jalview.git
19 years agoJpred to JNet
jprocter [Thu, 18 Aug 2005 10:41:04 +0000 (10:41 +0000)]
Jpred to JNet

19 years ago2_03 build project
amwaterhouse [Thu, 18 Aug 2005 10:38:13 +0000 (10:38 +0000)]
2_03 build project

19 years agoProceed with upperCase residue Release_2_03
amwaterhouse [Thu, 18 Aug 2005 09:47:32 +0000 (09:47 +0000)]
Proceed with upperCase residue

19 years agovarious case sensitivity bugs fixed in residue comparison functions.
jprocter [Thu, 18 Aug 2005 09:33:29 +0000 (09:33 +0000)]
various case sensitivity bugs fixed in residue comparison functions.

19 years agoUse aa index for aboveThreshold as well as colour index
amwaterhouse [Thu, 18 Aug 2005 09:20:07 +0000 (09:20 +0000)]
Use aa index for aboveThreshold as well as colour index

19 years agoClient threads for discovered web services.
jprocter [Wed, 17 Aug 2005 16:31:27 +0000 (16:31 +0000)]
Client threads for discovered web services.

19 years agoGUI modifications for service discovery.
jprocter [Wed, 17 Aug 2005 16:30:35 +0000 (16:30 +0000)]
GUI modifications for service discovery.

19 years agoGui Modifications for Service Discovery.
jprocter [Wed, 17 Aug 2005 16:30:02 +0000 (16:30 +0000)]
Gui Modifications for Service Discovery.

19 years ago<No Comment Entered>
jprocter [Wed, 17 Aug 2005 16:24:08 +0000 (16:24 +0000)]
<No Comment Entered>

19 years agoHas version, Groups are optional, trees added to schema
amwaterhouse [Wed, 17 Aug 2005 16:09:37 +0000 (16:09 +0000)]
Has version, Groups are optional, trees added to schema

19 years agoAdd attribute schemeName
amwaterhouse [Wed, 17 Aug 2005 16:08:47 +0000 (16:08 +0000)]
Add attribute schemeName

19 years agoAdd buildPropertiesFile to applet jar
amwaterhouse [Wed, 17 Aug 2005 16:08:12 +0000 (16:08 +0000)]
Add buildPropertiesFile to applet jar

19 years agoRead in version from build details file in applet jar
amwaterhouse [Wed, 17 Aug 2005 16:07:29 +0000 (16:07 +0000)]
Read in version from build details file in applet jar

19 years agoWeb Services moved from Calculate
amwaterhouse [Wed, 17 Aug 2005 15:40:56 +0000 (15:40 +0000)]
Web Services moved from Calculate

19 years agoCapitalise menus
amwaterhouse [Wed, 17 Aug 2005 15:36:11 +0000 (15:36 +0000)]
Capitalise menus

19 years agoMaintain list of webservices and query any Service Discovery services.
jprocter [Wed, 17 Aug 2005 15:31:32 +0000 (15:31 +0000)]
Maintain list of webservices and query any Service Discovery services.

19 years agoSimple Registry Service stubs
jprocter [Wed, 17 Aug 2005 15:23:34 +0000 (15:23 +0000)]
Simple Registry Service stubs

19 years agoFixed basic name to sequence ID matching (bug http://dragonfly.compbio.dundee.ac...
jprocter [Wed, 17 Aug 2005 15:20:10 +0000 (15:20 +0000)]
Fixed basic name to sequence ID matching (bug dragonfly.compbio.dundee.ac.uk/mantis/view.php?id=9227)
and improved code robustness when dealing with badly formed IDs (null strings).

19 years agoNo basicDirectoryModel on the Mac
amwaterhouse [Wed, 17 Aug 2005 14:11:58 +0000 (14:11 +0000)]
No basicDirectoryModel on the Mac

19 years agoSet size for mac users
amwaterhouse [Wed, 17 Aug 2005 14:11:34 +0000 (14:11 +0000)]
Set size for mac users

19 years agoError reply is kept separate from file type
amwaterhouse [Wed, 17 Aug 2005 13:43:42 +0000 (13:43 +0000)]
Error reply is kept separate from file type

19 years agoAdd names to schemes
amwaterhouse [Wed, 17 Aug 2005 13:05:00 +0000 (13:05 +0000)]
Add names to schemes

19 years agoNew image
amwaterhouse [Wed, 17 Aug 2005 13:04:37 +0000 (13:04 +0000)]
New image

19 years agoCheck default colour is not null
amwaterhouse [Wed, 17 Aug 2005 13:03:41 +0000 (13:03 +0000)]
Check default colour is not null

