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C
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D
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E
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W
A
add_computed_measurement() (epivizfileserver.measurements.measurementManager.MeasurementManager method)
add_genome() (epivizfileserver.measurements.measurementManager.MeasurementManager method)
add_new_collections() (epivizfileserver.measurements.measurementManager.EMDMeasurementMap method)
add_new_measurements() (epivizfileserver.measurements.measurementManager.EMDMeasurementMap method)
append() (epivizfileserver.measurements.measurementManager.MeasurementSet method)
B
BamFile (class in epivizfileserver.parser.BamFile)
BaseFile (class in epivizfileserver.parser.BaseFile)
BigBed (class in epivizfileserver.parser.BigBed)
BigWig (class in epivizfileserver.parser.BigWig)
bin_rows() (epivizfileserver.measurements.measurementClass.Measurement method)
(epivizfileserver.parser.BaseFile.BaseFile method)
(in module epivizfileserver.handler.handler)
(in module epivizfileserver.server.utils)
binFileData() (epivizfileserver.handler.handler.FileHandlerProcess method)
(epivizfileserver.handler.HandlerNoActor.FileHandlerProcess method)
C
cacheData (epivizfileserver.parser.BamFile.BamFile attribute)
(epivizfileserver.parser.BigWig.BigWig attribute)
(epivizfileserver.parser.GtfFile.GtfFile attribute)
(epivizfileserver.parser.GtfParsedFile.GtfParsedFile attribute)
(epivizfileserver.parser.GtfTabixFile.GtfTabixFile attribute)
(epivizfileserver.parser.HDF5File.HDF5File attribute)
(epivizfileserver.parser.SamFile.SamFile attribute)
(epivizfileserver.parser.TbxFile.TbxFile attribute)
(epivizfileserver.parser.TranscriptTbxFile.TranscriptTbxFile attribute)
clean_up() (in module epivizfileserver.server)
cleanFileOBJ() (epivizfileserver.handler.handler.FileHandlerProcess method)
(epivizfileserver.handler.HandlerNoActor.FileHandlerProcess method)
client (epivizfileserver.handler.handler.FileHandlerProcess attribute)
(epivizfileserver.handler.HandlerNoActor.FileHandlerProcess attribute)
columns (epivizfileserver.parser.BamFile.BamFile attribute)
(epivizfileserver.parser.BigWig.BigWig attribute)
(epivizfileserver.parser.GtfFile.GtfFile attribute)
(epivizfileserver.parser.GtfParsedFile.GtfParsedFile attribute)
(epivizfileserver.parser.GtfTabixFile.GtfTabixFile attribute)
(epivizfileserver.parser.HDF5File.HDF5File attribute)
(epivizfileserver.parser.SamFile.SamFile attribute)
(epivizfileserver.parser.TbxFile.TbxFile attribute)
(epivizfileserver.parser.TranscriptTbxFile.TranscriptTbxFile attribute)
ComputedMeasurement (class in epivizfileserver.measurements.measurementClass)
computeWrapper() (epivizfileserver.measurements.measurementClass.ComputedMeasurement method)
connection (epivizfileserver.measurements.measurementClass.DbMeasurement attribute)
create_fileHandler() (in module epivizfileserver.server)
create_parser_object() (epivizfileserver.measurements.measurementClass.FileMeasurement method)
(in module epivizfileserver.handler.utils)
(in module epivizfileserver.parser.utils)
(in module epivizfileserver.server.utils)
create_request() (in module epivizfileserver.server.request)
D
daskWrapper() (epivizfileserver.parser.BigWig.BigWig method)
DataRequest (class in epivizfileserver.server.request)
DbMeasurement (class in epivizfileserver.measurements.measurementClass)
decompress_binary() (epivizfileserver.parser.BaseFile.BaseFile method)
E
EMDMeasurementMap (class in epivizfileserver.measurements.measurementManager)
endian (epivizfileserver.parser.BaseFile.BaseFile attribute)
EpivizClient (class in epivizfileserver.client.EpivizClient)
