The CGView applet can be added to web pages, to display sequence feature information for circular genomes. The applet is not intended to be used as a means to generate images for publication (use the CGView application instead, or the PlasMapper server). The primary purpose of the applet is to allow dynamically generated sequence features to be visualized. For example, a program searching for sequence patterns might generate a tab-delimited feature file for the CGView applet, along with an HTML page containing the appropriate applet tag. The results could then be visualized by the program user, in a web browser. The CGView applet requires the latest version of the Java Plug-in. See the Java Plug-in home page for more information. Click here to test the CGView applet in your browser.
To use the CGView applet:
Download the CGView.jar file.
Place the file in the same directory as the HTML files on your web server.
Create a tab delimited file that describes the sequence features you want to display, or obtain an NCBI ptt file.
Use the applet tag (see example below) to incorporate the CGView applet into a web page. Change the "file" param value so that it matches the name of the feature file you created. he input file must end with an extension that tells CGView the format of the input file (.tab for the tab delimited format, or .ptt for the NCBI ptt format).
The applet tag shown below can be used to add the CGView applet to a web page. The value of the file parameter must be set to match the feature file name you are using. The height and width values can be adjusted. Five optional parameters are also available: hideLegend, hideFullViewLabels, labelFontSize, legendFontSize, and rulerFontSize. When hideLegend is set to T, legends are not shown in the applet. When hideFullViewLabels is set to T, labels are only drawn when the map is zoomed in. The font size options can be used to specify integer font sizes, instead of relying on CGView to choose font sizes. The Example pages using the applet are: example_1.html, example_2.html, and example_3.html.
<applet code="CGView.class" width="900" height="800" archive="CGView.jar">
<param NAME="file" VALUE="example_3_features.tab">
<param NAME="hideLegend" VALUE="T">
<param NAME="rulerFontSize" VALUE="10">
Stothard P, Wishart DS. Circular genome visualization and exploration
using CGView. Bioinformatics 21:537-539.