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Support for 3D hotspots #40

Merged
merged 103 commits into from
Jul 26, 2016
Merged

Support for 3D hotspots #40

merged 103 commits into from
Jul 26, 2016

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onursumer
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  • Adds visualization support for 3D hotspots
  • Single page front-end design with router for different views such as residue and gene pages.
  • Residue and Gene pages are using MutationMapper library
  • Major improvements for data import and management.
  • Better packaging of classes on the back-end.

Fixes the issue #39 and most of the issues in #35.

@onursumer
made MapConversion instance configurable with application.properties …
c0e5835 
…file
@onursumer
support for additional MAF fields
3993964
@onursumer
added functionality to process 3D hotspot mutations
fe3d654
@onursumer
improved tumor type value processing
4d711eb
@onursumer
added p-value column
7213201
@onursumer
added metadata to determine initial config
9754c75
@onursumer
added p value threshold option for display purposes,
390de2e 
 improved tooltip init
@onursumer
added functionality to generate tumor type composition by using the i…
4d10e79 
…nput MAF
@onursumer
added tumor type count calculation functionality
c300ece
@onursumer
now filtering out all mutations except missense when generating the 3…
1ce3fdb 
…D hotspots information
@onursumer
added new fields for 3D hotspots mutation data
3ff74ed
@onursumer
improved pdb chain field parsing
ac61c01
@onursumer
getters and setters for new HotspotMutation fields
2dfbd91
@onursumer
renamed codon to residue
81f10a8
@onursumer
improved mutation model
dd8d4f0
@onursumer
moved functionality related to data retrieval and persistence into re…
602eaea 
…pository classes
@onursumer
started implementing clustered hotspot mutation service
21ba42f
@onursumer
finished implementing clustered hotspot mutation service
3e9ec5b
@onursumer
minor update for the mutation model on the backend,
97bbadd 
improved p-value data handling and rendering on the frontend
@onursumer
added 3D hotspots specific columns
d1db8da
@onursumer
moved tooltip initialization into the new TooltipUtils class
9351fc6
@onursumer
now Cluster model has a list of residues
577afeb
@onursumer
factored out cell render functions into separate classes
7594120
@onursumer
added residue view
ae54c9a
@onursumer
updated Cluster model,
5a748cf 
added Cluster repository interface,
 updated repository interfaces
@onursumer
replaced domain package with model and persistence packages
54dbed8
@onursumer
added Cluster service, and API method to retrieve cluster data
dd66432
@onursumer
added p value field to the ClusteredHotspotMutation class
419fba8
@onursumer
3d mutation api now return only the cluster count instead of a full l…
6ed718b 
…ist of clusters,

 added client side cluster data proxy to retrieve clusters by hugo symbol and residue
@onursumer
now using routers to display each page within a different hash link
1c14c8b
@onursumer
fixed sorting behavior for various columns
5761779
@onursumer
updated the download file reference for internal profile
45fd650
@onursumer
manually removed the tracker from the 3Dmol library
9a22d9c
@onursumer
added 3d data files
16e8b4e
@onursumer
now residue table has a fixed width
692b82c
@onursumer
added a 3D hotspots logo
6b73c3a
@onursumer
disabled filtering residues upon mouse over the residues column, inst…
d999263 
…ead now filtering clusters with checkboxes
@onursumer
added gene page
38c5043
@onursumer
added tooltip for the cluster checkboxes
7393237
@onursumer
added gene page link to the residue page
ff24eb7
@onursumer
fixed the broken tooltip for residues column (fixed issue cBioPortal#39)
93ef162
@onursumer
added custom handlers for the diagram lollipop events
9d0ad13
@onursumer
improved residue select and highlight functionality
b732536
@onursumer
added classification legend to the residue view
a6367da
@onursumer
filtering by cluster now resets previous residue selection
de9e69c
@onursumer
updated the main page info for 3D profile
f2842f0
@onursumer
updated page title for 3D profile
419027e
@onursumer
updated tag line for 3D profile
37931c9
@onursumer
updated class values for hotspots
a2073de
@onursumer
updated 3D hotspots download file
e1ace6a
@onursumer
updated download file for public cancer hotspots
d04e704
@onursumer
added classification to the output file of the table download button
5923817
@onursumer
download button of the hotspots table now only downloads the visible …
87b096a 
…columns
@onursumer
for 3D hotspots disabled about link in the footer as well
81ce4e5
@onursumer
added data license (ODbL) information
b257eea
@onursumer
added separate properties files for each maven profile
466180c
@onursumer
updated maven profiles to enable inclusion and exclusion of certain r…
70e4a95 
…esource files
@onursumer onursumer self-assigned this Jul 26, 2016
@onursumer onursumer merged commit 3e07475 into cBioPortal:master Jul 26, 2016
@onursumer onursumer deleted the 3d branch July 26, 2016 15:53
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