jalview.git
17 years agoAnnotations do not extend when full alignment is adjusted
amwaterhouse [Fri, 4 May 2007 10:31:18 +0000 (10:31 +0000)]
Annotations do not extend when full alignment is adjusted

17 years agopdb id toUpperCase
amwaterhouse [Thu, 3 May 2007 14:41:17 +0000 (14:41 +0000)]
pdb id toUpperCase

17 years agooptimize repaints
amwaterhouse [Thu, 3 May 2007 14:40:57 +0000 (14:40 +0000)]
optimize repaints

17 years agoremove system.out
amwaterhouse [Thu, 3 May 2007 14:40:36 +0000 (14:40 +0000)]
remove system.out

17 years agofeature locations are retrieved by associated accession string and public debug repor...
jprocter [Wed, 2 May 2007 15:20:18 +0000 (15:20 +0000)]
feature locations are retrieved by associated accession string and public debug report request in case embl parsing fails

17 years agofeature locations are retrieved by associated accession string
jprocter [Wed, 2 May 2007 15:19:23 +0000 (15:19 +0000)]
feature locations are retrieved by associated accession string

17 years agopublic debug report log message to gather any cases where Das coordinate frame mappin...
jprocter [Wed, 2 May 2007 14:30:02 +0000 (14:30 +0000)]
public debug report log message to gather any cases where Das coordinate frame mapping fails

17 years agofixed getIntervals bug to ensure it returns range from start of token at fromPosition...
jprocter [Wed, 2 May 2007 14:28:40 +0000 (14:28 +0000)]
fixed getIntervals bug to ensure it returns range from start of token at fromPosition to end of token in toPosition in the direction from fromPosition to toPosition

17 years agodocumentation and proxy call to util.MapList.getToWord(mpos)
jprocter [Wed, 2 May 2007 14:27:25 +0000 (14:27 +0000)]
documentation and proxy call to util.MapList.getToWord(mpos)

17 years agoextractScores menu item disabled for release
jprocter [Wed, 2 May 2007 13:46:56 +0000 (13:46 +0000)]
extractScores menu item disabled for release

17 years agoonly return non-empty subsequences when getting selection as new sequences
jprocter [Wed, 2 May 2007 13:41:22 +0000 (13:41 +0000)]
only return non-empty subsequences when getting selection as new sequences

17 years agoAllow expansion of textarea for many sequence input
amwaterhouse [Wed, 2 May 2007 13:03:14 +0000 (13:03 +0000)]
Allow expansion of textarea for many sequence input

17 years agoAMSA input set padgaps true
amwaterhouse [Wed, 2 May 2007 13:02:47 +0000 (13:02 +0000)]
AMSA input set padgaps true

17 years agoconvert space to gapchar
amwaterhouse [Wed, 2 May 2007 13:02:21 +0000 (13:02 +0000)]
convert space to gapchar

17 years agoundo stackempty error fix, refactored do and undo() method to take array of alignment...
jprocter [Wed, 2 May 2007 12:25:44 +0000 (12:25 +0000)]
undo stackempty error fix, refactored do and undo() method to take array of alignments for operations that result in hide/show of alignment annotation, convenience method for getting alignment object array for all views

17 years agorefactored do and undo() method to take array of alignments for operations that resul...
jprocter [Wed, 2 May 2007 12:24:41 +0000 (12:24 +0000)]
refactored do and undo() method to take array of alignments for operations that result in hide/show of alignment annotation

17 years agocopy only the sequence associated alignment annotation displayed in the current view
jprocter [Wed, 2 May 2007 12:23:17 +0000 (12:23 +0000)]
copy only the sequence associated alignment annotation displayed in the current view

17 years agosubsequence bound checks and constructor for selectively duplicating sequence associa...
jprocter [Wed, 2 May 2007 12:21:26 +0000 (12:21 +0000)]
subsequence bound checks and constructor for selectively duplicating sequence associated alignment annotation in copy constructor

17 years agoreturn flag indicating if annotations were actually deleted from alignment
jprocter [Wed, 2 May 2007 12:20:10 +0000 (12:20 +0000)]
return flag indicating if annotations were actually deleted from alignment

17 years agochecks for negative start column in restrict
jprocter [Wed, 2 May 2007 12:19:55 +0000 (12:19 +0000)]
checks for negative start column in restrict

17 years agoPadgaps is false by default
amwaterhouse [Wed, 2 May 2007 10:47:29 +0000 (10:47 +0000)]
Padgaps is false by default

17 years agosetVisible flag sent to EditNameDialog
amwaterhouse [Tue, 1 May 2007 16:34:53 +0000 (16:34 +0000)]
setVisible flag sent to EditNameDialog

17 years agoPad gaps method
amwaterhouse [Tue, 1 May 2007 16:33:57 +0000 (16:33 +0000)]
Pad gaps method

