Rework TagPileup Window Graphics #119
Merged
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Collaborator
owlang
commented
May 24, 2023
owlang
commented
- Redo TagPileupWindow with Sally's window design and new cartoons (TagPileup Facelift #115)
- Add Jet/Rainbow color palette to BAM Correlation heatmap (BAM Correlation ColorMap Options #102)
- Fix BAM Correlation Heatmap Progress bar updates (BAM Genome Correlation Progress Bar not updating #118)
- other miscellaneous bug fixes and typos
- fill in more javadocs
Update TagPileup graphical interface according to new UI/UX specs. #115
#115 update file loader for Output Directory and Blacklist Filter to display a truncated file path (instead of just file name itself), so that just the last 30-50 characters are displayed. Full filepaths can always be displayed by hovering to get it in the tool tips. This involved creating a "getSubstringEnd" static method under the ExtensionFileFilter utility class. Bugfix: opening Output directory file selector and then "canceling" out to create a null reference that causes the script to throw an error when executing. This is fixed by adding handling for null output ("else" block added when updating "OUT_DRI").
Move singularity definition file into its own directory (for clarity and organization). Also give it a README for documenting usage.
-fixed bug -added JavaDocs for TagPileup classes under the `window_interface` package #115 Bug introduced during TagPileup facelift: selecting midpoint and then switching back to 5'end does not re-enable selection of separate strands. This is due to the `tglCombined.setEnabled(!activate)` line under the `allowReadChoice()` method that should be `tglCombined.setEnabled(!activate)`
This commit should not affect functional code. It is a pure javadocs update. Fix errors thrown during javadocs build: * typos in @see tags * unescaped characters like > < & updated to escaped equivalents > < %amp; * properly format links in HTML tags so they linkout * misspelled @param variables Fix warnings thrown during javadocs build: * add missing descriptions to @param and @return tags Reformat * For certain class/major method descriptions that run long, used Eclipse's default formatting to reformat the JavaDocs to wrap lines text Add more content * many classes missing JavaDoc content were filled in
-fixed bug related to combined/separate enabling/disabling -fixed bug related to output options enabling/disabling -streamline activateOutput() -add JavaDocs to helper methods allowReadChoice() and activateOutput() #115 Bug introduced during TagPileup facelift still not fixed (selecting midpoint and then switching back to 5'end does not re-enable selection of separate strands). This is was fixed by removing any activation/deactivation of tglCombined. Fixed another bug relating to activateOutput(). Unchecking and then rechecking "Output Heatmap Matrix" did not properly reactivate the heatmap components. To fix this, activateOutput() was streamlined to perform the check for both chckbxOutputCompositeData and chckbxOutputData as unchecked before disabling or renabling the Output directory button and label.
#102 charts.Heatmap - add JavaDocs - remove unused constructor - restructure to use different paint scales - implement a jet/rainbow paint scale and rename the red-white-blue paintscale BAMGenomeCorrelation -remove unused OUTPUT_STATUS in the script constructor -update suffix to append to basename with "_Correlation" descriptive string BAMGenomeCorrelationCLI -remove unused OUTPUT_STATUS in the script call BAMGenomeCorrelationOutput -remove unused OUTPUT_STATUS in the script call BAMGenomeCorrelationWindow -redesign window structure to organize/group options into subpanels -add options for selecting colorscales (jet vs rwb)
#118 fire property signal named "progress" fired by script class, caught by PropertyChangeListener added to instantiated script object in Output class. This PropertyChangeListener was configured to re-fire PropertyChangeEvent with same values, which is caught by PropertyChangeListener added to instantiated Output object in Window class. The rest follows the pattern laid out by other tools.
#102 update jet/rainbow color map to use the dark red for the higher value and the dark blue for the lower value
#118 Bug fix so that progress bar updates for BAM Genome Correlation. PropertyChangeListener needed to be added before script execution.
Missing input option validation added to PEStats on insert size min/max and num BAM files.
With this commit, decimal thresholding is supported with the `--absolute-threshold` tag
fix typo in signal duplication (signal_dup_description) constant
Add JavaDocs and reformat the JavaDocs of classes with in the charts directory
Add Gzip input support for Four color sequence plots. Include use of ExtensionFIleFilter.stripExtensionIgnoreGZ() which has been updated to not convert filename to all lower case. This method is used to generate default output filenames from both CLI and Window classes. Input extension checks were removed from CLI. #91
Mimic CLI of two-color heatmap tool in Window tool by using ExtensionFileFilter.stripExtensionIgnoreGZ() method to build the output PNG filename for Two-color heatmap.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.