epivizfileserver (module)
epivizfileserver.client (module)
epivizfileserver.client.EpivizClient (module)
epivizfileserver.handler (module)
epivizfileserver.handler.handler (module)
epivizfileserver.handler.HandlerNoActor (module)
epivizfileserver.handler.utils (module)
epivizfileserver.measurements (module)
epivizfileserver.measurements.measurementClass (module)
epivizfileserver.measurements.measurementManager (module)
epivizfileserver.parser (module)
epivizfileserver.parser.BamFile (module)
epivizfileserver.parser.BaseFile (module)
epivizfileserver.parser.BigBed (module)
epivizfileserver.parser.BigWig (module)
epivizfileserver.parser.GtfFile (module)
epivizfileserver.parser.GtfParsedFile (module)
epivizfileserver.parser.GtfTabixFile (module)
epivizfileserver.parser.GWASBigBed (module)
epivizfileserver.parser.HDF5File (module)
epivizfileserver.parser.Helper (module)
epivizfileserver.parser.InteractionBigBed (module)
epivizfileserver.parser.SamFile (module)
epivizfileserver.parser.TbxFile (module)
epivizfileserver.parser.TileDB (module)
epivizfileserver.parser.TranscriptTbxFile (module)
epivizfileserver.parser.utils (module)
epivizfileserver.server (module)
epivizfileserver.server.request (module)
epivizfileserver.server.utils (module)
epivizfileserver.trackhub (module)
epivizfileserver.trackhub.TrackHub (module)
EpivizRequest (class in epivizfileserver.server.request)
F
file (epivizfileserver.parser.BamFile.BamFile attribute)
(epivizfileserver.parser.GtfFile.GtfFile attribute)
(epivizfileserver.parser.GtfParsedFile.GtfParsedFile attribute)
(epivizfileserver.parser.GtfTabixFile.GtfTabixFile attribute)
(epivizfileserver.parser.HDF5File.HDF5File attribute)
(epivizfileserver.parser.SamFile.SamFile attribute)
(epivizfileserver.parser.TbxFile.TbxFile attribute)
(epivizfileserver.parser.TranscriptTbxFile.TranscriptTbxFile attribute)
FileHandlerProcess (class in epivizfileserver.handler.handler)
(class in epivizfileserver.handler.HandlerNoActor)
FileMeasurement (class in epivizfileserver.measurements.measurementClass)
fileSrc (epivizfileserver.parser.BamFile.BamFile attribute)
(epivizfileserver.parser.GtfFile.GtfFile attribute)
(epivizfileserver.parser.GtfParsedFile.GtfParsedFile attribute)
(epivizfileserver.parser.GtfTabixFile.GtfTabixFile attribute)
(epivizfileserver.parser.HDF5File.HDF5File attribute)
(epivizfileserver.parser.SamFile.SamFile attribute)
(epivizfileserver.parser.TbxFile.TbxFile attribute)
(epivizfileserver.parser.TranscriptTbxFile.TranscriptTbxFile attribute)
format_result() (in module epivizfileserver.server.utils)
formatAsJSON() (epivizfileserver.parser.BaseFile.BaseFile method)
G
get() (epivizfileserver.measurements.measurementManager.MeasurementSet method)
get_autosql() (epivizfileserver.parser.BigBed.BigBed method)
(epivizfileserver.parser.BigWig.BigWig method)
get_bin() (epivizfileserver.parser.BamFile.BamFile method)
(epivizfileserver.parser.GtfTabixFile.GtfTabixFile method)
(epivizfileserver.parser.SamFile.SamFile method)
(epivizfileserver.parser.TbxFile.TbxFile method)
get_bytes() (epivizfileserver.parser.BaseFile.BaseFile method)
get_bytes_http() (epivizfileserver.parser.BaseFile.BaseFile method)
get_cache() (epivizfileserver.parser.BigWig.BigWig method)
(epivizfileserver.parser.SamFile.SamFile method)
get_col_names() (epivizfileserver.parser.BamFile.BamFile method)
(epivizfileserver.parser.GtfFile.GtfFile method)
(epivizfileserver.parser.GtfParsedFile.GtfParsedFile method)
(epivizfileserver.parser.GtfTabixFile.GtfTabixFile method)
(epivizfileserver.parser.SamFile.SamFile method)
(epivizfileserver.parser.TbxFile.TbxFile method)
