VARNA: Visualization Applet for RNA

Adding text labels: The annotations example

Different types of textual annotations can be added to a VARNA drawing:

• A - Loop annotations: They are located in the barycenter of a loop, moving along with its bases. As for every other type of annotations, a custom font size can be specified through the color.
• B - Helix annotations: They are marking a whole helix, moving along with its bases and located within it. For every annotation, a custom color can be specified.
• C and D - Base annotations: Located on the side of a single base, they can be gently pushed further away to avoid a possible collision with a base number.
• E - Static annotations: They are drawn at a fixed positions within the panel.

Lastly, substructures can be automatically annotated, as was done in this example with terminal loops using the parameter autoTerminalLoops.

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<applet  code="VARNA.class"
	codebase="bin"
	archive="VARNA.jar"
	<param name="sequenceDBN" value=
	  "                                                       " />
	<param name="structureDBN" value=
	  "((((((.((((((........)))))).((((((.......))))))..))))))" />
	<param name="annotations" value=
	  "A:type=L,anchor=7,size=24;
	   B:type=H,anchor=6,color=#FF0000;
	   C:type=B,anchor=10,color=#0000FF;
	   D:type=B,anchor=11,color=#00FF00;
	   E:type=P,x=300,y=-60,size=34" />
	<param name="autoTerminalLoops" value="true" />
</applet>