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