Added -2 and -0.5 as exceptions for the magic numbers check.
Added descriptions of the main, gui and input packages by adding package-info.java files in these three packages.
Added APPLICATION_TITLE field (application name and version).
Used the FONT_NAME field for the definition of all font fields.
Commented out several unused fields.
Fixed lots of Checkstyle issues: added Javadocs, ...
Created determineReportDateRange method.
Added a private constructor.
Fixed lots of Checkstyle issues: switched UncommentedMain check off for main method, created POLL_INTERVAL_PIPELINE_LOG field, added & extended Javadocs, etc.
Changed PROPERTY_PROJECT_LOGO_FILE to point to "images\traitctmmlogo.png" instead of  "images\\traitctmm.jpg".
Added some TODOs to reorganize some directories.
Added some fields for log messages (this fixes several Checkstyle issues).
Changed ShowReportsFromDate to 07/07/2013 since the generated TIC files are from July 7th.
Get all dependencies except JCalendar 1.4 from the central Maven repository instead of from the local lib directory.
Defined properties for dependency and plugin versions.
Added Checkstyle plugin.
Replaced one dependency for Powermock by two dependencies as explained on the Powermock website.
Added Maven resources and JXR plugins to get rid of some Maven messages.
Changed name, version, description & build.directory and added packaging.
Added some comments and whitespace.
Resolved conflict after merge with master branch.
Added Javadocs, a hidden constructor, a default clause for a switch statement and finally a final keyword.
Added site directory to ProteomicsQCReportViewer\.gitignore.
Moved ProteomicsQCReportViewer.iml from main .gitignore to ProteomicsQCReportViewer\.gitignore.
Added Javadocs, put some strings before the .equals, catched more specific exceptions and finally replaced a few tabs by spaces.
Slight change to the NoWhitespaceAfter guideline: whitespace after typecast is ok, whitespace after unary minus or unary plus not.
Used logger instead of printStackTrace.
Added Javadocs, changed some comments and renamed some parameters & variables.
Merge pull request #11 from FreekDB/master

Mainly Checkstyle related improvements