ChangeLog.md

In hadexversum/IAOPeptideReader: A Web Application for Analysing IAO Peptide Files

v1.3.1 (2020-12-10):

• Updated shinytest snapshots.
• Disabled Input Summary Table screenshots.

v1.3.0 (2020-12-10):

• Added handling of sequence start value to JS.
• Added verification of sequence start input.
• Added verification of sequence start and length input values.

v1.2.7 (2020-12-10):

• Added sequence start to Input Summary Table.

v1.2.6 (2020-12-10):

• Added R part for minimum sequece start value.

v1.2.5 (2020-12-10):

• Removed redundant shinycssloaders dependency.

v1.2.4 (2020-12-10):

• Updated GitHub repository URL.

v1.2.3 (2020-12-10):

• Fixed Summary Table not being calculated after file upload.

v1.2.2 (2020-12-05):

• Updated documentation.

v1.2.1 (2020-12-05):

• Updated expected shinytest results.

v1.2.0 (2020-12-05):

• Renamed application to IAO Peptide Reader for it to be more precise as it does not process whole IAO.

v1.0.8 (2020-12-05):

• Added input summary table shiny tests.

v1.0.7 (2020-12-04):

• Added summary table shiny tests.

v1.0.6 (2020-12-03):

• Added file removal shiny tests.

v1.0.5 (2020-12-03):

• Added file upload tests utilizing shinytest package.

v1.0.4 (2020-11-25):

• Moved sample data from dev/data to inst/sample_data.

v1.0.3 (2020-11-25):

• Fixed doubled HTML id attribute.

v1.0.2 (2020-11-21):

• Rewritten iaoreader.redraw_vert method to not use iaoreader.drag_start_x which is changed too eagerly. This fixed disappearing measure values on K parameter change.
• Added iaoreader.vert_px_position utility method.

v1.0.1 (2020-11-20):

• Fixed vertical guides disappering on K parameter change.

v1.0.0 (2020-11-17):

• Removed development version notification.

v0.11.40 (2020-11-17):

• Added segment measure calculation example's description.

v0.11.39 (2020-11-17):

• Added image for the segment measure calculation example.

v0.11.38 (2020-11-17):

• Fixed drag vertical guides labels boxes not adjusting on font size change.

v0.11.37 (2020-11-17):

• Fixed drag vertical guides not being hidden on plot update.

v0.11.36 (2020-11-17):

• Added example of point measure calculation.

v0.11.35 (2020-11-17):

• Adjusted vertical position of the plot legend.

v0.11.34 (2020-11-17):

• Added description of segment measure variant.

v0.11.33 (2020-11-17):

• Added a structure for the measure calculation example.

v0.11.32 (2020-11-17):

• Rephrased first paragraph of measure info modal.

v0.11.31 (2020-11-17):

• Updated measure info modal structure.

v0.11.30 (2020-11-16):

• Updated phrasing.

v0.11.29 (2020-11-16):

• Removed redundant modal template.

v0.11.28 (2020-11-16):

• Added description to the measure info modal.

v0.11.27 (2020-11-13):

• Updated file info modal.

v0.11.26 (2020-11-11):

• Added plot setting to toggle the legend.

v0.11.25 (2020-11-11):

• Added plot setting to change legends font size.

v0.11.24 (2020-11-11):

• Improved legend scaling.

v0.11.23 (2020-11-11):

• Improved legend positioning.

v0.11.22 (2020-11-11):

• Simplified plot legends code.

v0.11.21 (2020-11-11):

• Added positioning to the plot legend.

v0.11.20 (2020-11-11):

• Added rough plot legend.

v0.11.19 (2020-11-02):

• Improved wording in few places.
• Improved few hover values.

v0.11.18 (2020-11-02):

• Added modal link to the measure info to the plot info modal.
• Added a new layer of modals with correct returns for following links from the plot info modal.

v0.11.17 (2020-11-02):

• Updated modal_link wrapper to make it possible to add a trailing dot - similarly to the external_link wrapper.
• Fixed class name in modal_link wrapper.

v0.11.16 (2020-11-02):

• Added information regarding vertical guides to the plot info modal.
• Ran the texts through Grammarly.
• Removed unnecessary class from plot info modal headers.

v0.11.15 (2020-11-02):

• Updated modal headers CSS.

v0.11.14 (2020-11-02):

• Added information regarding plot settings to the plot info modal.

v0.11.13 (2020-11-02):

• Added information regarding tooltip to the plot info modal.

v0.11.12 (2020-11-02):

• Created subfolder in the hosted images directory.

v0.11.11 (2020-11-02):

• Added modal structure for plot information.

v0.11.10 (2020-11-02):

• Removed redundant chdir argument.

v0.11.9 (2020-11-01):

• Fixed tooltip overflowing the svg tag.

v0.11.8 (2020-11-01):

• Added option to disable bolding the line under the mouse.

v0.11.7 (2020-11-01):

• Added option to disable the tooltip.

v0.11.6 (2020-11-01):

• Fixed tooltip getting disabled with mouseover vertical guide.
• Fixed thicker line getting stuck when cursor left the plot area.

v0.11.5 (2020-11-01):

• Now the line which has it's infromation displayed is marked by being thicker.

v0.11.4 (2020-11-01):

• Fixed assertions in two functions.

v0.11.3 (2020-10-31):

• Moved tooltip to top to avoid it getting obstructed by the click vert's measure value.
• Added tooltip background.
• Changed tooltip text color.
• Moved tooltip away from the cursor.

v0.11.2 (2020-10-31):

• Fixed tooltip not disappearing then moving out of plot area.
• Added text styling to the tooltip text.
• Added snapping of tooltip to integer values to avoid weird small moves.

v0.11.1 (2020-10-31):

• Added basic tooltip.

v0.11.0 (2020-10-31):

• Merged implementation of modals.

v0.10.25 (2020-10-25):

• Updated the file info modal.

v0.10.24 (2020-10-25):

• Set the field separator to comma and the decimal separator to dot in fread.

v0.10.23 (2020-10-09):

• Added information to the color palettes modal.
• Added styling to color palettes preview.

v0.10.22 (2020-10-08):

• Added colors palettes preview.

v0.10.21 (2020-10-08):

• Added blank modal for color palettes information.

v0.10.20 (2020-10-08):

• Updated modals file structure.
• Updated README.md accordingly.

v0.10.19 (2020-10-08):

• Added wrapper for creating label with link icon.

v0.10.18 (2020-10-08):

• Updated summary table description.
• Removed finished TODO elements.

v0.10.17 (2020-10-08):

• Updated modals flow.

v0.10.16 (2020-10-08):

• Added modal_link wrapper to facilitate opening modals with inline text links.

v0.10.15 (2020-10-08):

• Restructured modals.R file.

v0.10.14 (2020-10-07):

• Prepared structure for measure information modal.
• Added brief description of the summary table in the main panel.

v0.10.13 (2020-10-07):

• Renamed measure_info modal to k_param_info to separate these two informations.
• Changed cursor for the info icons.

v0.10.12 (2020-10-07):

• Removed unused add_class function.
• Fixed various typos.

v0.10.11 (2020-09-21):

• Added file structure description.

v0.10.10 (2020-09-21):

• Aligned Dismiss buttons in modals.

v0.10.9 (2020-09-21):

• Added table caption.

v0.10.8 (2020-09-16):

• Added example table to the modal with file structure details.

v0.10.7 (2020-09-14):

• Added an empty modal for informations about the measure.

v0.10.6 (2020-09-14):

• Created separate file for modals.

v0.10.5 (2020-09-14):

• Updated CSS to account for multiple icon buttons.

v0.10.4 (2020-09-14):

• Added basic modal.
• Updated modal CSS.

v0.10.3 (2020-09-14):

• Added invisible actionButton underneath the info-circle icon to facilitate communication with Shiny server.

v0.10.2 (2020-09-14):

• Added info-circle icon to file upload label for later addition of information modal.

v0.10.1 (2020-09-14):

• Moved d3.min.js to a separate directory.

v0.10.0 (2020-09-03):

• This marks end of implementation of measure values on the plot.
• Measure values now properly update when changing plot settings.
• Turned off measure value display if it is undefined.
• Changed the way height for measure values display is calculated to account for lines starting or ending within the segment.

v0.9.17 (2020-09-03):

• Added segment measure values to the plot. This took some adjustments in already existing interfaces.

v0.9.16 (2020-09-03):

• Fixed SVG download.

v0.9.15 (2020-09-03):

• Updated the draw_lambda_values function to account for segment measure.

v0.9.14 (2020-09-02):

• Added drag guides color selection to the plot settings.
• Opacity style now will be properly added to the downloaded SVG.

v0.9.13 (2020-09-02):

• Added JS interface for updating drag guides and area color.

v0.9.12 (2020-09-02):

• Improved drag colored area creation.

v0.9.11 (2020-09-02):

• Added colored area between the two drag ends.

v0.9.10 (2020-09-02):

• Parametrized the time minimum time difference after which dragging starts.
• Added check to not move drag ends if both start and end would end up on the same X-axis value.
• Renamed drag_t0 and drag_start_time to click_timestamp.

