouinIrradianceModel

getWavelength(OMSSensor) - Static method in class org.mbari.oasis.OMSUtil

getWavelength(String) - Static method in class org.mbari.oasis.OMSUtil

getYear(String) - Static method in class org.mbari.oasis.OMSUtil

Extract the year from filenames of types 'yyddd' or 'yyyyddd'.

getYear(String) - Static method in class org.mbari.oasis.OasisFileCoallator

Extract the year from filenames of types 'yyddd' or 'yyyydd'.

H

HRBinaryConverter - class org.mbari.hobilabs.HRBinaryConverter.

Useful class for converting binary hydrorad data files to ascii.

HRBinaryConverter(File, File, File, String) - Constructor for class org.mbari.hobilabs.HRBinaryConverter

HRBinaryConverter(String, String, String, String) - Constructor for class org.mbari.hobilabs.HRBinaryConverter

HRBinaryDecoder - class org.mbari.hobilabs.HRBinaryDecoder.

A decoder that reads information from binary Hydrorad files.

HRBinaryDecoder(File) - Constructor for class org.mbari.hobilabs.HRBinaryDecoder

HRBinaryDecoder(String) - Constructor for class org.mbari.hobilabs.HRBinaryDecoder

HRBinaryDecoder(String, boolean) - Constructor for class org.mbari.hobilabs.HRBinaryDecoder

HRBinaryDecoder(File, boolean) - Constructor for class org.mbari.hobilabs.HRBinaryDecoder

HRCalFileNameFilter - class org.mbari.hobilabs.HRCalFileNameFilter.

HRCalFileNameFilter(String, String) - Constructor for class org.mbari.hobilabs.HRCalFileNameFilter

HRCalibrationFileReader - class org.mbari.hobilabs.HRCalibrationFileReader.

This is not a complete reader yet.

HRCalibrationFileReader(File) - Constructor for class org.mbari.hobilabs.HRCalibrationFileReader

HRCalibrationFileReader(String) - Constructor for class org.mbari.hobilabs.HRCalibrationFileReader

HRDataCleaner - class org.mbari.oasis.HRDataCleaner.

Converts OASIS hydrorad data files to binary.

HRDataCleaner(File, File, String) - Constructor for class org.mbari.oasis.HRDataCleaner

The constructor doesn't check for read write access to any files.

HRDataCleaner(String, String, String) - Constructor for class org.mbari.oasis.HRDataCleaner

HRDataCleaner(String, String) - Constructor for class org.mbari.oasis.HRDataCleaner

This form of constructor will not append a prefix on to the output files

HRDataCleaner(File, File) - Constructor for class org.mbari.oasis.HRDataCleaner

This form of constructor will not append a prefix on to the output files

HRMain - class org.mbari.hobilabs.HRMain.

HRMain(File, File, String) - Constructor for class org.mbari.hobilabs.HRMain

HRMain(String, String, String) - Constructor for class org.mbari.hobilabs.HRMain

HRNetcdfArchive - class org.mbari.oasis.HRNetcdfArchive.

Title: HobiLabs data processing Description: Copyright: Copyright (c) Brian Schlining Company: MBARI

HRNetcdfArchive(String, File, String, File[]) - Constructor for class org.mbari.oasis.HRNetcdfArchive

HRNetcdfCoards - class org.mbari.oasis.HRNetcdfCoards.

Title: HobiLabs data processing Description: Creates COARDS compliant netcdf files Copyright: Copyright (c) Brian Schlining Company: MBARI

HRNetcdfCoards(String, File, String, File[]) - Constructor for class org.mbari.oasis.HRNetcdfCoards

HRNetcdfConstructor - class org.mbari.oasis.HRNetcdfConstructor.

Title: HobiLabs data processing Description: Copyright: Copyright (c) Brian Schlining Company: MBARI

HRNetcdfConstructor(String, File, String, File[]) - Constructor for class org.mbari.oasis.HRNetcdfConstructor

HRNetcdfFerret - class org.mbari.oasis.HRNetcdfFerret.

Title: HobiLabs data processing Description: Used for creating netcdf fiels to be read by ferret Copyright: Copyright (c) Brian Schlining Company: MBARI

HRNetcdfFerret(String, File, String, File[]) - Constructor for class org.mbari.oasis.HRNetcdfFerret

HRPacket - class org.mbari.hobilabs.HRPacket.

This does not use the traditional Java encapsulation of data.

HRPacket() - Constructor for class org.mbari.hobilabs.HRPacket

HRParser - class org.mbari.hobilabs.HRParser.

