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

A

accept(File) - Method in class org.ala.layers.util.SpatialConversionUtils.BaseFileNameInDirectoryFilter

accept(File, String) - Method in class org.ala.layers.util.SpatialConversionUtils.BaseFileNameInDirectoryFilter

addLayer(Layer) - Method in interface org.ala.layers.dao.LayerDAO

addLayer(Layer) - Method in class org.ala.layers.dao.LayerDAOImpl

addPolygon(SimpleRegion) - Method in class org.ala.layers.intersect.ComplexRegion

adds a new polygon note: if a mask is in use must call useMask again

addToShapeFileCache(String) - Method in class org.ala.layers.intersect.IntersectConfig

Add shape files to the shape file cache.

AnalysisLayer - Class in org.ala.layers.dto

AnalysisLayer() - Constructor for class org.ala.layers.dto.AnalysisLayer

AnalysisLayerDAO - Interface in org.ala.layers.dao

DAO for the Field object

AnalysisLayerDAOImpl - Class in org.ala.layers.dao

AnalysisLayerDAOImpl() - Constructor for class org.ala.layers.dao.AnalysisLayerDAOImpl

AnalysisLayerUtil - Class in org.ala.layers.util

AnalysisLayerUtil() - Constructor for class org.ala.layers.util.AnalysisLayerUtil

B

Bil2diva - Class in org.ala.layers.util

Bil2diva() - Constructor for class org.ala.layers.util.Bil2diva

bil2diva(String, String, String) - Static method in class org.ala.layers.util.Bil2diva

BOUNDING_BOX - Static variable in class org.ala.layers.intersect.SimpleRegion

shape type bounding box; upper, lower, left, right

buildFrom(double[]) - Static method in class org.ala.layers.legend.LegendEvaluate

buildFrom(int[]) - Static method in class org.ala.layers.legend.LegendEvaluate

buildFromGrid(String) - Static method in class org.ala.layers.grid.GridClassBuilder

buildZippedShapeFile(String, String, String, String) - Static method in class org.ala.layers.util.SpatialConversionUtils

byteorderLSB - Variable in class org.ala.layers.grid.GridGroup

byteorderLSB - Variable in class org.ala.layers.intersect.Grid

C

calculateArea(double[][]) - Static method in class org.ala.layers.util.SpatialUtil

calculateArea(String) - Static method in class org.ala.layers.util.SpatialUtil

calculateOccurrences(String, String) - Static method in class org.ala.layers.tabulation.TabulationUtil

calculateSpecies(String, String) - Static method in class org.ala.layers.tabulation.TabulationUtil

calculatetMinMax() - Method in class org.ala.layers.intersect.Grid

cellArea(double, double) - Static method in class org.ala.layers.util.SpatialUtil

CIRCLE - Static variable in class org.ala.layers.intersect.SimpleRegion

shape type circle; point and radius

Client - Class in org.ala.layers.client

Main CLI class to hook into layers-store

Client() - Constructor for class org.ala.layers.client.Client

colours - Static variable in class org.ala.layers.grid.GridClassBuilder

colours - Static variable in class org.ala.layers.legend.Legend

ComplexRegion - Class in org.ala.layers.intersect

ComplexRegion is a collection of SimpleRegion, expect POLYGONs for now.

ComplexRegion() - Constructor for class org.ala.layers.intersect.ComplexRegion

Constructor for empty ComplexRegion

convertLatToPixel(double) - Method in class org.ala.layers.intersect.SimpleRegion

convertLatToPixel(double) - Static method in class org.ala.layers.util.SpatialUtil

convertLngToPixel(double) - Method in class org.ala.layers.intersect.SimpleRegion

convertLngToPixel(double) - Static method in class org.ala.layers.util.SpatialUtil

convertMetersToLat(double) - Method in class org.ala.layers.intersect.SimpleRegion

convertMetersToLat(double) - Static method in class org.ala.layers.util.SpatialUtil

convertMetersToLng(double) - Method in class org.ala.layers.intersect.SimpleRegion

convertMetersToLng(double) - Static method in class org.ala.layers.util.SpatialUtil

convertMetersToPixels(double, double, int) - Method in class org.ala.layers.intersect.SimpleRegion

convertMetersToPixels(double, double, int) - Static method in class org.ala.layers.util.SpatialUtil

convertMetresToDecimalDegrees(Float) - Method in class org.ala.layers.dao.DistributionDAOImpl

WARNING: This conversion isnt accurate..

convertPixelsToMeters(int, double, int) - Method in class org.ala.layers.intersect.SimpleRegion

convertPixelsToMeters(int, double, int) - Static method in class org.ala.layers.util.SpatialUtil

convertPixelToLat(int) - Method in class org.ala.layers.intersect.SimpleRegion

convertPixelToLat(int) - Static method in class org.ala.layers.util.SpatialUtil

convertPixelToLng(int) - Method in class org.ala.layers.intersect.SimpleRegion

convertPixelToLng(int) - Static method in class org.ala.layers.util.SpatialUtil

create(String, String, String, String, String, String) - Static method in class org.ala.layers.dto.SearchObject

createCircleJs(double, double, double) - Static method in class org.ala.layers.util.SpatialConversionUtils

createPointOfInterest(String, String, String, Double, Double, Double, String, String, Double) - Method in interface org.ala.layers.dao.ObjectDAO

createPointOfInterest(String, String, String, Double, Double, Double, String, String, Double) - Method in class org.ala.layers.dao.ObjectDAOImpl

createUserUploadedObject(String, String, String, String) - Method in interface org.ala.layers.dao.ObjectDAO

createUserUploadedObject(String, String, String, String) - Method in class org.ala.layers.dao.ObjectDAOImpl

cutGridFiles(List<AnalysisLayer>, SimpleRegion) - Method in interface org.ala.layers.dao.AnalysisLayerDAO

cutGridFiles(List<AnalysisLayer>, SimpleRegion) - Method in class org.ala.layers.dao.AnalysisLayerDAOImpl

D

datatype - Variable in class org.ala.layers.grid.GridGroup

datatype - Variable in class org.ala.layers.intersect.Grid

deletePointOfInterest(int) - Method in interface org.ala.layers.dao.ObjectDAO

deletePointOfInterest(int) - Method in class org.ala.layers.dao.ObjectDAOImpl

deleteUserUploadedObject(int) - Method in interface org.ala.layers.dao.ObjectDAO

deleteUserUploadedObject(int) - Method in class org.ala.layers.dao.ObjectDAOImpl

determineGroupSizes(float[]) - Method in class org.ala.layers.legend.Legend

size is represented by number of unique values.

Distribution - Class in org.ala.layers.dto

This class serves as a model object for the "distributions" table

Distribution() - Constructor for class org.ala.layers.dto.Distribution

DistributionDAO - Interface in org.ala.layers.dao

DAO for the Field object

DistributionDAOImpl - Class in org.ala.layers.dao

DistributionDAOImpl() - Constructor for class org.ala.layers.dao.DistributionDAOImpl

DistributionGenerator - Class in org.ala.layers.distribution

DistributionGenerator() - Constructor for class org.ala.layers.distribution.DistributionGenerator

Diva2bil - Class in org.ala.layers.util

Diva2bil() - Constructor for class org.ala.layers.util.Diva2bil

diva2bil(String, String) - Static method in class org.ala.layers.util.Diva2bil

E

Envelope - Class in org.ala.layers.grid

Envelope() - Constructor for class org.ala.layers.grid.Envelope

equals(Object) - Method in class org.ala.layers.dto.Distribution

equals(Object) - Method in class org.ala.layers.dto.Objects

evaluateStdDev(float[]) - Method in class org.ala.layers.legend.Legend

range better on features lower is better

evaluateStdDevArea(float[]) - Method in class org.ala.layers.legend.Legend

range better on area lower is better

EXPERT_DISTRIBUTION - Static variable in class org.ala.layers.dto.Distribution

exportImage(float[], int, String, int, boolean) - Method in class org.ala.layers.legend.Legend

save to a file as a type (filename extension).

exportSLD(Grid, String, String, boolean, boolean) - Method in class org.ala.layers.legend.Legend

extractZippedShapeFile(File) - Static method in class org.ala.layers.util.SpatialConversionUtils

F

Facet - Class in org.ala.layers.dto

Facet() - Constructor for class org.ala.layers.dto.Facet

Field - Class in org.ala.layers.dto

This class serves as a model object for the "fields" table

Field() - Constructor for class org.ala.layers.dto.Field

FieldDAO - Interface in org.ala.layers.dao

DAO for the Field object

FieldDAOImpl - Class in org.ala.layers.dao

FieldDAOImpl() - Constructor for class org.ala.layers.dao.FieldDAOImpl

filename - Variable in class org.ala.layers.grid.GridGroup

filename - Variable in class org.ala.layers.intersect.Grid

fillAccMask(int, int, double, double, double, double, int, int, byte[][], boolean) - Method in class org.ala.layers.intersect.ComplexRegion

fillAccMask(double, double, double, double, int, int, byte[][], boolean) - Method in class org.ala.layers.intersect.SimpleRegion

fillAccMask_EPSG900913(int, int, double, double, double, double, int, int, byte[][], boolean) - Method in class org.ala.layers.intersect.ComplexRegion

fillAccMask_EPSG900913(double, double, double, double, int, int, byte[][], boolean) - Method in class org.ala.layers.intersect.SimpleRegion

findByCriteria(String, int) - Method in interface org.ala.layers.dao.SearchDAO

findByCriteria(String, int) - Method in class org.ala.layers.dao.SearchDAOImpl

findDistributionByLSIDOrName(String) - Method in interface org.ala.layers.dao.DistributionDAO

Find a distribution by name or LSID

findDistributionByLSIDOrName(String) - Method in class org.ala.layers.dao.DistributionDAOImpl

FixGridMinMax - Class in org.ala.layers.util

FixGridMinMax() - Constructor for class org.ala.layers.util.FixGridMinMax

G

generate(float[]) - Method in class org.ala.layers.legend.Legend

generate the legend cutoff points.

generate(float[], int) - Method in class org.ala.layers.legend.Legend

generate the legend cutoff points.

generate(float[], int) - Method in class org.ala.layers.legend.LegendEqualArea

generate(float[], int) - Method in class org.ala.layers.legend.LegendEqualSize

generate(float[], int) - Method in class org.ala.layers.legend.LegendEvenInterval

generate(float[], int) - Method in class org.ala.layers.legend.LegendEvenIntervalLog

generate(float[], int) - Method in class org.ala.layers.legend.LegendEvenIntervalLog10

generateGridLegend(String, String, int, boolean) - Static method in class org.ala.layers.legend.GridLegend

generateLegend(String) - Method in class org.ala.layers.legend.Legend

Produce image legend

geoJsonToWkt(String) - Static method in class org.ala.layers.util.SpatialConversionUtils

