jalview.git
18 years agovisWidth allows borders to be drawn around offscreen images when making images
amwaterhouse [Mon, 11 Sep 2006 15:27:34 +0000 (15:27 +0000)]
visWidth allows borders to be drawn around offscreen images when making images

18 years agoRemove system.out
amwaterhouse [Mon, 11 Sep 2006 14:44:48 +0000 (14:44 +0000)]
Remove system.out

18 years agogetVisibleIdWidth() for making images
amwaterhouse [Mon, 11 Sep 2006 11:30:23 +0000 (11:30 +0000)]
getVisibleIdWidth() for making images

18 years agoadded copy consensus sequence to consensus annotation popup menu
jprocter [Thu, 7 Sep 2006 11:39:36 +0000 (11:39 +0000)]
added copy consensus sequence to consensus annotation popup menu

18 years agogetVisibleContigs() returns start and end positions of visible regions of an alignmen...
jprocter [Tue, 5 Sep 2006 13:36:07 +0000 (13:36 +0000)]
getVisibleContigs() returns start and end positions of visible regions of an alignmentView.

18 years agojavadoc on contigs
jprocter [Tue, 5 Sep 2006 13:03:19 +0000 (13:03 +0000)]
javadoc on contigs

18 years agoDont look for middle mouse on the Mac
amwaterhouse [Fri, 1 Sep 2006 12:30:07 +0000 (12:30 +0000)]
Dont look for middle mouse on the Mac

18 years agoMAC moved to viewport
amwaterhouse [Fri, 1 Sep 2006 12:25:34 +0000 (12:25 +0000)]
MAC moved to viewport

18 years agofeature settings
amwaterhouse [Fri, 1 Sep 2006 11:23:03 +0000 (11:23 +0000)]
feature settings

18 years agoFeature Settings
amwaterhouse [Fri, 1 Sep 2006 11:22:33 +0000 (11:22 +0000)]
Feature Settings

18 years agoGraphHeight might be zero
amwaterhouse [Wed, 30 Aug 2006 16:10:07 +0000 (16:10 +0000)]
GraphHeight might be zero

18 years agojnet file is 1 to 1 mapping
amwaterhouse [Wed, 30 Aug 2006 16:09:47 +0000 (16:09 +0000)]
jnet file is 1 to 1 mapping

18 years agoRemove unnecessary separotor
amwaterhouse [Wed, 30 Aug 2006 16:09:25 +0000 (16:09 +0000)]
Remove unnecessary separotor

18 years agoGap added to aa3Hash
amwaterhouse [Wed, 30 Aug 2006 16:08:58 +0000 (16:08 +0000)]
Gap added to aa3Hash

18 years agoUser colours are case sensitive
amwaterhouse [Wed, 30 Aug 2006 16:08:36 +0000 (16:08 +0000)]
User colours are case sensitive

18 years agoCan shrink graph to zero
amwaterhouse [Tue, 29 Aug 2006 15:31:04 +0000 (15:31 +0000)]
Can shrink graph to zero

18 years agoNo stacktrace
amwaterhouse [Tue, 29 Aug 2006 15:24:40 +0000 (15:24 +0000)]
No stacktrace

18 years agocreateMapping alreadyMapped
amwaterhouse [Tue, 29 Aug 2006 15:24:22 +0000 (15:24 +0000)]
createMapping alreadyMapped

18 years agoAdditional repaint
amwaterhouse [Tue, 29 Aug 2006 15:22:59 +0000 (15:22 +0000)]
Additional repaint

18 years agojnetfile can be loaded onto alignment
amwaterhouse [Tue, 29 Aug 2006 15:22:15 +0000 (15:22 +0000)]
jnetfile can be loaded onto alignment

18 years agoSequenceMapping updated
amwaterhouse [Tue, 29 Aug 2006 15:21:39 +0000 (15:21 +0000)]
SequenceMapping updated

18 years agoJnet files sent to servlet as annotations
amwaterhouse [Tue, 29 Aug 2006 15:15:25 +0000 (15:15 +0000)]
Jnet files sent to servlet as annotations

18 years agounbalanced head tag
amwaterhouse [Thu, 24 Aug 2006 13:03:23 +0000 (13:03 +0000)]
unbalanced head tag

18 years agovolume 20
amwaterhouse [Wed, 23 Aug 2006 08:03:04 +0000 (08:03 +0000)]
volume 20

18 years ago2.1 updates
amwaterhouse [Tue, 22 Aug 2006 16:54:40 +0000 (16:54 +0000)]
2.1 updates

18 years agoadd link.gif Release_2_1
amwaterhouse [Tue, 22 Aug 2006 16:25:21 +0000 (16:25 +0000)]
add link.gif

18 years ago2.1 update
amwaterhouse [Tue, 22 Aug 2006 15:31:31 +0000 (15:31 +0000)]
2.1 update

18 years agoTo uppercase only visible
amwaterhouse [Tue, 22 Aug 2006 14:29:10 +0000 (14:29 +0000)]
To uppercase only visible

18 years agodocumentation - adding new Input data menu entries.
jprocter [Tue, 22 Aug 2006 13:47:47 +0000 (13:47 +0000)]
documentation - adding new Input data menu entries.

