René's URL Explorer Experiment

{"@context":"https://schema.org","@type":"DiscussionForumPosting","headline":"Q.  Inquiry for the Alignment Render in the BioJava.","articleBody":"Hello, \r\n\r\nI am software developer (new to biojava) currently using the Biojava API [biojava-core - 4.0.0 , alignment -1.9.3] for an application.\r\n\r\nWe are trying to accomplish Alignment render of the Query and the target \r\non Blast search like the image below. We are using the SmithWaterman algorithm for local Alignment. Now we are looking for a different way to visualize exactly where the sequence was aligned in our frontend application (we are using biojava in our backend side), like the following.\r\n\r\n```\r\nAAGAA\r\n||| |\r\nAAGGA\r\n```\r\n\r\nI found SimpleAlignment to render query and target alignment using TranslatedSequencePanel. but SimpleAlignment does not handle different length sequences and does not contain any gap-editing concepts. Upon further research I also came across formatOut  which return string with the format we were looking for. But formatOut is only available in biojava-legacy. Is there any way i can get the result like this one?\r\n![image](https://user-images.githubusercontent.com/31877486/138051362-026422d1-7f5a-4a8b-9993-4b85c76939c9.png)\r\n\r\nThanks!","author":{"url":"https://github.com/RoshanShrestha123","@type":"Person","name":"RoshanShrestha123"},"datePublished":"2021-10-20T07:56:47.000Z","interactionStatistic":{"@type":"InteractionCounter","interactionType":"https://schema.org/CommentAction","userInteractionCount":6},"url":"https://github.com/983/biojava/issues/983"}