GEONETWORK_URL_PLACEHOLDER - Static variable in class org.ala.layers.intersect.IntersectConfig

GEOSERVER_URL_PLACEHOLDER - Static variable in class org.ala.layers.intersect.IntersectConfig

get(String) - Method in class org.ala.layers.intersect.SimpleShapeFileCache

getAlaspatialOutputPath() - Static method in class org.ala.layers.intersect.IntersectConfig

getAlaspatialUrl() - Static method in class org.ala.layers.util.LayerProperties

getAll() - Method in class org.ala.layers.intersect.SimpleShapeFileCache

getAnalysisAlocCmd() - Static method in class org.ala.layers.util.LayerProperties

getAnalysisAlocEstimateAdd0() - Static method in class org.ala.layers.util.LayerProperties

getAnalysisAlocEstimateAdd1() - Static method in class org.ala.layers.util.LayerProperties

getAnalysisAlocEstimateAdd2() - Static method in class org.ala.layers.util.LayerProperties

getAnalysisAlocEstimateMult0() - Static method in class org.ala.layers.util.LayerProperties

getAnalysisAlocEstimateMult1() - Static method in class org.ala.layers.util.LayerProperties

getAnalysisAlocEstimateMult2() - Static method in class org.ala.layers.util.LayerProperties

getAnalysisAlocEstimateMult3() - Static method in class org.ala.layers.util.LayerProperties

getAnalysisEstimateSmoothing() - Static method in class org.ala.layers.util.LayerProperties

getAnalysisGdmCmd() - Static method in class org.ala.layers.util.LayerProperties

getAnalysisLayerDao() - Static method in class org.ala.layers.client.Client

getAnalysisLayerFilesPath() - Static method in class org.ala.layers.intersect.IntersectConfig

getAnalysisLayerInfo(String) - Method in class org.ala.layers.intersect.IntersectConfig

get info on an analysis layer

getAnalysisLayersByEnvCategory(String) - Method in interface org.ala.layers.dao.AnalysisLayerDAO

getAnalysisLayersByEnvCategory(String) - Method in class org.ala.layers.dao.AnalysisLayerDAOImpl

getAnalysisLayersByName(String[]) - Method in interface org.ala.layers.dao.AnalysisLayerDAO

getAnalysisLayersByName(String[]) - Method in class org.ala.layers.dao.AnalysisLayerDAOImpl

getAnalysisLayersDir() - Static method in class org.ala.layers.util.LayerProperties

getAnalysisLimitGridCells() - Static method in class org.ala.layers.util.LayerProperties

getAnalysisLimitOccurrences() - Static method in class org.ala.layers.util.LayerProperties

getAnalysisMaxentCmd() - Static method in class org.ala.layers.util.LayerProperties

getAnalysisMaxentEstimateMult0() - Static method in class org.ala.layers.util.LayerProperties

getAnalysisMaxentEstimateMult1() - Static method in class org.ala.layers.util.LayerProperties

getAnalysisMaxentEstimateMult2() - Static method in class org.ala.layers.util.LayerProperties

GetAnalysisMaxJobs() - Static method in class org.ala.layers.util.LayerProperties

getAnalysisResolutions() - Static method in class org.ala.layers.intersect.IntersectConfig

getAnalysisThreadCount() - Static method in class org.ala.layers.util.LayerProperties

getAnalysisWorkingDir() - Static method in class org.ala.layers.util.LayerProperties

getApiKeyCheckUrlTemplate() - Static method in class org.ala.layers.intersect.IntersectConfig

getArea() - Method in class org.ala.layers.dto.Tabulation

getArea_km() - Method in class org.ala.layers.dto.Distribution

getArea_km() - Method in class org.ala.layers.dto.GridClass

getArea_km() - Method in class org.ala.layers.dto.Objects

getArea_name() - Method in class org.ala.layers.dto.Distribution

getArrayMax(int[]) - Static method in class org.ala.layers.grid.Grid2Shape

getArrayMin(int[]) - Static method in class org.ala.layers.grid.Grid2Shape

getAuthority_() - Method in class org.ala.layers.dto.Distribution

getBaseOutputDir() - Static method in class org.ala.layers.util.LayerProperties

getBaseOutputURL() - Static method in class org.ala.layers.util.LayerProperties

getBbox() - Method in class org.ala.layers.dto.GridClass

getBbox() - Method in class org.ala.layers.dto.Objects

getBounding_box() - Method in class org.ala.layers.dto.Distribution

getBoundingBox() - Method in class org.ala.layers.intersect.ComplexRegion

gets the bounding box for shapes in this ComplexRegion

getBoundingBox() - Method in class org.ala.layers.intersect.SimpleRegion

gets the bounding box for types POLYGON and BOUNDING_BOX

getCaab_family_number() - Method in class org.ala.layers.dto.Distribution

getCaab_species_number() - Method in class org.ala.layers.dto.Distribution

getcellnumber(double, double) - Method in class org.ala.layers.grid.GridGroup

getcellnumber(double, double) - Method in class org.ala.layers.intersect.Grid

getChecklist_name() - Method in class org.ala.layers.dto.Distribution

getCitation_date() - Method in class org.ala.layers.dto.Layer

getClasses() - Method in class org.ala.layers.dto.IntersectionFile

getClassification1() - Method in class org.ala.layers.dto.Layer

getClassification2() - Method in class org.ala.layers.dto.Layer

getCoastal_fl() - Method in class org.ala.layers.dto.Distribution

getColour(float) - Method in class org.ala.layers.legend.Legend

Only correct when Legend is created with 10 divisions.

getColour(double, double, double) - Static method in class org.ala.layers.legend.Legend

colourize input between provided ranges.

getColumnIdx(String) - Method in class org.ala.layers.intersect.SimpleShapeFile

returns the position, zero indexed, of the provided column_name from within the .dbf

getColumnLookup(int) - Method in class org.ala.layers.intersect.SimpleShapeFile

returns set of values found in the .dbf file at a column number, zero base.

getColumnLookup() - Method in class org.ala.layers.intersect.SimpleShapeFile

getCommon_nam() - Method in class org.ala.layers.dto.Distribution

getConfig() - Method in interface org.ala.layers.dao.LayerIntersectDAO

Get initialised IntersectConfig.

getConfig() - Method in class org.ala.layers.dao.LayerIntersectDAOImpl

getConfigReloadWait() - Static method in class org.ala.layers.intersect.IntersectConfig

getCount() - Method in class org.ala.layers.dto.Facet

getCutoffFloats() - Method in class org.ala.layers.legend.Legend

get cutoff's

getCutoffs() - Method in class org.ala.layers.legend.Legend

get cutoff values as String includes group sizes if calculated

getData_resource_uid() - Method in class org.ala.layers.dto.Distribution

getDatalang() - Method in class org.ala.layers.dto.Layer

getDegrees() - Method in class org.ala.layers.dto.Objects

getDesc() - Method in class org.ala.layers.dto.Field

getDescription() - Method in class org.ala.layers.dto.Layer

getDescription() - Method in class org.ala.layers.dto.Objects

getDescription() - Method in class org.ala.layers.dto.SearchObject

getDescription() - Method in class org.ala.layers.dto.Uploaded

getDesmersal_fl() - Method in class org.ala.layers.dto.Distribution

getDisplayname() - Method in class org.ala.layers.dto.Layer

getDisplaypath() - Method in class org.ala.layers.dto.Layer

getDistance() - Method in class org.ala.layers.dto.Objects

getDistributionByLSID(String[]) - Method in interface org.ala.layers.dao.DistributionDAO

Find a distributions by LSIDs

getDistributionByLSID(String[]) - Method in class org.ala.layers.dao.DistributionDAOImpl

getDistributionBySpcode(long, String) - Method in interface org.ala.layers.dao.DistributionDAO

Find a distributions by SPCode

getDistributionBySpcode(long, String) - Method in class org.ala.layers.dao.DistributionDAOImpl

getdomain() - Method in class org.ala.layers.dto.Layer

getDoubleValue(String, String) - Method in class org.ala.layers.intersect.IniReader

getEnabled() - Method in class org.ala.layers.dto.Layer

getEnvCategories(List<AnalysisLayer>) - Method in interface org.ala.layers.dao.AnalysisLayerDAO

getEnvCategories(List<AnalysisLayer>) - Method in class org.ala.layers.dao.AnalysisLayerDAOImpl

getEnvironmentalvaluemax() - Method in class org.ala.layers.dto.Layer

getEnvironmentalvaluemin() - Method in class org.ala.layers.dto.Layer

getEnvironmentalvalueunits() - Method in class org.ala.layers.dto.Layer

getEstuarine_fl() - Method in class org.ala.layers.dto.Distribution

getExtent() - Method in class org.ala.layers.dto.Layer

getFamily() - Method in class org.ala.layers.dto.Distribution

getFamily_lsid() - Method in class org.ala.layers.dto.Distribution

getFid() - Method in class org.ala.layers.dto.Objects

getFid() - Method in class org.ala.layers.dto.SearchObject

getFid1() - Method in class org.ala.layers.dto.Tabulation

getFid2() - Method in class org.ala.layers.dto.Tabulation

getField() - Method in class org.ala.layers.dto.AnalysisLayer

getFieldById(String) - Method in interface org.ala.layers.dao.FieldDAO

getFieldById(String) - Method in class org.ala.layers.dao.FieldDAOImpl

getFieldDao() - Static method in class org.ala.layers.client.Client

getFieldId() - Method in class org.ala.layers.dto.IntersectionFile

getFieldId(String) - Static method in class org.ala.layers.tabulation.TabulationGenerator

getFieldIdFromFile(String) - Method in class org.ala.layers.intersect.IntersectConfig

