Widget Overview
The GenoViz Software Development Kit
includes six visualization widgets:
Each widget implements
the com.affymetrix.genoviz.widget.NeoWidgetI
interface.
NeoMap: Linear maps (physical, genetic, sequence, etc.)
The basic functionality of the NeoMap widget is to display
and manipulate arbitrary annotations along a linear map.
The application programming interface (API) supports adding annotations
in a variety of ways.
It also supports scrolling and zooming the view of the map,
selection of annotations, intelligent layout of annotations, and
rubberbanding.
In addition to the NeoMap, a number of different visual representations (glyphs)
of annotations are provided such as rectangles, arrows, and circles. Developers
can also easily create their own glyphs
without modifying the NeoMap implementation.
TieredNeoMap: Linear maps of category data
An extension of NeoMap, TieredNeoMaps have an integrated mechanism for displaying
data as belonging to one of several categories. Each category is assigned a tier,
which expands as necessary to display the data within it. Tiers can also be collapsed
or hidden to reduce cluttering of the display. A TieredLabelMap can be assigned to
the TieredNeoMap, which automatically keeps track of tiers' states and displays
a label of the same size off to one side of the map.
NeoAssembler: Sequence assemblies
The NeoAssembler widget displays DNA sequence assemblies
at a variety of resolutions.
The critical feature of the assembly viewer is the
ability to view individual sequence runs and consensus sequence
alongside each other. At resolutions > 1 pixel/base, aligned sequences
are represented as shaded rectangles with shading based on agreement
or disagreement with consensus. The font size for sequences can be
set, and at high enough resolution the base letters will be displayed
in addition to the background shading. For deep assemblies, the
sequences can be scrolled through while the consensus is held fixed.
Labels for the sequences are kept to the side, and events generated on
the NeoAssembler can be distinguished as occurring over the consensus,
labels, or aligned sequences. Although primarily designed to view DNA
assemblies from sequencing projects, the NeoAssembler can be used to
display any nucleotide or protein multiple sequence alignment.
NeoSeq: Biological sequences at residue resolution
The NeoSeq widget displays DNA sequences at base-pair resolution, or
proteins at amino-acid resolution, wrapping the residues so that
contiguous sequence is displayed as multiple lines, and a scrollbar is
provided to scroll through lines of sequence. Annotations along the
sequence can be represented as background color fills, outlines, or
font color. The size of the sequence font and the spacing of sequence lines are
configurable. Ranges of sequence can be selected, and the selected
sequence can be returned. Changes to the range of sequence displayed
generate NeoEvents that applets/applications can listen for.
NeoQualler: DNA base calling quality scores
The NeoQualler displays a histogram of quality scores
from a base calling program.
The bases and the bars graphing quality are color coded.
NeoTracer: DNA sequence trace data
The NeoTrace widget displays DNA trace data. The API supports input
of SCF and ABI trace files, as well as methods to add individual trace
data points and base calls. The trace widget displays four colored dye traces
alongside base calls. The API also supports calls mapping from trace
data points to called bases, such as retrieving the nearest called
base to a give trace data point and positioning the trace at a given
base position.
Next: Hello
- A First Use of a NeoMap