All Implemented Interfaces:

java.io.Closeable , java.lang.AutoCloseable
```
public final class TdfFile
 implements Closeable
                    
```
A Tiled Data Format (TDF) reader.
TDF format is a binary format for track data designed by IGV team for their browser.
TDF lacks an accurate and complete spec, thus the implementation is based on the high-level format overview in notes.txt and the sources of IGV itself.
See https://github.com/igvteam/igv/blob/master/src/org/broad/igv/tdf/notes.txt. See https://www.broadinstitute.org/software/igv/TDF.

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`public class`	`TdfFile.Companion`

Field Summary

Fields
Modifier and Type	Field	Description
`private final Integer`	`version`
`private final Set<String>`	`dataSetNames`
`private final Set<String>`	`groupNames`
`private final String`	`source`
`private final List<WindowFunction>`	`windowFunctions`
`private final TrackType`	`trackType`
`private final String`	`trackLine`
`private final List<String>`	`trackNames`
`private final String`	`build`
`private final Boolean`	`compressed`

Method Summary

Modifier and Type	Method	Description
`final List<TdfTile>`	`query(TdfDataset dataset, Integer startOffset, Integer endOffset, Function0<Unit> cancelledChecker)`	Returns a list of dataset tiles overlapping a given interval.
`final TdfSummary`	`summarize(String chromosome, Integer startOffset, Integer endOffset, Integer zoom, Function0<Unit> cancelledChecker)`	Returns a summary of the data within a given interval.
`final TdfTile`	`getTile(TdfDataset ds, Integer tileNumber)`
`final TdfDataset`	`getDataset(String chromosome, Integer zoom, WindowFunction windowFunction)`
`final TdfGroup`	`getGroup(String name)`
`Unit`	`close()`
`final String`	`component1()`
`final List<WindowFunction>`	`component5()`
`final TrackType`	`component6()`
`final String`	`component7()`
`final List<String>`	`component8()`
`final String`	`component9()`
`final Boolean`	`component10()`
`final TdfFile`	`copy(String source, RomBufferFactory buffFactory, TdfFile.Header header, TdfMasterIndex index, List<WindowFunction> windowFunctions, TrackType trackType, String trackLine, List<String> trackNames, String build, Boolean compressed)`
`final Integer`	`getVersion()`
`final Set<String>`	`getDataSetNames()`
`final Set<String>`	`getGroupNames()`
`final String`	`getSource()`
`final List<WindowFunction>`	`getWindowFunctions()`	Window functions supported by the data, e.g.
`final TrackType`	`getTrackType()`	Data type, e.g.
`final String`	`getTrackLine()`	Track description, see BED format spec for details.
`final List<String>`	`getTrackNames()`	Human-readable track names.
`final String`	`getBuild()`	Genome build, e.g.
`final Boolean`	`getCompressed()`	Whether the data sections are compressed with DEFLATE.

Methods inherited from class java.lang.AutoCloseable
equals, hashCode, toString
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

query
```
 final List<TdfTile> query(TdfDataset dataset, Integer startOffset, Integer endOffset, Function0<Unit> cancelledChecker)
```
Returns a list of dataset tiles overlapping a given interval.

Parameters:

dataset - dataset to query.

startOffset - 0-based start offset.

endOffset - 0-based end offset.

cancelledChecker - Throw cancelled exception to abort operation

summarize

 final TdfSummary summarize(String chromosome, Integer startOffset, Integer endOffset, Integer zoom, Function0<Unit> cancelledChecker)

Returns a summary of the data within a given interval.

getTile

 final TdfTile getTile(TdfDataset ds, Integer tileNumber)

getDataset

@JvmOverloads() final TdfDataset getDataset(String chromosome, Integer zoom, WindowFunction windowFunction)

getGroup
```
 final TdfGroup getGroup(String name)
```

close
```
 Unit close()
```

component1
```
 final String component1()
```

component5

 final List<WindowFunction> component5()

component6
```
 final TrackType component6()
```

component7
```
 final String component7()
```

component8
```
 final List<String> component8()
```

component9
```
 final String component9()
```

component10
```
 final Boolean component10()
```

copy

 final TdfFile copy(String source, RomBufferFactory buffFactory, TdfFile.Header header, TdfMasterIndex index, List<WindowFunction> windowFunctions, TrackType trackType, String trackLine, List<String> trackNames, String build, Boolean compressed)

getVersion
```
 final Integer getVersion()
```

getDataSetNames
```
 final Set<String> getDataSetNames()
```

getGroupNames
```
 final Set<String> getGroupNames()
```

getSource
```
 final String getSource()
```

getWindowFunctions
```
 final List<WindowFunction> getWindowFunctions()
```
Window functions supported by the data, e.g. "mean".

getTrackType
```
 final TrackType getTrackType()
```
Data type, e.g. "GENE_EXPRESSION".

getTrackLine
```
 final String getTrackLine()
```
Track description, see BED format spec for details.

getTrackNames
```
 final List<String> getTrackNames()
```
Human-readable track names.

getBuild
```
 final String getBuild()
```
Genome build, e.g. "hg38".

getCompressed
```
 final Boolean getCompressed()
```
Whether the data sections are compressed with DEFLATE.

Class TdfFile

Nested Class Summary

Field Summary

Method Summary

Methods inherited from class java.lang.AutoCloseable

Methods inherited from class java.lang.Object

Method Detail

query

summarize

getTile

getDataset

getGroup

close

component1

component5

component6

component7

component8

component9

component10

copy

getVersion

getDataSetNames

getGroupNames

getSource

getWindowFunctions

getTrackType

getTrackLine

getTrackNames

getBuild

getCompressed