17 years agoMake sure annots are alignment width
amwaterhouse [Tue, 1 May 2007 16:33:27 +0000 (16:33 +0000)]
Make sure annots are alignment width

17 years agouse jalviewLite to addFrame
amwaterhouse [Tue, 1 May 2007 14:18:56 +0000 (14:18 +0000)]
use jalviewLite to addFrame

17 years agoremove system.out
amwaterhouse [Tue, 1 May 2007 14:18:36 +0000 (14:18 +0000)]
remove system.out

17 years agoset chains available
amwaterhouse [Tue, 1 May 2007 13:58:22 +0000 (13:58 +0000)]
set chains available

17 years agoMultiple views/hidden region/undo out of index bug
amwaterhouse [Tue, 1 May 2007 13:40:02 +0000 (13:40 +0000)]
Multiple views/hidden region/undo out of index bug

17 years agoCan specify PDB chain to map sequence to - only used by applet so far
amwaterhouse [Tue, 1 May 2007 12:25:38 +0000 (12:25 +0000)]
Can specify PDB chain to map sequence to - only used by applet so far

17 years agojavadoc
jprocter [Tue, 1 May 2007 11:47:32 +0000 (11:47 +0000)]
javadoc

17 years agoremoveAlignmentAnnotation only removes annotation objects referenced by the alignment...
jprocter [Tue, 1 May 2007 11:46:38 +0000 (11:46 +0000)]
removeAlignmentAnnotation only removes annotation objects referenced by the alignmentI and will do nothing otherwise.

17 years agosort-by-score works of sequence-annotation, not alignment annotation vector
jprocter [Tue, 1 May 2007 10:42:59 +0000 (10:42 +0000)]
sort-by-score works of sequence-annotation, not alignment annotation vector

17 years agoSave seqset properties
amwaterhouse [Tue, 1 May 2007 10:04:43 +0000 (10:04 +0000)]
Save seqset properties

17 years agoSeqset properties saved
amwaterhouse [Tue, 1 May 2007 10:03:45 +0000 (10:03 +0000)]
Seqset properties saved

17 years ago2.3 what's new
jprocter [Tue, 1 May 2007 09:51:03 +0000 (09:51 +0000)]
2.3 what's new

17 years agopreliminary EMBL and mapping documentation
jprocter [Tue, 1 May 2007 09:50:49 +0000 (09:50 +0000)]
preliminary EMBL and mapping documentation

17 years ago'no sources selected' calls method on feature settings dialog to prompt user.
jprocter [Mon, 30 Apr 2007 15:36:20 +0000 (15:36 +0000)]
'no sources selected' calls method on feature settings dialog to prompt user.
fixed never-ending das feature retrieval bug.

17 years agofixed deadlock
jprocter [Mon, 30 Apr 2007 15:35:17 +0000 (15:35 +0000)]
fixed deadlock

17 years agosetVisible replaces show
amwaterhouse [Mon, 30 Apr 2007 15:02:27 +0000 (15:02 +0000)]
setVisible replaces show

17 years agoVersion 11.0.2
amwaterhouse [Mon, 30 Apr 2007 15:00:45 +0000 (15:00 +0000)]
Version 11.0.2

17 years agoREmoved
amwaterhouse [Mon, 30 Apr 2007 14:59:57 +0000 (14:59 +0000)]
REmoved

17 years agorebuild sort by scores menu when new annotation is available
jprocter [Mon, 30 Apr 2007 13:50:33 +0000 (13:50 +0000)]
rebuild sort by scores menu when new annotation is available

17 years agopad should leave null annotations array null
jprocter [Mon, 30 Apr 2007 13:48:36 +0000 (13:48 +0000)]
pad should leave null annotations array null

17 years agoconvenient creation of 'score only' annotation.
jprocter [Mon, 30 Apr 2007 13:24:07 +0000 (13:24 +0000)]
convenient creation of 'score only' annotation.

17 years agoparse alignment properties and add annotation rows for general alignment position...
jprocter [Mon, 30 Apr 2007 13:23:14 +0000 (13:23 +0000)]
parse alignment properties and add annotation rows for general alignment position annotation.

17 years agoalignment properties and embedded newick strings can be retrieved from parsed files
jprocter [Mon, 30 Apr 2007 13:22:25 +0000 (13:22 +0000)]
alignment properties and embedded newick strings can be retrieved from parsed files

17 years agodssp 7-state to three state lookup
jprocter [Mon, 30 Apr 2007 13:14:17 +0000 (13:14 +0000)]
dssp 7-state to three state lookup

17 years agojavadoc
jprocter [Mon, 30 Apr 2007 09:44:38 +0000 (09:44 +0000)]
javadoc

17 years agoremove excessive painting
amwaterhouse [Fri, 27 Apr 2007 16:21:01 +0000 (16:21 +0000)]
remove excessive painting

17 years agoREmove excessive painting
amwaterhouse [Fri, 27 Apr 2007 16:20:41 +0000 (16:20 +0000)]
REmove excessive painting

17 years agoRepaint after feature added
amwaterhouse [Fri, 27 Apr 2007 16:20:22 +0000 (16:20 +0000)]
Repaint after feature added

17 years agoPrevent err when editing and overview drawing
amwaterhouse [Fri, 27 Apr 2007 16:19:57 +0000 (16:19 +0000)]
Prevent err when editing and overview drawing

17 years agoFeatureRenderer mixups fixed
amwaterhouse [Fri, 27 Apr 2007 16:19:25 +0000 (16:19 +0000)]
FeatureRenderer mixups fixed

17 years agoRemove system.out AppletPDBViewer.java
amwaterhouse [Fri, 27 Apr 2007 15:36:36 +0000 (15:36 +0000)]
Remove system.out AppletPDBViewer.java

17 years agoCheck pdbid size >0
amwaterhouse [Fri, 27 Apr 2007 15:32:46 +0000 (15:32 +0000)]
Check pdbid size >0

17 years agoTrouble with featureRenderers fixed
amwaterhouse [Fri, 27 Apr 2007 15:32:12 +0000 (15:32 +0000)]
Trouble with featureRenderers fixed

17 years agoMove repaint in thread
amwaterhouse [Fri, 27 Apr 2007 14:53:33 +0000 (14:53 +0000)]
Move repaint in thread

17 years agoPut alignmentProperties in scrollpane
amwaterhouse [Fri, 27 Apr 2007 14:47:00 +0000 (14:47 +0000)]
Put alignmentProperties in scrollpane

17 years agoCheck feature group is visible for mouse over features
amwaterhouse [Fri, 27 Apr 2007 14:45:31 +0000 (14:45 +0000)]
Check feature group is visible for mouse over features

17 years agoremove System.out
amwaterhouse [Fri, 27 Apr 2007 14:45:04 +0000 (14:45 +0000)]
remove System.out

17 years agoAdd param to Jmol path
amwaterhouse [Fri, 27 Apr 2007 14:44:30 +0000 (14:44 +0000)]
Add param to Jmol path

17 years agopadGaps moved
amwaterhouse [Fri, 27 Apr 2007 14:44:10 +0000 (14:44 +0000)]
padGaps moved

17 years agoMake sure mainContainer and owner are not null
amwaterhouse [Fri, 27 Apr 2007 14:43:36 +0000 (14:43 +0000)]
Make sure mainContainer and owner are not null

17 years agoMust check that featureGroup is visible for mouse over features
amwaterhouse [Fri, 27 Apr 2007 14:43:20 +0000 (14:43 +0000)]
Must check that featureGroup is visible for mouse over features

17 years agoamendFeatures
amwaterhouse [Fri, 27 Apr 2007 14:42:59 +0000 (14:42 +0000)]
amendFeatures

17 years agopaintAlignment(true)
amwaterhouse [Fri, 27 Apr 2007 14:42:45 +0000 (14:42 +0000)]
paintAlignment(true)

17 years agoPlace new feature on top of existing features
amwaterhouse [Fri, 27 Apr 2007 14:42:27 +0000 (14:42 +0000)]
Place new feature on top of existing features

17 years agoMake sure sequence is in mouse over alignment
amwaterhouse [Fri, 27 Apr 2007 14:41:54 +0000 (14:41 +0000)]
Make sure sequence is in mouse over alignment

17 years agoAmend Features
amwaterhouse [Fri, 27 Apr 2007 14:41:30 +0000 (14:41 +0000)]
Amend Features

17 years agoColourByStructure not ready yet
amwaterhouse [Fri, 27 Apr 2007 14:40:59 +0000 (14:40 +0000)]
ColourByStructure not ready yet

17 years agonewlines in alignment properties converted to <br>
jprocter [Fri, 27 Apr 2007 12:24:40 +0000 (12:24 +0000)]
newlines in alignment properties converted to <br>

17 years agoblc header lines inserted as 'comment' alignment property
jprocter [Fri, 27 Apr 2007 12:24:09 +0000 (12:24 +0000)]
blc header lines inserted as 'comment' alignment property

17 years agoparsers can generate alignment properties
jprocter [Fri, 27 Apr 2007 12:23:33 +0000 (12:23 +0000)]
parsers can generate alignment properties

17 years agogetProperties returns nullk for no properties
jprocter [Fri, 27 Apr 2007 10:47:21 +0000 (10:47 +0000)]
getProperties returns nullk for no properties