19 years agoRemove user colour menu item
amwaterhouse [Wed, 17 Aug 2005 13:02:32 +0000 (13:02 +0000)]
Remove user colour menu item

19 years agoCheck default >0, not <1
amwaterhouse [Wed, 17 Aug 2005 11:01:55 +0000 (11:01 +0000)]
Check default >0, not <1

19 years agoConservation group colour saved
amwaterhouse [Wed, 17 Aug 2005 10:27:18 +0000 (10:27 +0000)]
Conservation group colour saved

19 years agoAdd SRS as default
amwaterhouse [Wed, 17 Aug 2005 09:59:00 +0000 (09:59 +0000)]
Add SRS as default

19 years agoReturn white userColourScheme, not null colourscheme
amwaterhouse [Wed, 17 Aug 2005 09:31:34 +0000 (09:31 +0000)]
Return white userColourScheme, not null colourscheme

19 years agoUse getDefault for exampleFile
amwaterhouse [Wed, 17 Aug 2005 09:30:56 +0000 (09:30 +0000)]
Use getDefault for exampleFile

19 years agoAdvice on proxy servers
amwaterhouse [Wed, 17 Aug 2005 09:13:22 +0000 (09:13 +0000)]
Advice on proxy servers

19 years agoRebuilt with new schema
amwaterhouse [Wed, 17 Aug 2005 09:12:03 +0000 (09:12 +0000)]
Rebuilt with new schema

19 years agoPut basic file chooser test in try catch loop
amwaterhouse [Wed, 17 Aug 2005 09:11:05 +0000 (09:11 +0000)]
Put basic file chooser test in try catch loop

19 years agoScheme name added
amwaterhouse [Wed, 17 Aug 2005 09:10:30 +0000 (09:10 +0000)]
Scheme name added

19 years agoUser colours have scheme name
amwaterhouse [Wed, 17 Aug 2005 09:10:06 +0000 (09:10 +0000)]
User colours have scheme name

19 years agoUser colours
amwaterhouse [Wed, 17 Aug 2005 09:09:18 +0000 (09:09 +0000)]
User colours

19 years agoNo score colour scheme, group colours saved if conservation applied
amwaterhouse [Wed, 17 Aug 2005 09:08:50 +0000 (09:08 +0000)]
No score colour scheme, group colours saved if conservation applied

19 years agoCalculation - consensus
amwaterhouse [Wed, 17 Aug 2005 09:08:20 +0000 (09:08 +0000)]
Calculation - consensus

19 years agoupdateUserColourMenu
amwaterhouse [Wed, 17 Aug 2005 09:06:39 +0000 (09:06 +0000)]
updateUserColourMenu

19 years agoDiscover user colours
amwaterhouse [Wed, 17 Aug 2005 09:06:10 +0000 (09:06 +0000)]
Discover user colours

19 years agoRemove redundant imports
amwaterhouse [Tue, 16 Aug 2005 08:51:32 +0000 (08:51 +0000)]
Remove redundant imports

19 years agoJalview Version:
amwaterhouse [Mon, 15 Aug 2005 14:08:45 +0000 (14:08 +0000)]
Jalview Version:

19 years agoOutput java version, os version on startup
amwaterhouse [Mon, 15 Aug 2005 14:08:13 +0000 (14:08 +0000)]
Output java version, os version on startup

19 years agoRemove null check
amwaterhouse [Mon, 15 Aug 2005 14:07:55 +0000 (14:07 +0000)]
Remove null check

19 years agoSparc for Solaris
amwaterhouse [Mon, 15 Aug 2005 13:58:34 +0000 (13:58 +0000)]
Sparc for Solaris

19 years agoUse default fileChooser for now
amwaterhouse [Mon, 15 Aug 2005 12:14:12 +0000 (12:14 +0000)]
Use default fileChooser for now

19 years agosuper.setconsensus
amwaterhouse [Mon, 15 Aug 2005 12:13:50 +0000 (12:13 +0000)]
super.setconsensus

19 years agoPercentage precalculated in aafrequency
amwaterhouse [Mon, 15 Aug 2005 12:13:33 +0000 (12:13 +0000)]
Percentage precalculated in aafrequency

19 years agoisGap slightly more efficient
amwaterhouse [Mon, 15 Aug 2005 12:13:00 +0000 (12:13 +0000)]
isGap slightly more efficient

19 years agoAdd taylor to default colour check
amwaterhouse [Mon, 15 Aug 2005 12:11:07 +0000 (12:11 +0000)]
Add taylor to default colour check

