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I get the warning “(old style Annotation) on new style Annotation::Collection”. What is wrong?

April 26, 2017annotation collection style warning wrong

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I get the warning “(old style Annotation) on new style Annotation::Collection”. What is wrong?

2 Answers

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Wow, you’re using an old version! You’ll see this error because the modules and interface has changed starting with BioPerl 1.0. Before v1.0 there was a Bio::Annotation module with add_Comment, add_Reference, each_Comment, and each_Reference methods. After v1.0 there is a Bio::Annotation::Collection module with add_Annotation(‘comment’, $ann) and get_Annotations(‘comment’). Please update your code in order to avoid seeing these warning messages. In the future the Reference objects will likely be implemented by the Bio::Biblio system but we hope to maintain a compatible API for these.

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This is because we have transitioned from the add_Comment/each_Comment, add_Reference/each_Reference style to add_Annotation(‘comment’, $ann)/get_Annotations(‘comment). Please update your code in order to avoid seeing these warning messages. The objects have also changed from the Bio::Annotation object to the Bio::Annotation::Collection object, starting with v. 1.0. This is a more general and extensible system. In the future the Reference objects will likely be implemented by the Bio::Biblio system but we hope to maintain a compatible API for these.