Remove custom annotations in batch

Paul Janszen

• April 23, 2024 07:21

Hello,

I'm trying to adapt a script for removal of annotations. This script is for the removal of standard annotations like Concatenated Sequence and Ligation.

However when I change the TYPE to a custom annotation type I get an error: The compilation failed at Line 9: error: cannot find symbol

// Remove Concatenated Sequence annotations
import java.util.stream.Collectors;
public static void modifySequence(DefaultSequenceDocument sequence) {
sequence
.setAnnotations(
sequence.getSequenceAnnotations()
.stream()
.filter(annotation -> !annotation.getType().equals(SequenceAnnotation.TYPE_CONCATENATED_SEQUENCE))
.collect(Collectors.toList()));
}

How can I adapt this script to remove custom annotations?

Thanks,

Paul

0

• 

  Matthew Cheung

  • April 24, 2024 10:07

  Hi Paul,

  The annotation type is just a String.  The various TYPE_XYZ variables are available for any built in types, but you can also just specify the String.  For example replacing TYPE_LIGATION with "ligation" will do the same thing.

  So for custom types that you have created, you can just specify the same String that was used to create it.

  0
• 

  Paul Janszen

  • April 24, 2024 11:55

  Hello Matthew,

  That doesn't work. I get these errors also with standard annotations:

  Standard annotation: Ligation:

  

  Custom annotation: Vhh Gene:

  

   

  This works for standard annotation LIGATION:

  

  0
• 

  Matthew Cheung

  • April 25, 2024 23:40
  • Edited

  Hi Paul,

  You need to replace the whole variable with a String.  e.g. 

  .filter(annotation -> !annotation.getType().equals("ligation"))

   

  0
• 

  Paul Janszen

  • April 29, 2024 13:51

  Hi Matthew,

  Sorry for the late reply. But your solution did work very well. Thank you!

  0

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