New Tool: FRiX Calculator and restructure main GUI #155
Conversation
This file contains 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
#138 Most tool group tab JPanels switched to BoxLayout with center stacking of function-initiated JPanels (initializeToolPanel). These were nested in a JScrollPane with vertical scrolling enabled as needed and horizontal scrolling disabled. Each intializeToolPanel used the GridBagLayout with 5px padding between components.
Move the ExcelAdapter JTable structure used by the scale-matrix tool to its own class within the objects package. This essentially enables pasting with Ctrl-V to the PastableeTable object (copy functions already enabled).
- update TagPileup to throw ScriptManager OptionExceptions for invalid PileupParameter values instead of "This should not print" print statements - also throw OptionException during CLI validation of input options - add javadocs to `getCLIcommand()` method - handle (catch and throw) exceptions for window_interface classes
charts.Histogram - include new histogram type formatted for FRiX tool cli.Peak_Analysis.FRiXCalculatorCLI - write CLI with Javadoc and Picocli decorators, validation methods, and CLI command building methods based on TagPileup (with unused elements stripped) main.ScriptManagerGUI - add FRiX Score Calculator to Peak_Analysis tab objects.ToolDescriptions - add FRiX Calculator description scripts.Peak_Analysis.FRiXCalculator - write FRiXCalculator script based on TagPileup and leveraging PileupExtract helper script util.BAMUtilities - modify BAMUtilities helper script for getting StandardizationRatio such that TagPileup behavior is unchanged but separates out statistics needed by FRiXCalculator window_interface.Peak_Analysis.FRiXCalculatorOutput/Window - build GUI interface for user selection of options and to display output
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.
Restructure main GUI to reduce code repetition and add new FRiX Calculator