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  1. Jalview
  2. JAL-2849

Sequence limits included in FASTA output regardless of user preference setting

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      Description

      FASTA files output by Jalview include sequence ID/start-end limits regardless of setting in preferences.

      The refactoring of the IO system introduced a generic suffix preference getter based on the Format class instance's name, unfortunately, the Capitalised format name was not being uppercased before the preference was being retrieved, breaking user preferences.


        public boolean getCacheSuffixDefault(FileFormatI format)
        {
          return Cache.getDefault(format.getName() + "_JVSUFFIX", true);
        }

        public String formatSequences(FileFormatI format, AlignmentI alignment,
                String[] omitHidden, int[] exportRange, HiddenColumns hidden)
        {
          return formatSequences(format, alignment, omitHidden, exportRange,
                  getCacheSuffixDefault(format), hidden, null);
        }

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            Assignee:
            jprocter Jim Procter
            Reporter:
            jprocter Jim Procter
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              Updated:
              Resolved: