Uploaded image for project: 'Jalview'
  1. Jalview
  2. JAL-3662

Jalview args CLI skips last format and outputs multiple files with input format

    XMLWordPrintable

    Details

    • Type: Bug
    • Status: Being documented
    • Priority: Critical
    • Resolution: Unresolved
    • Affects Version/s: 2.11.1.0
    • Fix Version/s: 2.11.1.0, 2.12.1
    • Component/s: Command Line Interface
    • Labels:
      None
    • Environment:
      Java and JavaScript

      Description

      logic in Jalview.java for final arguments processing reads two args at a time -- fileType and fileName. Fine for image types, but when it comes to actual alignmnt output, it skips the fileType just read and uses the input format instead.

      Variable "format" is being used instead of "outputFormat", and no check is done to see if the format is valid.

      Because there is no test, and because there is no break statement, any unidentified/misspelled arguments are collected and used for filenames for unwanted file saves.

      Jalview-JS/develop has a retooled section of this process that uses switch instead of multiple if/else blocks. For reference at least.

      CR to be attached momentarily.

        Attachments

          Issue Links

            Activity

              People

              Assignee:
              jprocter Jim Procter
              Reporter:
              hansonr Bob Hanson
              Votes:
              0 Vote for this issue
              Watchers:
              3 Start watching this issue

                Dates

                Created:
                Updated: