Comparing technical solutions for displaying alignments

With HTML/CSS
Pros
  • Directly shown in the browser
  • Suitable for all browsers
  • Simple
  • Fast
Cons
  • Limited interactivity
  • Limited functionality
With Java Web-start
Implementations: Strap
Pros
  • The speed of Java is suitable for 3D-visualization
  • Full application functionality is accessible via menu-bar and context menus
Cons
  • Requires Java
  • Takes a while before the alignment is shown
  • Occasionally Java-Web-start programs do not start
  • Security: The program uses the file system for data cache
Implementation:
With Java Applets
Pros
  • The speed of Java is suitable for 3D-Visualization
  • Security: Usually runs in a sand-box
  • Interactive user interface
  • Embedded in a web page
Cons
  • Requires the Java plugin
  • Occasionally fails to start
  • Takes a while before the alignment is shown
  • Occasionally the browser freezes or crashes
  • Large amounts of memory are taken up and might not be freed after closing the applet page.
  • Different applets may interfere with each other
Implementations:
Cinema, Jalview and PFaat
With Vector format
Pros
  • Scalable without raster effect
  • High quality graphics
  • Many display options
  • Looks always exactly the same independent of the viewer
Cons
  • Most browsers do not support vector image formats like PostScript, SVG and PDF and an external viewer is required.
  • No balloon messages
Implementation:
  • TexShade
  • ESPript
  • Boxshade