jalview.git
19 years agoReturn color.white if a gap char is detected
amwaterhouse [Fri, 14 Jan 2005 15:44:37 +0000 (15:44 +0000)]
Return color.white if a gap char is detected

19 years agogetValue method added
amwaterhouse [Thu, 13 Jan 2005 18:11:59 +0000 (18:11 +0000)]
getValue method added

19 years agoMaintain PID or conservation status when changing colour
amwaterhouse [Thu, 13 Jan 2005 18:11:16 +0000 (18:11 +0000)]
Maintain PID or conservation status when changing colour

19 years agoSequenceGroup is now an array
amwaterhouse [Thu, 13 Jan 2005 18:10:06 +0000 (18:10 +0000)]
SequenceGroup is now an array

19 years agoSend array of groups to renderer
amwaterhouse [Thu, 13 Jan 2005 18:08:41 +0000 (18:08 +0000)]
Send array of groups to renderer

19 years agoInitial selection bug fixed
amwaterhouse [Thu, 13 Jan 2005 18:07:42 +0000 (18:07 +0000)]
Initial selection bug fixed

19 years agoFindAllGroups added
amwaterhouse [Thu, 13 Jan 2005 18:06:55 +0000 (18:06 +0000)]
FindAllGroups added

19 years agoScrollbar at bottom of screen
amwaterhouse [Thu, 13 Jan 2005 18:05:57 +0000 (18:05 +0000)]
Scrollbar at bottom of screen

19 years agoGetResidueBoxColour altered for faster rendering
amwaterhouse [Thu, 13 Jan 2005 12:05:10 +0000 (12:05 +0000)]
GetResidueBoxColour altered for faster rendering

19 years agoRenderer already has graphics context
amwaterhouse [Thu, 13 Jan 2005 12:04:28 +0000 (12:04 +0000)]
Renderer already has graphics context

19 years agogetResidueBoxColour has been removed for faster rendering
amwaterhouse [Thu, 13 Jan 2005 12:03:41 +0000 (12:03 +0000)]
getResidueBoxColour has been removed for faster rendering

19 years agoIgnores gaps when searching
amwaterhouse [Thu, 13 Jan 2005 12:02:50 +0000 (12:02 +0000)]
Ignores gaps when searching

19 years agorandom change 3
jprocter [Wed, 12 Jan 2005 19:01:32 +0000 (19:01 +0000)]
random change 3

19 years agoanother dummy.
jprocter [Wed, 12 Jan 2005 18:32:34 +0000 (18:32 +0000)]
another dummy.

19 years agoGroup editing is done by control and alt key down
amwaterhouse [Wed, 12 Jan 2005 18:15:35 +0000 (18:15 +0000)]
Group editing is done by control and alt key down

19 years agoregular expression added
amwaterhouse [Wed, 12 Jan 2005 18:14:44 +0000 (18:14 +0000)]
regular expression added

19 years agodelete gaps bug fixed
amwaterhouse [Wed, 12 Jan 2005 18:14:27 +0000 (18:14 +0000)]
delete gaps bug fixed

19 years agomust append file:/// at beginning of file launch
amwaterhouse [Wed, 12 Jan 2005 18:13:54 +0000 (18:13 +0000)]
must append file:/// at beginning of file launch

19 years agoirrelevant comment.
jprocter [Wed, 12 Jan 2005 17:57:58 +0000 (17:57 +0000)]
irrelevant comment.

19 years agoDisplays number of matches found in search
amwaterhouse [Mon, 10 Jan 2005 17:39:32 +0000 (17:39 +0000)]
Displays number of matches found in search

19 years agojalview URL updated and authors in about file
amwaterhouse [Fri, 17 Dec 2004 15:39:39 +0000 (15:39 +0000)]
jalview URL updated and authors in about file

19 years agoMac osX doesnt like isControlDown, use alt instead
amwaterhouse [Fri, 17 Dec 2004 15:15:04 +0000 (15:15 +0000)]
Mac osX doesnt like isControlDown, use alt instead

19 years agoAll optionpane messages must be added to Desktop.desktop
amwaterhouse [Fri, 17 Dec 2004 15:14:22 +0000 (15:14 +0000)]
All optionpane messages must be added to Desktop.desktop

19 years agoIf screensize is small, setSize to be the screenSize
amwaterhouse [Fri, 17 Dec 2004 14:20:46 +0000 (14:20 +0000)]
If screensize is small, setSize to be the screenSize

19 years agoDoesn't draw the white box at the end of a line
amwaterhouse [Fri, 17 Dec 2004 14:20:04 +0000 (14:20 +0000)]
Doesn't draw the white box at the end of a line