v0.9.9 (2020-09-02):

• Added checks for time since clicking to differentiate dragging and single click.

v0.9.8 (2020-09-02):

• Moved mouseover guide to top and on click guide right below it.
• Fixed names of variables

v0.9.7 (2020-09-02):

• Added drag vertical guides.
• Made drawing lambda values optional to facilitate addition of drag vertical guides.

v0.9.6 (2020-09-02):

• Reordered color options in plot settings.
• Increased sidebar bottom padding.

v0.9.5 (2020-09-01):

• Changed the background display option behavior. Now it is handled via visibility rather than setting color to "".
• Now all elements - not only containers - with visibility: hidden won't be added to the SVG.

v0.9.4 (2020-09-01):

• Replaced svg tag background attribute with appending a background rect to the SVG.

v0.9.3 (2020-09-01):

• Elements with visibility: hidden won't be added to the SVG anymore.
• Added tags to .gitignore and .Rbuildignore.

v0.9.2 (2020-08-30):

• Moved the upload sample data button to be less prominent.
• Added percent symbol to the summary table.
• Added alignment to the summary table.

v0.9.1 (2020-08-30):

• Changed the development data upload to sample data upload.
• Updated CSS for the upload button.

v0.9.0 (2020-08-30):

• This version marks end of development of all application's main functionalities.
• Fixed overflow behavior in the summary table display.
• Added debounce to the summary table update trigger in order to fix the table not being updated quickly enough.
• Added column with file names to summary table.

v0.8.9 (2020-08-30):

• Added summary table display.
• Updated parsing function to convert to percent.

v0.8.8 (2020-08-30):

• Added function for calculating summary table data to the IAOReader class.
• Added Shiny handler for updating the plot.

v0.8.7 (2020-08-30):

• Added function for parsing lambda values to a data.frame from a JSON.

v0.8.6 (2020-08-28):

• Implemented SVG download.

v0.8.5 (2020-08-28):

• Reduced maximum title font size to 48px.
• Moved font size check to Shiny handler.

v0.8.4 (2020-08-28):

• Removed uses of dx and dy attributes from lambda values. This will help with SVG export.

v0.8.3 (2020-08-28):

• Changed the way the Y-axis ticks are not displayed.

v0.8.2 (2020-08-28):

• Added button for downloading plot as an SVG - for now it's just a prop.

v0.8.1 (2020-08-28):

• Adjusted top margins of Coverage Plot and Summary Table headers.

v0.7.23 (2020-08-28):

• Added option to include k parameter in plot title.
• Changed plot title setter to an update function.

v0.7.22 (2020-08-28):

• Changed plot title updating to setter.

v0.7.21 (2020-08-28):

• Added redraw_vert calls to Shiny handlers for options to update properly.

v0.7.20 (2020-08-28):

• Added vertical offset to the lambda values so that they don't obstruct lines.
• Reordered function calls within move_vert due to move_lambda_values using parameters set by draw_text_bbox called for axis label.

v0.7.19 (2020-08-28):

• Added redrawing mouseover vertical guide on font change.
• Reduced maximum X-axis font size to 26.
• Increased dy attribute of vertical guides axis label to not overlap with the plot.

v0.7.18 (2020-08-27):

• Added background boxes for vertical guide axis labels.
• Added iaoreader.redraw_vert call to the font size handler to update text box size.

v0.7.17 (2020-08-27):

• Reduced maximum X-axis font size to 30.
• Moved value verification to Shiny handler.

v0.7.16 (2020-08-24):

• Fixed an issue where lambda values would not reappear after setting update.
• Fixed an issue where lambda values would not update after adjusting k parameter.
• Added spacing between vertical guides and the lambda values.

v0.7.15 (2020-08-24):

• Fixed lambda values not being removed after disabling showing them.

v0.7.14 (2020-08-24):

• Fixed lambda values background color not updating on the persistent guide.

v0.7.13 (2020-08-22):

• Added checkbox for inverting lambda values background.

v0.7.12 (2020-08-22):

• Added lambda values box's color customization.

v0.7.11 (2020-08-22):

• Added an option to disable displaying the lambda values.

v0.7.10 (2020-08-22):

• Added box behind the lambda values displayed on the plot.
• Excluded lambda values text from the font size adjustment in plot settings.

v0.7.9 (2020-08-22):

• Added horizontal offset to the lambda values on the vertical guides.

v0.7.8 (2020-08-22):

• Moved lambda measure values to the lowers line for the persistent vertical guide.

v0.7.7 (2020-08-22):

• Added lambda measure values to the persistent vertical guide.

