jalview.git
17 years agoannotation and seqs vectors are protected members for use by file parsers for adding...
jprocter [Fri, 20 Apr 2007 14:05:50 +0000 (14:05 +0000)]
annotation and seqs vectors are protected members for use by file parsers for adding data for import.

17 years agotfactor annotation description includes full sequenceID
jprocter [Thu, 19 Apr 2007 16:25:22 +0000 (16:25 +0000)]
tfactor annotation description includes full sequenceID

17 years agotfactor and occupancy extracted from PDB file, and tfactor added as sequence associat...
jprocter [Thu, 19 Apr 2007 16:17:39 +0000 (16:17 +0000)]
tfactor and occupancy extracted from PDB file, and tfactor added as sequence associated alignment annotation.

17 years agobugfix
jprocter [Thu, 19 Apr 2007 16:16:23 +0000 (16:16 +0000)]
bugfix

17 years agofixed column selection cut/paste and self paste.
jprocter [Thu, 19 Apr 2007 15:23:18 +0000 (15:23 +0000)]
fixed column selection cut/paste and self paste.

17 years agosequence associated alignment annotation copy for column range selection
jprocter [Thu, 19 Apr 2007 15:22:40 +0000 (15:22 +0000)]
sequence associated alignment annotation copy for column range selection

17 years agoensure edit command gapChar is updated and used for padding when no alignmentI refere...
jprocter [Thu, 19 Apr 2007 15:21:16 +0000 (15:21 +0000)]
ensure edit command gapChar is updated and used for padding when no alignmentI reference is available

17 years agopadGaps flag in copy constructor
jprocter [Thu, 19 Apr 2007 15:00:52 +0000 (15:00 +0000)]
padGaps flag in copy constructor

17 years agojavadoc note on padding AlignmentAnnotation to alignment width
jprocter [Thu, 19 Apr 2007 14:55:39 +0000 (14:55 +0000)]
javadoc note on padding AlignmentAnnotation to alignment width

17 years agocopying sequenceMapping, restrict(alstart/end) and pad(alwidth) method.
jprocter [Thu, 19 Apr 2007 14:54:43 +0000 (14:54 +0000)]
copying sequenceMapping, restrict(alstart/end) and pad(alwidth) method.

17 years agoREPLACE added to edit command
amwaterhouse [Thu, 19 Apr 2007 14:42:24 +0000 (14:42 +0000)]
REPLACE added to edit command

17 years agoOnly setDropTarget if Desktop is not null
amwaterhouse [Thu, 19 Apr 2007 09:56:55 +0000 (09:56 +0000)]
Only setDropTarget if Desktop is not null

17 years agoValidate range for all annotations
amwaterhouse [Wed, 18 Apr 2007 16:11:28 +0000 (16:11 +0000)]
Validate range for all annotations

17 years agoRedundant code commented out
amwaterhouse [Wed, 18 Apr 2007 16:10:53 +0000 (16:10 +0000)]
Redundant code commented out

17 years agohastext = false
amwaterhouse [Wed, 18 Apr 2007 13:42:37 +0000 (13:42 +0000)]
hastext = false

17 years agodont set seqref null if index incorrect
amwaterhouse [Wed, 18 Apr 2007 13:35:07 +0000 (13:35 +0000)]
dont set seqref null if index incorrect

17 years agofeatureGroups not null
amwaterhouse [Wed, 18 Apr 2007 13:29:46 +0000 (13:29 +0000)]
featureGroups not null

17 years agoPad gaps when annotation editing
amwaterhouse [Wed, 18 Apr 2007 12:32:39 +0000 (12:32 +0000)]
Pad gaps when annotation editing

17 years agoquality has text false
amwaterhouse [Wed, 18 Apr 2007 12:06:17 +0000 (12:06 +0000)]
quality has text false

17 years agoQuality does not have text
amwaterhouse [Wed, 18 Apr 2007 12:04:28 +0000 (12:04 +0000)]
Quality does not have text

