X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=IDEAS.txt;h=3be0c198344fa99646809befb0554904007d4982;hb=db5333c93e7d29d2a6eb301a017300583bc9f44c;hp=bab0292f3f8e74864419908013df93242751be94;hpb=2a269830633463e5016d5c92ed672d9e312c9776;p=jabaws.git

diff --git a/IDEAS.txt b/IDEAS.txt
index bab0292..3be0c19 100644
--- a/IDEAS.txt
+++ b/IDEAS.txt
@@ -1,5 +1,35 @@
 FUTURE TODO
 
+Add interface for Jalview annotation 
+
+Develop generic Interface to return Jalview annotation for easy to add new 
+services (?) 
+
+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 
+
+New data model for representing psiblast,blast,phmmer,jackhmmer results
+
+new parsers for the above programmes output (Stockholm MSA format?)
+
+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 needs to be sent?   
+
+
+Add facility to distribute other results of the calculations like the trees and 
+annotation file for probcons. 
+
+(later) WRAP Amps
+
+(later) Implement utility to rerun died tasks from command line
+
 Registry for jalview WS - gives list of web services providers
  - checks the status of the web services
  - web service providers gives list of available WS