#8 Merged at 7d36217
  1. Lars Skjærven
  • OTHER: towards v2.3-1

  • ENHANCEMENT: plot.matrix.loadings() support "plot=FALSE" option to output loading matrix only

    • also minorly update to accept arguments passed to lattice::contourplot()
  • OTHER: fixed minor errors in plot.matrix.loadings.Rd

  • BUGFIX: Update to https for NCBI blast service

    NCBI blast moved from http to https. This updates: - get.blast.R - blast.pdb.R See Issue #407

  • OTHER: Update version path number

  • BUGFIX: get.seq.R - NCBI moved sites to HTTPS only

  • BUGFIX: get.seq.R - NCBI moved sites to HTTPS only (This is a copy from MASTER)

  • OTHER: upgrade development version

  • BUGFIX: hmmer fix for infinte mlog.evalue

  • BUGFIX: added box around hmmer plot in plot.blas.R

  • ENHANCEMENT: bio3d-web with no database

    • server/annotation.R use RDS files to store PDB/PFAM annotation data
  • ENHANCEMENT: switch from DT extension ColVis to Buttons

    removed dependency on deprecated DT ColVis extension replaced with DT extension Buttons

  • BUGFIX: must keep 'csv' button to show 'colvis' button

  • OTHER: shiny app update to use bio3d proper

    loads bio3d.view use bio3d proper with progress functions

  • OTHER: function name change: cmap.core() --> core.cmap() in server/fit.R

  • OTHER: updated README with more setup instructions

  • Issues #407: odd behavior resolved

Comments (4)

  1. Lars Skjærven author

    Shashank: Do you want to test this branch on your side? There are three main changes here:

    • removed dependency on mysql. using version from feature_shiny_nodb with flat file annotations.
    • removed dependency on deprecated DT ColVis extension replaced with DT extension Buttons.
    • switched to bio3d proper instead of special build inside branch (see recent merge to master)

    see file shiny_devel/pca-app/README for installation instructions

    Let me know if you want to keep these two branches separate for now.

    1. Shashank Jariwala

      Hi Lars, just going through the changes and setting up on my local machine.

      • Do we still want to keep the mysql option around? I have tried the _nodb version earlier, and it wasn't too bad; however, I haven't compared against mysql to actually know how much slower it is.
      • I will eventually find it once I pull _buttons dig into the code, but where exactly are we utilizing library(data.table)?
  2. Lars Skjærven author

    Hi Shashank, I use function rbindlist() in annotation.R line 32. This is needed since each annotation entry is stored in individual rds files. There was quite a speed up compared to regular rbind. The mysql version was slightly quicker as far as I remember, but negligible. In my opinion we can remove the mysql version.