get_columns() (epivizfileserver.measurements.measurementClass.ComputedMeasurement method)
(epivizfileserver.measurements.measurementClass.Measurement method)
get_data() (epivizfileserver.client.EpivizClient.EpivizClient method)
(epivizfileserver.measurements.measurementClass.ComputedMeasurement method)
(epivizfileserver.measurements.measurementClass.DbMeasurement method)
(epivizfileserver.measurements.measurementClass.FileMeasurement method)
(epivizfileserver.measurements.measurementClass.Measurement method)
(epivizfileserver.measurements.measurementClass.WebServerMeasurement method)
(epivizfileserver.parser.BaseFile.BaseFile method)
(epivizfileserver.parser.GtfFile.GtfFile method)
(epivizfileserver.parser.GtfParsedFile.GtfParsedFile method)
(epivizfileserver.parser.TbxFile.TbxFile method)
(epivizfileserver.server.request.DataRequest method)
(epivizfileserver.server.request.EpivizRequest method)
(epivizfileserver.server.request.MeasurementRequest method)
(epivizfileserver.server.request.SearchRequest method)
(epivizfileserver.server.request.SeqInfoRequest method)
get_file_object() (epivizfileserver.handler.handler.FileHandlerProcess method)
get_from_emd() (epivizfileserver.measurements.measurementManager.MeasurementManager method)
get_genomes() (epivizfileserver.measurements.measurementManager.MeasurementManager method)
get_measurement() (epivizfileserver.measurements.measurementManager.MeasurementManager method)
get_measurement_annotation() (epivizfileserver.measurements.measurementClass.Measurement method)
get_measurement_genome() (epivizfileserver.measurements.measurementClass.Measurement method)
get_measurement_id() (epivizfileserver.measurements.measurementClass.Measurement method)
get_measurement_max() (epivizfileserver.measurements.measurementClass.Measurement method)
get_measurement_metadata() (epivizfileserver.measurements.measurementClass.Measurement method)
get_measurement_min() (epivizfileserver.measurements.measurementClass.Measurement method)
get_measurement_name() (epivizfileserver.measurements.measurementClass.Measurement method)
get_measurement_source() (epivizfileserver.measurements.measurementClass.Measurement method)
get_measurement_type() (epivizfileserver.measurements.measurementClass.Measurement method)
get_measurements() (epivizfileserver.client.EpivizClient.EpivizClient method)
(epivizfileserver.measurements.measurementManager.MeasurementManager method)
(epivizfileserver.measurements.measurementManager.MeasurementSet method)
get_mids() (epivizfileserver.measurements.measurementManager.MeasurementSet method)
get_range_helper() (in module epivizfileserver.parser.Helper)
get_seq_info() (epivizfileserver.client.EpivizClient.EpivizClient method)
get_status() (epivizfileserver.measurements.measurementClass.FileMeasurement method)
(epivizfileserver.measurements.measurementClass.Measurement method)
(epivizfileserver.parser.BaseFile.BaseFile method)
(epivizfileserver.server.request.StatusRequest method)
getHeader() (epivizfileserver.parser.BigWig.BigWig method)
getId() (epivizfileserver.parser.BigWig.BigWig method)
getRange() (epivizfileserver.parser.BamFile.BamFile method)
(epivizfileserver.parser.BigWig.BigWig method)
(epivizfileserver.parser.GWASBigBed.GWASBigBed method)
(epivizfileserver.parser.GtfFile.GtfFile method)
(epivizfileserver.parser.GtfParsedFile.GtfParsedFile method)
(epivizfileserver.parser.GtfTabixFile.GtfTabixFile method)
(epivizfileserver.parser.HDF5File.HDF5File method)
(epivizfileserver.parser.InteractionBigBed.InteractionBigBed method)
(epivizfileserver.parser.SamFile.SamFile method)
(epivizfileserver.parser.TbxFile.TbxFile method)
(epivizfileserver.parser.TileDB.TileDB method)