HRParser is the main data parser engine for Decoders and Converters in the org.mbari.hobilabs.hr parckage.

HRParser(InputStream) - Constructor for class org.mbari.hobilabs.HRParser

HRParser will accept any InputStream.

HRParser(DataInputStream) - Constructor for class org.mbari.hobilabs.HRParser

HRUtil - class org.mbari.util.HRUtil.

HS2CalibrationFileReader - class org.mbari.hobilabs.HS2CalibrationFileReader.

Reads the HS2 calibration files.

HS2CalibrationFileReader(String) - Constructor for class org.mbari.hobilabs.HS2CalibrationFileReader

HS2CalibrationFileReader(File) - Constructor for class org.mbari.hobilabs.HS2CalibrationFileReader

HSDPacket - class org.mbari.hobilabs.HSDPacket.

Concrete subclass of HSPacket.

HSDPacket(long, int[], int[], int, int, byte) - Constructor for class org.mbari.hobilabs.HSDPacket

All the values are assigned in the constructor.

HSDParser - class org.mbari.hobilabs.HSDParser.

HSPacket - class org.mbari.hobilabs.HSPacket.

This abstract class spefies methods to store the type of data.

HSPacket(String) - Constructor for class org.mbari.hobilabs.HSPacket

HSParser - interface org.mbari.hobilabs.HSParser.

hasMoreElements() - Method in class org.mbari.oasis.OMSAttributeReader

Enumeration interface

hasMoreElements() - Method in class org.mbari.oasis.OMSVariableReader

Enumeration interface

I

ID() - Method in class org.mbari.io.FlatFileReader

Method declaration

IntTime - Variable in class org.mbari.hobilabs.HRPacket

interpLinear(double[], double[], double[]) - Static method in class org.mbari.util.MathUtil

interpLinear(long[], double[], long[]) - Static method in class org.mbari.util.MathUtil

isDirectory() - Method in class org.mbari.swing.tree.FileSystemNode

isEven(double) - Static method in class org.mbari.util.MathUtil

isExplored() - Method in class org.mbari.swing.tree.FileSystemNode

isLeaf() - Method in class org.mbari.swing.tree.FileSystemNode

isLeap(double) - Static method in class org.mbari.util.DateConverter

Check to see if a year is a leap year

isLeap(int) - Static method in class org.mbari.util.DateConverter

Check to see if a year is a leap year

isLeapYear(double) - Static method in class org.mbari.util.TimeUtil

Check to see if a year is a leap year

isLeapYear(int) - Static method in class org.mbari.util.TimeUtil

Check to see if a year is a leap year

J

JaiPngToGif - class org.mbari.oasis.JaiPngToGif.

JaiPngToGif() - Constructor for class org.mbari.oasis.JaiPngToGif

L

LONG_NAME - Static variable in class org.mbari.io.OasisPco2Reader

latitude - Variable in class org.mbari.util.SolarPosition

layoutContainer(Container) - Method in class org.mbari.awt.layout.VerticalFlowLayout

Lays out the container.

listen() - Method in class org.mbari.swing.DirectoryTree1

Listen for expansion of a node (i.e opening a directory).

longitude - Variable in class org.mbari.util.SolarPosition

M

MIDDLE - Static variable in class org.mbari.awt.layout.VerticalFlowLayout

Ma2Util - class org.mbari.ma2.Ma2Util.

Title: mbariMoos web application project Description: The goal of this project is to develop server side processes for use in disseminating OASIS and MOOS data sets.

MathUtil - class org.mbari.util.MathUtil.

Static methods for doing useful math

MathUtil() - Constructor for class org.mbari.util.MathUtil

MultiFileSelectPanel1 - class org.mbari.swing.MultiFileSelectPanel1.

This class allows a user to select multiple files from multiple directories.

MultiFileSelectPanel1(DefaultListModel) - Constructor for class org.mbari.swing.MultiFileSelectPanel1

MultiFileSelectPanel1() - Constructor for class org.mbari.swing.MultiFileSelectPanel1

main(String[]) - Static method in class org.mbari.gis.Drazen

main(String[]) - Static method in class org.mbari.hobilabs.HRBinaryConverter

main(String[]) - Static method in class org.mbari.hobilabs.HRMain

arg[0] = calfile directory arg[1] = binary data file arg[2] = destination directory

main(String[]) - Static method in class org.mbari.hobilabs.Test

main(String[]) - Static method in class org.mbari.io.DelimitedFile

For debugging

main(String[]) - Static method in class org.mbari.io.FlatFileReader

Method declaration

main(String[]) - Static method in class org.mbari.io.OasisPco2Reader2

main(String[]) - Static method in class org.mbari.io.OasisPco2Writer

main(String[]) - Static method in class org.mbari.model.solar.FrouinExtended

main(String[]) - Static method in class org.mbari.oasis.DuplicateRemover

Use as: org.mbari.oasis.DuplicateRemover

Inputs: filename = the name of the file to sort and remove duplicates from
dataDirectory = A directory of oasis data files.

