The following document contains release notes for Scaffold LFQ
Scaffold LFQ Version 4.0.2 (Released 2021-09-17)
Restored functionality of sample clustering in the heatmap
Changed background coloring of Protein # column header in Samples View
Scaffold LFQ Version 4.0.1 (Released 2021-03-18)
Added a "clear" button to the advanced filter dialog
Added tooltips to the column header in the Proteins view peptides table
Added support for FDR thresholding of MZID data using Percolator PEP or Byonic scores
Added a helpful message when an already-expired key is activated
Added drag-and-drop in the license entry dialog
Allow pasting or dropping License ID and Password at the same time in the license entry dialog
Allow assigning attributes by dragging an attribute folder onto a sample
Added feature to include current License ID when reporting errors
Show more detailed messages in the progress dialog
Added ability to copy selected text from the publish view
Added tooltips to violin plots
Updated colors, icons and GUI look-and-feel for Scaffold LFQ
Improved functionality of the volcano, quantitative scatter and PCA scores plots
Improved performance for internal utility methods
Improved some error messages when reading an invalid MZID file
Improved handling of file paths in an MZID when they are URL-encoded or contain special characters
Switched to bundling Java 11 JRE in installers
Improved GUI behavior in the bulk edit sample names dialog
Replaced "MZID-specified" with "externally-specified" in grouping and thresholding UI
Updated default locations for some image exports and attribute file export
Updated the Samples view color legend when switching "log intensities"
Fixed "No Clustering" optimization that could cause some groups that passed thresholds to not display
Fixed an infinite loop when trying to draw a box plot with few underlying items
Properly display percentage values in the color options dialog
Fixed incorrect scrolling to selected peptides in very long protein sequences
Fixed graphical artifacts in the protein sequence panel when resizing the window
Prevent the Proteins view from displaying filtered-out proteins
Report the cutoff for decreasing scores unambiguously in the publish view
Fixed bug in the summarization combo box that could prevent editing summarization
Corrected typo in installation error message
Fixed protein selection dropdown options after double-clicking a protein in the volcano plot
Fixed a bug causing the GO Term Filter to not appear when first applying GO terms
Fixed a bug that could cause incorrect normalization of counts for the selected protein after changing summarization or statistical test
Fixed a bug that could cause GO term clustering to randomly fail
Fixed a bug which could cause an error while recomputing heatmap clustering; improve performance of heatmap rebuilds
Fixed a bug that prevented proper opening of files when an attribute category's name contained leading or trailing whitespace
Fixed issues with cut-off text and keyboard focus traversal in the license entry dialog
Ensure that tooltips in quant trend charts correctly respect the "Log Intensities" option
Fixed a hang when copying an EMF image from the PCA scores plot
Fixed resizing of the Organize view when deleting a category; ensure buttons are consistently sized
Fixed a bug when imputing quantitative values with certain sample counts
Fixed an error when sample names contained long sequences of digits
Display group names in volcano plot tooltips instead of "null"
Do not show multiple rows for a protein group in the heatmap details
Do not display GO Terms that are associated with a protein with the "NOT" qualifier