getFieldName() - Method in class org.ala.layers.dto.IntersectionFile

getFieldname() - Method in class org.ala.layers.dto.Objects

getFieldname() - Method in class org.ala.layers.dto.SearchObject

getFields() - Method in interface org.ala.layers.dao.FieldDAO

getFields() - Method in class org.ala.layers.dao.FieldDAOImpl

getFieldsByDB() - Method in interface org.ala.layers.dao.FieldDAO

getFieldsByDB() - Method in class org.ala.layers.dao.FieldDAOImpl

getFieldsByDB() - Method in class org.ala.layers.intersect.IntersectConfig

getFileNames() - Method in class org.ala.layers.grid.GridCacheReader

getFilePath() - Method in class org.ala.layers.dto.IntersectionFile

getGdalDir() - Static method in class org.ala.layers.util.LayerProperties

getGdalPath() - Static method in class org.ala.layers.intersect.IntersectConfig

getGenus_lsid() - Method in class org.ala.layers.dto.Distribution

getGenus_name() - Method in class org.ala.layers.dto.Distribution

getGeom_idx() - Method in class org.ala.layers.dto.Distribution

getGeometry() - Method in class org.ala.layers.dto.Distribution

getGeometry() - Method in class org.ala.layers.dto.Objects

getGeometry() - Method in class org.ala.layers.dto.Tabulation

getGeometry() - Method in class org.ala.layers.dto.Uploaded

getGeometryCollectionParts(String) - Static method in class org.ala.layers.util.SpatialConversionUtils

getGeonetworkUrl() - Static method in class org.ala.layers.intersect.IntersectConfig

getGeoserverPassword() - Static method in class org.ala.layers.util.LayerProperties

getGeoserverUrl() - Static method in class org.ala.layers.intersect.IntersectConfig

getGeoserverUrl() - Static method in class org.ala.layers.util.LayerProperties

getGeoserverUsername() - Static method in class org.ala.layers.util.LayerProperties

getGid() - Method in class org.ala.layers.dto.Distribution

getGrid(String) - Static method in class org.ala.layers.intersect.Grid

getGrid() - Method in class org.ala.layers.intersect.Grid

getGridBufferSize() - Static method in class org.ala.layers.intersect.IntersectConfig

getGridCachePath() - Static method in class org.ala.layers.intersect.IntersectConfig

getGridCacheReaderCount() - Static method in class org.ala.layers.intersect.IntersectConfig

getGridEnvelopeAsMultiPolygon(String) - Static method in class org.ala.layers.grid.Envelope

Get a grid envelope as MultiPolygon.

getGridEnvelopeAsWkt(String) - Static method in class org.ala.layers.grid.Envelope

Get a grid envelope as WKT.

getGridSingleLayerEnvelopeAsWktIndexed(String, int[]) - Static method in class org.ala.layers.grid.Envelope

Get a grid envelope as WKT with index.

getGridStandardized(String) - Static method in class org.ala.layers.intersect.Grid

getGroup_name() - Method in class org.ala.layers.dto.Distribution

getGroupCount() - Method in class org.ala.layers.grid.GridCacheReader

getHeaderString() - Method in class org.ala.layers.intersect.SimpleShapeFile

gets shape header as String

getHeight() - Method in class org.ala.layers.intersect.SimpleRegion

getId() - Method in class org.ala.layers.dto.Field

getId() - Method in class org.ala.layers.dto.GridClass

getId() - Method in class org.ala.layers.dto.Layer

getId() - Method in class org.ala.layers.dto.LayerPid

getId() - Method in class org.ala.layers.dto.Objects

getId() - Method in class org.ala.layers.dto.SearchObject

getId() - Method in class org.ala.layers.dto.Uploaded

getImage_quality() - Method in class org.ala.layers.dto.Distribution

getImageMagickDir() - Static method in class org.ala.layers.util.LayerProperties

getIntegerValue(String, String) - Method in class org.ala.layers.intersect.IniReader

getIntersectionFile(String) - Method in class org.ala.layers.intersect.IntersectConfig

getIntersectionFiles() - Method in class org.ala.layers.intersect.IntersectConfig

getKeywords() - Method in class org.ala.layers.dto.Layer

getLastUpdated() - Method in class org.ala.layers.dto.Field

getLatitude(int) - Method in class org.ala.spatial.analysis.layers.Records

getLayer() - Method in class org.ala.layers.dto.AnalysisLayer

getLayerByDisplayName(String) - Method in interface org.ala.layers.dao.LayerDAO

getLayerByDisplayName(String) - Method in class org.ala.layers.dao.LayerDAOImpl

getLayerById(int) - Method in interface org.ala.layers.dao.LayerDAO

getLayerById(int) - Method in class org.ala.layers.dao.LayerDAOImpl

getLayerById(String) - Method in interface org.ala.layers.dao.LayerPidDAO

getLayerById(String) - Method in class org.ala.layers.dao.LayerPidDAOImpl

getLayerByIdForAdmin(int) - Method in interface org.ala.layers.dao.LayerDAO

getLayerByIdForAdmin(int) - Method in class org.ala.layers.dao.LayerDAOImpl

getLayerByName(String) - Method in interface org.ala.layers.dao.LayerDAO

getLayerByName(String) - Method in class org.ala.layers.dao.LayerDAOImpl

getLayerByNameForAdmin(String) - Method in interface org.ala.layers.dao.LayerDAO

getLayerByNameForAdmin(String) - Method in class org.ala.layers.dao.LayerDAOImpl

getLayerByPid(String) - Method in interface org.ala.layers.dao.LayerPidDAO

getLayerByPid(String) - Method in class org.ala.layers.dao.LayerPidDAOImpl

getLayerDao() - Static method in class org.ala.layers.client.Client

getLayerFilesPath() - Static method in class org.ala.layers.intersect.IntersectConfig

getLayerIndexUrl() - Static method in class org.ala.layers.intersect.IntersectConfig

getLayerIntersectDao() - Static method in class org.ala.layers.client.Client

getLayerName() - Method in class org.ala.layers.dto.IntersectionFile

getLayername() - Method in class org.ala.layers.util.LayerFilter

gets layer name

getLayerPath(String, String) - Static method in class org.ala.layers.tabulation.TabulationGenerator

getLayerPid() - Method in class org.ala.layers.dto.IntersectionFile

getLayerResolutionDefault() - Static method in class org.ala.layers.util.LayerProperties

getLayers() - Method in interface org.ala.layers.dao.LayerDAO

getLayers() - Method in class org.ala.layers.dao.LayerDAOImpl

getLayers() - Method in interface org.ala.layers.dao.LayerPidDAO

getLayers() - Method in class org.ala.layers.dao.LayerPidDAOImpl

getLayersByContextual() - Method in interface org.ala.layers.dao.LayerDAO

getLayersByContextual() - Method in class org.ala.layers.dao.LayerDAOImpl

getLayersByCriteria(String) - Method in interface org.ala.layers.dao.LayerDAO

getLayersByCriteria(String) - Method in class org.ala.layers.dao.LayerDAOImpl

getLayersByEnvironment() - Method in interface org.ala.layers.dao.LayerDAO

getLayersByEnvironment() - Method in class org.ala.layers.dao.LayerDAOImpl

getLayersForAdmin() - Method in interface org.ala.layers.dao.LayerDAO

getLayersForAdmin() - Method in class org.ala.layers.dao.LayerDAOImpl

getLicence_level() - Method in class org.ala.layers.dto.Layer

getLicence_link() - Method in class org.ala.layers.dto.Layer

getLicence_notes() - Method in class org.ala.layers.dto.Layer

getLinearColour(double, double, double, int, int) - Static method in class org.ala.layers.legend.Legend

getLoadedGrid(String) - Static method in class org.ala.layers.intersect.Grid

getLongitude(int) - Method in class org.ala.spatial.analysis.layers.Records

getLookuptablepath() - Method in class org.ala.layers.dto.Layer

getLsid() - Method in class org.ala.layers.dto.Distribution

getMax_depth() - Method in class org.ala.layers.dto.Distribution

getMaximum_value() - Method in class org.ala.layers.util.LayerFilter

for environmental gets maximum applied

getMaxlatitude() - Method in class org.ala.layers.dto.Layer

getMaxlongitude() - Method in class org.ala.layers.dto.Layer

getMaxShapeIdx() - Method in class org.ala.layers.dto.GridClass

getMddatest() - Method in class org.ala.layers.dto.Layer

getMdhrlv() - Method in class org.ala.layers.dto.Layer

getMetadata() - Method in class org.ala.layers.dto.LayerPid

getMetadata_u() - Method in class org.ala.layers.dto.Distribution

getMetadatapath() - Method in class org.ala.layers.dto.Layer

getMin_depth() - Method in class org.ala.layers.dto.Distribution

getMinimum_value() - Method in class org.ala.layers.util.LayerFilter

for environmental gets minimum applied

getMinlatitude() - Method in class org.ala.layers.dto.Layer

getMinlongitude() - Method in class org.ala.layers.dto.Layer

getMinMax() - Method in class org.ala.layers.legend.Legend

getMinShapeIdx() - Method in class org.ala.layers.dto.GridClass

getName() - Method in class org.ala.layers.dto.Facet

getName() - Method in class org.ala.layers.dto.Field

getName() - Method in class org.ala.layers.dto.GridClass

getName() - Method in class org.ala.layers.dto.IntersectionFile

getName() - Method in class org.ala.layers.dto.Layer

getName() - Method in class org.ala.layers.dto.Objects

getName() - Method in class org.ala.layers.dto.SearchObject

getName() - Method in class org.ala.layers.dto.Uploaded

getName1() - Method in class org.ala.layers.dto.Tabulation

getName2() - Method in class org.ala.layers.dto.Tabulation

getName_id() - Method in class org.ala.layers.dto.Objects

getNearestObjectByIdAndLocation(String, int, Double, Double) - Method in interface org.ala.layers.dao.ObjectDAO

getNearestObjectByIdAndLocation(String, int, Double, Double) - Method in class org.ala.layers.dao.ObjectDAOImpl

getNextValue(RandomAccessFile, Grid) - Static method in class org.ala.layers.grid.GridCacheBuilder

getNotes() - Method in class org.ala.layers.dto.Distribution

getNotes() - Method in class org.ala.layers.dto.Layer

getNumberOfPoints() - Method in class org.ala.layers.intersect.SimpleRegion

gets number of points for type POLYGON note: first point = last point

getNumberOfVertices(String) - Method in interface org.ala.layers.dao.DistributionDAO