v0.7.6 (2020-08-15):

• The lambda measure values are now displayed on the plot on mouseover.
• Restricted IAOReader lambda method to account only for currently displayed files.

v0.7.5 (2020-08-15):

• Added K penalty parameter customization to plot settings.

v0.7.4 (2020-08-15):

• Implemented lambda measure methods for IAOReader class.

v0.7.3 (2020-08-15):

• Implemented lambda and lambda_segment functions for single files.

v0.7.2 (2020-08-15):

• Replaced Remove label with trash bin icon in the input summary table.

v0.7.1 (2020-08-15):

• Adjusted plot title vertical placement.
• Updated global CSS overflow and scrolling properties.

v0.7.0 (2020-08-15):

• This version marks an end of implementation of plot settings regarding color and text properties of plot elements.
• Added numericInput for customizing axes labels font size.
• Added axes settings section to the plot settings.
• Fixed vertical guides label placement.

v0.6.22 (2020-08-15):

• Fixed ugly overflow of plot settings.
• Improved input settings table handling of many files.
• Removed outer padding of the sidebar.

v0.6.21 (2020-08-15):

• Added font-weight switch between bold and normal for the plot title.

v0.6.20 (2020-08-15):

• Added colorInput for title text color.

v0.6.19 (2020-08-15):

• Added numericInput for title font size.
• Added title font size verification before setting it.

v0.6.18 (2020-08-15):

• Fixed colorInputs width.
• Moved widths of inputs to a single variable for easier manipulation.
• Unified case in plot settings subtitles.

v0.6.17 (2020-08-15):

• Added title font size configuration interface to JS.

v0.6.16 (2020-08-15):

• Incorporated plot_settings class functionalities into the IAOReader class.
• Restructured www/js directory.

v0.6.15 (2020-08-15):

• Added colorInputs for axes and axes labels.
• Added default width to colorInput.

v0.6.14 (2020-08-15):

• Added styling for the axes and their labels.
• Added setters for setting these colors.

v0.6.13 (2020-08-15):

• Added colorInputs for both mouseover and persistent vertical guides.
• Changed default colors of the guides.

v0.6.12 (2020-08-15):

• Fixed show background checkbox making the background disappear indefinitely.

v0.6.11 (2020-08-15):

• TODOs and redundant functions clean-up.
• Reduced data sent to JS to Start, End and FileName columns.

v0.6.10 (2020-08-15):

• Implemented updateColorInput function to avoid code redundancy.

v0.6.9 (2020-08-15):

• Added colorInput to facilitate further additions of this input type.

v0.6.8 (2020-08-15):

• Improved background color setting implementation.

v0.6.7 (2020-08-15):

• Added setters for vertical lines' colors.

v0.6.6 (2020-08-14):

• Improved color plot settings arrangement and styling.

v0.6.5 (2020-08-14):

• Added checkbox for toggling the plot's background.
• Added initial color to the plot's background color input.

v0.6.4 (2020-08-14):

• Added color input for plot background.

v0.6.3 (2020-08-14):

• Increased top margin.
• Removed unused JS script.
• Added information about color palettes with URLs to palette update handler.

v0.6.2 (2020-08-14):

• Added a selectInput for picking a color palette of choice.
• Extended interface for plot settings generation to account for selectInputs.

v0.6.1 (2020-08-14):

• Updated plot settings headers.

v0.6.0 (2020-08-14):

• This version marks an end to vertical plot space optimization.
• Extended interface for plot settings generation.
• Used the updated interface for customizing the numericInput used for vertical offset between files.

v0.5.13 (2020-08-14):

• Fixed vertical offset adjustment after testing with multiple files.

v0.5.12 (2020-08-14):

• Added customization of the vertical spacing between files.

v0.5.11 (2020-08-14):

• Added plot setting for choosing whether to optimize the plot vertically.
• Added top margin to headers within plot settings.

v0.5.10 (2020-08-14):

• Fixed Y-axis range being to wide.

v0.5.9 (2020-08-14):

• Added function which adjusts height based on the calculated height differences and (hard-coded for now) offset.
• Added assertion to previously implemented function.

v0.5.8 (2020-08-14):

• Added function for calculating height differences between files on the plot.

v0.5.7 (2020-08-10):

• Added development disclaimer to the title panel.

v0.5.6 (2020-08-09):

• Added HTML title attribute to the IAO Reader in the title panel which indicates version of currently used application.

v0.5.5 (2020-08-09):

• Extended title panel with GitHub project's URL.

v0.5.4 (2020-08-09):

• Added sorting to the data preview.

v0.5.3 (2020-08-09):