19 years agoHashtable now in array, not vector
amwaterhouse [Mon, 15 Aug 2005 12:09:17 +0000 (12:09 +0000)]
Hashtable now in array, not vector

19 years agoIgnoreGapsConsensus
amwaterhouse [Mon, 15 Aug 2005 12:08:41 +0000 (12:08 +0000)]
IgnoreGapsConsensus

19 years agoDont color Checking... red
amwaterhouse [Mon, 15 Aug 2005 12:08:25 +0000 (12:08 +0000)]
Dont color Checking... red

19 years agoDeclare variables outside loops
amwaterhouse [Mon, 15 Aug 2005 12:04:32 +0000 (12:04 +0000)]
Declare variables outside loops

19 years agoCalculate gap and nogap ratio here
amwaterhouse [Mon, 15 Aug 2005 12:02:10 +0000 (12:02 +0000)]
Calculate gap and nogap ratio here

19 years agofixed leafMapping bug for Id's like SequenceX (where X=14 matches all X=1,10,11,12...
jprocter [Fri, 12 Aug 2005 14:26:15 +0000 (14:26 +0000)]
fixed leafMapping bug for Id's like SequenceX (where X=14 matches all X=1,10,11,12,13).
Fixes Mantis 0009227

19 years agoAdd notes on proxy settings
amwaterhouse [Tue, 9 Aug 2005 17:07:14 +0000 (17:07 +0000)]
Add notes on proxy settings

19 years agoInstallAnywhere readme
amwaterhouse [Tue, 9 Aug 2005 17:06:44 +0000 (17:06 +0000)]
InstallAnywhere readme

19 years agoNew classes
amwaterhouse [Tue, 9 Aug 2005 16:55:20 +0000 (16:55 +0000)]
New classes

19 years agoCache.getDefault
amwaterhouse [Tue, 9 Aug 2005 16:53:42 +0000 (16:53 +0000)]
Cache.getDefault

19 years agoProxy server, default browser, multiple links added
amwaterhouse [Tue, 9 Aug 2005 16:53:16 +0000 (16:53 +0000)]
Proxy server, default browser, multiple links added

19 years agocache.getDefault
amwaterhouse [Tue, 9 Aug 2005 16:53:05 +0000 (16:53 +0000)]
cache.getDefault

19 years agoTry/catch loading default icons
amwaterhouse [Tue, 9 Aug 2005 16:52:39 +0000 (16:52 +0000)]
Try/catch loading default icons

19 years agoSplash screen is repainted when checking latest version
amwaterhouse [Tue, 9 Aug 2005 16:52:09 +0000 (16:52 +0000)]
Splash screen is repainted when checking latest version

19 years agoHandle multiple url links
amwaterhouse [Tue, 9 Aug 2005 16:51:02 +0000 (16:51 +0000)]
Handle multiple url links

19 years agoCan give a name to new browser window
amwaterhouse [Tue, 9 Aug 2005 16:47:58 +0000 (16:47 +0000)]
Can give a name to new browser window

19 years agoProperties file is used in preference to viewport/cache/preferences replicating defaults
amwaterhouse [Tue, 9 Aug 2005 16:47:21 +0000 (16:47 +0000)]
Properties file is used in preference to viewport/cache/preferences replicating defaults

19 years agoEdit/add/delete a sequence link
amwaterhouse [Tue, 9 Aug 2005 16:46:08 +0000 (16:46 +0000)]
Edit/add/delete a sequence link

19 years agoApplet handles multiple sequence links
amwaterhouse [Tue, 9 Aug 2005 16:45:05 +0000 (16:45 +0000)]
Applet handles multiple sequence links

19 years agoAdd docs in build
amwaterhouse [Thu, 4 Aug 2005 08:16:31 +0000 (08:16 +0000)]
Add docs in build

19 years agoFix for user entering number in search window
amwaterhouse [Wed, 3 Aug 2005 15:07:41 +0000 (15:07 +0000)]
Fix for user entering number in search window

19 years agoVersion 2.02
amwaterhouse [Wed, 3 Aug 2005 13:13:25 +0000 (13:13 +0000)]
Version 2.02

19 years ago1 & -1
amwaterhouse [Wed, 3 Aug 2005 13:10:15 +0000 (13:10 +0000)]
1 & -1

19 years agoTrees aren't save in headless state in this version
amwaterhouse [Wed, 3 Aug 2005 13:09:36 +0000 (13:09 +0000)]
Trees aren't save in headless state in this version

