jalview.git
12 years agoinprogress
cmzmasek@gmail.com [Thu, 17 Jan 2013 00:18:36 +0000 (00:18 +0000)]
inprogress

12 years agoinprogress
cmzmasek@gmail.com [Thu, 17 Jan 2013 00:14:48 +0000 (00:14 +0000)]
inprogress

12 years agoinprogress
cmzmasek@gmail.com [Wed, 16 Jan 2013 23:30:15 +0000 (23:30 +0000)]
inprogress

12 years agoinprogress
cmzmasek@gmail.com [Wed, 16 Jan 2013 22:55:12 +0000 (22:55 +0000)]
inprogress

12 years agoinprogress
cmzmasek@gmail.com [Wed, 16 Jan 2013 22:40:12 +0000 (22:40 +0000)]
inprogress

12 years agoinprogress
cmzmasek@gmail.com [Wed, 16 Jan 2013 22:37:28 +0000 (22:37 +0000)]
inprogress

12 years agoinprogress
cmzmasek@gmail.com [Wed, 16 Jan 2013 22:28:32 +0000 (22:28 +0000)]
inprogress

12 years agoinprogress
cmzmasek@gmail.com [Wed, 16 Jan 2013 22:27:30 +0000 (22:27 +0000)]
inprogress

12 years agoinprogress
cmzmasek@gmail.com [Wed, 16 Jan 2013 03:12:01 +0000 (03:12 +0000)]
inprogress

12 years agoinprogress
cmzmasek@gmail.com [Wed, 16 Jan 2013 03:08:37 +0000 (03:08 +0000)]
inprogress

12 years agoinprogress
cmzmasek@gmail.com [Wed, 16 Jan 2013 02:56:03 +0000 (02:56 +0000)]
inprogress

12 years agonot needed
cmzmasek@gmail.com [Wed, 16 Jan 2013 01:06:32 +0000 (01:06 +0000)]
not needed

12 years agonot needed
cmzmasek@gmail.com [Wed, 16 Jan 2013 01:05:14 +0000 (01:05 +0000)]
not needed

12 years agoremoved clustalo
cmzmasek@gmail.com [Tue, 15 Jan 2013 18:42:36 +0000 (18:42 +0000)]
removed clustalo

12 years agoremoved clustalo
cmzmasek@gmail.com [Tue, 15 Jan 2013 18:41:59 +0000 (18:41 +0000)]
removed clustalo

12 years agoremoved clustalo
cmzmasek@gmail.com [Tue, 15 Jan 2013 18:41:46 +0000 (18:41 +0000)]
removed clustalo

12 years agoremoved clustalo
cmzmasek@gmail.com [Tue, 15 Jan 2013 18:36:58 +0000 (18:36 +0000)]
removed clustalo

12 years agofixed 2nd rio bug
cmzmasek@gmail.com [Tue, 15 Jan 2013 02:32:29 +0000 (02:32 +0000)]
fixed 2nd rio bug

12 years agofixed 2nd rio bug
cmzmasek@gmail.com [Tue, 15 Jan 2013 02:29:50 +0000 (02:29 +0000)]
fixed 2nd rio bug

12 years agoint => long for node id
cmzmasek@gmail.com [Sun, 13 Jan 2013 01:44:16 +0000 (01:44 +0000)]
int => long for node id
+ work on rio

12 years agoint => long for node id
cmzmasek@gmail.com [Sat, 12 Jan 2013 04:42:12 +0000 (04:42 +0000)]
int => long for node id
+ work on rio

12 years agomessed up at the moment
cmzmasek@gmail.com [Thu, 10 Jan 2013 22:18:39 +0000 (22:18 +0000)]
messed up at the moment

12 years agomessed up
cmzmasek [Thu, 10 Jan 2013 19:25:17 +0000 (19:25 +0000)]
messed up

12 years agomessed up at the moment
cmzmasek@gmail.com [Thu, 10 Jan 2013 18:30:08 +0000 (18:30 +0000)]
messed up at the moment

12 years agokepp only one dup min gt
cmzmasek@gmail.com [Wed, 9 Jan 2013 06:10:36 +0000 (06:10 +0000)]
kepp only one dup min gt

12 years agokepp only one dup min gt
cmzmasek@gmail.com [Wed, 9 Jan 2013 06:10:00 +0000 (06:10 +0000)]
kepp only one dup min gt

