Add UI for Threshold

[stevenDowns]

Project Changes

• Created a .gitignore file to prevent .class and .jar files from being checked in

Code Style Changes

• White space changes:
  • Adding a space between operators a==b becomes a == b
  • Adding a space after commas a,b becomes a, b
• large if blocks over the same value get rewritten as switch

Refactors

• Organized static values and user inputs used by Analyzer in the new object named CometConfiguration

New Functionality

• Added new object: CometConfiguration.
• Allow users to change the minimum threshold(numeric)
  • The threshold before was hardcoded to the Huang minimum threshold value.

[bgyori]

@stevenDowns thank you! The diff is quite extensive so I will need some time to review the changes.

[bgyori]

In a number of places, commented out code is left but indentation (and sometimes new lines) are removed. Can these be reverted to keep the original?

[stevenDowns]

OK, so you want to keep the commented out code? Is there a reason? there may be a better way to store it is why I ask.

[bgyori]

It might be fine to remove commented out code but keeping it in a mangled form doesn't make sense. My suggestion is just to revert these changes and keep the original, that's the easiest option I think.

[stevenDowns]

Sorry for the delay. I tried to go back through this file and add back the commented out code with their decompressed formats. If you spot a place I missed, put a comment at the line. I only went through this file, CometAnalyzer. If other files had this issue. I will look through them and try to restore the commented out code lines as they were.