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  1. Jalview
  2. JAL-2541

Delete/Cut selection doesn't relocate sequence features correctly when start of sequence is removed

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      Description

      Edit -> Cut of columns often leaves sequence features relocated or lost.
      To see this, load uniref50.fa and exampleFeatures.txt.
      Display only a few feature types e.g. PHOSPHORYLATION(T) and (S).
      Try cutting a few columns at a time, followed by Undo.
      Features quickly get mislocated.
      Happens in 2.10.1 desktop and applet.
      Not reproduced in 2.9 (but can't load exampleFeatures file due to a separate bug).

      Edit: In at least 2.10.3 onwards, this bug was caused by JAL-2822. To reproduce in 2.10.4 and 2.10.5, open the "Phospholation site view" in the example project, and select and delete the first three residues of FER3_RAPSA. Features (e.g. the variant (I->V)) are relocated three residues earlier than it should. Performing an undo and then a redo results in the features being located in the correct position in the modified sequence.

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          blocks

          Bug - A problem which impairs or prevents the functions of the product. JAL-2729 EditCommandTest fails in develop

          • Major - Major loss of function.
          • Closed

          Improvement - An improvement or enhancement to an existing feature or task. JAL-2574 Encapsulate find features for columns in Sequence

          • Major - Major loss of function.
          • Closed
          depends on

          Bug - A problem which impairs or prevents the functions of the product. JAL-2684 pairwise alignment of region selections do not inherit correct start/end position

          • Major - Major loss of function.
          • Closed

          Task - A task that needs to be done. JAL-2505 Make 'key' members of SequenceFeature final

          • Major - Major loss of function.
          • Closed

          Improvement - An improvement or enhancement to an existing feature or task. JAL-2822 Start and End should be updated when sequence data at beginning or end of alignment added/removed via 'Edit' sequence

          • Major - Major loss of function.
          • Closed
          related with

          Bug - A problem which impairs or prevents the functions of the product. JAL-2823 Edit sequence doesn't carry over and relocate sequence features and annotation

          • Critical - Crashes, loss of data, severe memory leak.
          • Open

          New Feature - A new feature of the product, which has yet to be developed. JAL-415 optionally relocate sequence features after a sequence edit

          • Major - Major loss of function.
          • Open

          Bug - A problem which impairs or prevents the functions of the product. JAL-2542 DBRefFetcher.transferReferences incorrectly relocates features

          • Major - Major loss of function.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. JAL-2829 Sequence.deleteChars (including gaps) makes incorrect new dataset sequence

          • Major - Major loss of function.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. JAL-2830 EditCommand Replace (on gapped sequence) mangles dataset sequence

          • Major - Major loss of function.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. JAL-3171 new alignment view doesn't share same dataset reference

          • Major - Major loss of function.
          • Closed

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              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              gmungoc Mungo Carstairs
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                Updated:
                Resolved: