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

Packages that use Chromatogram

Package	Description
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

Modifier and Type	Class	Description
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

Modifier and Type	Method	Description
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	AbstractChromatogram.reverseComplement()
Chromatogram	Chromatogram.reverseComplement()	Returns a new Chromatogram representing the reverse complement of this one.

Methods in org.biojava.bio.chromatogram with parameters of type Chromatogram

Modifier and Type	Method	Description
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

Modifier and Type	Method	Description
Chromatogram	ChromatogramGraphic.getChromatogram()	Accessor for the in-use chromatogram.

Methods in org.biojava.bio.chromatogram.graphic with parameters of type Chromatogram

Modifier and Type	Method	Description
float	ChromatogramNonlinearScaler.Identity.scale(Chromatogram c, int sampleIndex)
float	ChromatogramNonlinearScaler.scale(Chromatogram c, int sampleIndex)	Returns the remapped coordinate for the provided trace sample index of the given chromatogram.
float	FixedBaseWidthScaler.scale(Chromatogram c, int traceSampleIndex)
void	ChromatogramGraphic.setChromatogram(Chromatogram c)	Sets the chromatogram to draw.

Constructors in org.biojava.bio.chromatogram.graphic with parameters of type Chromatogram

Constructor	Description
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

Modifier and Type	Class	Description
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

Modifier and Type	Class	Description
class	SCF	A Chromatogram as loaded from an SCF v2 or v3 file.