Manual merge of Main.java Merge branch 'master' of https://github.com/FreekDB/trait_proteomics_qc_tool

Conflicts:
	ProteomicsQCReportViewer/src/nl/ctmm/trait/proteomics/qcviewer/Main.java
Manual merge of Main.java Merge branch 'master' of https://github.com/FreekDB/trait_proteomics_qc_tool

Conflicts:
	ProteomicsQCReportViewer/src/nl/ctmm/trait/proteomics/qcviewer/Main.java
ViewerFrame.java: Added sorting capability according to report index.
Main.java: Report units are sorted according to report index - before
updating report viewer.
Constants.java: Added constants specifying sort key strings
ReportUnit.java: Added special provision to sort according to report
index. 
ReportReader.java: Added a line for logging number of report units.
Manual merge of Main.java Merge branch 'master' of https://github.com/FreekDB/trait_proteomics_qc_tool

Conflicts:
	ProteomicsQCReportViewer/src/nl/ctmm/trait/proteomics/qcviewer/Main.java
Main:
- Removed unnecessary initialization for the logFileFlag field.
- Fixed some small Checkstyle issues (after running "mvn checkstyle:checkstyle" and checking "target\checkstyle-result.xml").

ReportUnit:
- Renamed the static getReportUnitComparator method to getComparator.

ViewerFrame:
- Changed a traditional for loop in the updateReportUnits method into a for each loop.