19 years agoLoading thread moved to io.FileLoader
amwaterhouse [Wed, 3 Aug 2005 13:08:43 +0000 (13:08 +0000)]
Loading thread moved to io.FileLoader

19 years agoUse Container to get fontMetrics
amwaterhouse [Wed, 3 Aug 2005 13:08:14 +0000 (13:08 +0000)]
Use Container to get fontMetrics

19 years agoFileLoading removed from desktop
amwaterhouse [Wed, 3 Aug 2005 13:07:39 +0000 (13:07 +0000)]
FileLoading removed from desktop

19 years agoCan run headless=true
amwaterhouse [Wed, 3 Aug 2005 13:07:11 +0000 (13:07 +0000)]
Can run headless=true

19 years agoUse font.getName, not font.getFontName
amwaterhouse [Tue, 2 Aug 2005 09:23:10 +0000 (09:23 +0000)]
Use font.getName, not font.getFontName

19 years agoRemove ref to ServletGUI
amwaterhouse [Fri, 29 Jul 2005 09:55:45 +0000 (09:55 +0000)]
Remove ref to ServletGUI

19 years agouse 1 & -1 if start/end not specified
amwaterhouse [Fri, 29 Jul 2005 09:53:09 +0000 (09:53 +0000)]
use 1 & -1 if start/end not specified

19 years agoif endRes <1, calc the endRes
amwaterhouse [Fri, 29 Jul 2005 09:48:19 +0000 (09:48 +0000)]
if endRes <1, calc the endRes

19 years agoCorrect label for end res in copy
amwaterhouse [Fri, 29 Jul 2005 09:39:20 +0000 (09:39 +0000)]
Correct label for end res in copy

19 years agov2.02 Release_2_02
amwaterhouse [Tue, 19 Jul 2005 09:37:53 +0000 (09:37 +0000)]
v2.02

19 years agobackslash irrelevant in java
amwaterhouse [Mon, 18 Jul 2005 16:15:23 +0000 (16:15 +0000)]
backslash irrelevant in java

19 years agoCopy seq ordering bug fixed
amwaterhouse [Mon, 18 Jul 2005 13:47:32 +0000 (13:47 +0000)]
Copy seq ordering bug fixed

19 years agoOutput redirected to output.txt
amwaterhouse [Mon, 18 Jul 2005 11:18:55 +0000 (11:18 +0000)]
Output redirected to output.txt

19 years agoRemove .txt, add command line instruction
amwaterhouse [Mon, 18 Jul 2005 11:18:11 +0000 (11:18 +0000)]
Remove .txt, add command line instruction

19 years agohomepage must have http:// at beginning
amwaterhouse [Tue, 12 Jul 2005 08:46:10 +0000 (08:46 +0000)]
homepage must have http:// at beginning

19 years agoput jalview.jar first in jnlp Release_2_01
amwaterhouse [Mon, 11 Jul 2005 16:05:15 +0000 (16:05 +0000)]
put jalview.jar first in jnlp

19 years agoVersion changes
amwaterhouse [Mon, 11 Jul 2005 15:56:39 +0000 (15:56 +0000)]
Version changes

19 years agoJnlp info updated
amwaterhouse [Mon, 11 Jul 2005 15:11:50 +0000 (15:11 +0000)]
Jnlp info updated

19 years agoMust check if group.sequences are null in remove gaps
amwaterhouse [Mon, 11 Jul 2005 14:46:23 +0000 (14:46 +0000)]
Must check if group.sequences are null in remove gaps

19 years agoConsume if enter pressed
amwaterhouse [Mon, 11 Jul 2005 14:38:35 +0000 (14:38 +0000)]
Consume if enter pressed

19 years agoListen for return key
amwaterhouse [Mon, 11 Jul 2005 14:32:47 +0000 (14:32 +0000)]
Listen for return key

19 years agocheck groupsize is non zero
amwaterhouse [Mon, 11 Jul 2005 14:05:44 +0000 (14:05 +0000)]
check groupsize is non zero

19 years agosetIconImage
amwaterhouse [Mon, 11 Jul 2005 13:58:31 +0000 (13:58 +0000)]
setIconImage

19 years agotypo
amwaterhouse [Mon, 11 Jul 2005 13:57:41 +0000 (13:57 +0000)]
typo

19 years agoimage changed
amwaterhouse [Mon, 11 Jul 2005 13:54:06 +0000 (13:54 +0000)]
image changed

19 years agoadded help and documentation for annotation editing.
jprocter [Mon, 11 Jul 2005 13:49:21 +0000 (13:49 +0000)]
added help and documentation for annotation editing.