main(String[]) - Static method in class org.mbari.oasis.HRDataCleaner

HRDataCleaner can be run from the command line as well as integrated into other programs.

main(String[]) - Static method in class org.mbari.oasis.HRNetcdfArchive

arg[0] = calfile directory arg[1] = binary data file arg[2] = destination directory

main(String[]) - Static method in class org.mbari.oasis.HRNetcdfCoards

arg[0] = calfile directory arg[1] = binary data file arg[2] = destination directory

main(String[]) - Static method in class org.mbari.oasis.HRNetcdfConstructor

arg[0] = calfile directory arg[1] = binary data file arg[2] = destination directory

main(String[]) - Static method in class org.mbari.oasis.HRNetcdfFerret

arg[0] = calfile directory arg[1] = binary data file arg[2] = destination directory

main(String[]) - Static method in class org.mbari.oasis.JaiPngToGif

main(String[]) - Static method in class org.mbari.oasis.NetcdfTest

main(String[]) - Static method in class org.mbari.oasis.OMSConfigReader

main(String[]) - Static method in class org.mbari.oasis.OMSMain

Method declaration

main(String[]) - Static method in class org.mbari.oasis.OMSNetcdfAppender

main(String[]) - Static method in class org.mbari.oasis.OMSVariableReader

main(String[]) - Static method in class org.mbari.oasis.OasisExtractor

main(String[]) - Static method in class org.mbari.oasis.OasisFileChecker

main(String[]) - Static method in class org.mbari.oasis.OasisFileCoallator

Allows the user to call this class from the command line Type 'java org.mbari.oasis.OasisFileCoallator' for help.

main(String[]) - Static method in class org.mbari.oasis.OasisHS2Processer

arg[0] = directory or file to parse If it's a directory the processer will loop through all files in the directory.

main(String[]) - Static method in class org.mbari.oasis.OasisPco2Netcdf

main(String[]) - Static method in class org.mbari.oasis.OasisRemoveDuplicates

main(String[]) - Static method in class org.mbari.oasis.OasisSpecprrNetcdf

main(String[]) - Static method in class org.mbari.oasis.Pco2Coards

main(String[]) - Static method in class org.mbari.oasis.Pco2Netcdf

main(String[]) - Static method in class org.mbari.swing.DirectoryTree1

main(String[]) - Static method in class org.mbari.swing.MultiFileSelectPanel1

main(String[]) - Static method in class org.mbari.util.DateConverter

Method declaration

minimumLayoutSize(Container) - Method in class org.mbari.awt.layout.VerticalFlowLayout

Returns the minimum size needed to layout the target container

mod(double, double) - Static method in class org.mbari.model.solar.FrouinExtended

mod(double, double) - Static method in class org.mbari.util.MathUtil

N

N - Variable in class org.mbari.hobilabs.HRPacket

NEWER_7_COLUMN - Static variable in class org.mbari.oasis.Pco2FileFormat

NEW_7_COLUMN - Static variable in class org.mbari.oasis.Pco2FileFormat

NcFilenameFilter - class org.mbari.io.NcFilenameFilter.

This filters for files with a .nc extension.

NcFilenameFilter() - Constructor for class org.mbari.io.NcFilenameFilter

NetcdfTest - class org.mbari.oasis.NetcdfTest.

NetcdfTest(String) - Constructor for class org.mbari.oasis.NetcdfTest

near(double[], double) - Static method in class org.mbari.util.MathUtil

Find the index of the value nearest to the key.

nextElement() - Method in class org.mbari.oasis.OMSAttributeReader

Enumeration interface

nextElement() - Method in class org.mbari.oasis.OMSVariableReader

Enumeration interface

O

OLD_6_COLUMN - Static variable in class org.mbari.oasis.Pco2FileFormat

OMSAbstractSchema - class org.mbari.oasis.OMSAbstractSchema.

OMSAbstractSchema(File) - Constructor for class org.mbari.oasis.OMSAbstractSchema

OMSAbstractSchemaConstructor - class org.mbari.oasis.OMSAbstractSchemaConstructor.

