Replace Map<String, HashSet<Score>> with ScoreManager and ScoreHolder classes to...

[jabaws.git] / TODO.txt

diff --git a/TODO.txt b/TODO.txt
index 79f6ca1..0acbf85 100644 (file)
--- a/TODO.txt
+++ b/TODO.txt
@@ -1,8 +1,49 @@
 TODO: \r
 \r
-Add globprot ws \r
+FIXME: \r
+Conecting to JABAWS version 2 service\r
+09-Feb-2011 15:27:53 compbio.ws.client.Jws2Client connect\r
+INFO: Connected successfully!\r
+Exception in thread "main" java.lang.NullPointerException\r
+       at compbio.ws.client.MetadataHelper.getParametersList(MetadataHelper.java:30)\r
+       at compbio.ws.client.Jws2Client.<init>(Jws2Client.java:179)\r
+       at compbio.ws.client.Jws2Client.main(Jws2Client.java:483)\r
+       \r
+       \r
+Need to pass predicted ranges to the client too - some are not straightforward to devise. \r
+This may require changes to SequenceAnnotation\r
+\r
+Globprot need a proper reference to bio python and sav_gol binaries -> they should be \r
+somehow taken from disembl. \r
+\r
+Add registry service to query services status\r
+\r
+Refactor web services checker to enable a programmatic access to its methods.\r
+Rename it to avoid confusion with jabaws client\r
+\r
+Finish the client\r
+\r
+Add interface for Jalview annotation \r
+Add the method to return Jalview Annotation to SequenceAnnotation IF  \r
+\r
+Develop generic Interface to return Jalview annotation for easy to add new \r
+services (?) \r
+\r
+Replace conservation.Method with server.ws.Method \r
+and try building WS. If this does not work - get rid of Method\r
+\r
+Output file parsing for stat reporting\r
+cluster engine stat of www-jws2 user\r
+\r
+integrate the above to tweak the size of the local job\r
+\r
+Add AACon ws\r
+Add iupred ws http://iupred.enzim.hu/\r
+Add globprot ws - does not report raw scores, just regions\r
 Add ronn ws\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
@@ -16,7 +57,7 @@ new parsers for the above programmes output (Stockholm MSA format?)
 \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
+What actually needs to be sent?   \r
 \r
 Add facility to distribute other results of the calculations like the trees and \r
 annotation file for probcons. \r