Update DevelopersInformation.md
Merge pull request #44 from FreekDB/master

Main and 9 other classes: fixed several FindBugs issues
Processing feedback of production version deployment on 23 August: 

1) Corrected report auto-refresh mechanism. 

ProgressLogReader.java: 
Added condition to infer changes to the log file. Added fields
currentLastLine and savedLastLine. 
pushPipelineStatus() now detects changes to the log file and invokes
Main.notifyProgressLogFileChanged(..) in case of change. 

Main.java:
Updated notifyProgressLogFileChanged(..) method. 
Added NO_NEW_REPORTS_MESSAGE. 
Removed NO_REPORTS_MESSAGE.
Processing feedback of production version deployment on 23 August: 

1) Enlarge TIC Graph pane to use full length of the monitor screen (~22
inches monitor). 

ViewerFrame.java: 
Increased CHART_PANEL_WIDTH from 800 to 1200. 
Increased DESKTOP_PANE_WIDTH from 1270 to 1670. 
Increased SORT_PANEL_WDITH from 700 to 840.
Increased METRIC_LABEL_WIDTH from 200 to 300. 
Increased STATUS_PANEL_WIDTH from 1333 to 1633. 
Increased CONTROL_PANEL_WIDTH from 1333 to 1633. 
Increased CONTROL_FRAME_WIDTH from 1333 to 1633. 
Reduced CONTROL_FRAME_HEIGHT from 165 to 155.
Reduced SPLIT_PANE_1_DIVIDER_LOCATION from 185 to 175. 
Increased spacing between control panel elements from DIMENSION_10X0 to
DIMENSION_25X0.
Specified setMaximumSize for zoomPanel. 
Specified setMaximumSize for sortPanel. 

2) Msrun name should be red in the TIC Graph. 

ChartUnit.java: 
Added code to paint chart title in Red. 

Other: 
Commented debug lines in ProgressLogReader.java.
Processing feedback of production version deployment on 23 August: 

3) Sometimes status is not fully visible in statusField.

ViewerFrame.java: 
Specified setMaximumSize and setMinimumSize for statusPanel. 
Added constants STATUS_FIELD_WIDTH and STATUS_FIELD_HEIGHT. 
Specified setMaximumSize, setMinimumSize and setPreferredSize for
statusField.
Processing feedback of production version deployment on 23 August: 

4) Viewer covers the Windows taskbar. 

ViewerFrame.java: 
Reduced VIEWER_HEIGHT from 1500 to 1350.  
Specified setMaximumSize for the viewer frame.
Working on the requirement: Export selected reports in PDF format
together with metrics values and TIC graph.
Following is coded:
1) Display PDF directory chooser form. 
2) Obtain directory location from the user to save the reports.
3) For every selected report unit, follow following steps:  
         i) Name the PDF file -> msrunname.pdf.
         ii) Create PDF document.
         iii) Add header to the PDF document.
         iv) Obtain TIC Chart of the Report Unit.   
         v) Add TIC Chart to the PDF document.
         vi) Obtain metrics listing and values table of the report unit. 
         vii) Add metrics listing and values table to the PDF document. 
         viii) Save PDF document to specified directory location. 
4) Notify user about saving PDF reports/handle error conditions. 

Look and feel optimization of the PDF report is to be done.
Removed OPL specific examples from the installation and user guide.
Working on look and feel optimization of the PDF report.

1) Specified column sizes.
2) Specified table header font and table content font. 
3) Added color to the table header.
Added following features to the PDF report:
 
1) Combine individual PDF reports into one single report;
2) Landscape layout of the page; 
3) Fit TIC Graph and metrics values table in one page; 
4) Remove "Index = n" from the TIC graph; and 
5) Add creation date/time in the report.
Merge branch 'master' of https://github.com/CTMM-TraIT/trait_proteomics_qc_tool.git

Conflicts:
	ProteomicsQCReportViewer/src/nl/ctmm/trait/proteomics/qcviewer/utils/ReportPDFExporter.java
Corrected logging message - removed use of String.format and extra
argument.
Modified ReportPDFExporter.java: 
1)The metrics values table displays sorted values. 
2)Removed seconds and milliseconds from creation date time stamp.
ReportPDFExporter.java: 
1) Added maxIntensity back to the TIC graph image. 
2) Used getTicChart().clone() while creating TIC graph.
Updated pom.xml. Removed unused dependency com.lowagie.
Addressed many CheckStyle warnings for the unit tests. 
Commented testGetNotAvailableImageException() method from UtilitiesTest.
This test is not necessary for the current version of report viewer.
Addressed requirement: Viewer customization according to the screen
size. 
ViewerFrame.java: 
Divided existing dimensions into variable dimensions and static
dimensions. 
Changed declaration of variable dimensions from final static to static. 
Changed names of variable dimensions to match with checkstyle variable
name requirements. 
Added method determineVariableDimensionsValues() to get screen size and
calculate values of variable dimensions according to screen size.
Added QuaMeter IDFree mode in TraIT Proteomics QC Pipeline. 

run_msqc_pipeline.py: 
1) Added variable _QUAMETER to specify QuaMeter installation folder. 
2) Added definition _run_quameter_idfree(...).
3) Added pipeline stage 5 - _run_quameter_idfree(...).

parse_metrics.py: 
1) Added variable quameter_metrics_file to specify QuaMeter output TSV
file. 
2) Added definition _extract_quameter_idfree_metrics(...) to extract
QuaMeter metrics from the TSV file. 
3) Added list metrics['QuaMeter'] to hold QuaMeter metrics.
4) Verified that QuaMeter metrics are written and saved in the
Metrics.json file.
parse_metrics.py: Restored generic_metrics['date'] statement.
Added support to parse QuaMeter IDFree metrics values from the
metrics.json file. 
DetailsFrame.java: Increased column sizes to accommodate QuaMeter
metrics keys, description and values. 
JsonMetricsReader.java: 
Changed function readJsonValues(...) to
readJsonValuesForGenericAndNISTMetrics(...).
Added function readJsonValuesForQuaMeterIDFreeMetrics(...) for reading
QuaMeter metrics values from the metrics.json file. 
ReportReader.java now uses readJsonValuesForGenericAndNISTMetrics(...)
and readJsonValuesForQuaMeterIDFreeMetrics(...). 
MetricsListing.txt: 
Added QUaMeter IDFree metrics keys and description in the
MetricsListing.txt file.