17 years agoAlignment of labels and text
amwaterhouse [Wed, 18 Apr 2007 12:03:49 +0000 (12:03 +0000)]
Alignment of labels and text

17 years agochecks for scrollbar height
amwaterhouse [Wed, 18 Apr 2007 12:03:28 +0000 (12:03 +0000)]
checks for scrollbar height

17 years agoDisable memory checker for now
amwaterhouse [Wed, 18 Apr 2007 12:02:16 +0000 (12:02 +0000)]
Disable memory checker for now

17 years agoadjustForAlignment on new seq ref
amwaterhouse [Wed, 18 Apr 2007 12:01:56 +0000 (12:01 +0000)]
adjustForAlignment on new seq ref

17 years agoCheck values not null in copy constructor
amwaterhouse [Wed, 18 Apr 2007 12:01:33 +0000 (12:01 +0000)]
Check values not null in copy constructor

17 years agomade compileApplet and obfuscate depend on the presence of a java 1.1 jdk to ensure...
jprocter [Wed, 18 Apr 2007 10:55:22 +0000 (10:55 +0000)]
made compileApplet and obfuscate depend on the presence of a java 1.1 jdk to ensure that applet jar is properly 1.1 compliant.

17 years agojava 1.1 compliance
jprocter [Wed, 18 Apr 2007 10:51:30 +0000 (10:51 +0000)]
java 1.1 compliance

17 years agobugfix for jalviewApplet run from command line.
jprocter [Tue, 17 Apr 2007 17:05:41 +0000 (17:05 +0000)]
bugfix for jalviewApplet run from command line.

17 years agobugfix.
jprocter [Tue, 17 Apr 2007 16:55:47 +0000 (16:55 +0000)]
bugfix.

17 years agojmol lib dependency for proguard and castorbinding target.
jprocter [Tue, 17 Apr 2007 16:39:45 +0000 (16:39 +0000)]
jmol lib dependency for proguard and castorbinding target.

17 years agouse of suffix string (filename.blc#suffixstring) to read a specified iteration from...
jprocter [Tue, 17 Apr 2007 15:58:47 +0000 (15:58 +0000)]
use of suffix string (filename.blc#suffixstring) to read a specified iteration from blc file.

17 years agorefactored to allow seeks on a FileParse datasource so IdentifyFile can be applied...
jprocter [Tue, 17 Apr 2007 15:57:41 +0000 (15:57 +0000)]
refactored to allow seeks on a FileParse datasource so IdentifyFile can be applied to an inputstream.

17 years agojavadoc
jprocter [Tue, 17 Apr 2007 15:55:04 +0000 (15:55 +0000)]
javadoc

17 years agoascii type
jprocter [Tue, 17 Apr 2007 11:32:26 +0000 (11:32 +0000)]
ascii type

17 years agopaste adds or creates full copies of objects in clipboard, and properly copies sequen...
jprocter [Tue, 17 Apr 2007 11:31:15 +0000 (11:31 +0000)]
paste adds or creates full copies of objects in clipboard, and properly copies sequence associated alignment annotation.

17 years agopdb files are global to all alignments with new mapping mechanism.
jprocter [Tue, 17 Apr 2007 11:29:11 +0000 (11:29 +0000)]
pdb files are global to all alignments with new mapping mechanism.

17 years agopaste/cut now adds or removes associated AlignmentAnnotation.
jprocter [Tue, 17 Apr 2007 11:05:40 +0000 (11:05 +0000)]
paste/cut now adds or removes associated AlignmentAnnotation.

17 years agocopy constructors and AlignmentAnnotation sequenceRef mechanisms for pasting sequence...
jprocter [Tue, 17 Apr 2007 11:03:38 +0000 (11:03 +0000)]
copy constructors and AlignmentAnnotation sequenceRef mechanisms for pasting sequences and annotation.

