dundee executable conf

[jabaws.git] / IDEAS.txt

diff --git a/IDEAS.txt b/IDEAS.txt
index e2f9f7d..ba3b9eb 100644 (file)
--- a/IDEAS.txt
+++ b/IDEAS.txt
@@ -1,5 +1,49 @@
 FUTURE TODO\r
-Registry for jalview WS - gives list of web services providers\r
+\r
+Pack the test cases and build file to run them in one of the distributives \r
+\r
+? Better native Mac support (and maybe abandon native windows support in \r
+favour of VM)\r
+\r
+Cluster stats: \r
+ -Remove hyperlinks from tasks which workdirs were removed \r
+ Way to do: Crawler is to update DB records if the directory is not found to prevent link \r
+generation for stats. \r
+ -graph generation \r
+ -user documentation (do not forget how to enable follow symlinks!)\r
+   \r
+Webpage for testing web services?\r
+\r
+Add interface for Jalview annotation \r
+\r
+Develop generic Interface to return Jalview annotation for easy to add new \r
+services (?) \r
+\r
+Philogeny Mrbayes + Philip\r
+ \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
+#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
+new parsers for the above programmes output (Stockholm MSA format?)\r
+\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 needs to be sent?   \r
+\r
+\r
+Add facility to distribute other results of the calculations like the trees and \r
+annotation file for probcons. \r
+\r
+(later) WRAP Amps\r
+\r
+(later) Implement utility to rerun died tasks from command line\r
+\r
 Registry for jalview WS - gives list of web services providers\r
  - checks the status of the web services\r
  - web service providers gives list of available WS\r
@@ -26,7 +70,17 @@ FUTURE TASKS
 Prepare HMM profile for the user alignment and call jnet - instead of jpred. \r
 JPRED REWRITING Wrap Jpred\r
 Wrap scanPS    \r
-Look at SIFTS at EBI \r
+\r
+CBS soft: \r
+Transmembrane regions\r
+Phosphorilation sites\r
+Glycozilation sites\r
+Signal P\r
+\r
+They all have SOAP WS...\r
+ \r
+CDD domains\r
+PFAM domains\r
  \r
 JPRED IMPROVEMENTS\r
 1) Make sure PSIBLAST does not generate large output (e.g. one approach is to stop on the first iteration\r
@@ -41,4 +95,9 @@ and if it is so, then use the family)
 /homes/ws-dev1/servers/Test/webapps/JalviewWS/WEB-INF/classes/vamsas/pl/bin/jpred3_submit_concise\r
 /homes/ws-dev1/servers/Test/webapps/TestJWS/WEB-INF/classes/vamsas/pl/bin/jpred3_submit_concise\r
 /homes/ws-dev1/servers/Test/webapps/JalviewWS-back/WEB-INF/classes/vamsas/pl/bin/jpred3_submit_concise\r
+\r
+\r
+JAXB - cannot serialize Maps and instance variables in Enums!\r
+Best replacement for Maps is a custom object for key->value pair and a HashSet for storing the pairs.\r
+JaxB cannot serialize instances of generic classes(?) \r
  
\ No newline at end of file