Returns the number of vertices that make up the distribution for the supplied lsid

getNumberOfVertices(String) - Method in class org.ala.layers.dao.DistributionDAOImpl

getObjectByFidAndName(String, String) - Method in interface org.ala.layers.dao.ObjectDAO

getObjectByFidAndName(String, String) - Method in class org.ala.layers.dao.ObjectDAOImpl

getObjectByIdAndLocation(String, Double, Double) - Method in interface org.ala.layers.dao.ObjectDAO

getObjectByIdAndLocation(String, Double, Double) - Method in class org.ala.layers.dao.ObjectDAOImpl

getObjectByPid(String) - Method in interface org.ala.layers.dao.ObjectDAO

getObjectByPid(String) - Method in class org.ala.layers.dao.ObjectDAOImpl

getObjectDao() - Static method in class org.ala.layers.client.Client

getObjects() - Method in interface org.ala.layers.dao.ObjectDAO

getObjects() - Method in class org.ala.layers.dao.ObjectDAOImpl

getObjects() - Method in class org.ala.layers.dto.Field

getObjectsById(String) - Method in interface org.ala.layers.dao.ObjectDAO

getObjectsById(String) - Method in class org.ala.layers.dao.ObjectDAOImpl

getObjectsByIdAndArea(String, Integer, String) - Method in interface org.ala.layers.dao.ObjectDAO

getObjectsByIdAndArea(String, Integer, String) - Method in class org.ala.layers.dao.ObjectDAOImpl

getObjectsByIdAndIntersection(String, Integer, LayerFilter) - Method in interface org.ala.layers.dao.ObjectDAO

getObjectsByIdAndIntersection(String, Integer, String) - Method in interface org.ala.layers.dao.ObjectDAO

getObjectsByIdAndIntersection(String, Integer, LayerFilter) - Method in class org.ala.layers.dao.ObjectDAOImpl

getObjectsByIdAndIntersection(String, Integer, String) - Method in class org.ala.layers.dao.ObjectDAOImpl

getObjectsGeometryById(String, String) - Method in interface org.ala.layers.dao.ObjectDAO

getObjectsGeometryById(String, String) - Method in class org.ala.layers.dao.ObjectDAOImpl

getObjectsIntersectingWithGeometry(String, String) - Method in interface org.ala.layers.dao.ObjectDAO

getObjectsIntersectingWithGeometry(String, String) - Method in class org.ala.layers.dao.ObjectDAOImpl

getObjectsIntersectingWithObject(String, String) - Method in interface org.ala.layers.dao.ObjectDAO

getObjectsIntersectingWithObject(String, String) - Method in class org.ala.layers.dao.ObjectDAOImpl

getObjectsWithinRadius(String, double, double, double) - Method in interface org.ala.layers.dao.ObjectDAO

getObjectsWithinRadius(String, double, double, double) - Method in class org.ala.layers.dao.ObjectDAOImpl

getOccurrences() - Method in class org.ala.layers.dto.Tabulation

getOccurrenceSpeciesRecordsFilename() - Static method in class org.ala.layers.intersect.IntersectConfig

getOverlapGridCells(double, double, double, double, int, int, byte[][], boolean) - Method in class org.ala.layers.intersect.ComplexRegion

determines overlap with a grid for type POLYGON when three_state_map is not null populate it with one of: GI_UNDEFINED GI_PARTIALLY_PRESENT GI_FULLY_PRESENT GI_ABSENCE

getOverlapGridCells(double, double, double, double, int, int, byte[][], boolean) - Method in class org.ala.layers.intersect.SimpleRegion

determines overlap with a grid for type POLYGON when three_state_map is not null populate it with one of: GI_UNDEFINED GI_PARTIALLY_PRESENT GI_FULLY_PRESENT GI_ABSENCE

getOverlapGridCells(double, double, double, double, int, int, byte[][]) - Method in class org.ala.layers.intersect.SimpleRegion

getOverlapGridCells_Acc(double, double, double, double, int, int, byte[][]) - Method in class org.ala.layers.intersect.SimpleRegion

stacks PARTIALLY_PRESENT shape outline onto three_state_map

getOverlapGridCells_Acc_EPSG900913(double, double, double, double, int, int, byte[][]) - Method in class org.ala.layers.intersect.SimpleRegion

stacks PARTIALLY_PRESENT shape outline onto three_state_map

getOverlapGridCells_Box(double, double, double, double, int, int, double[][], byte[][], boolean) - Method in class org.ala.layers.intersect.SimpleRegion

determines overlap with a grid for a BOUNDING_BOX

getOverlapGridCells_EPSG900913(double, double, double, double, int, int, byte[][], boolean) - Method in class org.ala.layers.intersect.ComplexRegion

getOverlapGridCells_EPSG900913(double, double, double, double, int, int, byte[][], boolean) - Method in class org.ala.layers.intersect.SimpleRegion

getOverlapGridCells_EPSG900913(double, double, double, double, int, int, byte[][]) - Method in class org.ala.layers.intersect.SimpleRegion

getOverlapGridCells_Polygon(double, double, double, double, int, int, byte[][], boolean) - Method in class org.ala.layers.intersect.SimpleRegion

determines overlap with a grid for POLYGON when three_state_map is not null populate it with one of: GI_UNDEFINED GI_PARTIALLY_PRESENT GI_FULLY_PRESENT GI_ABSENCE 1.

getOverlapGridCells_Polygon_Acc(double, double, double, double, int, int, byte[][]) - Method in class org.ala.layers.intersect.SimpleRegion

getOverlapGridCells_Polygon_Acc_EPSG900913(double, double, double, double, int, int, byte[][]) - Method in class org.ala.layers.intersect.SimpleRegion

getOverlapGridCells_Polygon_EPSG900913(double, double, double, double, int, int, byte[][], boolean) - Method in class org.ala.layers.intersect.SimpleRegion

getPath() - Method in class org.ala.layers.dto.Layer

getPath() - Method in class org.ala.layers.dto.LayerPid

getPath_1km() - Method in class org.ala.layers.dto.Layer

getPath_250m() - Method in class org.ala.layers.dto.Layer

getPath_orig() - Method in class org.ala.layers.dto.Layer

getPelagic_fl() - Method in class org.ala.layers.dto.Distribution

getPid() - Method in class org.ala.layers.dto.Distribution

getPid() - Method in class org.ala.layers.dto.Layer

getPid() - Method in class org.ala.layers.dto.LayerPid

getPid() - Method in class org.ala.layers.dto.Objects

getPid() - Method in class org.ala.layers.dto.SearchObject

getPid1() - Method in class org.ala.layers.dto.Tabulation

getPid2() - Method in class org.ala.layers.dto.Tabulation

getPointOfInterestDetails(int) - Method in interface org.ala.layers.dao.ObjectDAO

getPointOfInterestDetails(int) - Method in class org.ala.layers.dao.ObjectDAOImpl

getPointsOfInterestWithinRadius(double, double, double) - Method in interface org.ala.layers.dao.ObjectDAO

getPointsOfInterestWithinRadius(double, double, double) - Method in class org.ala.layers.dao.ObjectDAOImpl

getPolygons(ArrayList<Polygon>, int, BitSet, int, int, double, double, double, double) - Static method in class org.ala.layers.grid.Grid2Shape

getRecordsSize() - Method in class org.ala.spatial.analysis.layers.Records

getResolutions(List<AnalysisLayer>) - Method in interface org.ala.layers.dao.AnalysisLayerDAO

getResolutions(List<AnalysisLayer>) - Method in class org.ala.layers.dao.AnalysisLayerDAOImpl

getRespparty_role() - Method in class org.ala.layers.dto.Layer

getScale() - Method in class org.ala.layers.dto.Layer

getScientific() - Method in class org.ala.layers.dto.Distribution

getSdesc() - Method in class org.ala.layers.dto.Field

getShapeFields() - Method in class org.ala.layers.dto.IntersectionFile

getShapeFileCache() - Method in class org.ala.layers.intersect.IntersectConfig

getShapeFileFeatureAsWKT(File, int) - Static method in class org.ala.layers.util.SpatialConversionUtils

getShapeFileManifest(File) - Static method in class org.ala.layers.util.SpatialConversionUtils

getSid() - Method in class org.ala.layers.dto.Field

getSname() - Method in class org.ala.layers.dto.Field

getSortedLatitude(int) - Method in class org.ala.spatial.analysis.layers.Records

getSortedLongitude(int) - Method in class org.ala.spatial.analysis.layers.Records

getSortedSpecies(int) - Method in class org.ala.spatial.analysis.layers.Records

getSortedSpeciesNumber(int) - Method in class org.ala.spatial.analysis.layers.Records

getSource() - Method in class org.ala.layers.dto.Layer

getSource_link() - Method in class org.ala.layers.dto.Layer

getSpatialPortalAppName() - Static method in class org.ala.layers.intersect.IntersectConfig

getSpcode() - Method in class org.ala.layers.dto.Distribution

getSpecies() - Method in class org.ala.layers.dto.Tabulation

getSpecies(int) - Method in class org.ala.spatial.analysis.layers.Records

getSpeciesNumber(int) - Method in class org.ala.spatial.analysis.layers.Records

getSpeciesSize() - Method in class org.ala.spatial.analysis.layers.Records

getSpecific_n() - Method in class org.ala.layers.dto.Distribution

getSpid() - Method in class org.ala.layers.dto.Field

getStringValue(String, String) - Method in class org.ala.layers.intersect.IniReader

getTabulation(String, String, String) - Method in interface org.ala.layers.dao.TabulationDAO

getTabulation(String, String, String) - Method in class org.ala.layers.dao.TabulationDAOImpl

getTabulationSingle(String, String) - Method in interface org.ala.layers.dao.TabulationDAO

getTabulationSingle(String, String) - Method in class org.ala.layers.dao.TabulationDAOImpl

getThe_geom() - Method in class org.ala.layers.dto.LayerPid

getThreadCount() - Static method in class org.ala.layers.intersect.IntersectConfig

getType() - Method in class org.ala.layers.dto.Distribution

getType() - Method in class org.ala.layers.dto.Field

getType() - Method in class org.ala.layers.dto.IntersectionFile

getType() - Method in class org.ala.layers.dto.Layer

getType() - Method in class org.ala.layers.dto.LayerPid

getType() - Method in class org.ala.layers.intersect.SimpleRegion

getTypeName() - Method in class org.ala.layers.legend.Legend

return nice name for the method that this class uses to generate the cutoff points

getTypeName() - Method in class org.ala.layers.legend.LegendEqualArea

getTypeName() - Method in class org.ala.layers.legend.LegendEqualSize

getTypeName() - Method in class org.ala.layers.legend.LegendEvenInterval

getTypeName() - Method in class org.ala.layers.legend.LegendEvenIntervalLog

getTypeName() - Method in class org.ala.layers.legend.LegendEvenIntervalLog10

getUid() - Method in class org.ala.layers.dto.Layer

getUnique() - Method in class org.ala.layers.dto.LayerPid

getUploadedShapesFieldId() - Static method in class org.ala.layers.intersect.IntersectConfig

getValue() - Method in class org.ala.layers.intersect.ComplexRegion

gets integer value stored

getValues(double[][]) - Method in class org.ala.layers.intersect.Grid

getValues2(double[][]) - Method in class org.ala.layers.intersect.Grid

do get values of grid for provided points.

