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  1. UGENE
  2. UGENE-6749

Search by sequence names in the Alignment Editor



    • Type: New Feature
    • Status: Closed
    • Priority: Blocker
    • Resolution: Fixed
    • Affects Version/s: 34
    • Fix Version/s: 35
    • Component/s: Basic-MSA
    • Labels:
    • Story Points:
    • Epic Link:
    • Sprint:
      DEV-35-3, DEV-35-4, DEV-37-5
    • Affect Type:


      In UGENE 34 it is possible to search in sequences in an alignment (i.e. the sequence nucleotide or amino acid bases). This feature extends search to the sequence names in the Name List.

      The following should be done:

      1. Add "Search context" label (on Russian "Контекст поиска") and a combo box approximately as shown on the attached image. There should be the following values in the combo box:
        • "Sequences" (on Russian "Последовательности')
        • "Sequence names" (on Russian "Имена последовательностей")
      2. When "Sequences" is selected, the tab should work exactly as in UGENE 34 version.
      3. When "Sequence names" is selected, all three groups with parameters ("Search algorithms", "Search in", "Other settings") disappear. So there are only "Previous"/"Next" buttons and the labels below, if required.
      4. When "Sequence names" is selected and a pattern is input, the pattern should be searched in the sequence names:
        • If a sequence name contains a pattern, the sequence is considered to be one of the results.
        • The search takes into account Unicode characters (in particular, Russian characters, whitespaces, etc.).
        • After the search is done after the pattern input, the first found sequence is selected. The results label is updated accordingly: "Results: 1/found_results_num".
        • When other region in the alignment is selected or the alignment is edited, the results label is updated accordingly: "Results: -/found_results_num".
        • "Previous" and "Next" buttons "goes" to the previous/next result from the current selection (similarly to the sequences search implemented in UGENE-6746).
          #The "Info" label below should be the following (on macOS Ctrl+Enter is replaced by Cmd+Enter, see also similar feature in the SV):
        • For searching in sequences:
          Info: please input at least one sequence pattern to search for. Use Ctrl+Enter to input multiple patterns.
        • For searching in sequence names:
          Info: please input at least one pattern to search in the sequence names. Use Ctrl+Enter to input multiple patterns.
      5. Search in collapsing mode.
        The search only finds results in visible sequences. If the group is open, it will be searched inside it. If closed, then only in 1 group sequence. This is the meaning of the groups.
        After the results are found, the user can walk through them: Prev / Next. Clicking on these buttons does not change the number of results and does not open / close groups.


          Issue Links



              yalgaer Yuliya Algaer
              oigl Olga Golosova
              Assigned Tester:
              Svetlana Samoilenko
              2 Start watching this issue