Package: cgview (0.0.20100111-4)

[ Source: cgview  ]

Circular Genome Viewer

CGView is a Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web. Feature information and rendering options are supplied to the program using an XML file, a tab delimited file, or an NCBI ptt file. CGView converts the input into a graphical map (PNG, JPG, or Scalable Vector Graphics format), complete with labels, a title, legends, and footnotes. In addition to the default full view map, the program can generate a series of hyperlinked maps showing expanded views. The linked maps can be explored using any web browser, allowing rapid genome browsing, and facilitating data sharing. The feature labels in maps can be hyperlinked to external resources, allowing CGView maps to be integrated with existing web site content or databases.

In addition to the CGView application, an API is available for generating maps from within other Java applications, using the cgview package.

CGView can be used for any of the following:

 * Bacterial genome visualization and browsing - CGView can be
   incorporated into bacterial genome annotation pipelines, as a means
   of generating web content for data visualization and navigation. The
   PNG and image map content does not require Java applets or special
   browser plugins.
 * Genome poster generation - CGView can generate poster-sized images of
   circular genomes in rasterized image formats or in Scalable Vector
   Graphics format.
 * Sequence analysis visualization - CGView can be used to display the
   output of sequence analysis programs in a circular context.

CGView features:

 * Images can be generated in PNG, JPG, or SVG format. See the
   CGView gallery.
 * Static or interactive maps can be generated. The interactive maps
   make use of standard PNG images and HTML image maps. Scalable Vector
   Graphics output is included in the interactive maps (see example).
 * The XML input allows complete control over the appearance of the map.
 * Tab delimited input files and NCBI ptt files can be used as an
   alternative to the XML format.
 * The CGView API can be used to incorporate CGView into Java
   applications.
 * The CGView applet can be used to incorporate zoomable maps into web
   pages (see example).
 * The CGView Server can be used to generate maps online.

Other Packages Related to cgview

• dep: default-jre

  Standard Java or Java compatible Runtime

  or java10-runtime

  virtual package provided by default-jre, openjdk-11-jre

  or java11-runtime

  virtual package provided by default-jre, openjdk-11-jre

• dep: jarwrapper (>= 0.5)

  Run executable Java .jar files

• dep: libbatik-java

  xml.apache.org SVG Library

• dep: libcommons-lang-java

  Commons Lang - an extension of the java.lang package

• dep: libjargs-java

  Command-line argument parsing for Java

• dep: libxerces2-java

  Validating XML parser for Java with DOM level 3 support

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