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(java.io.File f)
          Creates a new Chromatogram object from the named file.
static Chromatogram ChromatogramFactory.create(java.io.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
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 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)
           
 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
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.