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  1. Jalview
  2. JAL-2390

Jalview throws Exception when running PCA on many sequences

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    Details

    • Type: Bug
    • Status: Open
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: 2.10.2
    • Fix Version/s: None
    • Component/s: analysis
    • Labels:
      None

      Description

      Found while testing JAL-2377 (develop branch). Create an alignment with 525 sequences by repeatedly copying uniref.fa (attached as bigal.fa). Select all and run PCA. Jalview logs an exception:
      java.lang.Exception: Too many iterations in tqli (max is 45)
      at jalview.math.Matrix.tqli(Matrix.java:421)
      at jalview.analysis.PCA.run(PCA.java:303)
      at jalview.viewmodel.PCAModel.run(PCAModel.java:76)
      at jalview.gui.PCAPanel.run(PCAPanel.java:224)
      at java.lang.Thread.run(Thread.java:745)

        Attachments

        1. bigal.fa
          105 kB
          Kira Mourão

          Issue Links

          related with

          Bug - A problem which impairs or prevents the functions of the product. JAL-1454 Jalview crashes when selecting PCA analysis

          • Major - Major loss of function.
          • Resolved

            Activity

              People

              Assignee:
              jprocter James Procter
              Reporter:
              kmourao Kira Mourão
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                Dates

                Created:
                Updated: