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## Uses of Interface
org.biojava.bio.chromatogram.Chromatogram

Packages that use Chromatogram
org.biojava.bio.chromatogram | Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.
org.biojava.bio.chromatogram.graphic | Tools for displaying chromatograms.
org.biojava.bio.program.abi | ABI Trace Handling.
org.biojava.bio.program.scf | Support for the SCF chromatogram format.

Uses of Chromatogram in org.biojava.bio.chromatogram

Classes in org.biojava.bio.chromatogram that implement Chromatogram
`class` | `AbstractChromatogram` A basic, abstract implementation of `Chromatogram`.
`class` | `SimpleChromatogram` A basic chromatogram implementation which provides public mutators for setting the various attributes of the chromatogram.

Methods in org.biojava.bio.chromatogram that return Chromatogram
`static Chromatogram` | `ChromatogramFactory.create(File f)` Creates a new `Chromatogram` object from the named file.
`static Chromatogram` | `ChromatogramFactory.create(InputStream in)` Creates a new `Chromatogram` object from the supplied stream.
`Chromatogram` | `Chromatogram.reverseComplement()` Returns a new `Chromatogram` representing the reverse complement of this one.
`Chromatogram` | `AbstractChromatogram.reverseComplement()`

Methods in org.biojava.bio.chromatogram with parameters of type Chromatogram
`static SymbolList` | `ChromatogramTools.getDNASequence(Chromatogram chromat)` Get the called DNA sequence from a chromatogram.
`static int` | `ChromatogramTools.getTraceOffset(Chromatogram chromat, int which)` Get a specific value from the trace offset sequence in the given chromatogram and extract its `int` value.
`static int[]` | `ChromatogramTools.getTraceOffsetArray(Chromatogram chromat)` Converts the peak offsets list of the given chromatogram into a new `int` array.
`static SymbolList` | `ChromatogramTools.getTraceOffsets(Chromatogram chromat)` Get the peak offsets for the called bases of a chromatogram.

Uses of Chromatogram in org.biojava.bio.chromatogram.graphic

Methods in org.biojava.bio.chromatogram.graphic that return Chromatogram
`Chromatogram` | `ChromatogramGraphic.getChromatogram()` Accessor for the in-use chromatogram.

Methods in org.biojava.bio.chromatogram.graphic with parameters of type Chromatogram
`float` | `FixedBaseWidthScaler.scale(Chromatogram c, int traceSampleIndex)`
`float` | `ChromatogramNonlinearScaler.scale(Chromatogram c, int sampleIndex)` Returns the remapped coordinate for the provided trace sample index of the given chromatogram.
`float` | `ChromatogramNonlinearScaler.Identity.scale(Chromatogram c, int sampleIndex)`
`void` | `ChromatogramGraphic.setChromatogram(Chromatogram c)` Sets the chromatogram to draw.

Constructors in org.biojava.bio.chromatogram.graphic with parameters of type Chromatogram
`ChromatogramGraphic(Chromatogram c)` Creates a new `ChromatogramGraphic`, initially displaying the given chromatogram.

Uses of Chromatogram in org.biojava.bio.program.abi

Classes in org.biojava.bio.program.abi that implement Chromatogram
`class` | `ABIFChromatogram` An implementation of `Chromatogram` to encapulsulate chromatogram data extracted from the files produced by ABI sequencers, such as the the 377 and the 3700.

Uses of Chromatogram in org.biojava.bio.program.scf

Classes in org.biojava.bio.program.scf that implement Chromatogram
`class` | `SCF` A `Chromatogram` as loaded from an SCF v2 or v3 file.

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