X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=TODO.txt;h=b6d15edac322c641c35b6c3415c247da7099f405;hb=a66674ad9520261789bbfe8401f88b37ae2a71a2;hp=a2126517291dcab94923539de76147520ad4f037;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;p=jabaws.git

diff --git a/TODO.txt b/TODO.txt
index a212651..b6d15ed 100644
--- a/TODO.txt
+++ b/TODO.txt
@@ -1,35 +1,51 @@
 TODO: 
 
-DONE: LocalExecutor service must be shutdown on web application undeploy event not on JVM shutdown. 
-This is because JVM is still running even after web application is shut down!
+Publish jabaws-discuss contact information
 
+Output file parsing for stat reporting
+cluster engine stat of www-jws2 user
 
-Good toString method for Limits (test with command line client -limits)
+integrate the above to tweak the size of the local job
 
-Add facility to distribute other results of the calculations like the trees and annotation file for probcons. 
+Add AACon ws
+Add iupred ws http://iupred.enzim.hu/
+Add globprot ws 
+Add ronn ws
 
-Use absolute path for web site download links as archives are not included into distro! 
+Philogeny Mrbayes + Philip
+ 
+USE CASE - TURN ALIGNMENT INTO PROFILE AND SEARCH SEQUENCE DATABASE USECASE
+- Receive user alignment 
+- use hmmerbuild to turn it to profile
+- use hmmersearch to search the database 
 
+#END OF - TURN ALIGNMENT INTO PROFILE AND SEARCH SEQUENCE DATABASE USECASE 
 
-(later) Define limits for presets
+New data model for representing psiblast,blast,phmmer,jackhmmer results
 
-Add documentation on Presets, Parameters and Limits
+new parsers for the above programmes output (Stockholm MSA format?)
 
-Explain how to define a limit
+Think hard on what to do with large output files? 
+e.g. serve the hits table in full, but retrieve alignments on demand.
+What actually neeeds to be sent?   
 
-Rearrange web site docs - add links to the top of the page to the topics discussed below
+Add facility to distribute other results of the calculations like the trees and 
+annotation file for probcons. 
 
-Put the documentation for various executables online
+# END OF SEARCHING SEQUENCE DATABASE USECASE
 
-Pack the test cases and build file to run them in one of the distributives 
+Good toString method for Limits (test with command line client -limits)
 
-Add test for repeated result collection from cluster engine 
+JABA DOCS
+(later) Define limits for presets - if required
+(later) Add documentation on Presets, Parameters and Limits
+(later) Explain how to define a limit
 
-Add logging facility to WSTester so more details of the problem can be reported
+Add test for repeated result collection from cluster engine
 
-Make left gradient image one-two characters larger + change "For developer ->For Developers"
+(low) Pack the test cases and build file to run them in one of the distributives 
 
-PART DONE: test local/cluster execution - test Load balancer
+(low) Add logging facility to WSTester so more details of the problem can be reported
 
 (low) Statistics collector for engines (number of operations/timing)
 
@@ -37,17 +53,23 @@ PART DONE: test local/cluster execution - test Load balancer
 
 (later) Implement utility to rerun died tasks
 
-(later) Progress bars - talk about (1. Proper time assessment vs low hustle option - dumping output to screen)
-
 (later) Add recognition for executables for the different architectures
 
 (later) use Latch to manage engine reservations. Reservations for parallel jobs? 
 
 DONE
+WILL NOT DO: Progress bars - needs assessing how long does it take to run a task
+DONE: LocalExecutor service must be shutdown on web application undeploy event not on JVM shutdown. 
+      This is because JVM is still running even after web application is shut down!
+DONE: Use absolute path for web site download links as archives are not included into distro!
+DONE: Rearrange web site docs - add links to the top of the page to the topics discussed below
+DONE: Put the documentation for various executables online
+DONE: Make left gradient image one-two characters larger + change "For developer ->For Developers"
+DONE: test local/cluster execution - test Load balancer
 DONE: Improve SimpleWS client so it can be scripted against: give user alignment and accept parameters
 DONE: Make a configuration tester class (check that configuration files point to the executables, and they can be executed)
 DONE: PUT CLIENT JAR INTO WEB-INF/LIB - most likely need to get rid of dist prefix in the build file
-DONE: Different packages for donwload and dundee. generic vs specific settings. 
+DONE: Different packages for download and dundee. generic vs specific settings. 
 DONE: JAVADOC
 DONE: Refactor EngineResourcesLeak tester to hide a map implementation!
 DONE: Compile executables for linux in the most generic way