OMSAbstractSchemaConstructor(File) - Constructor for class org.mbari.oasis.OMSAbstractSchemaConstructor

OMSAttributeReader - class org.mbari.oasis.OMSAttributeReader.

This class reads in data from a file in 'mooring'/data/specprr files and collects the netcdf specific information for attributes

OMSAttributeReader(String) - Constructor for class org.mbari.oasis.OMSAttributeReader

MooringAttributeReader reads in the Attributes in the main configuration file

OMSAttributeReader(File) - Constructor for class org.mbari.oasis.OMSAttributeReader

MooringAttributeReader reads in the Attributes in the main configuration file

OMSConfigReader - class org.mbari.oasis.OMSConfigReader.

OMSConfigReader(String) - Constructor for class org.mbari.oasis.OMSConfigReader

OMSConfigReader Reads in the Calibration file tree used for specprr instruments.

OMSConfigReader(File) - Constructor for class org.mbari.oasis.OMSConfigReader

OMSConfigReader Reads in the Calibration file tree used for specprr instruments.It defaults to the most current Configuration of the mooring

OMSConfigReader(String, double) - Constructor for class org.mbari.oasis.OMSConfigReader

OMSConfigReader Reads in the Calibration file tree used for specprr instruments

OMSConfigReader(File, double) - Constructor for class org.mbari.oasis.OMSConfigReader

OMSConfigReader Reads in the Calibration file tree used for specprr instruments

OMSMain - class org.mbari.oasis.OMSMain.

OMSMain is the main program for creating or adding to Oasis Mooring Spectroradiometer (OMS) netcdf files.

OMSNetcdfAppender - class org.mbari.oasis.OMSNetcdfAppender.

OMSNetcdfAppender is designed to append data onto existing Oasis Mooring specprr netcdf files.

OMSNetcdfAppender(String, String, String) - Constructor for class org.mbari.oasis.OMSNetcdfAppender

OMSSchemaConstructor - class org.mbari.oasis.OMSSchemaConstructor.

Setup a netCDF schema for specprr data collected through Oasis cans.

OMSSchemaConstructor(String) - Constructor for class org.mbari.oasis.OMSSchemaConstructor

Create a netCDF schema using information in the configuration files.

OMSSchemaConstructor(File) - Constructor for class org.mbari.oasis.OMSSchemaConstructor

OMSSensor - class org.mbari.oasis.OMSSensor.

OMSSensor (Oasis Mooring Specprr = OMS)

OMSSensor(String) - Constructor for class org.mbari.oasis.OMSSensor

Constructor creating an OMSSensor object from a line from a Calibration file

OMSUtil - class org.mbari.oasis.OMSUtil.

Utilties used for netcdf file construction

OMSVariableReader - class org.mbari.oasis.OMSVariableReader.

OMSVariableReader (OMS = Oasis Mooring Specprr) is used to get Variable information about the configuration that is stored in the configuration files

OMSVariableReader(String) - Constructor for class org.mbari.oasis.OMSVariableReader

OMSVariableReader reads in the Variables in the main configuration file

OMSVariableReader(File) - Constructor for class org.mbari.oasis.OMSVariableReader

OMSVariableReader reads in the Variables in the main configuration file

OasisExtractFilter - class org.mbari.io.OasisExtractFilter.

OasisExtractFilter(String) - Constructor for class org.mbari.io.OasisExtractFilter

OasisExtractor - class org.mbari.oasis.OasisExtractor.

OasisExtractor(String, String, int, int) - Constructor for class org.mbari.oasis.OasisExtractor

OasisFileChecker - class org.mbari.oasis.OasisFileChecker.

Checks files for duplicate data.

OasisFileCoallator - class org.mbari.oasis.OasisFileCoallator.

Combine files created by Bob Herlein's extract program into a single data file.

OasisFileReader - class org.mbari.io.OasisFileReader.

Reads files created by Bob Herlein's extract program and combined using concat.awk or OasisFileCoallator.java into a double array

OasisFileReader(String) - Constructor for class org.mbari.io.OasisFileReader

Constructor makes a quick pass through the file to intialize memory.

OasisFileReader(File) - Constructor for class org.mbari.io.OasisFileReader

OasisHS2Parser - class org.mbari.oasis.OasisHS2Parser.

OasisHS2Parser(File, Writer, Properties) - Constructor for class org.mbari.oasis.OasisHS2Parser

OasisHS2Processer - class org.mbari.oasis.OasisHS2Processer.

Used to process an HS2 data file or directory full of HS2 data files into a single text file.

OasisHS2Processer(String, String, String) - Constructor for class org.mbari.oasis.OasisHS2Processer

OasisPco2Netcdf - class org.mbari.oasis.OasisPco2Netcdf.