getValues3(double[][], int) - Method in class org.ala.layers.intersect.Grid

getValueString(int) - Method in class org.ala.layers.intersect.SimpleShapeFile

getWidth() - Method in class org.ala.layers.intersect.SimpleRegion

getWmsurl() - Method in class org.ala.layers.dto.Distribution

getWmsurl() - Method in class org.ala.layers.dto.Objects

getYear(int) - Method in class org.ala.spatial.analysis.layers.Records

GI_ABSENCE - Static variable in class org.ala.layers.intersect.SimpleRegion

ABSENCE state for grid intersection output

GI_FULLY_PRESENT - Static variable in class org.ala.layers.intersect.SimpleRegion

FULLY PRESENT state for grid intersection output

GI_PARTIALLY_PRESENT - Static variable in class org.ala.layers.intersect.SimpleRegion

PARTiALLy PRESENT state for grid intersection output

GI_UNDEFINED - Static variable in class org.ala.layers.intersect.SimpleRegion

UNDEFINED state for grid intersection output can be considered ABSENCE

Grid - Class in org.ala.layers.intersect

Grid.java Created on June 24, 2005, 4:12 PM

Grid(String) - Constructor for class org.ala.layers.intersect.Grid

loads grd for gri file reference

grid2Multipolygon(BitSet, int, int, double, double, double, double) - Static method in class org.ala.layers.grid.Grid2Shape

grid2Multipolygon(float[], double, double, int, int, double, double, double, double) - Static method in class org.ala.layers.grid.Grid2Shape

Grid2Shape - Class in org.ala.layers.grid

Grid2Shape() - Constructor for class org.ala.layers.grid.Grid2Shape

grid2Wkt(BitSet, int, int, double, double, double, double) - Static method in class org.ala.layers.grid.Grid2Shape

grid2Wkt(float[], double, double, int, int, double, double, double, double) - Static method in class org.ala.layers.grid.Grid2Shape

grid2WktIndexed(BitSet, int, int, double, double, double, double, int) - Static method in class org.ala.layers.grid.Grid2Shape

grid2WktIndexed(float[], double, double, int, int, double, double, double, double, int[]) - Static method in class org.ala.layers.grid.Grid2Shape

GridCacheBuilder - Class in org.ala.layers.grid

GridCacheBuilder() - Constructor for class org.ala.layers.grid.GridCacheBuilder

GridCacheReader - Class in org.ala.layers.grid

GridCacheReader(String) - Constructor for class org.ala.layers.grid.GridCacheReader

GridClass - Class in org.ala.layers.dto

GridClass() - Constructor for class org.ala.layers.dto.GridClass

GridClassBuilder - Class in org.ala.layers.grid

GridClassBuilder() - Constructor for class org.ala.layers.grid.GridClassBuilder

GridFileLegends - Class in org.ala.layers.legend

Produces legend cutoff values for environmental layers

GridFileLegends(String, String, boolean, String[], FileWriter) - Constructor for class org.ala.layers.legend.GridFileLegends

GridGroup - Class in org.ala.layers.grid

GridGroup(String) - Constructor for class org.ala.layers.grid.GridGroup

GridLegend - Class in org.ala.layers.legend

GridLegend(String, String, boolean, String[], FileWriter, int, boolean) - Constructor for class org.ala.layers.legend.GridLegend

H

hashCode() - Method in class org.ala.layers.dto.Distribution

hashCode() - Method in class org.ala.layers.dto.Objects

I

identifyOutlierPointsForDistribution(String, Map<String, Map<String, Double>>) - Method in interface org.ala.layers.dao.DistributionDAO

Identify points which fall outside an expert distribution

identifyOutlierPointsForDistribution(String, Map<String, Map<String, Double>>) - Method in class org.ala.layers.dao.DistributionDAOImpl

IniReader - Class in org.ala.layers.intersect

Provides read only access to an ini file.

IniReader(String) - Constructor for class org.ala.layers.intersect.IniReader

Constructor loads ini file into the document object.

intersect(double[][], String[], int, int) - Method in class org.ala.layers.intersect.SimpleShapeFile

use when created from a shape file identifies the index within a lookup list provided for each provided point, or -1 for not found.

intersect(double, double) - Method in class org.ala.layers.intersect.SimpleShapeFile

IntersectCallback - Interface in org.ala.layers.dao

IntersectConfig - Class in org.ala.layers.intersect

IntersectConfig(FieldDAO, LayerDAO) - Constructor for class org.ala.layers.intersect.IntersectConfig

intersectGrid(String, double[][], StringBuilder) - Method in class org.ala.layers.intersect.SamplingThread

intersectGridAsContextual(String, HashMap<Integer, GridClass>, double[][], StringBuilder) - Method in class org.ala.layers.intersect.SamplingThread

intersectInt(double, double) - Method in class org.ala.layers.intersect.SimpleShapeFile

IntersectionFile - Class in org.ala.layers.dto

IntersectionFile(String, String, String, String, String, String, String, String, HashMap<Integer, GridClass>) - Constructor for class org.ala.layers.dto.IntersectionFile

IntersectUtil - Class in org.ala.layers.util

IntersectUtil() - Constructor for class org.ala.layers.util.IntersectUtil

isAddtomap() - Method in class org.ala.layers.dto.Field

isAnalysis() - Method in class org.ala.layers.dto.Field

isDefaultlayer() - Method in class org.ala.layers.dto.Field

isEnabled() - Method in class org.ala.layers.dto.Field

isGrid() - Method in class org.ala.layers.dto.Layer

isIndb() - Method in class org.ala.layers.dto.Field

isIntersect() - Method in class org.ala.layers.dto.Field

isLayerbranch() - Method in class org.ala.layers.dto.Field

isLocalSampling() - Method in class org.ala.layers.intersect.IntersectConfig

isNamesearch() - Method in class org.ala.layers.dto.Field

isShape() - Method in class org.ala.layers.dto.Layer

isValid(double) - Method in class org.ala.layers.util.LayerFilter

isWithin(double, double) - Method in class org.ala.layers.intersect.ComplexRegion

returns true when the point provided is within the ComplexRegion uses mask when available note: type UNDEFINED implies no boundary, always returns true.

isWithin(double, double) - Method in class org.ala.layers.intersect.SimpleRegion

returns true when the point provided is within the SimpleRegion note: type UNDEFINED implies no boundary, always returns true.

isWithin_EPSG900913(double, double) - Method in class org.ala.layers.intersect.ComplexRegion

isWithin_EPSG900913(double, double) - Method in class org.ala.layers.intersect.SimpleRegion

isWKTValid(String) - Static method in class org.ala.layers.util.SpatialConversionUtils

L

Layer - Class in org.ala.layers.dto

This class serves as a model object for a list of layers served by the ALA Spatial Portal

Layer() - Constructor for class org.ala.layers.dto.Layer

Layer(String, String) - Constructor for class org.ala.layers.dto.Layer

LayerDAO - Interface in org.ala.layers.dao

DAO for the Layer object

LayerDAOImpl - Class in org.ala.layers.dao

LayerDAOImpl() - Constructor for class org.ala.layers.dao.LayerDAOImpl

LayerFilter - Class in org.ala.layers.util

container for layer filter; - includes minimum and maximum for environmental layers - includes catagory names and indexes of selected for contextual layers

LayerFilter(String, double, double) - Constructor for class org.ala.layers.util.LayerFilter

LayerIntersectDAO - Interface in org.ala.layers.dao

LayerIntersectDAOImpl - Class in org.ala.layers.dao

Implementation of the sampling.

LayerIntersectDAOImpl() - Constructor for class org.ala.layers.dao.LayerIntersectDAOImpl

LayerPid - Class in org.ala.layers.dto

This class serves as a model object for the "layerpids" table

LayerPid() - Constructor for class org.ala.layers.dto.LayerPid

LayerPidDAO - Interface in org.ala.layers.dao

DAO for the LayerPid object

LayerPidDAOImpl - Class in org.ala.layers.dao

LayerPidDAOImpl() - Constructor for class org.ala.layers.dao.LayerPidDAOImpl

LayerProperties - Class in org.ala.layers.util

LayerProperties() - Constructor for class org.ala.layers.util.LayerProperties

Legend - Class in org.ala.layers.legend

Legend() - Constructor for class org.ala.layers.legend.Legend

LegendEqualArea - Class in org.ala.layers.legend

generates legend using equal size of unique values in each catagory.

LegendEqualArea() - Constructor for class org.ala.layers.legend.LegendEqualArea

LegendEqualSize - Class in org.ala.layers.legend

generates legend using equal size of unique values in each catagory.

LegendEqualSize() - Constructor for class org.ala.layers.legend.LegendEqualSize

LegendEvaluate - Class in org.ala.layers.legend

LegendEvaluate() - Constructor for class org.ala.layers.legend.LegendEvaluate

LegendEvenInterval - Class in org.ala.layers.legend

generates legend with even interval cutoff's.

LegendEvenInterval() - Constructor for class org.ala.layers.legend.LegendEvenInterval

LegendEvenIntervalLog - Class in org.ala.layers.legend

generates legend with even interval cutoff's.

LegendEvenIntervalLog() - Constructor for class org.ala.layers.legend.LegendEvenIntervalLog

LegendEvenIntervalLog10 - Class in org.ala.layers.legend

generates legend with even interval cutoff's.