• Added title panel.

v0.5.2 (2020-08-09):

• Updated Travis config.
• This version marks start of differentiation between master and devel branches.

v0.5.1 (2020-08-09):

• Continuous delivery config update.

v0.5.0 (2020-08-09):

• Added continuous delivery to the shinyapps.io.

v0.4.25 (2020-08-09):

• Added run_app argument to run_shiny_app to allow deployment of the application to shinyapps.io.

v0.4.24 (2020-08-09):

• Removed shinipsum hidden dependency.

v0.4.23 (2020-08-07):

• Added information about maximum sequence length currently displayed to the Sequence Length section of the sidebar.

v0.4.22 (2020-08-01):

• Updated CSS.

v0.4.21 (2020-07-31):

• Added scrolling to the Input Summary Table when there are too many files.
• Added page title.

v0.4.20 (2020-07-31):

• Removed redundant functions used in the verification of the data.
• Removed unused tests.

v0.4.19 (2020-07-29):

• Fixed verification error messages.
• Updated and extended tests.

v0.4.18 (2020-07-29):

• Added type verification to Protein and State columns.

v0.4.17 (2020-07-17):

• Added error handling to file reading.

v0.4.16 (2020-07-17):

• Added accept parameter to the fileInput in the sidebar. Now the browser will suggest .csv data format.

v0.4.15 (2020-07-17):

• Renamed shiny_app folder to IAOReader in the inst subdirectory.

v0.4.14 (2020-06-28):

• Added ColorBrewer object for managing color palettes.
• Implemented setter for color palettes.

v0.4.13 (2020-06-28):

• Colors are only assigned to the displayed files now.
• Removed ColorId - now lines get colored based on the file name.
• Moved color_pallette to plot_settings.
• Vertically centered checkboxes with CSS.

v0.4.12 (2020-06-28):

• Added getter for currently displayed files to the JavaScript class.

v0.4.11 (2020-06-28):

• Disabled Y axis ticks.
• Added missing fonts.

v0.4.10 (2020-06-28):

• Implemented the displayed file hiding in the JavaScript.

v0.4.9 (2020-06-28):

• Prepared the R side for file display toggling.

v0.4.8 (2020-06-28):

• Fixed observers from Input Summary table not being properly deleted. The list of observers was being reset before the observers were destroyed.

v0.4.7 (2020-06-28):

• Extended input_ids in files input meta which were used in Input Summary table. This should solve some issues with overlapping input_ids.
• Fixed if added in previous version.

v0.4.6 (2020-06-28):

• Added button for uploading the development data usually used for testing.

v0.4.5 (2020-06-27):

• Reorganised data flow in IAOReader. Now the data is filtered only once every plot redraw.

v0.4.4 (2020-06-27):

• Moved the data preparation to IAOReader class method.

v0.4.3 (2020-06-21):

• Fixed y axis value calculation by moving it to data filtering.

v0.4.2 (2020-06-21):

• Added lines coloring by file.

v0.4.1 (2020-06-03):

• Fixed the Plot Settings Reset button. It no longer tries to reset objects which are not meta elements.

v0.4.0 (2020-05-31):

• This version has functional vertical guides (mouseover and on click).
• Extended the plot settings generation interface to allow addition of manual shiny elements.

v0.3.19 (2020-05-31):

• Added resetting of the guides to their initial state on data redraw.

v0.3.18 (2020-05-31):

• Added a plot settings to toggle line marking by the vertical guides.

v0.3.17 (2020-05-30):

• Added "snapping" to the mark_lines method effectively fixing lines not being marked although the vert was overlapping given line.

v0.3.16 (2020-05-30):

• Added handler for resetting the mouseover vertical guide on svg mouse exit.

v0.3.15 (2020-05-30):

• Added coloring lines to the persistent vertical guide.

v0.3.14 (2020-05-30):

• Added coloring lines under the mouseover vertical guide.
• Added unmark_lines function.
• Removed changing visibility to visible on every move_vert call.

v0.3.13 (2020-05-30):

• Changed single value margin to a separate value for each side.

v0.3.12 (2020-05-30):

• Moved vertical guides colors to CSS variables.
• Fixed starting position of the mouseover vert.

v0.3.11 (2020-05-30):

• Added function for adding class to lines.

v0.3.10 (2020-05-29):

• Added X axis value labels to vertical guides. Extended them to imitate axis ticks.
• Parametrized vertical guides' colors.

v0.3.9 (2020-05-29):

• Changed the vertical guides to actually be g tags containing lines. This will allow easier addition of labels.

v0.3.8 (2020-05-29):