19 years agoFixed bug in editing by group
amwaterhouse [Fri, 17 Dec 2004 14:19:17 +0000 (14:19 +0000)]
Fixed bug in editing by group

19 years agoHide apply and undo buttons
amwaterhouse [Fri, 17 Dec 2004 14:18:43 +0000 (14:18 +0000)]
Hide apply and undo buttons

19 years agoUse the isGap method in utils
amwaterhouse [Fri, 17 Dec 2004 14:18:13 +0000 (14:18 +0000)]
Use the isGap method in utils

19 years agoOutput new alignment bug fixed
amwaterhouse [Thu, 16 Dec 2004 15:45:38 +0000 (15:45 +0000)]
Output new alignment bug fixed

19 years agoilen and jlen no longer +1
amwaterhouse [Thu, 16 Dec 2004 13:19:57 +0000 (13:19 +0000)]
ilen and jlen no longer +1

19 years agoRemove redundancy implemented
amwaterhouse [Thu, 16 Dec 2004 13:19:14 +0000 (13:19 +0000)]
Remove redundancy implemented

19 years agocolours are right, but not the conservation bit!!
amwaterhouse [Wed, 15 Dec 2004 17:29:19 +0000 (17:29 +0000)]
colours are right, but not the conservation bit!!

19 years agono need to send sequence to determine residue colour
amwaterhouse [Wed, 15 Dec 2004 17:28:54 +0000 (17:28 +0000)]
no need to send sequence to determine residue colour

19 years agoAdded for the moment, only used by ClustalxColourScheme
amwaterhouse [Wed, 15 Dec 2004 17:28:07 +0000 (17:28 +0000)]
Added for the moment, only used by ClustalxColourScheme

19 years agoNo need to sened sequence to determine residue colour
amwaterhouse [Wed, 15 Dec 2004 17:27:31 +0000 (17:27 +0000)]
No need to sened sequence to determine residue colour

19 years agoisGap method implemented in utils, and optimized
amwaterhouse [Wed, 15 Dec 2004 17:26:47 +0000 (17:26 +0000)]
isGap method implemented in utils, and optimized

19 years agoisGap method implemented in utils
amwaterhouse [Wed, 15 Dec 2004 17:25:25 +0000 (17:25 +0000)]
isGap method implemented in utils

19 years agoGSlider replaces GConservationIncrementPanel
amwaterhouse [Wed, 15 Dec 2004 17:24:14 +0000 (17:24 +0000)]
GSlider replaces GConservationIncrementPanel

19 years agono more group editing mode. clustal implemented
amwaterhouse [Wed, 15 Dec 2004 17:23:28 +0000 (17:23 +0000)]
no more group editing mode. clustal implemented

19 years agoDisplays full id with the help of nowrap
amwaterhouse [Wed, 15 Dec 2004 17:22:43 +0000 (17:22 +0000)]
Displays full id with the help of nowrap

19 years agoNew class
amwaterhouse [Wed, 15 Dec 2004 17:22:04 +0000 (17:22 +0000)]
New class

19 years agoColourScheme no longer requires sequence
amwaterhouse [Wed, 15 Dec 2004 17:21:35 +0000 (17:21 +0000)]
ColourScheme no longer requires sequence

19 years agoEnd of GroupEditing, GroupDefiningMode!!!!!
amwaterhouse [Wed, 15 Dec 2004 17:20:32 +0000 (17:20 +0000)]
End of GroupEditing, GroupDefiningMode!!!!!

19 years agoRegister with paintrefresher
amwaterhouse [Wed, 15 Dec 2004 17:19:48 +0000 (17:19 +0000)]
Register with paintrefresher

19 years agoIf selection altered, update RubberbandGroup
amwaterhouse [Wed, 15 Dec 2004 17:19:15 +0000 (17:19 +0000)]
If selection altered, update RubberbandGroup

19 years agoAll colours added, also sequence menu added
amwaterhouse [Wed, 15 Dec 2004 17:18:39 +0000 (17:18 +0000)]
All colours added, also sequence menu added

19 years agoRight mouse brings up Popupmenu
amwaterhouse [Wed, 15 Dec 2004 17:17:51 +0000 (17:17 +0000)]
Right mouse brings up Popupmenu

19 years agoColourScheme findColour no longer needs sequence
amwaterhouse [Wed, 15 Dec 2004 17:17:16 +0000 (17:17 +0000)]
ColourScheme findColour no longer needs sequence

19 years agoIf selection altered, update Rubberband group also
amwaterhouse [Wed, 15 Dec 2004 17:16:06 +0000 (17:16 +0000)]
If selection altered, update Rubberband group also

19 years agoREpainting after graph panel setVisible fixed
amwaterhouse [Wed, 15 Dec 2004 17:15:25 +0000 (17:15 +0000)]
REpainting after graph panel setVisible fixed

