{"action":"closed","issue":{"url":"https://api.github.com/repos/CompEvol/beast2/issues/523","repository_url":"https://api.github.com/repos/CompEvol/beast2","labels_url":"https://api.github.com/repos/CompEvol/beast2/issues/523/labels{/name}","comments_url":"https://api.github.com/repos/CompEvol/beast2/issues/523/comments","events_url":"https://api.github.com/repos/CompEvol/beast2/issues/523/events","html_url":"https://github.com/CompEvol/beast2/issues/523","id":140591948,"number":523,"title":"BEAUti does not allow tree not to be estimated in Initialization panel","user":{"login":"rbouckaert","id":3612959,"avatar_url":"https://avatars.githubusercontent.com/u/3612959?v=3","gravatar_id":"","url":"https://api.github.com/users/rbouckaert","html_url":"https://github.com/rbouckaert","followers_url":"https://api.github.com/users/rbouckaert/followers","following_url":"https://api.github.com/users/rbouckaert/following{/other_user}","gists_url":"https://api.github.com/users/rbouckaert/gists{/gist_id}","starred_url":"https://api.github.com/users/rbouckaert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rbouckaert/subscriptions","organizations_url":"https://api.github.com/users/rbouckaert/orgs","repos_url":"https://api.github.com/users/rbouckaert/repos","events_url":"https://api.github.com/users/rbouckaert/events{/privacy}","received_events_url":"https://api.github.com/users/rbouckaert/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2016-03-14T06:54:39Z","updated_at":"2016-03-16T02:55:44Z","closed_at":"2016-03-16T02:55:44Z","body":"\"I found that the reason the tree estimate checkbox doesn't work is because it is getting overriden by the following lines in the \r\nBeautiDoc.scrubAll function\r\n         for (BEASTInterface plugin : pluginmap.values()) {\r\n               if (plugin instanceof Tree) {\r\n                   Tree tree = (Tree) plugin;\r\n                   tree.isEstimatedInput.setValue(false, tree);\r\n               }\r\n           }\r\n           for (BEASTInterface plugin : pPartition[2]) {\r\n               // TODO: this might not be a valid type conversion from TreeInterface to Tree\r\n               Tree tree = (Tree) ((GenericTreeLikelihood) plugin).treeInput.get();\r\n               tree.isEstimatedInput.setValue(true, tree);\r\n           }\r\nCommenting those lines out does not obviously break anything (by which I mean Beauti doesn't crash and the unit tests in test.beast.app.beauti behave the same way) and restores the expected behaviour of the checkbox\""}}