Add support for command-line interface options

[Robert Leach]

USE CASE: WHAT DO YOU WANT TO DO?

Run various treeview operations from the command line without the GUI.

STEPS TO REPRODUCE AN ISSUE (OR TRIGGER A NEW FEATURE)

1. Invoke TreeView from the command line with options such as a file name/path to open: java -jar treeview.jar -r /path/to/file.cdt

CURRENT BEHAVIOR

Some command line options still exist as leftovers from java TreeView 2, but are not intentionally implemented and are not supported.

EXPECTED BEHAVIOR

A suite of options should be implemented so that various operations can be performed without the GUI. These options should be supported:

• input file
• column & row data start indexes & delimiter options (to skip import dialog)
• Cluster (inc. row/col similarity metric, ignore zeros, and linkage method)
• Min, middle, & max data values for left, middle, & right color thumbs
• A way to zoom to a specific area (possibly even select)
• possibly various color setting options
• possibly various label setting options
• Export (format, paper size, orientation, region, aspect, row labels, column labels, show selection)
• An option to run with or without the GUI

All the options should be documented somewhere in how to use them - perhaps a usage output?

The main idea here would be to allow people to run TreeView operations in a pipeline in order to get back an exported image or data. If run without the GUI, the user would have to select either clustering or export or both.

DEVELOPERS ONLY SECTION

SUGGESTED CHANGE (Pseudocode optional)

Some options already exist in a vestigial fashion. Test them and fix those that don't work. Implement those that are absent. Write up the documentation on the implemented options and put them on the website & in the help menu.

FILES AFFECTED (where the changes will be implemented) - developers only

unknown

LEVEL OF EFFORT - developers only

major

COMMENTS

This was a feature request from an external user who was running Treeview as a part of a pipeline that included opening treeview with a given input file.