• Added persistent vertical guide appearing on click.
• Added removal of the persistent guide on double click.
• Renamed mouse_in_svg function to mouse_out_of_bonds to be more descriptive.

v0.3.7 (2020-05-29):

• Parametrized the moved vert in moving functions.
• Separated verts_g and vert creation for easier addition of new guides.
• Added section headers to the IAOReader class.

v0.3.6 (2020-05-29):

• Added utility functions for handling vertical guide and mouse.

v0.3.5 (2020-05-29):

• Added mousemove handler for the vertical guide.
• Renamed draw_vert to move_vert which is more appropriate.

v0.3.4 (2020-05-29):

• Added rounding of X value to which the draw_vert method moves the vertical guide.
• Moved declaration of attributes for the guide to constructor.

v0.3.3 (2020-05-29):

• Cleaned-up JS classes constructors.

v0.3.2 (2020-05-29):

• Added function for drawing vertical guide.
• Added plot setting do disable the line.

v0.3.1 (2020-05-29):

• Fixed the overextending Y axis.

v0.3.0 (2020-05-29):

• Now the plot data is filtered solely by the JS. This marks an end of rewriting old code into proper JS classes.
• Removed the updater of plot settings as they should be handler properly now.

v0.2.37 (2020-05-29):

• Rewritten y_scale to be created by IAOReader class.
• Removed redundant variables and attributes.
• Updated the checks for whether the data has been already passed to the IAOReader class object.

v0.2.36 (2020-05-29):

• Moved IAOReader.plot_data to plot_data_raw and added filtered data as IAOReader.plot_data getter.

v0.2.35 (2020-05-29):

• Moved plot data transformation to endpoint responsible for updating it in IAOReader class object.

v0.2.34 (2020-05-29):

• The plot data is now stored in the IAOReader object.

v0.2.33 (2020-05-29):

• Split handler which sent data and seq length into two.

v0.2.32 (2020-05-29):

• Moved Shiny handlers to a single file.

v0.2.31 (2020-05-29):

• Rewritten x_scale to be created by IAOReader class.

v0.2.30 (2020-05-29):

• Moved creation of g tags for X and Y axes and lines to IAOReader constructor.

v0.2.29 (2020-05-29):

• Moved plot data drawing to IAOReader class.

v0.2.28 (2020-05-29):

• Created www/js/classes directory and adjusted sourcing in ui.R.

v0.2.27 (2020-05-29):

• Added PlotSettings class for managing configurable plot elements.
• Rewritten the plot title to utilize this class.
• Moved plot title handler file to plot_settings.js due to rather brief nature of the handlers.

v0.2.26 (2020-05-27):

• Moved the creation of IAOReader class object to a Shiny handler. This way the svg can be created in class' constructor which in turn allows to reduce amount of workarounds.
• Removed the plot title fix as it is no longer necessary.

v0.2.25 (2020-05-27):

• Implemented IAOReader JS class for better handling of the application.
• Rewritten svg canvas creation to use the IAOReader class.
• Added temporary fix for plot title which is created too early.

v0.2.24 (2020-05-27):

• Centered the plot title.

v0.2.23 (2020-05-27):

• Reorganized scripts in the www subdirectory.
• Updated Plot Settings mapping to include input_id provided by hand.
• Changed the way scripts and CSS are attached.

v0.2.22 (2020-05-23):

• Fixed plot by adding y offset to data transformation.

v0.2.21 (2020-05-23):

• Changing the sequence length is now tied to data redrawing.
• Moved X axis creation to plot updating.

v0.2.20 (2020-05-23):

• Added wonky data plotting.

v0.2.19 (2020-05-23):

• Added drawing of Y axis to plot data updater.
• Increased margin.
• Moved plot title.
• Added early stops to the plot handlers if the plot does not exist yet.

v0.2.18 (2020-05-23):

• Added handler for drawing X axis of the plot.

v0.2.17 (2020-05-23):

• Added _x, _y, and _margin attributes to the svg to parametrize those values throughout the plot.

v0.2.16 (2020-05-23):

• Split utils.R into separate files.

v0.2.15 (2020-05-23):

• Updated JS files style.
• Changed svg removal to a check before creation.

v0.2.14 (2020-05-23):

• The JS plot is now deleted on data upload before appending a new one.
• Reduced the amount of data sent to JS to only unique records.

v0.2.13 (2020-03-20):

• Implemented plot title updater handler.
• Added forced update for all Plot Settings after the new filtered data is plotted.
• Set suspendWhenHidden to FALSE for the Plot Settings uiOutput. This allows the UI and server generator create it before the user visits the Plot Settings tab which is crucial for proper application of the settings.
• Fixed typo in plot.js.