17 years agocopy constructor and ascii type change.
jprocter [Tue, 17 Apr 2007 11:02:43 +0000 (11:02 +0000)]
copy constructor and ascii type change.

17 years agoproper copy constructor (not clone)
jprocter [Tue, 17 Apr 2007 11:01:57 +0000 (11:01 +0000)]
proper copy constructor (not clone)

17 years agoApplet remembers PDBEntries, can launch multiple structures from popupmenu
amwaterhouse [Tue, 17 Apr 2007 10:42:39 +0000 (10:42 +0000)]
Applet remembers PDBEntries, can launch multiple structures from popupmenu

17 years agoAdd system.out for Mcview / Jmol detection
amwaterhouse [Tue, 17 Apr 2007 09:37:10 +0000 (09:37 +0000)]
Add system.out for Mcview / Jmol detection

17 years agoRemove system.out
amwaterhouse [Tue, 17 Apr 2007 09:35:45 +0000 (09:35 +0000)]
Remove system.out

17 years agodrawSequence must be synchronized
amwaterhouse [Mon, 16 Apr 2007 11:24:16 +0000 (11:24 +0000)]
drawSequence must be synchronized

17 years agoToo many calls to paintAlignment
amwaterhouse [Mon, 16 Apr 2007 11:23:25 +0000 (11:23 +0000)]
Too many calls to paintAlignment

17 years agoFeatureRenderer takes alignmentPanel
amwaterhouse [Fri, 13 Apr 2007 15:52:18 +0000 (15:52 +0000)]
FeatureRenderer takes alignmentPanel

17 years agoCheck alignment has same sequence
amwaterhouse [Fri, 13 Apr 2007 15:51:20 +0000 (15:51 +0000)]
Check alignment has same sequence

17 years agobasic support for multi-exon CDS features
jprocter [Thu, 12 Apr 2007 14:46:07 +0000 (14:46 +0000)]
basic support for multi-exon CDS features

17 years agoNumber pad keys can be used in cursor mode
amwaterhouse [Thu, 12 Apr 2007 14:00:59 +0000 (14:00 +0000)]
Number pad keys can be used in cursor mode

17 years agoSetTargetColour before dialog.show
amwaterhouse [Wed, 11 Apr 2007 14:30:49 +0000 (14:30 +0000)]
SetTargetColour before dialog.show

17 years agoModified to compile applet with Jmol jar present
amwaterhouse [Wed, 11 Apr 2007 14:29:44 +0000 (14:29 +0000)]
Modified to compile applet with Jmol jar present

17 years agofixed for display of 'null' group features
jprocter [Wed, 11 Apr 2007 14:16:55 +0000 (14:16 +0000)]
fixed for display of 'null' group features

17 years agofixed base lookup bug in dna pairwise alignment and ensured abiguous and non-standard...
jprocter [Wed, 11 Apr 2007 13:57:45 +0000 (13:57 +0000)]
fixed base lookup bug in dna pairwise alignment and ensured abiguous and non-standard aa and na codes are preserved in aligned sequences.

17 years agoCan add features with no group
amwaterhouse [Wed, 11 Apr 2007 13:02:43 +0000 (13:02 +0000)]
Can add features with no group

17 years agoAdjustment for hidden columns
amwaterhouse [Wed, 11 Apr 2007 13:01:44 +0000 (13:01 +0000)]
Adjustment for hidden columns

17 years agoUse same mouse events as scalePanel
amwaterhouse [Wed, 11 Apr 2007 13:01:18 +0000 (13:01 +0000)]
Use same mouse events as scalePanel

17 years agoAmend features/annotations in applet
amwaterhouse [Wed, 11 Apr 2007 13:00:48 +0000 (13:00 +0000)]
Amend features/annotations in applet

17 years agoUsed several places
amwaterhouse [Wed, 11 Apr 2007 13:00:28 +0000 (13:00 +0000)]
Used several places

17 years agoIf hiddenColumns are null, then column is viisble
amwaterhouse [Wed, 11 Apr 2007 13:00:09 +0000 (13:00 +0000)]
If hiddenColumns are null, then column is viisble

