{"action":"created","comment":{"url":"https://api.github.com/repos/OpenMS/OpenMS/pulls/comments/44142365","id":44142365,"diff_hunk":"@@ -60,191 +59,106 @@ namespace OpenMS\n \n   PeptideHit AScore::compute(PeptideHit & hit, RichPeakSpectrum & real_spectrum, double fragment_mass_tolerance, bool fragment_mass_unit_ppm) const","path":"src/openms/source/ANALYSIS/ID/AScore.cpp","position":19,"original_position":19,"commit_id":"e5f51d13091d44ad150bd7c56143b4924d73041c","original_commit_id":"e5f51d13091d44ad150bd7c56143b4924d73041c","user":{"login":"timosachsenberg","id":5803621,"avatar_url":"https://avatars.githubusercontent.com/u/5803621?v=3","gravatar_id":"","url":"https://api.github.com/users/timosachsenberg","html_url":"https://github.com/timosachsenberg","followers_url":"https://api.github.com/users/timosachsenberg/followers","following_url":"https://api.github.com/users/timosachsenberg/following{/other_user}","gists_url":"https://api.github.com/users/timosachsenberg/gists{/gist_id}","starred_url":"https://api.github.com/users/timosachsenberg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/timosachsenberg/subscriptions","organizations_url":"https://api.github.com/users/timosachsenberg/orgs","repos_url":"https://api.github.com/users/timosachsenberg/repos","events_url":"https://api.github.com/users/timosachsenberg/events{/privacy}","received_events_url":"https://api.github.com/users/timosachsenberg/received_events","type":"User","site_admin":false},"body":"could probably be const PeptideHit &","created_at":"2015-11-06T14:41:22Z","updated_at":"2015-11-06T14:41:22Z","html_url":"https://github.com/OpenMS/OpenMS/pull/1692#discussion_r44142365","pull_request_url":"https://api.github.com/repos/OpenMS/OpenMS/pulls/1692","_links":{"self":{"href":"https://api.github.com/repos/OpenMS/OpenMS/pulls/comments/44142365"},"html":{"href":"https://github.com/OpenMS/OpenMS/pull/1692#discussion_r44142365"},"pull_request":{"href":"https://api.github.com/repos/OpenMS/OpenMS/pulls/1692"}}},"pull_request":{"url":"https://api.github.com/repos/OpenMS/OpenMS/pulls/1692","id":49943566,"html_url":"https://github.com/OpenMS/OpenMS/pull/1692","diff_url":"https://github.com/OpenMS/OpenMS/pull/1692.diff","patch_url":"https://github.com/OpenMS/OpenMS/pull/1692.patch","issue_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1692","number":1692,"state":"open","locked":false,"title":"Fix phospho scoring","user":{"login":"PetraGutenbrunner","id":6952271,"avatar_url":"https://avatars.githubusercontent.com/u/6952271?v=3","gravatar_id":"","url":"https://api.github.com/users/PetraGutenbrunner","html_url":"https://github.com/PetraGutenbrunner","followers_url":"https://api.github.com/users/PetraGutenbrunner/followers","following_url":"https://api.github.com/users/PetraGutenbrunner/following{/other_user}","gists_url":"https://api.github.com/users/PetraGutenbrunner/gists{/gist_id}","starred_url":"https://api.github.com/users/PetraGutenbrunner/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/PetraGutenbrunner/subscriptions","organizations_url":"https://api.github.com/users/PetraGutenbrunner/orgs","repos_url":"https://api.github.com/users/PetraGutenbrunner/repos","events_url":"https://api.github.com/users/PetraGutenbrunner/events{/privacy}","received_events_url":"https://api.github.com/users/PetraGutenbrunner/received_events","type":"User","site_admin":false},"body":"Refactoring:\r\n* divided compute into more sub-methods\r\n* changed the access of all methods except compute from public to protected\r\n\r\nAScore.cpp:\r\n62: copy hit, to not loose the previous peptide hit settings\r\n\r\n65: score set to zero, the new score type \"peptide score\" has a different meaning. \r\n    If for any reason it is not possible to calculate the peptide score, the score should be\r\n    0 to avoid a score mixed up.\r\n\r\n82-116: calculate also peptide score for peptides without a phospho event, phospho site \r\n    or where number of possible sites are equal to the number of phospho events\r\n\r\n369 - computeSiteDeterminingIons: calculation of the number of different speaks between the theoretical spectra of the two best scoring peptide permutations, respectively. \r\n\r\n363 - computePermutations_: if there is no phospho-event no permutation calculation needs to be done\r\n\r\n482 - peakPickingPerWindowsInSpectrum_: instead of starting the spectrum at 0, the lowest m/z value is rounded down to the next hundred value. 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