v0.2.12 (2020-03-20):

• Hidden Plot Settings until a correct file is uploaded.

v0.2.11 (2020-03-20):

• Changed splitLayout in Sequence Length to a manual split layout to improve formatting.
• Added text wrapping to the maximum sequence length output.

v0.2.10 (2020-03-20):

• Added handler for creating an empty canvas for the plot.
• Created mock handler for updating the data on the plot.

v0.2.9 (2020-03-19):

• Added d3.min.js script.
• Changed the mock plot to an empty div for the real plot.

v0.2.8 (2020-03-18):

• Updated Sequence Length section CSS and alignment.

v0.2.7 (2020-03-17):

• Updated Input Summary Table CSS:
  • Added alternating colors to the table rows.
  • Removed unnecessary margins from the selectInputs.
  • Shrunk the buttons.
  • Moved the header row width settings to the CSS file.
  • Updated header padding.
  • Shortened Sequence Length to Seq. Length.
  • Replaced button's error hover tooltip with a proper one.

v0.2.6 (2020-03-17):

• Updated Input Summary Table CSS:
  • Changed colour of error rows.
  • Improved coloring of header row.
  • Added padding to the cells.
  • Aligned text cells.
  • Handled text overflow in text cells.
  • Added mouseover hints for file names (to show full name when truncated).
  • Removed empty header cell from over the buttons.

v0.2.5 (2020-03-17):

• Disabled selectInput creation for the wrong files.

v0.2.4 (2020-03-14):

• Added sequence length verification and mouseover information.

v0.2.3 (2020-03-14):

• Moved data_preview.R sourcing to the file which calls data_preview module.
• Added file sourcing summary for the application.

v0.2.2 (2020-03-14):

• Renamed buttons in Input Summary Table to not suggest that user's file will be deleted from their system.

v0.2.1 (2020-03-11):

• Added resetting of the observers list within input_settings_rv on a new file upload.
• Updated TODO.md.

v0.2.0 (2020-03-11):

• The data is now saved only for correct files.
• The saved data now includes only the columns used by the app.
• Connected Data Preview to the uploaded files.
• Added placeholders for when there is no file uploaded.
• This update marks the end of file management and settings development as well as Data Preview tab implementation. However, the CSS for the Input Summary Table and styling of Data Preview table are yet to be improved.

v0.1.28 (2020-03-10):

• Improved the way the maximum sequence length is handled.

v0.1.27 (2020-03-10):

• Deletion handler now properly deletes data associated with the file.
• Added data preparation for passing it over to the JS.

v0.1.26 (2020-03-10):

• Improved saving the files meta information to input_settings_rv and added saving of the data to that structure.
• Minor other improvements.

v0.1.25 (2020-03-10):

• Handled case when all files are deleted through the Input Files Summary table.
• Improved setting the protein and state during Input Files Summary table UI creation.

v0.1.24 (2020-03-10):

• Fixed the bug of observers not being deleted mentioned in previous change log entry.
• Removed redundant codecov.yml configuration file.

v0.1.23 (2020-03-10):

• Changed files_meta to a reactiveVal to support deleting objects from it.
• Implemented delete button handler in the server function generator.
• Added preserving of the selected values through the deletions.
• Note: current version contains a bug where the observers aren't deleted properly on new files upload.

v0.1.22 (2020-03-09):

• Updated the data for the Input Files Summary testing.
• Implemented server function generation with select input updaters for the Input Files Summary.

v0.1.21 (2020-03-09):

• Fixed the read_protein_state_mapping function for data.table arguments added tests for the this case.

v0.1.20 (2020-03-09):

• Added automatic updating of the sequence length input when the files are uploaded.
• Added req to in the maximum sequence length reactive to avoid calculation when there is no correct file uploaded.

v0.1.19 (2020-03-09):

• Improved handling of the wrong files in the sidebars. Now the UI is more informative about the issues.

v0.1.18 (2020-03-09):

• Added wrapper for attaching scripts.
• Restructured the run_shiny_app function to source the files in inst folder. This fixes the bug (or rather namespace issue) where package's imported functions are not found by the Shiny application.
• Reordered CSS file a little.

v0.1.17 (2020-03-08):

• Added a function for reading the (protein, state) mapping.
• Updated badges in README.md after renaming the repository.

v0.1.16 (2020-03-08):

• Fixed handling NA values in the verify_column_types function.

v0.1.15 (2020-03-02):

• Added sequence length calculation for each file.
• Updated the mock information about maximum sequence length to be a value read from input files.

v0.1.14 (2020-03-02):

