jalview.git
18 years agoAllow for non graph annotations in combobox
amwaterhouse [Fri, 3 Feb 2006 17:42:19 +0000 (17:42 +0000)]
Allow for non graph annotations in combobox

18 years agoReading features files readded as ref to FeatureRenderer is required
amwaterhouse [Fri, 3 Feb 2006 17:41:43 +0000 (17:41 +0000)]
Reading features files readded as ref to FeatureRenderer is required

18 years agohas ref to annotation
amwaterhouse [Fri, 3 Feb 2006 17:40:49 +0000 (17:40 +0000)]
has ref to annotation

18 years agoAdd annotation with sequence ref updated
amwaterhouse [Fri, 3 Feb 2006 17:40:26 +0000 (17:40 +0000)]
Add annotation with sequence ref updated

18 years agoReads annotation files
amwaterhouse [Fri, 3 Feb 2006 17:39:41 +0000 (17:39 +0000)]
Reads annotation files

18 years agoApplet draws line graphs
amwaterhouse [Fri, 3 Feb 2006 17:39:03 +0000 (17:39 +0000)]
Applet draws line graphs

18 years agoApplet reads in annotation files
amwaterhouse [Fri, 3 Feb 2006 17:38:42 +0000 (17:38 +0000)]
Applet reads in annotation files

18 years agoAA properties added
amwaterhouse [Fri, 3 Feb 2006 17:37:32 +0000 (17:37 +0000)]
AA properties added

18 years agoAA Properties
amwaterhouse [Fri, 3 Feb 2006 17:36:59 +0000 (17:36 +0000)]
AA Properties

18 years agoNew images
amwaterhouse [Fri, 3 Feb 2006 17:36:35 +0000 (17:36 +0000)]
New images

18 years agoUpdated images
amwaterhouse [Fri, 3 Feb 2006 17:36:22 +0000 (17:36 +0000)]
Updated images

18 years agoremoved
amwaterhouse [Fri, 3 Feb 2006 17:36:09 +0000 (17:36 +0000)]
removed

18 years agoRemoved
amwaterhouse [Fri, 3 Feb 2006 17:35:14 +0000 (17:35 +0000)]
Removed

18 years agoCancel button is now close button
amwaterhouse [Mon, 30 Jan 2006 17:14:47 +0000 (17:14 +0000)]
Cancel button is now close button

18 years agoDont draw origin beyond end of alignment
amwaterhouse [Mon, 30 Jan 2006 17:14:22 +0000 (17:14 +0000)]
Dont draw origin beyond end of alignment

18 years agoNo need for apply button, just update colours when events occur
amwaterhouse [Mon, 30 Jan 2006 15:33:08 +0000 (15:33 +0000)]
No need for apply button, just update colours when events occur

18 years agoGet min and max colour added
amwaterhouse [Mon, 30 Jan 2006 15:32:37 +0000 (15:32 +0000)]
Get min and max colour added

18 years agoCan be used for annotation colouring
amwaterhouse [Mon, 30 Jan 2006 14:58:09 +0000 (14:58 +0000)]
Can be used for annotation colouring

18 years agoFaster paint
amwaterhouse [Mon, 30 Jan 2006 14:57:43 +0000 (14:57 +0000)]
Faster paint

18 years agoUse Antialias flag
amwaterhouse [Mon, 30 Jan 2006 14:57:20 +0000 (14:57 +0000)]
Use Antialias flag

18 years agoSmooth fonts added
amwaterhouse [Mon, 30 Jan 2006 14:57:06 +0000 (14:57 +0000)]
Smooth fonts added

18 years agoNull sequence check
amwaterhouse [Mon, 30 Jan 2006 14:56:51 +0000 (14:56 +0000)]
Null sequence check

18 years agoMonospaced indicator
amwaterhouse [Mon, 30 Jan 2006 14:55:58 +0000 (14:55 +0000)]
Monospaced indicator

18 years agoUnix drag and drop implemented
amwaterhouse [Mon, 30 Jan 2006 14:55:40 +0000 (14:55 +0000)]
Unix drag and drop implemented

18 years agoGraphGroups added
amwaterhouse [Mon, 30 Jan 2006 14:55:17 +0000 (14:55 +0000)]
GraphGroups added

18 years agoFast paint update
amwaterhouse [Mon, 30 Jan 2006 14:54:54 +0000 (14:54 +0000)]
Fast paint update

18 years agoAnti alias flag
amwaterhouse [Mon, 30 Jan 2006 14:54:27 +0000 (14:54 +0000)]
Anti alias flag