19 years agoSliderPanel added, edit is by mouse click
amwaterhouse [Wed, 15 Dec 2004 17:14:48 +0000 (17:14 +0000)]
SliderPanel added, edit is by mouse click

19 years agoRemoved, SliderPanel replaces this class
amwaterhouse [Wed, 15 Dec 2004 17:14:04 +0000 (17:14 +0000)]
Removed, SliderPanel replaces this class

19 years agoisGap method added to utils
amwaterhouse [Wed, 15 Dec 2004 17:11:34 +0000 (17:11 +0000)]
isGap method added to utils

19 years agoDont try{}catch the findColour method, lets fix this now
amwaterhouse [Tue, 14 Dec 2004 17:37:06 +0000 (17:37 +0000)]
Dont try{}catch the findColour method, lets fix this now

19 years agoHTML ouput is now identical to onscreen view
amwaterhouse [Tue, 14 Dec 2004 17:35:55 +0000 (17:35 +0000)]
HTML ouput is now identical to onscreen view

19 years agoEnable PID menuitem
amwaterhouse [Tue, 14 Dec 2004 17:35:27 +0000 (17:35 +0000)]
Enable PID menuitem

19 years agoPID Colour scheme now operational!
amwaterhouse [Tue, 14 Dec 2004 17:34:50 +0000 (17:34 +0000)]
PID Colour scheme now operational!

19 years agoAdd Jims name!
amwaterhouse [Tue, 14 Dec 2004 15:41:21 +0000 (15:41 +0000)]
Add Jims name!

19 years agoGetcolours is not needed ????
amwaterhouse [Tue, 14 Dec 2004 14:54:51 +0000 (14:54 +0000)]
Getcolours is not needed ????

19 years agoScalepanel has new constructor
amwaterhouse [Tue, 14 Dec 2004 14:52:39 +0000 (14:52 +0000)]
Scalepanel has new constructor

19 years agoIncrement panel must call globalcolour or seqeuncegroup colour
amwaterhouse [Tue, 14 Dec 2004 14:51:55 +0000 (14:51 +0000)]
Increment panel must call globalcolour or seqeuncegroup colour

19 years agoAllow userdefined colours for groups
amwaterhouse [Tue, 14 Dec 2004 14:51:11 +0000 (14:51 +0000)]
Allow userdefined colours for groups

19 years agoCan now select groups using column selection
amwaterhouse [Tue, 14 Dec 2004 14:50:31 +0000 (14:50 +0000)]
Can now select groups using column selection

19 years agoUserdefinedcolours works for groups as well
amwaterhouse [Tue, 14 Dec 2004 14:49:55 +0000 (14:49 +0000)]
Userdefinedcolours works for groups as well

19 years agoHastable is not used anywhere
amwaterhouse [Tue, 14 Dec 2004 14:48:58 +0000 (14:48 +0000)]
Hastable is not used anywhere

19 years agoNew class for defining groups and selections
amwaterhouse [Tue, 14 Dec 2004 11:24:26 +0000 (11:24 +0000)]
New class for defining groups and selections

19 years agoCopy, cut and move now done via popup menu
amwaterhouse [Tue, 14 Dec 2004 11:23:07 +0000 (11:23 +0000)]
Copy, cut and move now done via popup menu

19 years agoSelection of sequences is continuous
amwaterhouse [Tue, 14 Dec 2004 11:22:30 +0000 (11:22 +0000)]
Selection of sequences is continuous

19 years agoDrawing of group and rubberband corrected
amwaterhouse [Tue, 14 Dec 2004 11:21:26 +0000 (11:21 +0000)]
Drawing of group and rubberband corrected

19 years agoSequence selection now done via popup menu
amwaterhouse [Tue, 14 Dec 2004 11:20:51 +0000 (11:20 +0000)]
Sequence selection now done via popup menu

19 years agomust allow for alignment width
amwaterhouse [Tue, 14 Dec 2004 11:20:18 +0000 (11:20 +0000)]
must allow for alignment width

19 years agoCopy, move and delete now done via Popup menu
amwaterhouse [Tue, 14 Dec 2004 11:19:46 +0000 (11:19 +0000)]
Copy, move and delete now done via Popup menu

19 years agoAddOrRemove function added, start and end res fixed
amwaterhouse [Tue, 14 Dec 2004 11:19:04 +0000 (11:19 +0000)]
AddOrRemove function added, start and end res fixed

19 years agoIf groups doesnt contain group, addition is allowed
amwaterhouse [Tue, 14 Dec 2004 11:18:12 +0000 (11:18 +0000)]
If groups doesnt contain group, addition is allowed

