Deprecate jtv#68
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WilliamKMLai merged 4 commits intomasterfrom Dec 21, 2021
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Affected tools are TagPileup in Read_Analysis and the two sort tools in Coordinate_Manipulation Remove the util.JTVOutput class that writes a JTV file. Remove the code within the SortBED and SortGFF script classes that call the JTVOutput class to generate the JTV. Remove the code within the TagPileup script class that calls the JTVOutput class to generate the JTV. Remove the JTV-related variables stored in the PileupParameters class that TagPileup uses. Remove the code within the CLI and window_interface class that set the PileupParameter values.
Since the JTV file type was deprecated, the command line interface of Tag Pileup does not use color information because it only stores the values of the composite plot rather than generating the PNG (see separate composite plot tool). As a result, the PileupParameters object is used by the script TagPileup object and the colors are used only by the Output window from the GUI interface. It is redundant to pass the color information to the script when it is only used by the output window. PileupParameters.java--color information (Anti, Sense, and Combined) are removed from the object. TagPileupOutput--constructor adjusted to accept an ArrayList of Color objects and the composite plot figures are adjusted to use this ArrayList for generating the composite plot object. Two whitespace formatting changes are also included here. TagPileupWindow--The code for changing the PileupParameters color fields is adjusted to create a new ArrayList of Color objects to pass to the TagPileupOutput object.
TagPileupWindow contained logically redundant if-statement checks that were merged in this commit. i.e. the chckbxOutputData was checked for if it was *not selected* and then for if it was *selected* which was logically merged with an added "else" statement
Two writer objects were not closed in the TagPileup script. This was fixed in this commit (along with some cosmetic code indentation adjustments)
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Merge commits addressing issue #64 to master.