12 years agoiterating rio + cleanup
cmzmasek@gmail.com [Wed, 9 Jan 2013 05:15:59 +0000 (05:15 +0000)]
iterating rio + cleanup

12 years agoiterating rio + cleanup
cmzmasek@gmail.com [Wed, 9 Jan 2013 05:14:18 +0000 (05:14 +0000)]
iterating rio + cleanup

12 years agoiterating nexus test
cmzmasek@gmail.com [Wed, 9 Jan 2013 05:13:15 +0000 (05:13 +0000)]
iterating nexus test

12 years agoiterating nexus
cmzmasek@gmail.com [Wed, 9 Jan 2013 04:37:05 +0000 (04:37 +0000)]
iterating nexus

12 years agoiterating nexus
cmzmasek@gmail.com [Wed, 9 Jan 2013 04:06:08 +0000 (04:06 +0000)]
iterating nexus

12 years agoiterating rio + cleanup
cmzmasek@gmail.com [Tue, 8 Jan 2013 23:56:21 +0000 (23:56 +0000)]
iterating rio + cleanup

12 years agoinprogress
cmzmasek@gmail.com [Tue, 8 Jan 2013 20:34:31 +0000 (20:34 +0000)]
inprogress

12 years agoinprogress
cmzmasek@gmail.com [Tue, 8 Jan 2013 20:31:11 +0000 (20:31 +0000)]
inprogress

12 years agoinprogress
cmzmasek@gmail.com [Tue, 8 Jan 2013 20:14:47 +0000 (20:14 +0000)]
inprogress

12 years agoiterating rio + cleanup
cmzmasek@gmail.com [Tue, 8 Jan 2013 03:30:13 +0000 (03:30 +0000)]
iterating rio + cleanup

12 years agoiterating rio + cleanup
cmzmasek@gmail.com [Mon, 7 Jan 2013 22:59:41 +0000 (22:59 +0000)]
iterating rio + cleanup

12 years agoinprogress
cmzmasek@gmail.com [Mon, 7 Jan 2013 22:07:56 +0000 (22:07 +0000)]
inprogress

12 years agoin progress
cmzmasek [Mon, 7 Jan 2013 04:24:20 +0000 (04:24 +0000)]
in progress

12 years agoremoved view as NHX
cmzmasek@gmail.com [Sat, 5 Jan 2013 20:04:59 +0000 (20:04 +0000)]
removed view as NHX

12 years agoremoved view as NHX
cmzmasek@gmail.com [Sat, 5 Jan 2013 20:03:51 +0000 (20:03 +0000)]
removed view as NHX

12 years agofurther reduction of NHX fields
cmzmasek@gmail.com [Sat, 5 Jan 2013 05:14:27 +0000 (05:14 +0000)]
further reduction of NHX fields
iterating NHX parser
clean up

12 years agofurther reduction of NHX fields
cmzmasek@gmail.com [Sat, 5 Jan 2013 05:05:26 +0000 (05:05 +0000)]
further reduction of NHX fields
iterating NHX parser
clean up

12 years agofurther reduction of NHX fields
cmzmasek@gmail.com [Sat, 5 Jan 2013 05:00:34 +0000 (05:00 +0000)]
further reduction of NHX fields
iterating NHX parser
clean up

12 years agoiterating nh parser
cmzmasek@gmail.com [Sat, 5 Jan 2013 04:03:13 +0000 (04:03 +0000)]
iterating nh parser

12 years agoiterating nh parser
cmzmasek@gmail.com [Sat, 5 Jan 2013 04:02:53 +0000 (04:02 +0000)]
iterating nh parser

12 years agoremoved save as NHX
cmzmasek@gmail.com [Sat, 5 Jan 2013 03:23:47 +0000 (03:23 +0000)]
removed save as NHX

12 years agoremoved save as NHX
cmzmasek@gmail.com [Sat, 5 Jan 2013 03:20:46 +0000 (03:20 +0000)]
removed save as NHX

12 years agoremoved view as NHX
cmzmasek@gmail.com [Sat, 5 Jan 2013 02:37:37 +0000 (02:37 +0000)]
removed view as NHX

12 years agofixed hmmscan summary (inprot things are disables for now)
cmzmasek@gmail.com [Sat, 5 Jan 2013 00:58:24 +0000 (00:58 +0000)]
fixed hmmscan summary (inprot things are disables for now)

12 years agoinprogress
cmzmasek@gmail.com [Sat, 5 Jan 2013 00:56:20 +0000 (00:56 +0000)]
inprogress