Constructs a netCDF file from pCO2 data files created by 'extract' (i.e.

OasisPco2Netcdf(String, String, String, String) - Constructor for class org.mbari.oasis.OasisPco2Netcdf

OasisPco2Netcdf(String, File, File, File) - Constructor for class org.mbari.oasis.OasisPco2Netcdf

OasisPco2Reader - class org.mbari.io.OasisPco2Reader.

Read a concatenated file of pC02 data.

OasisPco2Reader(String) - Constructor for class org.mbari.io.OasisPco2Reader

Create a OasisPco2Reader and intialize memory.

OasisPco2Reader(File) - Constructor for class org.mbari.io.OasisPco2Reader

Create a OasisPco2Reader and intialize memory.

OasisPco2Reader2 - class org.mbari.io.OasisPco2Reader2.

Read a concatenated file of pC02 data.

OasisPco2Reader2(String) - Constructor for class org.mbari.io.OasisPco2Reader2

Create a OasisPco2Reader and intialize memory.

OasisPco2Reader2(File) - Constructor for class org.mbari.io.OasisPco2Reader2

Create a OasisPco2Reader and intialize memory.

OasisPco2Writer - class org.mbari.io.OasisPco2Writer.

OasisPco2Writer(String) - Constructor for class org.mbari.io.OasisPco2Writer

OasisRemoveDuplicates - class org.mbari.oasis.OasisRemoveDuplicates.

Checks files for duplicate data.

OasisSpecprrNetcdf - class org.mbari.oasis.OasisSpecprrNetcdf.

OasisSpecprrNetcdf(String, String, String, String) - Constructor for class org.mbari.oasis.OasisSpecprrNetcdf

OasisSpecprrNetcdf(String, File, File, File) - Constructor for class org.mbari.oasis.OasisSpecprrNetcdf

OceanUtil - class org.mbari.util.OceanUtil.

order(String[], int[]) - Static method in class org.mbari.util.StringUtil

Useful method for ordering a 1-D array based on an array of indices

orderVector(double[], int[]) - Static method in class org.mbari.util.MathUtil

Useful method for ordering a 1-D array based on an array of indices

orderVector(float[], int[]) - Static method in class org.mbari.util.MathUtil

orderVector(long[], int[]) - Static method in class org.mbari.util.MathUtil

org.mbari.awt.layout - package org.mbari.awt.layout

org.mbari.gis - package org.mbari.gis

org.mbari.gis.util - package org.mbari.gis.util

org.mbari.hobilabs - package org.mbari.hobilabs

org.mbari.io - package org.mbari.io

org.mbari.ma2 - package org.mbari.ma2

org.mbari.model.solar - package org.mbari.model.solar

org.mbari.oasis - package org.mbari.oasis

org.mbari.swing - package org.mbari.swing

org.mbari.swing.tree - package org.mbari.swing.tree

org.mbari.util - package org.mbari.util

P

Pco2 - class org.mbari.oasis.Pco2.

Container for format of pCO2 data files

Pco2Coards - class org.mbari.oasis.Pco2Coards.

Constructs a netCDF file from pCO2 data files created by 'extract' (i.e.

Pco2Coards(String, String, String, String) - Constructor for class org.mbari.oasis.Pco2Coards

Pco2Coards(String, File, File, File) - Constructor for class org.mbari.oasis.Pco2Coards

Pco2FileFormat - class org.mbari.oasis.Pco2FileFormat.

Title: MBARI Java development Description: Copyright: Copyright (c) 2001 Company: MBARI

Pco2FileFormat(int) - Constructor for class org.mbari.oasis.Pco2FileFormat

Pco2Netcdf - class org.mbari.oasis.Pco2Netcdf.

Constructs a netCDF file from pCO2 data files created by 'extract' (i.e.

Pco2Netcdf(String, String, String, String, int) - Constructor for class org.mbari.oasis.Pco2Netcdf

Pco2Netcdf(String, File, File, File, int) - Constructor for class org.mbari.oasis.Pco2Netcdf

Pco2Reader - class org.mbari.oasis.Pco2Reader.

Read a concatenated file of pC02 data.

Pco2Reader(File) - Constructor for class org.mbari.oasis.Pco2Reader

Create a OasisPco2Reader and intialize memory.

Pco2Reader(String) - Constructor for class org.mbari.oasis.Pco2Reader

Create a OasisPco2Reader and intialize memory.

Pco2Reader(File, int) - Constructor for class org.mbari.oasis.Pco2Reader

Create a OasisPco2Reader and intialize memory.