18 years agoDrop annotations onto alignment
amwaterhouse [Mon, 30 Jan 2006 14:54:07 +0000 (14:54 +0000)]
Drop annotations onto alignment

18 years agoSmooth fonts, annotation Colour
amwaterhouse [Mon, 30 Jan 2006 14:53:37 +0000 (14:53 +0000)]
Smooth fonts, annotation Colour

18 years agoSmooth font option
amwaterhouse [Mon, 30 Jan 2006 14:53:04 +0000 (14:53 +0000)]
Smooth font option

18 years agoAddAnnotation with start index
amwaterhouse [Mon, 30 Jan 2006 14:48:47 +0000 (14:48 +0000)]
AddAnnotation with start index

18 years agoNew Class
amwaterhouse [Mon, 30 Jan 2006 14:46:40 +0000 (14:46 +0000)]
New Class

18 years agoNew files
amwaterhouse [Mon, 30 Jan 2006 14:46:15 +0000 (14:46 +0000)]
New files

18 years agoFaster painting
amwaterhouse [Mon, 30 Jan 2006 14:45:37 +0000 (14:45 +0000)]
Faster painting

18 years agoAllow features in overview window
amwaterhouse [Mon, 30 Jan 2006 14:45:10 +0000 (14:45 +0000)]
Allow features in overview window

18 years agoAllow embedded applet
amwaterhouse [Mon, 30 Jan 2006 14:43:58 +0000 (14:43 +0000)]
Allow embedded applet

18 years agoPIR file IO now preserves and parses Modeller style colon-separated fields
jprocter [Thu, 12 Jan 2006 15:07:50 +0000 (15:07 +0000)]
PIR file IO now preserves and parses Modeller style colon-separated fields

18 years agoDBRefEntry made for sequences retrieved from the PDB
jprocter [Thu, 12 Jan 2006 13:34:59 +0000 (13:34 +0000)]
DBRefEntry made for sequences retrieved from the PDB

18 years ago<No Comment Entered>
jprocter [Thu, 12 Jan 2006 13:32:33 +0000 (13:32 +0000)]
<No Comment Entered>

18 years agoensured properties are loaded before loggers are initialised.
jprocter [Thu, 12 Jan 2006 12:21:21 +0000 (12:21 +0000)]
ensured properties are loaded before loggers are initialised.

18 years agorefactored Alignframe padGaps code to Alignment and Added AlignmentI method.
jprocter [Wed, 11 Jan 2006 13:27:21 +0000 (13:27 +0000)]
refactored Alignframe padGaps code to Alignment and Added AlignmentI method.

18 years agoCheck for null StringBuffer in getPDB
amwaterhouse [Thu, 22 Dec 2005 17:07:07 +0000 (17:07 +0000)]
Check for null StringBuffer in getPDB

18 years agoCheck for null StringBuffer in getPDB
amwaterhouse [Thu, 22 Dec 2005 16:46:46 +0000 (16:46 +0000)]
Check for null StringBuffer in getPDB

18 years agoJar file 20% smaller
amwaterhouse [Thu, 22 Dec 2005 16:01:52 +0000 (16:01 +0000)]
Jar file 20% smaller

18 years agoReduced jar size by 20%
amwaterhouse [Thu, 22 Dec 2005 16:00:57 +0000 (16:00 +0000)]
Reduced jar size by 20%

18 years agoAllow embedded applet
amwaterhouse [Thu, 22 Dec 2005 16:00:30 +0000 (16:00 +0000)]
Allow embedded applet

18 years agograph now has type, not a boolean
amwaterhouse [Thu, 22 Dec 2005 15:59:52 +0000 (15:59 +0000)]
graph now has type, not a boolean

18 years agoWatch for trim left/right null widths
amwaterhouse [Thu, 22 Dec 2005 15:59:21 +0000 (15:59 +0000)]
Watch for trim left/right null widths

18 years agoREGEX CANNOT BE STATIC
amwaterhouse [Thu, 22 Dec 2005 15:58:38 +0000 (15:58 +0000)]
REGEX CANNOT BE STATIC

18 years agoWrapped search scrolls to visible result
amwaterhouse [Thu, 22 Dec 2005 15:58:09 +0000 (15:58 +0000)]
Wrapped search scrolls to visible result

18 years agoRemove import
amwaterhouse [Thu, 22 Dec 2005 15:57:35 +0000 (15:57 +0000)]
Remove import

18 years agoAnnotations.Graph can be bargraph, linegraph
amwaterhouse [Thu, 22 Dec 2005 15:57:25 +0000 (15:57 +0000)]
Annotations.Graph can be bargraph, linegraph

18 years agoRemove printPoints
amwaterhouse [Thu, 22 Dec 2005 15:56:37 +0000 (15:56 +0000)]
Remove printPoints

18 years agoRemove main method
amwaterhouse [Thu, 22 Dec 2005 15:56:20 +0000 (15:56 +0000)]
Remove main method

18 years agoLoad assocated tree
amwaterhouse [Thu, 22 Dec 2005 15:55:58 +0000 (15:55 +0000)]
Load assocated tree

18 years agoTodo notes for feature issue: 0011711
jprocter [Fri, 16 Dec 2005 15:34:18 +0000 (15:34 +0000)]
Todo notes for feature issue:   0011711

18 years agoClose body and html, dont put in table
amwaterhouse [Thu, 15 Dec 2005 15:09:23 +0000 (15:09 +0000)]
Close body and html, dont put in table

18 years agoPrevents confusing extra line being output in Java Console
amwaterhouse [Thu, 15 Dec 2005 14:54:26 +0000 (14:54 +0000)]
Prevents confusing extra line being output in Java Console

18 years agoSetMenuBar(null) when closing frames. Prevents a bug in JVMs post 1.4
amwaterhouse [Thu, 15 Dec 2005 14:17:12 +0000 (14:17 +0000)]
SetMenuBar(null) when closing frames. Prevents a bug in JVMs post 1.4

18 years agoBroken link fixed
amwaterhouse [Tue, 13 Dec 2005 11:09:07 +0000 (11:09 +0000)]
Broken link fixed

18 years agoBroken link fixed
amwaterhouse [Tue, 13 Dec 2005 11:01:55 +0000 (11:01 +0000)]
Broken link fixed

18 years agoVersion update
amwaterhouse [Tue, 13 Dec 2005 10:37:03 +0000 (10:37 +0000)]
Version update

18 years agoBuilds web TOC for help files
amwaterhouse [Tue, 13 Dec 2005 10:36:47 +0000 (10:36 +0000)]
Builds web TOC for help files

18 years agoLink to applets.html
amwaterhouse [Tue, 13 Dec 2005 10:36:03 +0000 (10:36 +0000)]
Link to applets.html

18 years agoApplet new features
amwaterhouse [Mon, 12 Dec 2005 18:01:20 +0000 (18:01 +0000)]
Applet new features

18 years agoRemove unused mappings
amwaterhouse [Mon, 12 Dec 2005 18:00:56 +0000 (18:00 +0000)]
Remove unused mappings

18 years agoGetAlignment uses active alignment window
amwaterhouse [Mon, 12 Dec 2005 18:00:26 +0000 (18:00 +0000)]
GetAlignment uses active alignment window

18 years agoInlude mcview in build applet
amwaterhouse [Mon, 12 Dec 2005 17:57:02 +0000 (17:57 +0000)]
Inlude mcview in build applet

18 years agoChange dataset name
amwaterhouse [Mon, 12 Dec 2005 15:53:10 +0000 (15:53 +0000)]
Change dataset name

18 years agoChange title
amwaterhouse [Mon, 12 Dec 2005 15:51:48 +0000 (15:51 +0000)]
Change title

18 years agoRelease date
amwaterhouse [Mon, 12 Dec 2005 14:47:52 +0000 (14:47 +0000)]
Release date

18 years agoDOnt mention WSWublast for now
amwaterhouse [Mon, 12 Dec 2005 14:47:41 +0000 (14:47 +0000)]
DOnt mention WSWublast for now

18 years agoJbinit
amwaterhouse [Mon, 12 Dec 2005 14:20:09 +0000 (14:20 +0000)]
Jbinit

18 years agoFont size label
amwaterhouse [Mon, 12 Dec 2005 14:15:03 +0000 (14:15 +0000)]
Font size label

18 years agoDont bother with WSWUBlast for now
amwaterhouse [Mon, 12 Dec 2005 14:14:28 +0000 (14:14 +0000)]
Dont bother with WSWUBlast for now

18 years agoFOnt size -3 for labels
amwaterhouse [Mon, 12 Dec 2005 13:31:49 +0000 (13:31 +0000)]
FOnt size -3 for labels

18 years ago Check if user cancelled before making image
amwaterhouse [Mon, 12 Dec 2005 13:31:29 +0000 (13:31 +0000)]
 Check if user cancelled before making image

18 years agoSet font italic
amwaterhouse [Mon, 12 Dec 2005 12:24:57 +0000 (12:24 +0000)]
Set font italic

18 years agoFont changes on export png/eps
amwaterhouse [Mon, 12 Dec 2005 12:24:24 +0000 (12:24 +0000)]
Font changes on export png/eps

18 years agoGetmask is slightly wider
amwaterhouse [Mon, 12 Dec 2005 10:45:39 +0000 (10:45 +0000)]
Getmask is slightly wider

18 years agoadded description of how PDB structures can be associated with
jprocter [Fri, 9 Dec 2005 18:48:09 +0000 (18:48 +0000)]
added description of how PDB structures can be associated with
sequences (and so viewed in the PDB viewer).

