May 2010 Commit Log

Number of Commits:

26

Number of Active Developers:

1

jprocter 2010-05-21 11:08 #26

more robust discovery and preset support

32 lines of code changed in:

• src/jalview/gui: AlignFrame.java (+3 -12)
• src/jalview/ws/jws2: Jws2Discoverer.java (+29 -1)

jprocter 2010-05-21 11:07 #25

preset and argument support

74 lines of code changed in:

• src/jalview/ws/jws2: MsaWSClient.java (+55 -5), MsaWSThread.java (+19 -5)

jprocter 2010-05-21 11:07 #24

comment about trapping OOMs

11 lines of code changed in:

• src/jalview/ws: JobStateSummary.java (+11 -2)

jprocter 2010-05-21 11:06 #23

commented out debug code

7 lines of code changed in:

• src/jalview/ws/jws1: MsaWSThread.java (+7)

jprocter 2010-05-21 10:35 #22

quick workaround for JAL-537.

309 lines of code changed in:

• src/jalview/gui: Console.java (+305 -65), Desktop.java (+4 -4)

jprocter 2010-05-17 17:15 #21

status can be null to begin with

6 lines of code changed in:

• src/jalview/ws/jws2: JWs2Job.java (+6 -6)

jprocter 2010-05-17 17:14 #20

pullJobExecutionStats for JAL-493

27 lines of code changed in:

• src/jalview/ws/jws2: MsaWSThread.java (+27 -4)

jprocter 2010-05-17 17:13 #19

minor fix for * JAL-537

7 lines of code changed in:

• src/jalview/gui: Console.java (+7 -3)

jprocter 2010-05-17 17:12 #18

more robust jws2 service discovery

187 lines of code changed in:

• src/jalview/gui: AlignFrame.java (+141 -73), Desktop.java (+3 -3)
• src/jalview/ws/jws2: Jws2Discoverer.java (+43 -6)

jprocter 2010-05-17 17:12 #17

refactored old jalview service code to its own package.

3744 lines of code changed in:

• src/jalview/ws: AWSThread.java (+1), Discoverer.java (del), JPredClient.java (del), JPredThread.java (del), JWS1Thread.java (del), MsaWSClient.java (del), MsaWSThread.java (del), SeqSearchWSClient.java (del), SeqSearchWSThread.java (del), WS1Client.java (del), WSJob.java (del)
• src/jalview/ws/jws1: Discoverer.java (new 455), JPredClient.java (new 390), JPredThread.java (new 667), JWS1Thread.java (new 48), MsaWSClient.java (new 234), MsaWSThread.java (new 715), SeqSearchWSClient.java (new 315), SeqSearchWSThread.java (new 681), WS1Client.java (new 113), WSJob.java (new 125)

jprocter 2010-05-17 11:17 #16

always pass full web service exception details to the log

2 lines of code changed in:

• src/jalview/ws: AWSThread.java (+2 -1)

jprocter 2010-05-17 10:56 #15

always pass full web service exception details to the log

2 lines of code changed in:

• src/jalview/ws: AWSThread.java (+2 -5)

jprocter 2010-05-17 10:56 #14

always log info about services that are discovered

1 lines of code changed in:

• src/jalview/ws/jws2: Jws2Discoverer.java (+1 -1)

jprocter 2010-05-14 18:09 #13

First patch for * JAL-493
- bespoke build of the jalview ws2 client library with refactored base client.

0 lines of code changed in:

• lib: min-jws2-client-1.0.jar (new)

jprocter 2010-05-14 18:08 #12

First patch for * JAL-493

2052 lines of code changed in:

• src/jalview/gui: AlignFrame.java (+15 -4)
• src/jalview/ws: AWSThread.java (new 344), AWsJob.java (new 200), Discoverer.java (+2 -2), JPredClient.java (+1 -1), JPredThread.java (changed), JWS1Thread.java (new), JobStateSummary.java (new 129), MsaWSClient.java (+2 -2), MsaWSThread.java (changed), SeqSearchWSClient.java (changed), SeqSearchWSThread.java (changed), WS1Client.java (new), WSClient.java (+1 -85), WSJob.java (new), WSThread.java (del)
• src/jalview/ws/jws2: AWS2Thread.java (new 16), JWs2Job.java (new 126), Jws2Client.java (new 54), Jws2Discoverer.java (new 192), MsaWSClient.java (new 205), MsaWSThread.java (new 765)

jprocter 2010-05-14 18:04 #11

standard function for bootstrapping discovery threads

9 lines of code changed in:

• src/jalview/bin: Jalview.java (+2 -2)
• src/jalview/gui: Desktop.java (+7 -1)

jprocter 2010-05-14 18:03 #10

allow initLogger to be called multiple times

5 lines of code changed in:

• src/jalview/bin: Cache.java (+5 -1)

jprocter 2010-05-14 15:37 #9

partial patch for * JAL-466
allows finder to be instantiated for an explicit alignment panel and viewport.

27 lines of code changed in:

• src/jalview/gui: Finder.java (+27 -2)

jprocter 2010-05-14 12:46 #8

fix for JAL-533

3 lines of code changed in:

• src/jalview/schemes: ClustalxColourScheme.java (+3 -2)

jprocter 2010-05-12 10:37 #7

debug comment

2 lines of code changed in:

• src/jalview/gui: AlignmentPanel.java (+2 -1)

jprocter 2010-05-12 10:37 #6

patch for JAL-528

2 lines of code changed in:

• src/jalview/gui: SeqPanel.java (+2 -1)

jprocter 2010-05-12 09:38 #5

fix for JAL-527

16 lines of code changed in:

• src/jalview/analysis: AlignSeq.java (+16 -5)

jprocter 2010-05-01 18:31 #4

jalview 2.5 documentation (still)

26 lines of code changed in:

• help: help.jhm (+1), helpTOC.xml (+4 -2)
• help/html: jalviewjnlp.html (+2 -2)
• help/html/features: annotation.html (+1 -1), featuresFormat.html (+1 -1)
• help/html/menus: popupMenu.html (+3 -2)
• help/html/webServices: index.html (+14 -9)

jprocter 2010-05-01 16:50 #3

branched 2.5 version

0 lines of code changed in:

• RELEASE (changed)

jprocter 2010-05-01 16:40 #2

relocatable reference to build file and dropped groovy library from classpath

5 lines of code changed in:

• .classpath (-1)
• .externalToolBuilders: Jalview Release indices [Builder].launch (+5 -5)

jprocter 2010-05-01 16:25 #1

href for version

1 lines of code changed in:

• help/html: releases.html (+1 -1)

April 2010 »