19 years agoHashtable size must allow for total-start
amwaterhouse [Tue, 14 Dec 2004 11:17:27 +0000 (11:17 +0000)]
Hashtable size must allow for total-start

19 years agoChoosing sort again reverses the sort order
amwaterhouse [Tue, 14 Dec 2004 11:16:47 +0000 (11:16 +0000)]
Choosing sort again reverses the sort order

19 years agoNo longer exclusive to SequenceGroups
amwaterhouse [Fri, 10 Dec 2004 14:42:12 +0000 (14:42 +0000)]
No longer exclusive to SequenceGroups

19 years agoNow allows multi coloured HTML output
amwaterhouse [Fri, 10 Dec 2004 14:39:22 +0000 (14:39 +0000)]
Now allows multi coloured HTML output

19 years agoColours set globally in viewport
amwaterhouse [Fri, 10 Dec 2004 14:38:41 +0000 (14:38 +0000)]
Colours set globally in viewport

19 years agoLooks to viewportfor global settings
amwaterhouse [Fri, 10 Dec 2004 14:37:55 +0000 (14:37 +0000)]
Looks to viewportfor global settings

19 years agoAddition of rubberband
amwaterhouse [Fri, 10 Dec 2004 14:37:09 +0000 (14:37 +0000)]
Addition of rubberband

19 years agoNow draws group, rubberband
amwaterhouse [Fri, 10 Dec 2004 14:36:33 +0000 (14:36 +0000)]
Now draws group, rubberband

19 years agosequence selection modified
amwaterhouse [Fri, 10 Dec 2004 14:35:18 +0000 (14:35 +0000)]
sequence selection modified

19 years agoSELECTED IDS COLOURED LIGHT GRAY
amwaterhouse [Fri, 10 Dec 2004 14:34:27 +0000 (14:34 +0000)]
SELECTED IDS COLOURED LIGHT GRAY

19 years agoCOnservationSelected and rubberband method setup
amwaterhouse [Fri, 10 Dec 2004 14:33:53 +0000 (14:33 +0000)]
COnservationSelected and rubberband method setup

19 years agoColour scheme new global implementation
amwaterhouse [Fri, 10 Dec 2004 14:33:08 +0000 (14:33 +0000)]
Colour scheme new global implementation

19 years agoColour etc is now globally set
amwaterhouse [Fri, 10 Dec 2004 14:32:06 +0000 (14:32 +0000)]
Colour etc is now globally set

19 years agoCheck if sequence is in group before adding
amwaterhouse [Fri, 10 Dec 2004 14:31:01 +0000 (14:31 +0000)]
Check if sequence is in group before adding

19 years agoUse cross platform lookandfeel
amwaterhouse [Fri, 10 Dec 2004 14:30:25 +0000 (14:30 +0000)]
Use cross platform lookandfeel

19 years agoDont use updateResidueView
amwaterhouse [Fri, 3 Dec 2004 17:40:05 +0000 (17:40 +0000)]
Dont use updateResidueView

19 years agoSpace char added
amwaterhouse [Fri, 3 Dec 2004 16:36:35 +0000 (16:36 +0000)]
Space char added

19 years agoremove import of jbgui
amwaterhouse [Fri, 3 Dec 2004 16:36:08 +0000 (16:36 +0000)]
remove import of jbgui

19 years agodefault gap char is -
amwaterhouse [Fri, 3 Dec 2004 16:34:51 +0000 (16:34 +0000)]
default gap char is -

19 years agowont work at present, renderer is null
amwaterhouse [Fri, 3 Dec 2004 16:34:21 +0000 (16:34 +0000)]
wont work at present, renderer is null

19 years agoremove splashscreenclosing line
amwaterhouse [Fri, 3 Dec 2004 16:32:56 +0000 (16:32 +0000)]
remove splashscreenclosing line

19 years agoPreparing for groupselect mode
amwaterhouse [Fri, 3 Dec 2004 16:32:23 +0000 (16:32 +0000)]
Preparing for groupselect mode

19 years agoav.charWidth is now an int
amwaterhouse [Fri, 3 Dec 2004 16:31:09 +0000 (16:31 +0000)]
av.charWidth is now an int

19 years agosend SequenceGroup to renderer
amwaterhouse [Fri, 3 Dec 2004 16:30:17 +0000 (16:30 +0000)]
send SequenceGroup to renderer

19 years agocharWidth is now an int
amwaterhouse [Fri, 3 Dec 2004 16:29:38 +0000 (16:29 +0000)]
charWidth is now an int

19 years agoText alignment changes
amwaterhouse [Fri, 3 Dec 2004 16:29:08 +0000 (16:29 +0000)]
Text alignment changes