LegendEvenIntervalLog10() - Constructor for class org.ala.layers.legend.LegendEvenIntervalLog10

listColumns() - Method in class org.ala.layers.intersect.SimpleShapeFile

returns a list of column names in the .dbf file

listTabulations() - Method in interface org.ala.layers.dao.TabulationDAO

listTabulations() - Method in class org.ala.layers.dao.TabulationDAOImpl

load() - Method in class org.ala.layers.intersect.IntersectConfig

loadRegion(String) - Method in class org.ala.layers.intersect.SimpleShapeFile

save partial file (enough to reload and use intersect function)

loadShapeInRegion(String, int) - Static method in class org.ala.layers.intersect.SimpleShapeFile

save partial file (enough to reload and use intersect function)

logger - Variable in class org.ala.layers.intersect.Grid

Log4j instance

logger - Variable in class org.ala.layers.intersect.IniReader

Log4j instance

logger - Variable in class org.ala.layers.intersect.SimpleShapeFileCache

Log4j instance

M

main(String[]) - Static method in class org.ala.layers.client.Client

main(String[]) - Static method in class org.ala.layers.distribution.DistributionGenerator

main(String[]) - Static method in class org.ala.layers.grid.GridCacheBuilder

main(String[]) - Static method in class org.ala.layers.grid.GridCacheReader

main(String[]) - Static method in class org.ala.layers.grid.GridClassBuilder

main(String[]) - Static method in class org.ala.layers.intersect.Test

main(String[]) - Static method in class org.ala.layers.legend.GridLegend

main(String[]) - Static method in class org.ala.layers.pid.PidGenerator

main(String[]) - Static method in class org.ala.layers.stats.ObjectsStatsGenerator

main(String[]) - Static method in class org.ala.layers.tabulation.TabulationGenerator

main(String[]) - Static method in class org.ala.layers.util.AnalysisLayerUtil

main(String[]) - Static method in class org.ala.layers.util.Bil2diva

main(String[]) - Static method in class org.ala.layers.util.Diva2bil

main(String[]) - Static method in class org.ala.layers.util.FixGridMinMax

main(String[]) - Static method in class org.ala.layers.util.IntersectUtil

maxval - Variable in class org.ala.layers.intersect.Grid

mergeMissingValues(Grid, boolean) - Method in class org.ala.layers.intersect.Grid

mintLayerPid(AndsPidClient.HandleType, String) - Static method in class org.ala.layers.pid.PidGenerator

minval - Variable in class org.ala.layers.intersect.Grid

N

ncols - Variable in class org.ala.layers.grid.GridGroup

ncols - Variable in class org.ala.layers.intersect.Grid

nodatavalue - Variable in class org.ala.layers.grid.GridGroup

nodatavalue - Variable in class org.ala.layers.intersect.Grid

nrows - Variable in class org.ala.layers.grid.GridGroup

nrows - Variable in class org.ala.layers.intersect.Grid

O

ObjectDAO - Interface in org.ala.layers.dao

DAO for the Object object

ObjectDAOImpl - Class in org.ala.layers.dao

ObjectDAOImpl() - Constructor for class org.ala.layers.dao.ObjectDAOImpl

Objects - Class in org.ala.layers.dto

This class serves as a model object for a list of objects served by the ALA Spatial Portal

Objects() - Constructor for class org.ala.layers.dto.Objects

ObjectsStatsGenerator - Class in org.ala.layers.stats

This class generates bbox and area_km attributes for entries in the objects table.

ObjectsStatsGenerator() - Constructor for class org.ala.layers.stats.ObjectsStatsGenerator

org.ala.layers.client - package org.ala.layers.client

org.ala.layers.dao - package org.ala.layers.dao

org.ala.layers.distribution - package org.ala.layers.distribution

org.ala.layers.dto - package org.ala.layers.dto

org.ala.layers.grid - package org.ala.layers.grid

org.ala.layers.intersect - package org.ala.layers.intersect

org.ala.layers.legend - package org.ala.layers.legend

org.ala.layers.pid - package org.ala.layers.pid

org.ala.layers.stats - package org.ala.layers.stats

org.ala.layers.tabulation - package org.ala.layers.tabulation

org.ala.layers.util - package org.ala.layers.util

org.ala.spatial.analysis.layers - package org.ala.spatial.analysis.layers

P

parseComplexRegion(String[]) - Static method in class org.ala.layers.intersect.ComplexRegion

parseLayerFilter(String) - Static method in class org.ala.layers.util.LayerFilter

parseLayerFilters(String) - Static method in class org.ala.layers.util.LayerFilter

parseSimpleRegion(String) - Static method in class org.ala.layers.intersect.SimpleRegion

defines a region by a points string, POLYGON only TODO: define better format for parsing, including BOUNDING_BOX and CIRCLE

parseWKT(String) - Static method in class org.ala.layers.intersect.SimpleShapeFile

defines a region by a points string, POLYGON only TODO: define better format for parsing, including BOUNDING_BOX and CIRCLE

PidGenerator - Class in org.ala.layers.pid

PidGenerator() - Constructor for class org.ala.layers.pid.PidGenerator

planeDistance(double, double, double, double, int) - Static method in class org.ala.layers.util.SpatialUtil

pointsOfInterestGeometryIntersect(String) - Method in interface org.ala.layers.dao.ObjectDAO

pointsOfInterestGeometryIntersect(String) - Method in class org.ala.layers.dao.ObjectDAOImpl

pointsOfInterestObjectIntersect(String) - Method in interface org.ala.layers.dao.ObjectDAO

pointsOfInterestObjectIntersect(String) - Method in class org.ala.layers.dao.ObjectDAOImpl

POLYGON - Static variable in class org.ala.layers.intersect.SimpleRegion

shape type polygon; list of points as longitude, latitude pairs last point == first point

printMinMax() - Method in class org.ala.layers.intersect.Grid

progressMessage(String) - Method in interface org.ala.layers.dao.IntersectCallback

Q

queryDistributions(String, double, double, Integer, String, String, String[]) - Method in interface org.ala.layers.dao.DistributionDAO

queryDistributions(String, double, double, Boolean, Boolean, Boolean, Boolean, String, Integer, String, String[], String[], String[], String[], String, String[]) - Method in interface org.ala.layers.dao.DistributionDAO

queryDistributions(String, double, double, Integer, String, String, String[]) - Method in class org.ala.layers.dao.DistributionDAOImpl

queryDistributions(String, double, double, Boolean, Boolean, Boolean, Boolean, String, Integer, String, String[], String[], String[], String[], String, String[]) - Method in class org.ala.layers.dao.DistributionDAOImpl

queryDistributionsByRadius(float, float, float, double, double, Boolean, Boolean, Boolean, Boolean, String, Integer, String, String[], String[], String[], String[], String, String[]) - Method in interface org.ala.layers.dao.DistributionDAO

queryDistributionsByRadius(float, float, float, double, double, Integer, String, String[], String[], String[], String[], String, String[]) - Method in class org.ala.layers.dao.DistributionDAOImpl

queryDistributionsByRadius(float, float, float, double, double, Boolean, Boolean, Boolean, Boolean, String, Integer, String, String[], String[], String[], String[], String, String[]) - Method in class org.ala.layers.dao.DistributionDAOImpl

Query by radius

queryDistributionsByRadiusFamilyCounts(float, float, float, double, double, Boolean, Boolean, Boolean, Boolean, String, Integer, String, String[], String[], String[], String[], String, String[]) - Method in interface org.ala.layers.dao.DistributionDAO

queryDistributionsByRadiusFamilyCounts(float, float, float, double, double, Boolean, Boolean, Boolean, Boolean, String, Integer, String, String[], String[], String[], String[], String, String[]) - Method in class org.ala.layers.dao.DistributionDAOImpl

Query by radius

queryDistributionsFamilyCounts(String, double, double, Boolean, Boolean, Boolean, Boolean, String, Integer, String, String[], String[], String[], String[], String, String[]) - Method in interface org.ala.layers.dao.DistributionDAO

queryDistributionsFamilyCounts(String, double, double, Boolean, Boolean, Boolean, Boolean, String, Integer, String, String[], String[], String[], String[], String, String[]) - Method in class org.ala.layers.dao.DistributionDAOImpl

R

Records - Class in org.ala.spatial.analysis.layers

Records(String, String, double[], String, SimpleRegion) - Constructor for class org.ala.spatial.analysis.layers.Records

Records(String, String, double[], String, SimpleRegion, String) - Constructor for class org.ala.spatial.analysis.layers.Records

Records(String) - Constructor for class org.ala.spatial.analysis.layers.Records

Records(String, SimpleRegion) - Constructor for class org.ala.spatial.analysis.layers.Records

reload() - Method in interface org.ala.layers.dao.LayerIntersectDAO

Refresh properties and table images.

reload() - Method in class org.ala.layers.dao.LayerIntersectDAOImpl

removeSpeciesNames() - Method in class org.ala.spatial.analysis.layers.Records

requiresReload() - Method in class org.ala.layers.intersect.IntersectConfig

run() - Method in class org.ala.layers.intersect.SamplingThread

S

sample(double, double) - Method in class org.ala.layers.grid.GridCacheReader

sample(double, double) - Method in class org.ala.layers.grid.GridGroup

sample(double[][], IntersectionFile, StringBuilder) - Method in class org.ala.layers.intersect.SamplingThread

sampling(String, double, double) - Method in interface org.ala.layers.dao.LayerIntersectDAO

Sampling one point Must have local access to layer files and db connection.

sampling(String, String) - Method in interface org.ala.layers.dao.LayerIntersectDAO

Sampling

sampling(String[], double[][]) - Method in interface org.ala.layers.dao.LayerIntersectDAO

Sampling

sampling(String[], double[][], IntersectCallback) - Method in interface org.ala.layers.dao.LayerIntersectDAO

Sampling

sampling(IntersectionFile[], double[][]) - Method in interface org.ala.layers.dao.LayerIntersectDAO

Sampling

sampling(double, double) - Method in interface org.ala.layers.dao.LayerIntersectDAO

Sampling one point, all cached fields.

sampling(String, double, double) - Method in class org.ala.layers.dao.LayerIntersectDAOImpl

Single coordinate sampling.

sampling(double, double) - Method in class org.ala.layers.dao.LayerIntersectDAOImpl

sampling(String, String) - Method in class org.ala.layers.dao.LayerIntersectDAOImpl

sampling(String[], double[][], IntersectCallback) - Method in class org.ala.layers.dao.LayerIntersectDAOImpl

sampling(String[], double[][]) - Method in class org.ala.layers.dao.LayerIntersectDAOImpl

sampling(IntersectionFile[], double[][]) - Method in class org.ala.layers.dao.LayerIntersectDAOImpl

samplingFull(String, double, double) - Method in interface org.ala.layers.dao.LayerIntersectDAO

Sampling one point, multiple fields.

samplingFull(String, double, double) - Method in class org.ala.layers.dao.LayerIntersectDAOImpl

SamplingThread - Class in org.ala.layers.intersect

SamplingThread(LinkedBlockingQueue<Integer>, CountDownLatch, IntersectionFile[], double[][], ArrayList<String>, int, SimpleShapeFileCache, int, IntersectCallback) - Constructor for class org.ala.layers.intersect.SamplingThread

saveGridAsImage(byte[][]) - Method in class org.ala.layers.intersect.SimpleRegion

saveShapefile(File, String, String, String) - Static method in class org.ala.layers.util.SpatialConversionUtils

