Uploaded image for project: 'Jalview'
  1. Jalview
  2. JAL-1954

cannot import pfam format files with tab separators

    XMLWordPrintable

    Details

    • Type: Bug
    • Status: Open
    • Priority: Critical
    • Resolution: Unresolved
    • Affects Version/s: 2.9, 2.9.0b1, 2.9.0b2
    • Fix Version/s: None
    • Component/s: file format issue
    • Labels:
      None

      Description

      I picked an arbitrary page from PANDIT to try and load an alignment from:
      http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi?action=browse&fam=PF00903&field=nam-dsq

      Copying and pasting the alignment data directly into Jalview or importing via a text file lead to an 'unsupported format' message, however checking with the Identify.main routine and stepping through with a debugger the PFAM parser extracts valid sequence data.

      It looks like the 'hasValidSequence()' method is too strict to allow the data from this page to be imported.

      -- Correction

      After trying a simple test datafile - it seems all PFAM files imported get rejected by the hasValidSequence() test

        Attachments

          Issue Links

            Activity

              People

              Assignee:
              jprocter James Procter
              Reporter:
              jprocter James Procter
              Votes:
              0 Vote for this issue
              Watchers:
              1 Start watching this issue

                Dates

                Created:
                Updated: