jalview.git
18 years agopart finished (still finishing the updateJalview method of VamsasDatastore)
jprocter [Mon, 27 Mar 2006 17:42:19 +0000 (17:42 +0000)]
part finished (still finishing the updateJalview method of VamsasDatastore)

18 years agopreliminary notes on javliew sync with vamsas document
jprocter [Mon, 27 Mar 2006 08:39:24 +0000 (08:39 +0000)]
preliminary notes on javliew sync with vamsas document

18 years agomodified constructor for jalview.gui.VamsasClient
jprocter [Sun, 26 Mar 2006 18:29:01 +0000 (18:29 +0000)]
modified constructor for jalview.gui.VamsasClient

18 years agorefactored VamsasClient to jalview.gui, and created Vamsas session menu.
jprocter [Sun, 26 Mar 2006 12:29:34 +0000 (12:29 +0000)]
refactored VamsasClient to jalview.gui, and created Vamsas session menu.

18 years agobasic VamsasSession gui bits.
jprocter [Sat, 25 Mar 2006 16:33:09 +0000 (16:33 +0000)]
basic VamsasSession gui bits.

18 years agoFeature settings Root_VamJalview_2_07b+
amwaterhouse [Fri, 24 Mar 2006 16:29:00 +0000 (16:29 +0000)]
Feature settings

18 years agoHas its own featureRenderer
amwaterhouse [Fri, 24 Mar 2006 16:28:29 +0000 (16:28 +0000)]
Has its own featureRenderer

18 years agoGroup colours not used
amwaterhouse [Fri, 24 Mar 2006 15:36:53 +0000 (15:36 +0000)]
Group colours not used

18 years agoAssociated Data menu item
amwaterhouse [Fri, 24 Mar 2006 15:36:33 +0000 (15:36 +0000)]
Associated Data menu item

18 years agoCursor added
amwaterhouse [Fri, 24 Mar 2006 15:36:04 +0000 (15:36 +0000)]
Cursor added

18 years agoTypo
amwaterhouse [Fri, 24 Mar 2006 15:35:44 +0000 (15:35 +0000)]
Typo

18 years agofr.transferSettings
amwaterhouse [Fri, 24 Mar 2006 15:35:31 +0000 (15:35 +0000)]
fr.transferSettings

18 years agoFeatureSettings bug fixed
amwaterhouse [Fri, 24 Mar 2006 15:35:10 +0000 (15:35 +0000)]
FeatureSettings bug fixed

18 years agoFeature added to group search results
amwaterhouse [Fri, 24 Mar 2006 15:34:48 +0000 (15:34 +0000)]
Feature added to group search results

18 years agoGroups compatibility
amwaterhouse [Fri, 24 Mar 2006 15:34:21 +0000 (15:34 +0000)]
Groups compatibility

18 years agoNo need to hava SSX as array
amwaterhouse [Fri, 24 Mar 2006 15:33:44 +0000 (15:33 +0000)]
No need to hava SSX as array

18 years agoCursoMode added
amwaterhouse [Fri, 24 Mar 2006 15:33:20 +0000 (15:33 +0000)]
CursoMode added

18 years agoLoad data file added
amwaterhouse [Fri, 24 Mar 2006 15:32:50 +0000 (15:32 +0000)]
Load data file added

18 years agoTrim line
amwaterhouse [Fri, 24 Mar 2006 15:32:22 +0000 (15:32 +0000)]
Trim line

18 years agoFeatures added to group Uniprot
amwaterhouse [Fri, 24 Mar 2006 15:32:08 +0000 (15:32 +0000)]
Features added to group Uniprot

18 years agoAdd check if sequence already exists
amwaterhouse [Fri, 24 Mar 2006 15:31:42 +0000 (15:31 +0000)]
Add check if sequence already exists

18 years agoFeaturesGroup added to constructor
amwaterhouse [Fri, 24 Mar 2006 15:31:11 +0000 (15:31 +0000)]
FeaturesGroup added to constructor

18 years ago1 too many
amwaterhouse [Fri, 24 Mar 2006 15:29:33 +0000 (15:29 +0000)]
1 too many

18 years agoFeatures added to group search results
amwaterhouse [Fri, 24 Mar 2006 15:28:54 +0000 (15:28 +0000)]
Features added to group search results

18 years ago-1 +1 check removed
amwaterhouse [Fri, 24 Mar 2006 15:28:30 +0000 (15:28 +0000)]
-1 +1 check removed

18 years ago1 too many in drawgraph
amwaterhouse [Fri, 24 Mar 2006 15:27:59 +0000 (15:27 +0000)]
1 too many in drawgraph

18 years agoAnnotation colour scheme added
amwaterhouse [Fri, 24 Mar 2006 15:27:21 +0000 (15:27 +0000)]
Annotation colour scheme added

18 years agoCalled from AnnotationColourChooser and Feature Settings
amwaterhouse [Fri, 24 Mar 2006 15:26:37 +0000 (15:26 +0000)]
Called from AnnotationColourChooser and Feature Settings

18 years agoAnnotation colours added to applet
amwaterhouse [Fri, 24 Mar 2006 15:25:59 +0000 (15:25 +0000)]
Annotation colours added to applet

18 years agoZSort no longer static
amwaterhouse [Fri, 24 Mar 2006 15:25:09 +0000 (15:25 +0000)]
ZSort no longer static

18 years agoHas own featurerenderer
amwaterhouse [Fri, 24 Mar 2006 15:24:53 +0000 (15:24 +0000)]
Has own featurerenderer

18 years agoRearranged text
amwaterhouse [Mon, 20 Mar 2006 14:48:50 +0000 (14:48 +0000)]
Rearranged text

18 years agoCorrect reference
amwaterhouse [Mon, 20 Mar 2006 14:42:37 +0000 (14:42 +0000)]
Correct reference

18 years agotypo
amwaterhouse [Mon, 20 Mar 2006 14:34:20 +0000 (14:34 +0000)]
typo

18 years agoReference added
amwaterhouse [Mon, 20 Mar 2006 14:34:06 +0000 (14:34 +0000)]
Reference added

18 years agoadded example jnlp to memory settings help
jprocter [Mon, 20 Mar 2006 10:02:06 +0000 (10:02 +0000)]
added example jnlp to memory settings help

18 years agoadded link to example jnlp file
jprocter [Mon, 20 Mar 2006 09:56:54 +0000 (09:56 +0000)]
added link to example jnlp file

18 years agoexample jnlp file for users to edit and save locally
jprocter [Mon, 20 Mar 2006 09:56:41 +0000 (09:56 +0000)]
example jnlp file for users to edit and save locally

18 years agojnet method description correction.
jprocter [Fri, 17 Mar 2006 08:51:44 +0000 (08:51 +0000)]
jnet method description correction.

18 years agoFix for Finn Drablos bug. Must use equals for comparing strings
amwaterhouse [Thu, 16 Mar 2006 17:25:35 +0000 (17:25 +0000)]
Fix for Finn Drablos bug. Must use equals for comparing strings

18 years agohistoryItem.restore
amwaterhouse [Thu, 16 Mar 2006 15:31:36 +0000 (15:31 +0000)]
historyItem.restore

18 years agoHideSequences
amwaterhouse [Thu, 16 Mar 2006 15:31:02 +0000 (15:31 +0000)]
HideSequences

18 years agogetWidth and getHeight just once
amwaterhouse [Thu, 16 Mar 2006 15:30:41 +0000 (15:30 +0000)]
getWidth and getHeight just once

18 years ago-1 to drawGraphs
amwaterhouse [Thu, 16 Mar 2006 15:30:13 +0000 (15:30 +0000)]
-1 to drawGraphs

18 years agoisVisible and hiddenboundary added
amwaterhouse [Thu, 16 Mar 2006 15:29:55 +0000 (15:29 +0000)]
isVisible and hiddenboundary added

18 years agoUserColors not used here
amwaterhouse [Thu, 16 Mar 2006 15:29:34 +0000 (15:29 +0000)]
UserColors not used here

18 years agoHidden Rows
amwaterhouse [Thu, 16 Mar 2006 15:29:10 +0000 (15:29 +0000)]
Hidden Rows

18 years agoReveal
amwaterhouse [Thu, 16 Mar 2006 15:28:57 +0000 (15:28 +0000)]
Reveal

18 years agoFaster
amwaterhouse [Thu, 16 Mar 2006 15:28:41 +0000 (15:28 +0000)]
Faster

18 years agoHide Sequences
amwaterhouse [Thu, 16 Mar 2006 15:28:30 +0000 (15:28 +0000)]
Hide Sequences

18 years agoTooltip for hidden columns
amwaterhouse [Thu, 16 Mar 2006 15:28:13 +0000 (15:28 +0000)]
Tooltip for hidden columns

18 years agoHidden column adjustments
amwaterhouse [Thu, 16 Mar 2006 15:27:47 +0000 (15:27 +0000)]
Hidden column adjustments

18 years agoScrolls when editing
amwaterhouse [Thu, 16 Mar 2006 15:27:23 +0000 (15:27 +0000)]
Scrolls when editing

18 years agoGethidden sequences
amwaterhouse [Thu, 16 Mar 2006 15:21:58 +0000 (15:21 +0000)]
Gethidden sequences

18 years agoHiddenSequence methods
amwaterhouse [Thu, 16 Mar 2006 15:21:24 +0000 (15:21 +0000)]
HiddenSequence methods

18 years agogetHiddenSequences
amwaterhouse [Thu, 16 Mar 2006 15:20:57 +0000 (15:20 +0000)]
getHiddenSequences

18 years agoKeeps a record of hidden sequences
amwaterhouse [Thu, 16 Mar 2006 15:20:31 +0000 (15:20 +0000)]
Keeps a record of hidden sequences

18 years agoAllow loading from Zip files
amwaterhouse [Thu, 16 Mar 2006 15:19:24 +0000 (15:19 +0000)]
Allow loading from Zip files

18 years agoLoad tree
amwaterhouse [Thu, 16 Mar 2006 15:18:55 +0000 (15:18 +0000)]
Load tree

18 years agoCandP takes AlignFrame, not applet
amwaterhouse [Thu, 16 Mar 2006 15:18:17 +0000 (15:18 +0000)]
CandP takes AlignFrame, not applet

18 years agoFastpaint updates
amwaterhouse [Thu, 16 Mar 2006 15:18:02 +0000 (15:18 +0000)]
Fastpaint updates

18 years agoCheck endres when drawing graphs
amwaterhouse [Thu, 16 Mar 2006 15:17:14 +0000 (15:17 +0000)]
Check endres when drawing graphs

18 years agoCut and paste may be inserted into Dialog frame
amwaterhouse [Thu, 16 Mar 2006 15:16:45 +0000 (15:16 +0000)]
Cut and paste may be inserted into Dialog frame

18 years agoFastest implementation so far
amwaterhouse [Thu, 16 Mar 2006 15:16:21 +0000 (15:16 +0000)]
Fastest implementation so far

18 years agoExtra argument false
amwaterhouse [Thu, 16 Mar 2006 15:16:03 +0000 (15:16 +0000)]
Extra argument false

18 years agoScroll implemented for applet editing
amwaterhouse [Thu, 16 Mar 2006 15:15:18 +0000 (15:15 +0000)]
Scroll implemented for applet editing

18 years agoSelection Group rendering updated
amwaterhouse [Thu, 16 Mar 2006 15:15:05 +0000 (15:15 +0000)]
Selection Group rendering updated

18 years agoReduced arguments for speed
amwaterhouse [Thu, 16 Mar 2006 15:14:28 +0000 (15:14 +0000)]
Reduced arguments for speed

18 years agoCan be used for user features
amwaterhouse [Thu, 16 Mar 2006 15:14:09 +0000 (15:14 +0000)]
Can be used for user features

18 years agoAdd new feature from seqrch results
amwaterhouse [Thu, 16 Mar 2006 15:13:55 +0000 (15:13 +0000)]
Add new feature from seqrch results

18 years agoFeature rendering in groups
amwaterhouse [Thu, 16 Mar 2006 15:13:43 +0000 (15:13 +0000)]
Feature rendering in groups

18 years agoOut of bounds check
amwaterhouse [Thu, 16 Mar 2006 15:12:26 +0000 (15:12 +0000)]
Out of bounds check

18 years agoadded description of alignment quality scores and separated
jprocter [Thu, 16 Mar 2006 10:24:50 +0000 (10:24 +0000)]
added description of alignment quality scores and separated
description of conservation calculation from the instructions for
colouring alignments by it.

18 years agomethods for searching DBRef lists
jprocter [Tue, 14 Mar 2006 11:22:04 +0000 (11:22 +0000)]
methods for searching DBRef lists

18 years agofixes bug 0013013 but reveals lack of a 'features retrieved' flag that should be...
jprocter [Mon, 13 Mar 2006 16:52:54 +0000 (16:52 +0000)]
fixes bug 0013013 but reveals lack of a 'features retrieved' flag that should be set when a sequence's uniprot record has been retrieved and all its sequence features have been added.

18 years agobug fix for 0013013
jprocter [Mon, 13 Mar 2006 16:46:36 +0000 (16:46 +0000)]
bug fix for 0013013

18 years agoSequences can have a description
amwaterhouse [Wed, 8 Mar 2006 17:04:57 +0000 (17:04 +0000)]
Sequences can have a description

18 years agoFeatures may belong to a feature group
amwaterhouse [Wed, 8 Mar 2006 17:04:41 +0000 (17:04 +0000)]
Features may belong to a feature group

18 years agoIdentifyFile should not be static
amwaterhouse [Wed, 8 Mar 2006 16:58:51 +0000 (16:58 +0000)]
IdentifyFile should not be static

18 years agoCan read from zip file
amwaterhouse [Wed, 8 Mar 2006 16:58:16 +0000 (16:58 +0000)]
Can read from zip file

18 years agoBlank space is white
amwaterhouse [Wed, 8 Mar 2006 16:55:43 +0000 (16:55 +0000)]
Blank space is white

18 years agoReveal All added
amwaterhouse [Wed, 8 Mar 2006 16:55:30 +0000 (16:55 +0000)]
Reveal All added

18 years ago<= fastPaints hidden columns
amwaterhouse [Wed, 8 Mar 2006 16:54:51 +0000 (16:54 +0000)]
<= fastPaints hidden columns

18 years agoCheck for visibleGroup==null
amwaterhouse [Wed, 8 Mar 2006 16:54:28 +0000 (16:54 +0000)]
Check for visibleGroup==null

18 years agoIdentfyFile should not be static
amwaterhouse [Wed, 8 Mar 2006 16:53:36 +0000 (16:53 +0000)]
IdentfyFile should not be static

18 years agoRevealAllHiddenColumns
amwaterhouse [Wed, 8 Mar 2006 16:53:18 +0000 (16:53 +0000)]
RevealAllHiddenColumns

18 years agoAllow for hidden columns
amwaterhouse [Wed, 8 Mar 2006 16:52:59 +0000 (16:52 +0000)]
Allow for hidden columns

18 years agoAble to read resources from Zip file
amwaterhouse [Wed, 8 Mar 2006 16:51:44 +0000 (16:51 +0000)]
Able to read resources from Zip file

18 years agoBlank space is white
amwaterhouse [Wed, 8 Mar 2006 16:50:34 +0000 (16:50 +0000)]
Blank space is white

18 years agoPASTE is constant in AppletFormatAdapter
amwaterhouse [Wed, 8 Mar 2006 16:49:09 +0000 (16:49 +0000)]
PASTE is constant in AppletFormatAdapter

18 years agoPack resources in Zip file
amwaterhouse [Wed, 8 Mar 2006 16:48:32 +0000 (16:48 +0000)]
Pack resources in Zip file

18 years agofixed after refactoring of SequenceFeature[] seq.getSequenceFeatures
jprocter [Wed, 1 Mar 2006 16:23:15 +0000 (16:23 +0000)]
fixed after refactoring of SequenceFeature[] seq.getSequenceFeatures

18 years agopropagate SearchResult object use to MCView's highlighted residue renderer.
jprocter [Wed, 1 Mar 2006 14:03:52 +0000 (14:03 +0000)]
propagate SearchResult object use to MCView's highlighted residue renderer.

18 years agoP1 changed to N1
amwaterhouse [Fri, 24 Feb 2006 11:48:23 +0000 (11:48 +0000)]
P1 changed to N1

18 years agoAdd Annotation to specific sequence
amwaterhouse [Fri, 24 Feb 2006 11:47:51 +0000 (11:47 +0000)]
Add Annotation to specific sequence

18 years agoCannot delete residues
amwaterhouse [Fri, 24 Feb 2006 11:47:03 +0000 (11:47 +0000)]
Cannot delete residues

18 years agoFeatures now array
amwaterhouse [Fri, 24 Feb 2006 11:46:41 +0000 (11:46 +0000)]
Features now array

18 years agoKeeps original threshold value
amwaterhouse [Fri, 24 Feb 2006 11:45:36 +0000 (11:45 +0000)]
Keeps original threshold value

18 years agosetShowSequenceFeatures
amwaterhouse [Fri, 24 Feb 2006 11:44:59 +0000 (11:44 +0000)]
setShowSequenceFeatures

18 years agoFirst attempt at hidden regions
amwaterhouse [Fri, 24 Feb 2006 11:44:36 +0000 (11:44 +0000)]
First attempt at hidden regions