SearchDAO - Interface in org.ala.layers.dao

SearchDAOImpl - Class in org.ala.layers.dao

SearchDAOImpl() - Constructor for class org.ala.layers.dao.SearchDAOImpl

SearchObject - Class in org.ala.layers.dto

SearchObject DTO

SearchObject() - Constructor for class org.ala.layers.dto.SearchObject

setAddtomap(Boolean) - Method in class org.ala.layers.dto.Field

setAnalysis(Boolean) - Method in class org.ala.layers.dto.Field

setArea(Double) - Method in class org.ala.layers.dto.Tabulation

setArea_km(Double) - Method in class org.ala.layers.dto.Distribution

setArea_km(Double) - Method in class org.ala.layers.dto.GridClass

setArea_km(Double) - Method in class org.ala.layers.dto.Objects

setArea_name(String) - Method in class org.ala.layers.dto.Distribution

setAuthority_(String) - Method in class org.ala.layers.dto.Distribution

setBbox(String) - Method in class org.ala.layers.dto.GridClass

setBbox(String) - Method in class org.ala.layers.dto.Objects

setBounding_box(String) - Method in class org.ala.layers.dto.Distribution

setBox(double, double, double, double) - Method in class org.ala.layers.intersect.SimpleRegion

defines the SimpleRegion as type BOUNDING_BOX

setCaab_family_number(String) - Method in class org.ala.layers.dto.Distribution

setCaab_species_number(String) - Method in class org.ala.layers.dto.Distribution

setChecklist_name(String) - Method in class org.ala.layers.dto.Distribution

setCircle(double, double, double) - Method in class org.ala.layers.intersect.SimpleRegion

defines the SimpleRegion as type CIRCLE

setCitation_date(String) - Method in class org.ala.layers.dto.Layer

setClasses(HashMap<Integer, GridClass>) - Method in class org.ala.layers.dto.IntersectionFile

setClassification1(String) - Method in class org.ala.layers.dto.Layer

setClassification2(String) - Method in class org.ala.layers.dto.Layer

setCoastal_fl(Integer) - Method in class org.ala.layers.dto.Distribution

setCoastal_fl(Boolean) - Method in class org.ala.layers.dto.Distribution

setCommon_nam(String) - Method in class org.ala.layers.dto.Distribution

setCount(Integer) - Method in class org.ala.layers.dto.Facet

setCurrentLayer(IntersectionFile) - Method in interface org.ala.layers.dao.IntersectCallback

setCurrentLayerIdx(Integer) - Method in interface org.ala.layers.dao.IntersectCallback

setData_resource_uid(String) - Method in class org.ala.layers.dto.Distribution

setDatalang(String) - Method in class org.ala.layers.dto.Layer

setDataSource(DataSource) - Method in class org.ala.layers.dao.AnalysisLayerDAOImpl

setDataSource(DataSource) - Method in class org.ala.layers.dao.DistributionDAOImpl

setDataSource(DataSource) - Method in class org.ala.layers.dao.FieldDAOImpl

setDataSource(DataSource) - Method in class org.ala.layers.dao.LayerDAOImpl

setDataSource(DataSource) - Method in class org.ala.layers.dao.LayerPidDAOImpl

setDataSource(DataSource) - Method in class org.ala.layers.dao.ObjectDAOImpl

setDataSource(DataSource) - Method in class org.ala.layers.dao.SearchDAOImpl

setDataSource(DataSource) - Method in class org.ala.layers.dao.TabulationDAOImpl

setDefaultlayer(Boolean) - Method in class org.ala.layers.dto.Field

setDegrees(Double) - Method in class org.ala.layers.dto.Objects

setDesc(String) - Method in class org.ala.layers.dto.Field

setDescription(String) - Method in class org.ala.layers.dto.Layer

setDescription(String) - Method in class org.ala.layers.dto.Objects

setDescription(String) - Method in class org.ala.layers.dto.SearchObject

setDescription(String) - Method in class org.ala.layers.dto.Uploaded

setDesmersal_fl(Boolean) - Method in class org.ala.layers.dto.Distribution

setDesmersal_fl(Integer) - Method in class org.ala.layers.dto.Distribution

setDisplayname(String) - Method in class org.ala.layers.dto.Layer

setDisplaypath(String) - Method in class org.ala.layers.dto.Layer

setDistance(Double) - Method in class org.ala.layers.dto.Objects

setDomain(String) - Method in class org.ala.layers.dto.Layer

setEnabled(Boolean) - Method in class org.ala.layers.dto.Field

setEnabled(Boolean) - Method in class org.ala.layers.dto.Layer

setEnvironmentalvaluemax(String) - Method in class org.ala.layers.dto.Layer

setEnvironmentalvaluemin(String) - Method in class org.ala.layers.dto.Layer

setEnvironmentalvalueunits(String) - Method in class org.ala.layers.dto.Layer

setEstuarine_fl(Integer) - Method in class org.ala.layers.dto.Distribution

setEstuarine_fl(Boolean) - Method in class org.ala.layers.dto.Distribution

setExtent(String) - Method in class org.ala.layers.dto.Layer

setFamily(String) - Method in class org.ala.layers.dto.Distribution

setFamily_lsid(String) - Method in class org.ala.layers.dto.Distribution

setFid(String) - Method in class org.ala.layers.dto.Objects

setFid(String) - Method in class org.ala.layers.dto.SearchObject

setFid1(String) - Method in class org.ala.layers.dto.Tabulation

setFid2(String) - Method in class org.ala.layers.dto.Tabulation

setField(Field) - Method in class org.ala.layers.dto.AnalysisLayer

setFieldId(String) - Method in class org.ala.layers.dto.IntersectionFile

setFieldName(String) - Method in class org.ala.layers.dto.IntersectionFile

setFieldname(String) - Method in class org.ala.layers.dto.Objects

setFieldname(String) - Method in class org.ala.layers.dto.SearchObject

setFilePath(String) - Method in class org.ala.layers.dto.IntersectionFile

setGenus_lsid(String) - Method in class org.ala.layers.dto.Distribution

setGenus_name(String) - Method in class org.ala.layers.dto.Distribution

setGeom_idx(Long) - Method in class org.ala.layers.dto.Distribution

setGeometry(String) - Method in class org.ala.layers.dto.Distribution

setGeometry(String) - Method in class org.ala.layers.dto.Objects

setGeometry(String) - Method in class org.ala.layers.dto.Tabulation

setGeometry(String) - Method in class org.ala.layers.dto.Uploaded

setGid(Long) - Method in class org.ala.layers.dto.Distribution

setGroup_name(String) - Method in class org.ala.layers.dto.Distribution

setId(String) - Method in class org.ala.layers.dto.Field

setId(Integer) - Method in class org.ala.layers.dto.GridClass

setId(Long) - Method in class org.ala.layers.dto.Layer

setId(String) - Method in class org.ala.layers.dto.LayerPid

setId(String) - Method in class org.ala.layers.dto.Objects

setId(String) - Method in class org.ala.layers.dto.SearchObject

setId(String) - Method in class org.ala.layers.dto.Uploaded

setImage_quality(String) - Method in class org.ala.layers.dto.Distribution

setIndb(Boolean) - Method in class org.ala.layers.dto.Field

setIntersect(Boolean) - Method in class org.ala.layers.dto.Field

setKeywords(String) - Method in class org.ala.layers.dto.Layer

setLastUpdated(Date) - Method in class org.ala.layers.dto.Field

setLayer(Layer) - Method in class org.ala.layers.dto.AnalysisLayer

setLayerbranch(Boolean) - Method in class org.ala.layers.dto.Field

setLayerName(String) - Method in class org.ala.layers.dto.IntersectionFile

setLayerPid(String) - Method in class org.ala.layers.dto.IntersectionFile

setLayersToSample(IntersectionFile[]) - Method in interface org.ala.layers.dao.IntersectCallback