getRecord() (epivizfileserver.handler.handler.FileHandlerProcess method)
(epivizfileserver.handler.HandlerNoActor.FileHandlerProcess method)
getTree() (epivizfileserver.parser.BigWig.BigWig method)
getTreeBytes() (epivizfileserver.parser.BigWig.BigWig method)
getValues() (epivizfileserver.parser.BigWig.BigWig method)
getZoom() (epivizfileserver.parser.BigWig.BigWig method)
getZoomHeader() (epivizfileserver.parser.BigWig.BigWig method)
GtfFile (class in epivizfileserver.parser.GtfFile)
GtfParsedFile (class in epivizfileserver.parser.GtfParsedFile)
GtfTabixFile (class in epivizfileserver.parser.GtfTabixFile)
GWASBigBed (class in epivizfileserver.parser.GWASBigBed)
H
handleFile() (epivizfileserver.handler.handler.FileHandlerProcess method)
(epivizfileserver.handler.HandlerNoActor.FileHandlerProcess method)
handleSearch() (epivizfileserver.handler.handler.FileHandlerProcess method)
(epivizfileserver.handler.HandlerNoActor.FileHandlerProcess method)
HDF5File (class in epivizfileserver.parser.HDF5File)
HEADER_STRUCT (epivizfileserver.parser.BaseFile.BaseFile attribute)
I
import_ahub() (epivizfileserver.measurements.measurementManager.MeasurementManager method)
import_dbm() (epivizfileserver.measurements.measurementManager.MeasurementManager method)
import_emd() (epivizfileserver.measurements.measurementManager.MeasurementManager method)
import_files() (epivizfileserver.measurements.measurementManager.MeasurementManager method)
import_records() (epivizfileserver.measurements.measurementManager.MeasurementManager method)
import_trackhub() (epivizfileserver.measurements.measurementManager.MeasurementManager method)
init() (epivizfileserver.measurements.measurementManager.EMDMeasurementMap method)
init_collections() (epivizfileserver.measurements.measurementManager.EMDMeasurementMap method)
init_measurements() (epivizfileserver.measurements.measurementManager.EMDMeasurementMap method)
InteractionBigBed (class in epivizfileserver.parser.InteractionBigBed)
is_computed() (epivizfileserver.measurements.measurementClass.Measurement method)
is_file() (epivizfileserver.measurements.measurementClass.Measurement method)
is_gene() (epivizfileserver.measurements.measurementClass.Measurement method)
is_local() (epivizfileserver.parser.BaseFile.BaseFile method)
L
local (epivizfileserver.parser.BaseFile.BaseFile attribute)
locateTree() (epivizfileserver.parser.BigWig.BigWig method)
M
magic (epivizfileserver.parser.BigBed.BigBed attribute)
(epivizfileserver.parser.BigWig.BigWig attribute)
(epivizfileserver.parser.GWASBigBed.GWASBigBed attribute)
(epivizfileserver.parser.InteractionBigBed.InteractionBigBed attribute)
MAXWORKER (in module epivizfileserver.server)
Measurement (class in epivizfileserver.measurements.measurementClass)
MeasurementManager (class in epivizfileserver.measurements.measurementManager)
MeasurementRequest (class in epivizfileserver.server.request)
measurements (epivizfileserver.measurements.measurementManager.MeasurementManager attribute)
MeasurementSet (class in epivizfileserver.measurements.measurementManager)
P
parse_attribute() (epivizfileserver.parser.GtfFile.GtfFile method)
(epivizfileserver.parser.GtfParsedFile.GtfParsedFile method)
parse_genome() (epivizfileserver.trackhub.TrackHub.TrackHub method)
parse_genomeTracks() (epivizfileserver.trackhub.TrackHub.TrackHub method)
parse_header() (epivizfileserver.parser.BaseFile.BaseFile method)
(epivizfileserver.parser.BigWig.BigWig method)
parse_hub() (epivizfileserver.trackhub.TrackHub.TrackHub method)
parse_trackDb() (epivizfileserver.trackhub.TrackHub.TrackHub method)
parse_url() (epivizfileserver.parser.BaseFile.BaseFile method)
