{"action":"created","comment":{"url":"https://api.github.com/repos/biocore/scikit-bio/pulls/comments/29956761","id":29956761,"diff_hunk":"@@ -585,73 +569,18 @@ def is_empty(self):\n         \"\"\"\n         return self.sequence_count() == 0\n \n-    def is_valid(self):\n-        \"\"\"Return True if the SequenceCollection is valid\n-\n-        Returns\n-        -------\n-        bool\n-            ``True`` if `self` is valid, and ``False`` otherwise.\n-\n-        Notes\n-        -----\n-        Validity is defined as having no sequences containing characters\n-        outside of their valid character sets.\n-\n-        See Also\n-        --------\n-        skbio.alignment.BiologicalSequence.is_valid\n-\n-        Examples\n-        --------\n-        >>> from skbio.alignment import SequenceCollection\n-        >>> from skbio.sequence import DNA, RNA\n-        >>> sequences = [DNA('ACCGT', id=\"seq1\"),\n-        ...              DNA('AACCGGT', id=\"seq2\")]\n-        >>> s1 = SequenceCollection(sequences)\n-        >>> print(s1.is_valid())\n-        True\n-        >>> sequences = [RNA('ACCGT', id=\"seq1\"),\n-        ...              RNA('AACCGGT', id=\"seq2\")]\n-        >>> s1 = SequenceCollection(sequences)\n-        >>> print(s1.is_valid())\n-        False\n-\n-        \"\"\"\n-        return self._validate_character_set()\n-\n     def iteritems(self):\n         \"\"\"Generator of id, sequence tuples\n \n         Returns\n         -------\n         generator of tuples\n-            Each tuple contains ordered\n-            (`skbio.sequence.BiologicalSequence.id`,\n-            `skbio.sequence.BiologicalSequence`) pairs.\n+            Each tuple contains ordered (`skbio.id`, `skbio.Sequence`) pairs.","path":"skbio/alignment/_alignment.py","position":505,"original_position":505,"commit_id":"07f75cd59c63f24a8c9e12dd20a0e151ef39b36f","original_commit_id":"85fba44ee0ecf7663f5a695376d8121d97334a47","user":{"login":"gregcaporaso","id":192372,"avatar_url":"https://avatars.githubusercontent.com/u/192372?v=3","gravatar_id":"","url":"https://api.github.com/users/gregcaporaso","html_url":"https://github.com/gregcaporaso","followers_url":"https://api.github.com/users/gregcaporaso/followers","following_url":"https://api.github.com/users/gregcaporaso/following{/other_user}","gists_url":"https://api.github.com/users/gregcaporaso/gists{/gist_id}","starred_url":"https://api.github.com/users/gregcaporaso/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gregcaporaso/subscriptions","organizations_url":"https://api.github.com/users/gregcaporaso/orgs","repos_url":"https://api.github.com/users/gregcaporaso/repos","events_url":"https://api.github.com/users/gregcaporaso/events{/privacy}","received_events_url":"https://api.github.com/users/gregcaporaso/received_events","type":"User","site_admin":false},"body":"Oops, that was my over-zealous find/replace. ","created_at":"2015-05-08T17:04:16Z","updated_at":"2015-05-08T17:04:16Z","html_url":"https://github.com/biocore/scikit-bio/pull/920#discussion_r29956761","pull_request_url":"https://api.github.com/repos/biocore/scikit-bio/pulls/920","_links":{"self":{"href":"https://api.github.com/repos/biocore/scikit-bio/pulls/comments/29956761"},"html":{"href":"https://github.com/biocore/scikit-bio/pull/920#discussion_r29956761"},"pull_request":{"href":"https://api.github.com/repos/biocore/scikit-bio/pulls/920"}}},"pull_request":{"url":"https://api.github.com/repos/biocore/scikit-bio/pulls/920","id":35018382,"html_url":"https://github.com/biocore/scikit-bio/pull/920","diff_url":"https://github.com/biocore/scikit-bio/pull/920.diff","patch_url":"https://github.com/biocore/scikit-bio/pull/920.patch","issue_url":"https://api.github.com/repos/biocore/scikit-bio/issues/920","number":920,"state":"open","locked":false,"title":"First pass at Sequence 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an extremely detailed review, we can go over this next week in person.","created_at":"2015-05-08T15:19:06Z","updated_at":"2015-05-08T17:04:16Z","closed_at":null,"merged_at":null,"merge_commit_sha":"c1e0173f7b16031be726ca9a20db8afeafca2a54","assignee":null,"milestone":{"url":"https://api.github.com/repos/biocore/scikit-bio/milestones/13","html_url":"https://github.com/biocore/scikit-bio/milestones/0.3.0:%20Sequences,%20Collections,%20and%20Alignments,%20oh%20my!","labels_url":"https://api.github.com/repos/biocore/scikit-bio/milestones/13/labels","id":976974,"number":13,"title":"0.3.0: Sequences, Collections, and Alignments, oh my!","description":"Clean up `Alignment` API and better integrate alignment algorithms with sequence objects and 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