setLicence_level(String) - Method in class org.ala.layers.dto.Layer

setLicence_link(String) - Method in class org.ala.layers.dto.Layer

setLicence_notes(String) - Method in class org.ala.layers.dto.Layer

setLookuptablepath(String) - Method in class org.ala.layers.dto.Layer

setLsid(String) - Method in class org.ala.layers.dto.Distribution

setMax_depth(Double) - Method in class org.ala.layers.dto.Distribution

setMaxlatitude(Double) - Method in class org.ala.layers.dto.Layer

setMaxlongitude(Double) - Method in class org.ala.layers.dto.Layer

setMaxShapeIdx(Integer) - Method in class org.ala.layers.dto.GridClass

setMddatest(String) - Method in class org.ala.layers.dto.Layer

setMdhrlv(String) - Method in class org.ala.layers.dto.Layer

setMetadata(String) - Method in class org.ala.layers.dto.LayerPid

setMetadata_u(String) - Method in class org.ala.layers.dto.Distribution

setMetadatapath(String) - Method in class org.ala.layers.dto.Layer

setMin_depth(Double) - Method in class org.ala.layers.dto.Distribution

setMinlatitude(Double) - Method in class org.ala.layers.dto.Layer

setMinlongitude(Double) - Method in class org.ala.layers.dto.Layer

setMinShapeIdx(Integer) - Method in class org.ala.layers.dto.GridClass

setName(String) - Method in class org.ala.layers.dto.Facet

setName(String) - Method in class org.ala.layers.dto.Field

setName(String) - Method in class org.ala.layers.dto.GridClass

setName(String) - Method in class org.ala.layers.dto.IntersectionFile

setName(String) - Method in class org.ala.layers.dto.Layer

setName(String) - Method in class org.ala.layers.dto.Objects

setName(String) - Method in class org.ala.layers.dto.SearchObject

setName(String) - Method in class org.ala.layers.dto.Uploaded

setName1(String) - Method in class org.ala.layers.dto.Tabulation

setName2(String) - Method in class org.ala.layers.dto.Tabulation

setName_id(int) - Method in class org.ala.layers.dto.Objects

setNamesearch(Boolean) - Method in class org.ala.layers.dto.Field

setNone() - Method in class org.ala.layers.intersect.SimpleRegion

defines the SimpleRegion as type UNDEFINED

setNotes(String) - Method in class org.ala.layers.dto.Distribution

setNotes(String) - Method in class org.ala.layers.dto.Layer

setObjects(List<Objects>) - Method in class org.ala.layers.dto.Field

setOccurrences(int) - Method in class org.ala.layers.dto.Tabulation

setPath(String) - Method in class org.ala.layers.dto.Layer

setPath(String) - Method in class org.ala.layers.dto.LayerPid

setPath250m(String) - Method in class org.ala.layers.dto.Layer

setPath_1km(String) - Method in class org.ala.layers.dto.Layer

setPath_orig(String) - Method in class org.ala.layers.dto.Layer

setPelagic_fl(Double) - Method in class org.ala.layers.dto.Distribution

setPid(String) - Method in class org.ala.layers.dto.Distribution

setPid(String) - Method in class org.ala.layers.dto.Layer

setPid(String) - Method in class org.ala.layers.dto.LayerPid

setPid(String) - Method in class org.ala.layers.dto.Objects

setPid(String) - Method in class org.ala.layers.dto.SearchObject

setPid1(String) - Method in class org.ala.layers.dto.Tabulation

setPid2(String) - Method in class org.ala.layers.dto.Tabulation

setPolygon(double[]) - Method in class org.ala.layers.intersect.SimpleRegion

defines the SimpleRegion as type POLYGON

setRespparty_role(String) - Method in class org.ala.layers.dto.Layer

setScale(String) - Method in class org.ala.layers.dto.Layer

setScientific(String) - Method in class org.ala.layers.dto.Distribution

setSdesc(String) - Method in class org.ala.layers.dto.Field

setShapeFields(String) - Method in class org.ala.layers.dto.IntersectionFile

setSid(String) - Method in class org.ala.layers.dto.Field

setSname(String) - Method in class org.ala.layers.dto.Field

setSource(String) - Method in class org.ala.layers.dto.Layer

setSource_link(String) - Method in class org.ala.layers.dto.Layer

setSpcode(Long) - Method in class org.ala.layers.dto.Distribution

setSpcode(Double) - Method in class org.ala.layers.dto.Distribution

setSpecies(int) - Method in class org.ala.layers.dto.Tabulation

setSpecific_n(String) - Method in class org.ala.layers.dto.Distribution

setSpid(String) - Method in class org.ala.layers.dto.Field

setThe_geom(String) - Method in class org.ala.layers.dto.LayerPid

setType(String) - Method in class org.ala.layers.dto.Distribution

setType(String) - Method in class org.ala.layers.dto.Field

setType(String) - Method in class org.ala.layers.dto.IntersectionFile

setType(String) - Method in class org.ala.layers.dto.Layer

setType(int) - Method in class org.ala.layers.dto.LayerPid

setUid(String) - Method in class org.ala.layers.dto.Layer

setUnique(String) - Method in class org.ala.layers.dto.LayerPid

setValue(int) - Method in class org.ala.layers.intersect.ComplexRegion

sets integer value stored

setValue(String, String, String) - Method in class org.ala.layers.intersect.IniReader

setViewName(String) - Method in class org.ala.layers.dao.DistributionDAOImpl

setWmsurl(String) - Method in class org.ala.layers.dto.Distribution

setWmsurl(String) - Method in class org.ala.layers.dto.Objects

SimpleRegion - Class in org.ala.layers.intersect

SimpleRegion enables point to shape intersections, where the shape is stored within SimpleRegion as a circle, bounding box or polygon.

SimpleRegion() - Constructor for class org.ala.layers.intersect.SimpleRegion

Constructor for a SimpleRegion with no shape

SimpleShapeFile - Class in org.ala.layers.intersect

SimpleShapeFile is a representation of a Shape File for intersections with points .shp MULTIPOLYGON only .dbf can read values from String and Number columns only TODO: finish serialization

SimpleShapeFile(String, String) - Constructor for class org.ala.layers.intersect.SimpleShapeFile

Constructor for a SimpleShapeFile, requires .dbf and .shp files present on the fileprefix provided.

SimpleShapeFileCache - Class in org.ala.layers.intersect

SimpleShapeFileCache(String[], String[], String[]) - Constructor for class org.ala.layers.intersect.SimpleShapeFileCache

sortedRowStarts(double, int, double) - Method in class org.ala.spatial.analysis.layers.Records

sortedStarts(double, double, double) - Method in class org.ala.spatial.analysis.layers.Records

SpatialConversionUtils - Class in org.ala.layers.util

Utilities for converting spatial data between formats

SpatialConversionUtils() - Constructor for class org.ala.layers.util.SpatialConversionUtils

SpatialConversionUtils.BaseFileNameInDirectoryFilter - Class in org.ala.layers.util

SpatialConversionUtils.BaseFileNameInDirectoryFilter(String, File, List<File>) - Constructor for class org.ala.layers.util.SpatialConversionUtils.BaseFileNameInDirectoryFilter

SpatialUtil - Class in org.ala.layers.util

SpatialUtil() - Constructor for class org.ala.layers.util.SpatialUtil

SPECIES_CHECKLIST - Static variable in class org.ala.layers.dto.Distribution

streamGrid2Wkt(OutputStream, BitSet, int, int, double, double, double, double) - Static method in class org.ala.layers.grid.Grid2Shape

streamGrid2Wkt(OutputStream, float[], double, double, int, int, double, double, double, double) - Static method in class org.ala.layers.grid.Grid2Shape

streamGrid2WktIndexed(OutputStream, BitSet, int, int, double, double, double, double, int[], StringBuilder, int) - Static method in class org.ala.layers.grid.Grid2Shape

streamGridEnvelopeAsWkt(String, OutputStream) - Static method in class org.ala.layers.grid.Envelope

Stream a grid envelope as WKT.

streamObjectsGeometryById(OutputStream, String, String) - Method in interface org.ala.layers.dao.ObjectDAO

streamObjectsGeometryById(OutputStream, String, String) - Method in class org.ala.layers.dao.ObjectDAOImpl

T

Tabulation - Class in org.ala.layers.dto

Tabulation() - Constructor for class org.ala.layers.dto.Tabulation

TabulationDAO - Interface in org.ala.layers.dao

DAO for the Field object

TabulationDAOImpl - Class in org.ala.layers.dao

TabulationDAOImpl() - Constructor for class org.ala.layers.dao.TabulationDAOImpl

TabulationGenerator - Class in org.ala.layers.tabulation

TabulationGenerator() - Constructor for class org.ala.layers.tabulation.TabulationGenerator

TabulationUtil - Class in org.ala.layers.tabulation

TabulationUtil() - Constructor for class org.ala.layers.tabulation.TabulationUtil

Test - Class in org.ala.layers.intersect

Test() - Constructor for class org.ala.layers.intersect.Test

toArray() - Method in class org.ala.layers.dto.Layer

toMap() - Method in class org.ala.layers.dto.Layer

toString() - Method in class org.ala.layers.dto.Layer

U

UNDEFINED - Static variable in class org.ala.layers.intersect.SimpleRegion

shape type not declared

units - Variable in class org.ala.layers.intersect.Grid

update(String[], String[], String[]) - Method in class org.ala.layers.intersect.SimpleShapeFileCache

updateLayer(Layer) - Method in interface org.ala.layers.dao.LayerDAO

updateLayer(Layer) - Method in class org.ala.layers.dao.LayerDAOImpl

updateNames(String, String) - Method in class org.ala.layers.grid.GridCacheReader

updateObjectNames() - Method in interface org.ala.layers.dao.ObjectDAO

updateObjectNames() - Method in class org.ala.layers.dao.ObjectDAOImpl

updatePointOfInterest(int, String, String, String, Double, Double, Double, String, String, Double) - Method in interface org.ala.layers.dao.ObjectDAO

updatePointOfInterest(int, String, String, String, Double, Double, Double, String, String, Double) - Method in class org.ala.layers.dao.ObjectDAOImpl

updateUserUploadedObject(int, String, String, String, String) - Method in interface org.ala.layers.dao.ObjectDAO

updateUserUploadedObject(int, String, String, String, String) - Method in class org.ala.layers.dao.ObjectDAOImpl

Uploaded - Class in org.ala.layers.dto

This class serves as a model object for the "uploaded" table

Uploaded() - Constructor for class org.ala.layers.dto.Uploaded

useMask(int, int, int) - Method in class org.ala.layers.intersect.ComplexRegion

builds a grid (mask) to speed up isWithin.

V

valid - Variable in class org.ala.layers.grid.GridGroup

valid - Variable in class org.ala.layers.intersect.Grid

valueExists(String, String) - Method in class org.ala.layers.intersect.IniReader

values - Variable in class org.ala.layers.grid.GridGroup

values - Variable in class org.ala.layers.intersect.Grid

W

write(String) - Method in class org.ala.layers.intersect.IniReader

write(Map<String, String>, String) - Method in class org.ala.layers.intersect.IniReader

writeGrid(String, int[], double, double, double, double, double, double, int, int) - Method in class org.ala.layers.intersect.Grid

for DomainGenerator writes out a list of double (same as getGrid() returns) to a file byteorderlsb data type, FLOAT

writeGrid(String, double[], double, double, double, double, double, double, int, int) - Method in class org.ala.layers.intersect.Grid

for grid cutter writes out a list of double (same as getGrid() returns) to a file byteorderlsb data type, FLOAT

writeGrid(String, float[], double, double, double, double, double, double, int, int) - Method in class org.ala.layers.intersect.Grid

writeHeader(String, double, double, double, double, double, double, int, int, double, double) - Method in class org.ala.layers.intersect.Grid

writeHeader(String, double, double, double, double, double, double, int, int, double, double, String, String) - Method in class org.ala.layers.intersect.Grid

writeSampleToStream(String[], String[], ArrayList<String>, OutputStream) - Static method in class org.ala.layers.util.IntersectUtil

write sample output into a stream.

X

xmax - Variable in class org.ala.layers.grid.GridGroup

xmax - Variable in class org.ala.layers.intersect.Grid

xmin - Variable in class org.ala.layers.grid.GridGroup

xmin - Variable in class org.ala.layers.intersect.Grid

xres - Variable in class org.ala.layers.grid.GridGroup

xres - Variable in class org.ala.layers.intersect.Grid

Y

ymax - Variable in class org.ala.layers.grid.GridGroup

ymax - Variable in class org.ala.layers.intersect.Grid

ymin - Variable in class org.ala.layers.grid.GridGroup

ymin - Variable in class org.ala.layers.intersect.Grid

yres - Variable in class org.ala.layers.grid.GridGroup

yres - Variable in class org.ala.layers.intersect.Grid

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