17 years agodocumentation and getProperties method
jprocter [Fri, 27 Apr 2007 10:46:49 +0000 (10:46 +0000)]
documentation and getProperties method

17 years agoaligned boxes
amwaterhouse [Fri, 27 Apr 2007 10:00:27 +0000 (10:00 +0000)]
aligned boxes

17 years agoThresholdIsMin available in applet
amwaterhouse [Fri, 27 Apr 2007 09:54:58 +0000 (09:54 +0000)]
ThresholdIsMin available in applet

17 years agoSet black if colour null
amwaterhouse [Fri, 27 Apr 2007 09:54:41 +0000 (09:54 +0000)]
Set black if colour null

17 years agoAlignment properties available
amwaterhouse [Fri, 27 Apr 2007 09:54:13 +0000 (09:54 +0000)]
Alignment properties available

17 years agohide the initial window after selection made
amwaterhouse [Fri, 27 Apr 2007 09:53:47 +0000 (09:53 +0000)]
hide the initial window after selection made

17 years agoone colour flag in annotation export
amwaterhouse [Fri, 27 Apr 2007 09:53:27 +0000 (09:53 +0000)]
one colour flag in annotation export

17 years agobugfix for deleted annotation undo
jprocter [Fri, 27 Apr 2007 08:51:13 +0000 (08:51 +0000)]
bugfix for deleted annotation undo

17 years agoAnnotation gradient will use direct colours if no graph exists
amwaterhouse [Fri, 27 Apr 2007 08:50:06 +0000 (08:50 +0000)]
Annotation gradient will use direct colours if no graph exists

17 years agoAllow threshold to be min/max
amwaterhouse [Fri, 27 Apr 2007 08:21:09 +0000 (08:21 +0000)]
Allow threshold to be min/max

17 years agohide annotation colouring options
amwaterhouse [Fri, 27 Apr 2007 08:20:45 +0000 (08:20 +0000)]
hide annotation colouring options

17 years agoDont colour labels
amwaterhouse [Fri, 27 Apr 2007 08:20:03 +0000 (08:20 +0000)]
Dont colour labels

17 years agoadded/tested sort by scores menu and added basic extractScores function.
jprocter [Thu, 26 Apr 2007 17:16:07 +0000 (17:16 +0000)]
added/tested sort by scores menu and added basic extractScores function.

17 years agouse hasScore method to test presence of score in annotation.
jprocter [Thu, 26 Apr 2007 17:15:13 +0000 (17:15 +0000)]
use hasScore method to test presence of score in annotation.

17 years agoadded 'sort by sequence associated annotation score'
jprocter [Thu, 26 Apr 2007 17:13:47 +0000 (17:13 +0000)]
added 'sort by sequence associated annotation score'

17 years agobug fixed basic score extraction by regex on description method
jprocter [Thu, 26 Apr 2007 17:13:12 +0000 (17:13 +0000)]
bug fixed basic score extraction by regex on description method

17 years agoget annotation by label string
jprocter [Thu, 26 Apr 2007 17:12:27 +0000 (17:12 +0000)]
get annotation by label string

17 years agofix '\0' bug from score-only positional annotation
jprocter [Thu, 26 Apr 2007 17:11:56 +0000 (17:11 +0000)]
fix '\0' bug from score-only positional annotation

17 years agoscore is a double, fix bugs for score only annotation not being associated with sequences
jprocter [Thu, 26 Apr 2007 17:11:27 +0000 (17:11 +0000)]
score is a double, fix bugs for score only annotation not being associated with sequences

17 years agodouble sort functions
jprocter [Thu, 26 Apr 2007 17:10:20 +0000 (17:10 +0000)]
double sort functions

17 years agototal annotation score is a double for maximum precision.
jprocter [Thu, 26 Apr 2007 17:10:05 +0000 (17:10 +0000)]
total annotation score is a double for maximum precision.

17 years agocheck for null ss character
amwaterhouse [Thu, 26 Apr 2007 15:14:51 +0000 (15:14 +0000)]
check for null ss character

17 years agocolourText = false
amwaterhouse [Thu, 26 Apr 2007 15:14:31 +0000 (15:14 +0000)]
colourText = false

17 years agoscore and visible copy construction
jprocter [Thu, 26 Apr 2007 15:02:37 +0000 (15:02 +0000)]
score and visible copy construction

17 years agoEdit seqs
amwaterhouse [Thu, 26 Apr 2007 11:51:26 +0000 (11:51 +0000)]
Edit seqs

17 years agoquick fix for verbose fortranesque comments in preamble of AMPS BLC files (lines...
jprocter [Thu, 26 Apr 2007 11:24:42 +0000 (11:24 +0000)]
quick fix for verbose fortranesque comments in preamble of AMPS BLC files (lines were being recognised as JPred concise files)