{"action":"created","comment":{"url":"https://api.github.com/repos/OpenMS/OpenMS/pulls/comments/33855867","id":33855867,"diff_hunk":"@@ -120,6 +120,83 @@ namespace OpenMS\n       setValidFormats_(\"out\", ListUtils::create<String>(\"tsv\"));\n     }\n \n+    /// Helper:\n+    /// gets peptide_evidences with data from internal structures,\n+    /// a row with information about the PeptideHit in general\n+    /// a reference to a vector of rows\n+    /// and adds a row for each PeptideEvidence to rows.\n+    static void addPepEvidenceToRows(const vector<PeptideEvidence>& peptide_evidences, MzTabPSMSectionRow& row, MzTabPSMSectionRows& rows)\n+    {\n+      if (!peptide_evidences.empty())\n+      {\n+        for (Size i = 0; i != peptide_evidences.size(); ++i)\n+        {\n+          // get AABefore and AAAfter as well as start and end for all pep evidences\n+\n+          // pre/post\n+          // from spec: Amino acid preceding the peptide (coming from the PSM) in the protein\n+          // sequence. If unknown “null” MUST be used, if the peptide is N-terminal “-“\n+          // MUST be used.\n+          if (peptide_evidences[i].getAABefore() == PeptideEvidence::UNKNOWN_AA)\n+          {\n+            row.pre = MzTabString(\"null\");\n+          }\n+          else if (peptide_evidences[i].getAABefore() == PeptideEvidence::N_TERMINAL_AA)\n+          {\n+            row.pre = MzTabString(\"-\");\n+          }\n+          else\n+          {\n+            row.pre = MzTabString(String(peptide_evidences[i].getAABefore()));\n+          }\n+\n+          if (peptide_evidences[i].getAAAfter() == PeptideEvidence::UNKNOWN_AA)\n+          {\n+            row.post = MzTabString(\"null\");\n+          }\n+          else if (peptide_evidences[i].getAAAfter() == PeptideEvidence::C_TERMINAL_AA)\n+          {\n+            row.post = MzTabString(\"-\");\n+          }\n+          else\n+          {\n+            row.post = MzTabString(String(peptide_evidences[i].getAAAfter()));\n+          }\n+\n+          // start/end\n+          if (peptide_evidences[i].getStart() == PeptideEvidence::UNKNOWN_POSITION)\n+          {\n+            row.start = MzTabString(\"-\");\n+          }\n+          else\n+          {\n+            row.start = MzTabString(String(peptide_evidences[i].getStart() + 1)); // counting in mzTab starts at 1\n+          }\n+\n+          if (peptide_evidences[i].getEnd() == PeptideEvidence::UNKNOWN_POSITION)\n+          {\n+            row.end = MzTabString(\"-\");\n+          }\n+          else\n+          {\n+            row.end = MzTabString(String(peptide_evidences[i].getEnd() + 1)); // counting in mzTab starts at 1\n+          }\n+\n+          row.accession = MzTabString(peptide_evidences[i].getProteinAccession());\n+\n+          rows.push_back(row);\n+        }\n+      }\n+      else\n+      { // report without pep evidence information\n+        row.pre = MzTabString(\"-\");","path":"src/topp/MzTabExporter.cpp","position":73,"original_position":73,"commit_id":"24a9a2cfa1c37c7ab5da3c3fa470e61da7935604","original_commit_id":"24a9a2cfa1c37c7ab5da3c3fa470e61da7935604","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":"I don't know this by heat but did you check if \"-\" or \"null\" is correct?","created_at":"2015-07-03T10:57:13Z","updated_at":"2015-07-03T10:57:13Z","html_url":"https://github.com/OpenMS/OpenMS/pull/1490#discussion_r33855867","pull_request_url":"https://api.github.com/repos/OpenMS/OpenMS/pulls/1490","_links":{"self":{"href":"https://api.github.com/repos/OpenMS/OpenMS/pulls/comments/33855867"},"html":{"href":"https://github.com/OpenMS/OpenMS/pull/1490#discussion_r33855867"},"pull_request":{"href":"https://api.github.com/repos/OpenMS/OpenMS/pulls/1490"}}},"pull_request":{"url":"https://api.github.com/repos/OpenMS/OpenMS/pulls/1490","id":38977785,"html_url":"https://github.com/OpenMS/OpenMS/pull/1490","diff_url":"https://github.com/OpenMS/OpenMS/pull/1490.diff","patch_url":"https://github.com/OpenMS/OpenMS/pull/1490.patch","issue_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1490","number":1490,"state":"open","locked":false,"title":"[FEATURE] Better protein ID support for mzTabExporter","user":{"login":"jpfeuffer","id":8102638,"avatar_url":"https://avatars.githubusercontent.com/u/8102638?v=3","gravatar_id":"","url":"https://api.github.com/users/jpfeuffer","html_url":"https://github.com/jpfeuffer","followers_url":"https://api.github.com/users/jpfeuffer/followers","following_url":"https://api.github.com/users/jpfeuffer/following{/other_user}","gists_url":"https://api.github.com/users/jpfeuffer/gists{/gist_id}","starred_url":"https://api.github.com/users/jpfeuffer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jpfeuffer/subscriptions","organizations_url":"https://api.github.com/users/jpfeuffer/orgs","repos_url":"https://api.github.com/users/jpfeuffer/repos","events_url":"https://api.github.com/users/jpfeuffer/events{/privacy}","received_events_url":"https://api.github.com/users/jpfeuffer/received_events","type":"User","site_admin":false},"body":"mzTabExporter now writes multiple PeptideEvidences of a PeptideID in multiple PSM rows as suggested by the format. Enables reporting of shared peptides.\r\nAlso adds meta value support for PRT level. Currently adds a column for every occurring meta 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