parse_url_http() (epivizfileserver.parser.BaseFile.BaseFile method)
parseLeafDataNode() (epivizfileserver.parser.BigBed.BigBed method)
(epivizfileserver.parser.BigWig.BigWig method)
pickleFileObject() (epivizfileserver.handler.handler.FileHandlerProcess method)
(epivizfileserver.handler.HandlerNoActor.FileHandlerProcess method)
process_emd_record() (epivizfileserver.measurements.measurementManager.EMDMeasurementMap method)
Q
query() (epivizfileserver.measurements.measurementClass.DbMeasurement method)
(epivizfileserver.measurements.measurementClass.Measurement method)
R
read_10x_hdf5() (epivizfileserver.parser.HDF5File.HDF5File method)
readRtreeHeaderNode() (epivizfileserver.parser.BigWig.BigWig method)
readRtreeNode() (epivizfileserver.parser.BigWig.BigWig method)
records (epivizfileserver.handler.handler.FileHandlerProcess attribute)
(epivizfileserver.handler.HandlerNoActor.FileHandlerProcess attribute)
S
SamFile (class in epivizfileserver.parser.SamFile)
schedulePickle() (in module epivizfileserver.server)
search_gene() (epivizfileserver.measurements.measurementClass.FileMeasurement method)
(epivizfileserver.parser.GtfFile.GtfFile method)
(epivizfileserver.parser.GtfParsedFile.GtfParsedFile method)
searchGene() (epivizfileserver.parser.GtfFile.GtfFile method)
(epivizfileserver.parser.GtfParsedFile.GtfParsedFile method)
(epivizfileserver.parser.TbxFile.TbxFile method)
SearchRequest (class in epivizfileserver.server.request)
SeqInfoRequest (class in epivizfileserver.server.request)
set_cache() (epivizfileserver.parser.BigWig.BigWig method)
(epivizfileserver.parser.SamFile.SamFile method)
setRecord() (epivizfileserver.handler.handler.FileHandlerProcess method)
(epivizfileserver.handler.HandlerNoActor.FileHandlerProcess method)
setup_after_connection() (in module epivizfileserver.server)
setup_app() (in module epivizfileserver.server)
setup_connection() (in module epivizfileserver.server)
simplified_bin_rows() (epivizfileserver.parser.BaseFile.BaseFile method)
StatusRequest (class in epivizfileserver.server.request)
SUMMARY_STRUCT (epivizfileserver.parser.BaseFile.BaseFile attribute)
sync() (epivizfileserver.measurements.measurementManager.EMDMeasurementMap method)
sync_collections() (epivizfileserver.measurements.measurementManager.EMDMeasurementMap method)
sync_measurements() (epivizfileserver.measurements.measurementManager.EMDMeasurementMap method)
T
TbxFile (class in epivizfileserver.parser.TbxFile)
TileDB (class in epivizfileserver.parser.TileDB)
to_DF() (epivizfileserver.parser.BamFile.BamFile method)
to_msgpack() (epivizfileserver.parser.BamFile.BamFile method)
toDataFrame() (in module epivizfileserver.parser.utils)
toDF() (epivizfileserver.parser.GtfTabixFile.GtfTabixFile method)
(epivizfileserver.parser.SamFile.SamFile method)
(epivizfileserver.parser.TbxFile.TbxFile method)
TrackHub (class in epivizfileserver.trackhub.TrackHub)
TranscriptTbxFile (class in epivizfileserver.parser.TranscriptTbxFile)
traverseRtreeNodes() (epivizfileserver.parser.BigWig.BigWig method)
tree (epivizfileserver.parser.BigWig.BigWig attribute)
U
use_emd() (epivizfileserver.measurements.measurementManager.MeasurementManager method)
V
validate_params() (epivizfileserver.server.request.DataRequest method)
(epivizfileserver.server.request.EpivizRequest method)
(epivizfileserver.server.request.MeasurementRequest method)
(epivizfileserver.server.request.SearchRequest method)
(epivizfileserver.server.request.SeqInfoRequest method)
version (epivizfileserver.client.EpivizClient.EpivizClient attribute)
W
WebServerMeasurement (class in epivizfileserver.measurements.measurementClass)
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