Initial commit
Merge branch 'master' of github.com:BaderLab/EnrichmentMapApp
Update README.md
Update README.md
Fixed issue when no genesets pass filter defaulting to compute overlap between all genesets in the gmt file and issue with rpt setting of phenotype not being propagted to the map
added missing file from build (missing because using same instance of source tree for both branches working on.  Separated branches to separate instances of sourcetree to avoid confusion in future)  Fixed test cases to compensate for change in compute similarity behaviour
added a gitignore file so don't accidentally miss adding a new source file.
add file that tracks build number
initial version of wiki manual
revamp structure of manual.  Added edb, expanded RPT description, combined coeffecient, expansion of what parameters mean,
Verified that previous issues reported by Veronique relating to missing rows from the export expressin file were gone in current version.  (issue was relating to session file.  incorrect loading in version 1.2 made it seem data was missing from current version but on re creating the session and re-loading it all the data was there)
Added option to see the values associated with the color in the heatmap.  Through back and forth with veronique got visualization to what users would want.  Add switch to turn off or on values and colors are there all the time
Fixed issue with mouse over of heat map cells (no longer require click, changed it to mouse over)
Fixed missing phenotypes from re-factored build (now phenotypes are in the parameters panel and used for heatmap column annotation.)
Fixed sort arrow --> didn't work because it has been doctored so that when gsea rankings are shown the leading edge is always on top.  for dataset that are from GSEa results this results in all sorting only being done in ascending.  Fixed so doctoring only happens when the leading edge is being displayed.  Arrow now working.
Fixed visualization of expression heat map with regards to spacing of columns being wonnky depending on in values were turned on or off
Got rid of duplicate expression files if dataset 1 and dataset 2 share the same expression file.  (didn't change the data structure but changed how the heatmap displays the data when the files are the smae.
fixed issue with reset button not working
Fixed classes not being coloured in the heatmap when there was a class file --> also added the feature of the user being able to specify the path to the class file instead of having the feature only when the user loads GSEA data through an rpt.
Fixed issues with sorting of the table (introduced when added values to heatmap.  Missing comparator for the new data type in the table sort method).
fixed minor issue with reset (forgot to blank class files)
fixed ticket 175 (drproject) - regarding leading edge not working for blue sets on re-loaded session.
fixed ticket #198
Also added similiarity cut off label to enrichment map input panel
ticket #213 - issue with deleting post analysis node and edges from and stored session and trying to reload the node (usually done with different paramters) but only the node gets added back.  When nodes and edges are deleted they are not deleted from the set of genesets and gene set similarity.  On recomputed if the edge existed in the set I didn't re-create it.  Change this to updated the gene set similarity and it get re-added.  Also fixed issues with stored old sessions missing GSEA ranking and issue with expression data coming from rank files in the edb directory.
Fixed misc bugs with heatmap and post analysis.  fixed GSEA ranking not working for second dataset.
Add to data support to commandtool interface.
Fixed issue with rank files being used as expression files - added dummy description file so the rank file looks more llike the expression file.
Transferred post-analysis-panel modifications to EMRefactor branch
Added the N, n, m, k values used for Hypergeometric test calculation as edge attributes