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Packages that use Chromatogram | |
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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 |
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Classes in org.biojava.bio.chromatogram that implement Chromatogram | |
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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 | |
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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()
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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 | |
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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 |
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Methods in org.biojava.bio.chromatogram.graphic that return Chromatogram | |
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Chromatogram |
ChromatogramGraphic.getChromatogram()
Accessor for the in-use chromatogram. |
Methods in org.biojava.bio.chromatogram.graphic with parameters of type Chromatogram | |
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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)
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float |
FixedBaseWidthScaler.scale(Chromatogram c,
int traceSampleIndex)
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void |
ChromatogramGraphic.setChromatogram(Chromatogram c)
Sets the chromatogram to draw. |
Constructors in org.biojava.bio.chromatogram.graphic with parameters of type Chromatogram | |
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ChromatogramGraphic(Chromatogram c)
Creates a new ChromatogramGraphic , initially displaying
the given chromatogram. |
Uses of Chromatogram in org.biojava.bio.program.abi |
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Classes in org.biojava.bio.program.abi that implement Chromatogram | |
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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 |
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Classes in org.biojava.bio.program.scf that implement Chromatogram | |
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class |
SCF
A Chromatogram as loaded from an
SCF v2 or v3 file. |
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