18 years agoRearranged 'What's new' and debugged/verified the sequence fetcher and
jprocter [Fri, 9 Dec 2005 18:47:23 +0000 (18:47 +0000)]
Rearranged 'What's new' and debugged/verified the sequence fetcher and
pdbviewer/viewingpdbs entries.

18 years agofixed pdbentry creation and multiple uniprot or pdb entry retrieval.
jprocter [Fri, 9 Dec 2005 16:02:40 +0000 (16:02 +0000)]
fixed pdbentry creation and multiple uniprot or pdb entry retrieval.

18 years agoChange order of repaint if wrapped
amwaterhouse [Fri, 9 Dec 2005 14:25:10 +0000 (14:25 +0000)]
Change order of repaint if wrapped

18 years agoApplet Structure viewer has all colours available
amwaterhouse [Fri, 9 Dec 2005 14:10:59 +0000 (14:10 +0000)]
Applet Structure viewer has all colours available

18 years agoCan be used by PDBViewer
amwaterhouse [Fri, 9 Dec 2005 13:35:03 +0000 (13:35 +0000)]
Can be used by PDBViewer

18 years agoAll colours added to Structure viewer
amwaterhouse [Fri, 9 Dec 2005 13:34:46 +0000 (13:34 +0000)]
All colours added to Structure viewer

18 years agoOnly load the tree file once, for first alignment
amwaterhouse [Fri, 9 Dec 2005 11:13:18 +0000 (11:13 +0000)]
Only load the tree file once, for first alignment

18 years agoKeylistener added to frame and seqcanvas
amwaterhouse [Fri, 9 Dec 2005 11:12:56 +0000 (11:12 +0000)]
Keylistener added to frame and seqcanvas

18 years agocontext dependent title for when called from desktop or alignment window menu
jprocter [Thu, 8 Dec 2005 16:45:04 +0000 (16:45 +0000)]
context dependent title for when called from desktop or alignment window menu

18 years agochanged WhatsNew to a folder and modified preferences and seqfetcher
jprocter [Thu, 8 Dec 2005 16:19:51 +0000 (16:19 +0000)]
changed WhatsNew to a folder and modified preferences and seqfetcher
entries.

18 years agoIf dataset seq exists for paste to existing alignment, make a ref
amwaterhouse [Thu, 8 Dec 2005 16:18:10 +0000 (16:18 +0000)]
If dataset seq exists for paste to existing alignment, make a ref

18 years agoadded some error checking and instruction dialogs
jprocter [Thu, 8 Dec 2005 16:10:39 +0000 (16:10 +0000)]
added some error checking and instruction dialogs

18 years agoShould call deselectAll when escape pressed
amwaterhouse [Thu, 8 Dec 2005 15:39:46 +0000 (15:39 +0000)]
Should call deselectAll when escape pressed

18 years agoDont repaint if component has been removed
amwaterhouse [Thu, 8 Dec 2005 15:34:59 +0000 (15:34 +0000)]
Dont repaint if component has been removed

18 years agoSeqColoursReady
amwaterhouse [Thu, 8 Dec 2005 15:34:29 +0000 (15:34 +0000)]
SeqColoursReady

18 years agomodified jnet parsing exception report string.
jprocter [Thu, 8 Dec 2005 14:09:17 +0000 (14:09 +0000)]
modified jnet parsing exception report string.

18 years agoexception checks for (de)uniquify
jprocter [Thu, 8 Dec 2005 14:08:22 +0000 (14:08 +0000)]
exception checks for (de)uniquify

18 years agoClustal colour added to table
amwaterhouse [Thu, 8 Dec 2005 13:42:00 +0000 (13:42 +0000)]
Clustal colour added to table

18 years agoSeqColoursReady boolean added
amwaterhouse [Thu, 8 Dec 2005 12:04:29 +0000 (12:04 +0000)]
SeqColoursReady boolean added