X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=IDEAS.txt;h=ba3b9eb1ac22961ee4d25a21132e26295712ade4;hb=29b08ed1511c3d09d6dff7699569096af72c5af0;hp=e2f9f7df32642b7bce31036701f25195c82e03c0;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;p=jabaws.git

diff --git a/IDEAS.txt b/IDEAS.txt
index e2f9f7d..ba3b9eb 100644
--- a/IDEAS.txt
+++ b/IDEAS.txt
@@ -1,5 +1,49 @@
 FUTURE TODO
-Registry for jalview WS - gives list of web services providers
+
+Pack the test cases and build file to run them in one of the distributives 
+
+? Better native Mac support (and maybe abandon native windows support in 
+favour of VM)
+
+Cluster stats: 
+ -Remove hyperlinks from tasks which workdirs were removed 
+ Way to do: Crawler is to update DB records if the directory is not found to prevent link 
+generation for stats. 
+ -graph generation 
+ -user documentation (do not forget how to enable follow symlinks!)
+   
+Webpage for testing web services?
+
+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
@@ -26,7 +70,17 @@ FUTURE TASKS
 Prepare HMM profile for the user alignment and call jnet - instead of jpred. 
 JPRED REWRITING Wrap Jpred
 Wrap scanPS    
-Look at SIFTS at EBI 
+
+CBS soft: 
+Transmembrane regions
+Phosphorilation sites
+Glycozilation sites
+Signal P
+
+They all have SOAP WS...
+ 
+CDD domains
+PFAM domains
  
 JPRED IMPROVEMENTS
 1) Make sure PSIBLAST does not generate large output (e.g. one approach is to stop on the first iteration
@@ -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
 /homes/ws-dev1/servers/Test/webapps/TestJWS/WEB-INF/classes/vamsas/pl/bin/jpred3_submit_concise
 /homes/ws-dev1/servers/Test/webapps/JalviewWS-back/WEB-INF/classes/vamsas/pl/bin/jpred3_submit_concise
+
+
+JAXB - cannot serialize Maps and instance variables in Enums!
+Best replacement for Maps is a custom object for key->value pair and a HashSet for storing the pairs.
+JaxB cannot serialize instances of generic classes(?) 
  
\ No newline at end of file