17 years agofeatureAdded not in applet
amwaterhouse [Wed, 11 Apr 2007 12:59:27 +0000 (12:59 +0000)]
featureAdded not in applet

17 years agoPaste menu item dispalyed on right click. Memory settings visible in this version
amwaterhouse [Thu, 5 Apr 2007 11:22:35 +0000 (11:22 +0000)]
Paste menu item dispalyed on right click. Memory settings visible in this version

17 years agoPasted file doesnt have title and not reloadable
amwaterhouse [Thu, 5 Apr 2007 11:22:05 +0000 (11:22 +0000)]
Pasted file doesnt have title and not reloadable

17 years agocall getAllframes on desktop instance
amwaterhouse [Thu, 5 Apr 2007 11:21:18 +0000 (11:21 +0000)]
call getAllframes on desktop instance

17 years agonewFEatures flag for seq type
amwaterhouse [Wed, 4 Apr 2007 15:18:56 +0000 (15:18 +0000)]
newFEatures flag for seq type

17 years agoUse newFeatures flag
amwaterhouse [Wed, 4 Apr 2007 15:11:59 +0000 (15:11 +0000)]
Use newFeatures flag

17 years agocombobox for overlapping features
amwaterhouse [Wed, 4 Apr 2007 14:40:16 +0000 (14:40 +0000)]
combobox for overlapping features

17 years agopaintALignment
amwaterhouse [Wed, 4 Apr 2007 14:39:50 +0000 (14:39 +0000)]
paintALignment

17 years agoflag for dasCoordSysFound added
amwaterhouse [Wed, 4 Apr 2007 13:10:57 +0000 (13:10 +0000)]
flag for dasCoordSysFound added

17 years agoThrow exception if pdb result size is zero
amwaterhouse [Wed, 4 Apr 2007 13:06:15 +0000 (13:06 +0000)]
Throw exception if pdb result size is zero

17 years agodoco change.
jprocter [Mon, 2 Apr 2007 15:52:47 +0000 (15:52 +0000)]
doco change.

17 years agoupdate settings for new groups (always displayed) and new feature types (containing...
jprocter [Mon, 2 Apr 2007 15:10:39 +0000 (15:10 +0000)]
update settings for new groups (always displayed) and new feature types (containing group is checked and type is checked and displayed on top)

17 years agobugfix + create/amend whilst feature panel open (still fixing)
jprocter [Mon, 2 Apr 2007 14:52:11 +0000 (14:52 +0000)]
bugfix + create/amend whilst feature panel open (still fixing)

17 years agotypo fix.
jprocter [Mon, 2 Apr 2007 14:07:40 +0000 (14:07 +0000)]
typo fix.

17 years agoAllow for scroll bar height
amwaterhouse [Mon, 2 Apr 2007 13:57:55 +0000 (13:57 +0000)]
Allow for scroll bar height

17 years agofeaturesAdded method introduced for consistency with application for notifying gui...
jprocter [Mon, 2 Apr 2007 13:12:19 +0000 (13:12 +0000)]
featuresAdded method introduced for consistency with application for notifying gui when features have been modified/created.

17 years agofr==null check.
jprocter [Mon, 2 Apr 2007 13:11:13 +0000 (13:11 +0000)]
fr==null check.

17 years agofeature group state and type order preference storage/retrieval.
jprocter [Mon, 2 Apr 2007 13:10:05 +0000 (13:10 +0000)]
feature group state and type order preference storage/retrieval.

17 years agofeaturesAdded call for transferred PDB features
jprocter [Mon, 2 Apr 2007 13:09:32 +0000 (13:09 +0000)]
featuresAdded call for transferred PDB features

17 years agofeaturesAdded() method, state change support between feature setting box and featureR...
jprocter [Mon, 2 Apr 2007 13:08:20 +0000 (13:08 +0000)]
featuresAdded() method, state change support between feature setting box and featureRenderer, feature ordering conserved between group selections, new features appear on top of old, and 'optimise' feature ordering button added.