• Hidden everything but the file upload input until a file is uploaded.

v0.1.13 (2020-03-02):

• Added data (including few incorrect files) for testing the application during the development.
• Minor update in README.md.

v0.1.12 (2020-03-02):

• Added mouseover hint with error messages on rows with incorrect inputs in the Input Summary table.

v0.1.11 (2020-03-02):

• Moved Input Summary table generation to the server function.
• Implemented function generating single Input Summary table's row UI.

v0.1.10 (2020-03-02):

• Updated README.md and excluded option to run directly from GitHub (the imported packages would not be loaded).
• Fixed misspells in the file upload handler.

v0.1.9 (2020-03-02):

• Fixed few typos and variable names.
• Changed Travis notifications frequency.
• Added license badge.

v0.1.8 (2020-03-02):

• Implemented the vefify_iao_data function and added tests.
• Updated the error messages returned by the two subfunctions of the above function.
• Updated the .travis.yml file with lines which should prevent the build from failing on OSX with R 3.4.

v0.1.7 (2020-02-29):

• Implemented the verify_column_types function and added tests.

v0.1.6 (2020-02-29):

• Implemented the verify_colnames function and added tests.

v0.1.5 (2020-02-29):

• Added reactive for holding files meta information which have not been fully implemented yet.
• Added functions signatures for verifying IAO file's correctness.

v0.1.4 (2020-02-28):

• Added documentation.
• Updated NAMESPACE to not override imports.

v0.1.3 (2020-02-28):

• Added license.
• Added Travis.
• Added Appveyor.
• Added code coverage.
• Removed finished points from the TODO.md.

v0.1.2 (2020-02-28):

• Created server file for Input Settings with mock fileInput handler and an outline of the handler which will be implemented.
• Added Remarks section to the README.md.

v0.1.1 (2020-02-28):

• Added function for extending an objects class by reference.
• Added tests for the above function.
• The above two changes resulted in adding a new import (data.table) and a new suggestion (testthat).

v0.1.0 (2020-02-27):

• Merged refactoring-from-scratch branch into master and cleaned up after the merge.

v0.0.16 (2020-02-26):

• Moved single element CSS to the element definition.
• Added some sidebar global CSS.
• Added full Input Settings tab mock UI.

v0.0.15 (2020-02-25):

• Added default values to the input mapping.
• Added button for resetting plot settings to default.

v0.0.14 (2020-02-24):

• Moved inputs generation for the Plot Settings tab to the server function.
• Moved the input mapping to a reactive inside the server function.
• Created basic connection from R server function to JS.

v0.0.13 (2020-02-24):

• Added wrapper for creating plot settings inputs.
• Added chdir argument to source calls.
• Finished variables, functions and files names refactoring.

v0.0.12 (2020-02-24):

• Added tabs to the sidebar panel.

v0.0.11 (2020-02-23):

• Added DT package as an import.
• Created mock DT table in the Data Preview tab.

v0.0.10 (2020-02-23):

• Renamed files names to match the function naming convention.
• Split out a part of server.R in preparation for multiple file structure.

v0.0.9 (2020-02-23):

• Added ids to main panel and sidebar panel for easy distinguishing main panel from sidebar panel in CSS.
• Added side padding to main panel contents.

v0.0.8 (2020-02-13):

• Added selectInput with mock choices for selecting file for preview.
• Updated CSS of the main panel and the newly added selectInput.

v0.0.7 (2020-02-12):

• Updated functions naming convention.
• Added tabsetPanel and tabs to the main panel.
• Added mock summary table to the Peptide Coverage tab.

v0.0.6 (2020-02-12):

• Moved main panel and sidebar panel objects to function to allow top-bottom structure of the scripts.
• Added shinipsum as a requirement for development.
• Created a plot output for the application's main plot.

v0.0.5 (2020-02-12):

• Fixed an issue with UI using function defined below the UI definition.

v0.0.4 (2020-02-12):

• Created structure for sidebar page.
• Extender folder structure in preparation for UI development.
• Attached HaDeX theme.
• Fixed typo in README.md.

v0.0.3 (2020-02-11):

• Added a simple CSS theme.
• Created README.md with installation instructions and updated .Rbuildignore.

v0.0.2 (2020-02-11):

• Added a simple application with one output filled out in the server function.
• Added exported function run_shiny_app to run the application located inside package's files.

v0.0.1 (2020-02-06):

• Updated the TODO.md list with further plan for the development.

v0.0.0 (2020-02-06):

• Created an empty package's structure from scratch.

hadexversum/IAOPeptideReader documentation built on March 3, 2021, 12:33 a.m.