12 years agoinprogress
cmzmasek@gmail.com [Sat, 5 Jan 2013 00:43:44 +0000 (00:43 +0000)]
inprogress

12 years agoinprogress
cmzmasek@gmail.com [Sat, 5 Jan 2013 00:42:04 +0000 (00:42 +0000)]
inprogress

12 years agoinprogress
cmzmasek@gmail.com [Sat, 5 Jan 2013 00:10:30 +0000 (00:10 +0000)]
inprogress

12 years agoinprogress
cmzmasek@gmail.com [Sat, 5 Jan 2013 00:03:18 +0000 (00:03 +0000)]
inprogress

12 years agoinprogress
cmzmasek@gmail.com [Sat, 5 Jan 2013 00:01:10 +0000 (00:01 +0000)]
inprogress

12 years agoinprogress
cmzmasek@gmail.com [Fri, 4 Jan 2013 23:59:19 +0000 (23:59 +0000)]
inprogress

12 years agoinprogress
cmzmasek@gmail.com [Fri, 4 Jan 2013 23:49:29 +0000 (23:49 +0000)]
inprogress

12 years agoinprogress
cmzmasek@gmail.com [Fri, 4 Jan 2013 22:00:42 +0000 (22:00 +0000)]
inprogress

12 years agoinprogress
cmzmasek@gmail.com [Fri, 4 Jan 2013 21:54:26 +0000 (21:54 +0000)]
inprogress

12 years agoinprogress
cmzmasek@gmail.com [Fri, 4 Jan 2013 21:36:13 +0000 (21:36 +0000)]
inprogress

12 years agoinprogress
cmzmasek@gmail.com [Fri, 4 Jan 2013 21:34:02 +0000 (21:34 +0000)]
inprogress

12 years agoinprogress
cmzmasek@gmail.com [Fri, 4 Jan 2013 21:13:45 +0000 (21:13 +0000)]
inprogress

12 years agoinprogress
cmzmasek@gmail.com [Fri, 4 Jan 2013 21:11:27 +0000 (21:11 +0000)]
inprogress

12 years agoinprogress
cmzmasek@gmail.com [Fri, 4 Jan 2013 21:10:42 +0000 (21:10 +0000)]
inprogress

12 years agoinprogress
cmzmasek@gmail.com [Fri, 4 Jan 2013 02:28:05 +0000 (02:28 +0000)]
inprogress

12 years agoinprogress
cmzmasek@gmail.com [Thu, 3 Jan 2013 23:07:19 +0000 (23:07 +0000)]
inprogress

12 years agoinprogress
cmzmasek@gmail.com [Thu, 3 Jan 2013 22:55:18 +0000 (22:55 +0000)]
inprogress

12 years agoiterating nh parser
cmzmasek@gmail.com [Thu, 3 Jan 2013 22:54:57 +0000 (22:54 +0000)]
iterating nh parser

12 years agoif ( !lineage.get( i ).equalsIgnoreCase( up_taxonomy.getLineage().get( i ) ) ) {
cmzmasek [Sun, 30 Dec 2012 05:27:19 +0000 (05:27 +0000)]
if ( !lineage.get( i ).equalsIgnoreCase( up_taxonomy.getLineage().get( i ) ) ) {

becomes:

if ( i == up_taxonomy.getLineage().size() || !lineage.get( i ).equalsIgnoreCase( up_taxonomy.getLineage().get( i ) ) ) {

12 years agoin progress
cmzmasek [Sun, 30 Dec 2012 02:31:08 +0000 (02:31 +0000)]
in progress

12 years agoin progress
cmzmasek [Sun, 30 Dec 2012 02:05:30 +0000 (02:05 +0000)]
in progress

12 years agoCan now set the initial window size via configuration file for application and ArchA...
cmzmasek [Sun, 30 Dec 2012 01:28:39 +0000 (01:28 +0000)]
Can now set the initial window size via configuration file for application and ArchA applet.

12 years agoCan now set the initial window size via configuration file for application and ArchA...
cmzmasek [Sun, 30 Dec 2012 01:28:24 +0000 (01:28 +0000)]
Can now set the initial window size via configuration file for application and ArchA applet.

12 years agoCan now set the initial window size via configuration file for application and ArchA...
cmzmasek [Sun, 30 Dec 2012 00:31:49 +0000 (00:31 +0000)]
Can now set the initial window size via configuration file for application and ArchA applet.