17 years agoadded feature type order preference attribute and visible feature group state element
jprocter [Mon, 2 Apr 2007 13:05:09 +0000 (13:05 +0000)]
added feature type order preference attribute and visible feature group state element

17 years agoNew seq feature name not added here
amwaterhouse [Mon, 2 Apr 2007 12:52:40 +0000 (12:52 +0000)]
New seq feature name not added here

17 years agogetAllFeaturesAtRes replace by findFeaturesAtRes
amwaterhouse [Mon, 2 Apr 2007 12:51:14 +0000 (12:51 +0000)]
getAllFeaturesAtRes replace by findFeaturesAtRes

17 years agoaddElement
amwaterhouse [Mon, 2 Apr 2007 12:50:07 +0000 (12:50 +0000)]
addElement

17 years agodestroy destroyed
amwaterhouse [Mon, 2 Apr 2007 12:38:13 +0000 (12:38 +0000)]
destroy destroyed

17 years agodestroy destroyed
amwaterhouse [Mon, 2 Apr 2007 12:29:21 +0000 (12:29 +0000)]
destroy destroyed

17 years agoDestroy alignment moved to finalize
amwaterhouse [Mon, 2 Apr 2007 12:28:28 +0000 (12:28 +0000)]
Destroy alignment moved to finalize

17 years agoChain might be null
amwaterhouse [Mon, 2 Apr 2007 11:21:35 +0000 (11:21 +0000)]
Chain might be null

17 years agoDestroy Alignment when closing frame
amwaterhouse [Mon, 2 Apr 2007 11:21:13 +0000 (11:21 +0000)]
Destroy Alignment when closing frame

17 years agoDestroy aligment method added
amwaterhouse [Mon, 2 Apr 2007 11:17:25 +0000 (11:17 +0000)]
Destroy aligment method added

17 years agoMust allow for scrollbar height
amwaterhouse [Mon, 2 Apr 2007 11:16:53 +0000 (11:16 +0000)]
Must allow for scrollbar height

17 years agoPick atom highlighted
amwaterhouse [Tue, 27 Mar 2007 09:14:02 +0000 (09:14 +0000)]
Pick atom highlighted

17 years agoUpdated PDB loading params
amwaterhouse [Tue, 27 Mar 2007 09:02:34 +0000 (09:02 +0000)]
Updated PDB loading params

17 years agoJmol calls user colours
amwaterhouse [Mon, 26 Mar 2007 17:29:37 +0000 (17:29 +0000)]
Jmol calls user colours

17 years agoJalview colour schemes added
amwaterhouse [Mon, 26 Mar 2007 17:28:56 +0000 (17:28 +0000)]
Jalview colour schemes added

17 years agoAdd seq mapping for multiple seq 2 pdbs
amwaterhouse [Mon, 26 Mar 2007 17:25:41 +0000 (17:25 +0000)]
Add seq mapping for multiple seq 2 pdbs

17 years agoMenu changes
amwaterhouse [Mon, 26 Mar 2007 17:25:14 +0000 (17:25 +0000)]
Menu changes

17 years agofix single sequence features added rendering bug.
jprocter [Mon, 26 Mar 2007 14:31:39 +0000 (14:31 +0000)]
fix single sequence features added rendering bug.

17 years agoPDB residue numberings transfered and alignment view refreshed to update featureRenderer.
jprocter [Mon, 26 Mar 2007 14:19:52 +0000 (14:19 +0000)]
PDB residue numberings transfered and alignment view refreshed to update featureRenderer.

17 years agogrammar.
jprocter [Mon, 26 Mar 2007 14:15:54 +0000 (14:15 +0000)]
grammar.

17 years agoupdates to console
amwaterhouse [Fri, 23 Mar 2007 17:26:20 +0000 (17:26 +0000)]
updates to console