Pco2Reader(String, int) - Constructor for class org.mbari.oasis.Pco2Reader

Create a OasisPco2Reader and intialize memory.

Pco2Reader(File, Pco2FileFormat) - Constructor for class org.mbari.oasis.Pco2Reader

Create a OasisPco2Reader and intialize memory.

Pco2Reader(String, Pco2FileFormat) - Constructor for class org.mbari.oasis.Pco2Reader

Create a OasisPco2Reader and intialize memory.

PixCount - Variable in class org.mbari.hobilabs.HRPacket

PixInc - Variable in class org.mbari.hobilabs.HRPacket

Pixel - Variable in class org.mbari.hobilabs.HRPacket

Process - Variable in class org.mbari.hobilabs.HRPacket

parse() - Method in class org.mbari.hobilabs.HRParser

Call this method to start the actual processing.

parse(String) - Static method in class org.mbari.hobilabs.HSDParser

parse() - Method in interface org.mbari.hobilabs.HSParser

parseFile() - Method in class org.mbari.hobilabs.HRParser

Deprecated. Use parse() instead

posFft(int, double, double, double) - Static method in class org.mbari.model.solar.FrouinExtended

subroutine pos_fft (j,tu,xlon,xlat,asol,phi0) parameter (pi=3.14159265,fac=pi/180.) solar position (zenithal angle asol,azimuthal angle phi0 in degrees) j is the day number in the year mean solar time (heure decimale)

posSol(int, int, double, double, double) - Static method in class org.mbari.model.solar.FrouinExtended

Subroutine from 6S package to get Sun position

preferredLayoutSize(Container) - Method in class org.mbari.awt.layout.VerticalFlowLayout

Returns the preferred dimensions given the components in the target container.

pressureToDepth(double, double) - Static method in class org.mbari.util.OceanUtil

Calculate ocean depth from measured pressure and latitude.
Example: depth_(5000,36) -> 4906.08
depth_(1000,90) -> 9674.23 UNESCO 44 p28

Note: For more accurate results an additional factor of the ratio of the actual geopotential anomaly/gravity must be added.

process() - Method in class org.mbari.hobilabs.HRMain

process() - Method in class org.mbari.oasis.HRNetcdfArchive

process() - Method in class org.mbari.oasis.HRNetcdfCoards

process() - Method in class org.mbari.oasis.HRNetcdfConstructor

process() - Method in class org.mbari.oasis.HRNetcdfFerret

process() - Method in class org.mbari.oasis.OasisHS2Processer

Method called to read the calibration file and store it as a properties object.

R

RawTime - Variable in class org.mbari.hobilabs.HRPacket

read() - Method in class org.mbari.io.AsciiHexInputStream

Read a single byte (2 ASCII characters).

read() - Method in class org.mbari.io.AsciiHexReader

Read a single byte (2 ASCII characters).

read() - Method in class org.mbari.io.DelimitedFile

This method does the actual reading of the data file.

readBoolean() - Method in class org.mbari.io.AsciiHexReader

readByte() - Method in class org.mbari.io.AsciiHexReader

Reads and returns one input byte.

readChar() - Method in class org.mbari.io.AsciiHexReader

Reads an input char and returns the char value.

readDouble() - Method in class org.mbari.io.AsciiHexReader

Reads eight input bytes and returns a double value.

readFile() - Method in class org.mbari.io.DelimitedFile

Deprecated. 08 Feb 2002; use read() instead

readFile() - Method in class org.mbari.io.FlatFileReader

This method does the actual reading of the data file.

readFile() - Method in class org.mbari.io.OasisFileReader

Read a data file.

readFloat() - Method in class org.mbari.io.AsciiHexReader

Reads four input bytes and returns a float value.

readFully(byte[]) - Method in class org.mbari.io.AsciiHexReader

See the general contract of the readFully method of DataInput.

readFully(byte[], int, int) - Method in class org.mbari.io.AsciiHexReader

See the general contract of the readFully method of DataInput.

readInt() - Method in class org.mbari.io.AsciiHexReader

Reads four input bytes and returns an int value.

readLine() - Method in class org.mbari.io.AsciiHexReader

Reads the next line of text from the input stream.

readLong() - Method in class org.mbari.io.AsciiHexReader

Reads eight input bytes and returns a long value.

readShort() - Method in class org.mbari.io.AsciiHexReader

Reads two input bytes and returns a short value.

readUTF() - Method in class org.mbari.io.AsciiHexReader

Reads in a string that has been encoded using a modified UTF-8 format.

readUnsignedByte() - Method in class org.mbari.io.AsciiHexReader

Reads one input byte, zero-extends it to type int, and returns the result, which is therefore in the range 0 through 255.

readUnsignedShort() - Method in class org.mbari.io.AsciiHexReader

Reads two input bytes and returns an int value in the range 0 through 65535.

rem(double, double) - Static method in class org.mbari.util.MathUtil

S

Scale - Variable in class org.mbari.hobilabs.HRPacket

SolarPosition - class org.mbari.util.SolarPosition.

