jalview.git
11 years agokeep tilde annotation
cmzmasek [Sun, 20 Jan 2013 06:33:18 +0000 (06:33 +0000)]
keep tilde annotation

11 years agokeep tilde annotation
cmzmasek [Sun, 20 Jan 2013 05:24:13 +0000 (05:24 +0000)]
keep tilde annotation

11 years agoinprogress
cmzmasek@gmail.com [Sat, 19 Jan 2013 02:31:30 +0000 (02:31 +0000)]
inprogress

11 years agoinprogress
cmzmasek@gmail.com [Fri, 18 Jan 2013 23:29:13 +0000 (23:29 +0000)]
inprogress

11 years agoinprogress
cmzmasek@gmail.com [Fri, 18 Jan 2013 23:27:45 +0000 (23:27 +0000)]
inprogress

11 years agoinprogress
cmzmasek@gmail.com [Fri, 18 Jan 2013 23:20:59 +0000 (23:20 +0000)]
inprogress

11 years agoinprogress
cmzmasek@gmail.com [Fri, 18 Jan 2013 22:48:33 +0000 (22:48 +0000)]
inprogress

11 years agocommented out unneed output
cmzmasek@gmail.com [Thu, 17 Jan 2013 22:53:08 +0000 (22:53 +0000)]
commented out unneed output

11 years agocommented out unneed output
cmzmasek@gmail.com [Thu, 17 Jan 2013 22:25:00 +0000 (22:25 +0000)]
commented out unneed output

11 years agoin progress
cmzmasek [Thu, 17 Jan 2013 19:35:33 +0000 (19:35 +0000)]
in progress

11 years agoinprogress
cmzmasek@gmail.com [Thu, 17 Jan 2013 02:33:15 +0000 (02:33 +0000)]
inprogress

11 years agoinprogress
cmzmasek@gmail.com [Thu, 17 Jan 2013 02:27:28 +0000 (02:27 +0000)]
inprogress

11 years agoinprogress
cmzmasek@gmail.com [Thu, 17 Jan 2013 00:28:36 +0000 (00:28 +0000)]
inprogress

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

11 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

11 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

11 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

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

11 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

11 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

11 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

11 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

11 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

11 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

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

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

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

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

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

11 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)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

11 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 ) ) ) {

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

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

11 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.

11 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.

11 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.

11 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.

11 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

11 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

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

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

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

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

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

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

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

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

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