12 years agoCan now set the initial window size via configuration file for application and ArchA...
cmzmasek [Sun, 30 Dec 2012 00:31:31 +0000 (00:31 +0000)]
Can now set the initial window size via configuration file for application and ArchA applet.

12 years agomoved to: https://sites.google.com/site/cmzmasek/home/software/forester
cmzmasek@gmail.com [Sat, 29 Dec 2012 20:32:33 +0000 (20:32 +0000)]
moved to: https://sites.google.com/site/cmzmasek/home/software/forester

12 years agoancestor analysis fails on this
cmzmasek@gmail.com [Sat, 29 Dec 2012 01:24:21 +0000 (01:24 +0000)]
ancestor analysis fails on this

12 years ago"rio" work
cmzmasek@gmail.com [Thu, 27 Dec 2012 03:29:57 +0000 (03:29 +0000)]
"rio" work

12 years ago"rio" work
cmzmasek@gmail.com [Thu, 27 Dec 2012 03:29:34 +0000 (03:29 +0000)]
"rio" work

12 years agoinprogress
cmzmasek@gmail.com [Thu, 27 Dec 2012 00:07:27 +0000 (00:07 +0000)]
inprogress

12 years agorio - gsdir work...
cmzmasek [Wed, 26 Dec 2012 06:15:37 +0000 (06:15 +0000)]
rio - gsdir work...

12 years agorio - gsdir work...
cmzmasek [Wed, 26 Dec 2012 06:14:32 +0000 (06:14 +0000)]
rio - gsdir work...

12 years agorio - gsdir work...
cmzmasek [Wed, 26 Dec 2012 06:09:43 +0000 (06:09 +0000)]
rio - gsdir work...

12 years agoin progress
cmzmasek [Wed, 26 Dec 2012 02:41:00 +0000 (02:41 +0000)]
in progress

12 years agoin progress
cmzmasek [Tue, 25 Dec 2012 06:20:08 +0000 (06:20 +0000)]
in progress

12 years agoremove single node root
cmzmasek [Mon, 24 Dec 2012 20:44:46 +0000 (20:44 +0000)]
remove single node root

12 years agoremove single node root
cmzmasek [Mon, 24 Dec 2012 19:53:37 +0000 (19:53 +0000)]
remove single node root

12 years agoinprogress
cmzmasek@gmail.com [Sat, 22 Dec 2012 05:34:03 +0000 (05:34 +0000)]
inprogress

12 years agoinprogress
cmzmasek@gmail.com [Sat, 22 Dec 2012 05:33:40 +0000 (05:33 +0000)]
inprogress

12 years agonot needed anymore
cmzmasek@gmail.com [Sat, 22 Dec 2012 05:00:49 +0000 (05:00 +0000)]
not needed anymore

12 years agonot needed anymore
cmzmasek@gmail.com [Sat, 22 Dec 2012 04:57:06 +0000 (04:57 +0000)]
not needed anymore

12 years agodecorator fixed
cmzmasek@gmail.com [Fri, 21 Dec 2012 20:57:49 +0000 (20:57 +0000)]
decorator fixed

12 years agodecorator fixed
cmzmasek@gmail.com [Fri, 21 Dec 2012 20:57:20 +0000 (20:57 +0000)]
decorator fixed

12 years agomidpoint rooting is faster
cmzmasek@gmail.com [Fri, 21 Dec 2012 02:07:49 +0000 (02:07 +0000)]
midpoint rooting is faster

12 years agoerror things
cmzmasek@gmail.com [Thu, 20 Dec 2012 20:51:31 +0000 (20:51 +0000)]
error things

12 years agoEdited wiki page RIO through web user interface.
cmzmasek@gmail.com [Thu, 20 Dec 2012 18:46:18 +0000 (18:46 +0000)]
Edited wiki page RIO through web user interface.

12 years agoEdited wiki page RIO through web user interface.
cmzmasek@gmail.com [Thu, 20 Dec 2012 18:24:30 +0000 (18:24 +0000)]
Edited wiki page RIO through web user interface.

12 years agoEdited wiki page RIO through web user interface.
cmzmasek@gmail.com [Thu, 20 Dec 2012 18:22:13 +0000 (18:22 +0000)]
Edited wiki page RIO through web user interface.

12 years agoEdited wiki page RIO through web user interface.
cmzmasek@gmail.com [Thu, 20 Dec 2012 18:21:29 +0000 (18:21 +0000)]
Edited wiki page RIO through web user interface.