Checked values against MLML/OCEANS toolbox functions (which are considered truth) distance came out EXACTLY as the matlab functions.

SolarPosition(long, double, double) - Constructor for class org.mbari.util.SolarPosition

SolarPosition(Date, double, double) - Constructor for class org.mbari.util.SolarPosition

SolarUtil - class org.mbari.util.SolarUtil.

SolarUtil() - Constructor for class org.mbari.util.SolarUtil

StringUtil - class org.mbari.util.StringUtil.

SystemUtil - class org.mbari.util.SystemUtil.

Static methods (i.e.

SystemUtil() - Constructor for class org.mbari.util.SystemUtil

schema - Variable in class org.mbari.oasis.OMSAbstractSchema

schema - Variable in class org.mbari.oasis.OMSAbstractSchemaConstructor

sensor - Variable in class org.mbari.oasis.OMSConfigReader

seperate() - Method in class org.mbari.oasis.HRDataCleaner

This method will start the processing.

serialDaysToUtc(double) - Static method in class org.mbari.util.DateConverter

Convert from serial days, the format used by matlab, (Serial days.01 jan 0000 00:00:00 = Day 1) to UTC (milliseconds since 01 Jan 1970 00:00:00).

serialDaysToUtc(double) - Static method in class org.mbari.util.TimeUtil

Convert from serial days, the format used by matlab, (Serial days.01 jan 0000 00:00:00 = Day 1) to UTC (milliseconds since 01 Jan 1970 00:00:00).

set(Date, Date, String) - Method in class org.mbari.oasis.CalibrationHistory

Adds a calibration file to the history.

set(long, long, String) - Method in class org.mbari.oasis.CalibrationHistory

Adds a calibration file to the history.

setChooser(JFileChooser) - Method in class org.mbari.swing.FileChoicePanelOpen1

Sets the chooser used by this component.

setChooser(JFileChooser) - Method in class org.mbari.swing.FileChoicePanelSave1

Sets the chooser used by this component.

setChooser(JFileChooser) - Method in class org.mbari.swing.FileListPanel1

Sets the chooser used by this component.

setChooser(JFileChooser) - Method in class org.mbari.swing.FileOpenPanel1

Sets the chooser used by this component.

setChooser(JFileChooser) - Method in class org.mbari.swing.FileSavePanel1

Sets the chooser used by this component.

setCommentTag(String) - Method in class org.mbari.io.DelimitedFile

setData(HRPacket[]) - Method in class org.mbari.hobilabs.HRBinaryDecoder

setData(int, int, double) - Method in class org.mbari.io.FlatFileReader

This method is used to replace a single value in the array of data read from a flat file.

setDefault(String) - Method in class org.mbari.oasis.CalibrationHistory

Sets the default calibration file

setDefaultListModel(DefaultListModel) - Method in class org.mbari.swing.MultiFileSelectPanel1

setDelimiter(String) - Method in class org.mbari.io.DelimitedFile

setFile(File) - Method in class org.mbari.swing.FileChoicePanelOpen1

setFile(File) - Method in class org.mbari.swing.FileChoicePanelSave1

setFile(File) - Method in class org.mbari.swing.FileOpenPanel1

setFile(File) - Method in class org.mbari.swing.FileSavePanel1

setHasColumnNames(boolean) - Method in class org.mbari.io.DelimitedFile

setHgap(int) - Method in class org.mbari.awt.layout.VerticalFlowLayout

Sets the horizontal gap between components.

setHorizontalFill(boolean) - Method in class org.mbari.awt.layout.VerticalFlowLayout

setInstrumentType(String) - Method in class org.mbari.oasis.CalibrationHistory

Useful for setting or changing the instrument type

setVerticalFill(boolean) - Method in class org.mbari.awt.layout.VerticalFlowLayout

setVgap(int) - Method in class org.mbari.awt.layout.VerticalFlowLayout

Sets the vertical gap between components.

sign(double) - Static method in class org.mbari.model.solar.FrouinExtended

sign(double) - Static method in class org.mbari.util.MathUtil

skipBytes(int) - Method in class org.mbari.io.AsciiHexReader

See the general contract of the skipBytes method of DataInput.

