{"action":"created","issue":{"url":"https://api.github.com/repos/SynBioDex/libSBOLj/issues/348","repository_url":"https://api.github.com/repos/SynBioDex/libSBOLj","labels_url":"https://api.github.com/repos/SynBioDex/libSBOLj/issues/348/labels{/name}","comments_url":"https://api.github.com/repos/SynBioDex/libSBOLj/issues/348/comments","events_url":"https://api.github.com/repos/SynBioDex/libSBOLj/issues/348/events","html_url":"https://github.com/SynBioDex/libSBOLj/issues/348","id":154294322,"number":348,"title":"JavaDoc for sortedComponents method in ComponentDefinition class","user":{"login":"mehersam","id":7087523,"avatar_url":"https://avatars.githubusercontent.com/u/7087523?v=3","gravatar_id":"","url":"https://api.github.com/users/mehersam","html_url":"https://github.com/mehersam","followers_url":"https://api.github.com/users/mehersam/followers","following_url":"https://api.github.com/users/mehersam/following{/other_user}","gists_url":"https://api.github.com/users/mehersam/gists{/gist_id}","starred_url":"https://api.github.com/users/mehersam/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mehersam/subscriptions","organizations_url":"https://api.github.com/users/mehersam/orgs","repos_url":"https://api.github.com/users/mehersam/repos","events_url":"https://api.github.com/users/mehersam/events{/privacy}","received_events_url":"https://api.github.com/users/mehersam/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/SynBioDex/libSBOLj/milestones/3","html_url":"https://github.com/SynBioDex/libSBOLj/milestones/SBOL%202.1","labels_url":"https://api.github.com/repos/SynBioDex/libSBOLj/milestones/3/labels","id":1409072,"number":3,"title":"SBOL 2.1","description":"","creator":{"login":"cjmyers","id":3507191,"avatar_url":"https://avatars.githubusercontent.com/u/3507191?v=3","gravatar_id":"","url":"https://api.github.com/users/cjmyers","html_url":"https://github.com/cjmyers","followers_url":"https://api.github.com/users/cjmyers/followers","following_url":"https://api.github.com/users/cjmyers/following{/other_user}","gists_url":"https://api.github.com/users/cjmyers/gists{/gist_id}","starred_url":"https://api.github.com/users/cjmyers/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cjmyers/subscriptions","organizations_url":"https://api.github.com/users/cjmyers/orgs","repos_url":"https://api.github.com/users/cjmyers/repos","events_url":"https://api.github.com/users/cjmyers/events{/privacy}","received_events_url":"https://api.github.com/users/cjmyers/received_events","type":"User","site_admin":false},"open_issues":6,"closed_issues":67,"state":"open","created_at":"2015-11-12T19:22:12Z","updated_at":"2016-05-11T23:36:22Z","due_on":"2016-04-30T06:00:00Z","closed_at":null},"comments":2,"created_at":"2016-05-11T17:05:50Z","updated_at":"2016-05-12T23:11:56Z","closed_at":null,"body":"Specify how the Components are being sorted. Mention how the sorting functionality works"},"comment":{"url":"https://api.github.com/repos/SynBioDex/libSBOLj/issues/comments/218911619","html_url":"https://github.com/SynBioDex/libSBOLj/issues/348#issuecomment-218911619","issue_url":"https://api.github.com/repos/SynBioDex/libSBOLj/issues/348","id":218911619,"user":{"login":"cjmyers","id":3507191,"avatar_url":"https://avatars.githubusercontent.com/u/3507191?v=3","gravatar_id":"","url":"https://api.github.com/users/cjmyers","html_url":"https://github.com/cjmyers","followers_url":"https://api.github.com/users/cjmyers/followers","following_url":"https://api.github.com/users/cjmyers/following{/other_user}","gists_url":"https://api.github.com/users/cjmyers/gists{/gist_id}","starred_url":"https://api.github.com/users/cjmyers/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cjmyers/subscriptions","organizations_url":"https://api.github.com/users/cjmyers/orgs","repos_url":"https://api.github.com/users/cjmyers/repos","events_url":"https://api.github.com/users/cjmyers/events{/privacy}","received_events_url":"https://api.github.com/users/cjmyers/received_events","type":"User","site_admin":false},"created_at":"2016-05-12T23:11:56Z","updated_at":"2016-05-12T23:11:56Z","body":"There are indeed some weird corner cases.  To say how things resolve, you need to look at the compareTo methods in each Location class.\n\nIn the example you give, SA1 would come before SA2, since the start is before the cut.  However, looking at the code, I’m not sure things are consistent about GenericLocations.  I thought I made it put them either all at the beginning or end, but I’m really not sure.\n\nTo be honest, I don’t think this function makes much sense when things are overlapping or unspecified.  For GenericLocation, one must use the sequenceConstraints for the sort. \n\nWe definitely need several tests to see if this is at least doing something consistent.\n\nChris\n\n> On May 12, 2016, at 12:28 AM, zgzn <notifications@github.com> wrote:\n> \n> Updated method comments for getSortedComponents and getSortedSequenceAnnotations in ComponentDefinition. It would be nice to test these methods to validate the method comments. It is interesting to see how SAs in a ComponentDefinition instance are sorted if they each have different location type. For example, SA1 has a range, and SA2 has a cut and it is located within the range of SA1, and SA3 has a generic location which does not have a specific value of its location.\n> \n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly or view it on GitHub <https://github.com/SynBioDex/libSBOLj/issues/348#issuecomment-218671190>\n\n"}}