Uses of Interface
org.biojava.bio.chromatogram.Chromatogram
Packages that use Chromatogram
Package
Description
Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.
Tools for displaying chromatograms.
ABI Trace Handling.
Support for the SCF chromatogram format.
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Uses of Chromatogram in org.biojava.bio.chromatogram
Classes in org.biojava.bio.chromatogram that implement ChromatogramModifier and TypeClassDescriptionclass
A basic, abstract implementation ofChromatogram
.class
A basic chromatogram implementation which provides public mutators for setting the various attributes of the chromatogram.Methods in org.biojava.bio.chromatogram that return ChromatogramModifier and TypeMethodDescriptionstatic Chromatogram
Creates a newChromatogram
object from the named file.static Chromatogram
ChromatogramFactory.create
(InputStream in) Creates a newChromatogram
object from the supplied stream.AbstractChromatogram.reverseComplement()
Chromatogram.reverseComplement()
Returns a newChromatogram
representing the reverse complement of this one.Methods in org.biojava.bio.chromatogram with parameters of type ChromatogramModifier and TypeMethodDescriptionstatic final SymbolList
ChromatogramTools.getDNASequence
(Chromatogram chromat) Get the called DNA sequence from a chromatogram.static final int
ChromatogramTools.getTraceOffset
(Chromatogram chromat, int which) Get a specific value from the trace offset sequence in the given chromatogram and extract itsint
value.static final int[]
ChromatogramTools.getTraceOffsetArray
(Chromatogram chromat) Converts the peak offsets list of the given chromatogram into a newint
array.static final 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 ChromatogramModifier and TypeMethodDescriptionChromatogramGraphic.getChromatogram()
Accessor for the in-use chromatogram.Methods in org.biojava.bio.chromatogram.graphic with parameters of type ChromatogramModifier and TypeMethodDescriptionfloat
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 ChromatogramModifierConstructorDescriptionCreates a newChromatogramGraphic
, initially displaying the given chromatogram. -
Uses of Chromatogram in org.biojava.bio.program.abi
Classes in org.biojava.bio.program.abi that implement ChromatogramModifier and TypeClassDescriptionclass
An implementation ofChromatogram
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