sortFiles(OMSSensor[]) - Method in class org.mbari.oasis.OMSSchemaConstructor

Sorts an array of Strings alphabetically

sortFiles(String[]) - Static method in class org.mbari.oasis.OMSUtil

Sorts an array of Strings alphabetically

sortFiles(Collator, String[]) - Static method in class org.mbari.oasis.OasisFileCoallator

Sorts the array of filename by name

start() - Method in class org.mbari.oasis.OasisExtractor

T

TOP - Static variable in class org.mbari.awt.layout.VerticalFlowLayout

Temp - Variable in class org.mbari.hobilabs.HRPacket

Test - class org.mbari.hobilabs.Test.

Test() - Constructor for class org.mbari.hobilabs.Test

TimeUtil - class org.mbari.util.TimeUtil.

Utilities for converting between diferent types of commonly used scientific date formats

TimeUtil() - Constructor for class org.mbari.util.TimeUtil

test() - Static method in class org.mbari.io.OasisPco2Reader

test() - Static method in class org.mbari.oasis.Pco2Reader

testFrouinExtended() - Static method in class org.mbari.model.solar.FrouinExtended

time - Variable in class org.mbari.util.SolarPosition

timeD - Variable in class org.mbari.oasis.OMSAbstractSchema

timeD - Variable in class org.mbari.oasis.OMSAbstractSchemaConstructor

toSerialDays(Date) - Static method in class org.mbari.util.DateConverter

Convert a date object ot serial days

toSerialDays(Date) - Static method in class org.mbari.util.TimeUtil

Convert a date object ot serial days

toString() - Method in class org.mbari.swing.tree.FileSystemNode

U

UNITS - Static variable in class org.mbari.io.OasisPco2Reader

uniqueSort(double[]) - Static method in class org.mbari.util.MathUtil

Returns an array of indices indicating the order the data should be sorted in.

uniqueSort(long[]) - Static method in class org.mbari.util.MathUtil

Returns an array of indices indicating the order the data should be sorted in.

utcToSerialDays(long) - Static method in class org.mbari.util.DateConverter

Convert from UTC (milliseconds since 01 Jan 1970 00:00:00) to serial days, the format used by matlab (Serial days.

utcToSerialDays(double) - Static method in class org.mbari.util.DateConverter

Convert from UTC (milliseconds since 01 Jan 1970 00:00:00) to serial days, the format used by matlab (Serial days.

utcToSerialDays(long) - Static method in class org.mbari.util.TimeUtil

Convert from UTC (milliseconds since 01 Jan 1970 00:00:00) to serial days, the format used by matlab (Serial days.

utcToSerialDays(double) - Static method in class org.mbari.util.TimeUtil

Convert from UTC (milliseconds since 01 Jan 1970 00:00:00) to serial days, the format used by matlab (Serial days.

V

VerticalFlowLayout - class org.mbari.awt.layout.VerticalFlowLayout.

VFlowLayout is similar to FlowLayout except it lays out components vertically.

VerticalFlowLayout() - Constructor for class org.mbari.awt.layout.VerticalFlowLayout

Construct a new VerticalFlowLayout with a middle alignemnt, and the fill to edge flag set.

VerticalFlowLayout(boolean, boolean) - Constructor for class org.mbari.awt.layout.VerticalFlowLayout

Construct a new VerticalFlowLayout with a middle alignemnt.

VerticalFlowLayout(int) - Constructor for class org.mbari.awt.layout.VerticalFlowLayout

Construct a new VerticalFlowLayout with a middle alignemnt.

VerticalFlowLayout(int, boolean, boolean) - Constructor for class org.mbari.awt.layout.VerticalFlowLayout

Construct a new VerticalFlowLayout.

VerticalFlowLayout(int, int, int, boolean, boolean) - Constructor for class org.mbari.awt.layout.VerticalFlowLayout

Construct a new VerticalFlowLayout.

Voltage - Variable in class org.mbari.hobilabs.HRPacket

validSensor - Variable in class org.mbari.oasis.OMSConfigReader

varSol(int, int) - Static method in class org.mbari.model.solar.FrouinExtended

Subroutine from 6S package to get Earth-Sun distance correction calculation of the variability of the solar constant during the year.

variables - Variable in class org.mbari.oasis.OMSAbstractSchema

variables - Variable in class org.mbari.oasis.OMSAbstractSchemaConstructor

W

write(String) - Method in class org.mbari.io.OasisPco2Writer

Z

zenith - Variable in class org.mbari.util.SolarPosition

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