18 years agoadded note on column-separability
jprocter [Tue, 22 Aug 2006 13:25:47 +0000 (13:25 +0000)]
added note on column-separability

18 years agodocumentation
jprocter [Tue, 22 Aug 2006 13:13:23 +0000 (13:13 +0000)]
documentation

18 years agogetSequenceStrings() bug fixed.
jprocter [Tue, 22 Aug 2006 13:01:50 +0000 (13:01 +0000)]
getSequenceStrings() bug fixed.

18 years agoRemove group when hiding cols from scalePanel
amwaterhouse [Tue, 22 Aug 2006 10:39:03 +0000 (10:39 +0000)]
Remove group when hiding cols from scalePanel

18 years ago2006
amwaterhouse [Tue, 22 Aug 2006 09:11:05 +0000 (09:11 +0000)]
2006

18 years agoPut transparency back
amwaterhouse [Tue, 22 Aug 2006 09:10:48 +0000 (09:10 +0000)]
Put transparency back

18 years agomake 1.1 compatible
amwaterhouse [Tue, 22 Aug 2006 09:10:28 +0000 (09:10 +0000)]
make 1.1 compatible

18 years agohidden region recovery in JPred and new hidden region pruning function
jprocter [Tue, 22 Aug 2006 08:34:04 +0000 (08:34 +0000)]
hidden region recovery in JPred and new hidden region pruning function

18 years agooff by one bug in hiden column unmarshalling
jprocter [Tue, 22 Aug 2006 08:32:40 +0000 (08:32 +0000)]
off by one bug in hiden column unmarshalling

18 years agoheader updated
amwaterhouse [Mon, 21 Aug 2006 15:36:21 +0000 (15:36 +0000)]
header updated

18 years agoheader updated
amwaterhouse [Mon, 21 Aug 2006 15:29:26 +0000 (15:29 +0000)]
header updated

18 years agovalidate groupPanel
amwaterhouse [Mon, 21 Aug 2006 14:48:49 +0000 (14:48 +0000)]
validate groupPanel

18 years agovalidate groupPanel
amwaterhouse [Mon, 21 Aug 2006 14:39:50 +0000 (14:39 +0000)]
validate groupPanel

18 years agoAdd uniprot DBref
amwaterhouse [Mon, 21 Aug 2006 14:39:36 +0000 (14:39 +0000)]
Add uniprot DBref

18 years agoRemove system.out
amwaterhouse [Mon, 21 Aug 2006 14:14:07 +0000 (14:14 +0000)]
Remove system.out

18 years ago1.1 compatible
amwaterhouse [Mon, 21 Aug 2006 14:13:49 +0000 (14:13 +0000)]
1.1 compatible

18 years agoRefactored Jnet and added hidden columns support.
jprocter [Mon, 21 Aug 2006 13:41:41 +0000 (13:41 +0000)]
Refactored Jnet and added hidden columns support.
fixed undo-redo bug, hidden columns are moved with gapped columns and delete columns and undo-redo.

18 years agofixed undo-redo bug, hidden columns are moved with gapped columns and delete columns...
jprocter [Mon, 21 Aug 2006 13:40:54 +0000 (13:40 +0000)]
fixed undo-redo bug, hidden columns are moved with gapped columns and delete columns and undo-redo

18 years agoremoveGaps method can record changes in alignment columns to pass to ColumnSelection
jprocter [Mon, 21 Aug 2006 13:03:28 +0000 (13:03 +0000)]
removeGaps method can record changes in alignment columns to pass to ColumnSelection

18 years agofix for truncation of sequence associated annotation mapped onto alignment
jprocter [Mon, 21 Aug 2006 12:51:46 +0000 (12:51 +0000)]
fix for truncation of sequence associated annotation mapped onto alignment

18 years agoadded shiftList to record changes in alignment column positions.
jprocter [Mon, 21 Aug 2006 12:46:32 +0000 (12:46 +0000)]
added shiftList to record changes in alignment column positions.

18 years agoremove gaps method from AlignFrame.remove_gaps_actionPerformed
jprocter [Mon, 21 Aug 2006 12:45:09 +0000 (12:45 +0000)]
remove gaps method from AlignFrame.remove_gaps_actionPerformed

18 years agoinverse ShiftList and SequenceI.gapMap->ShiftList methods.
jprocter [Mon, 21 Aug 2006 12:43:39 +0000 (12:43 +0000)]
inverse ShiftList and SequenceI.gapMap->ShiftList methods.

18 years agoavoid null pointer exceptions
jprocter [Mon, 21 Aug 2006 12:42:25 +0000 (12:42 +0000)]
avoid null pointer exceptions

18 years agojavadoc
jprocter [Sun, 20 Aug 2006 12:00:35 +0000 (12:00 +0000)]
javadoc

18 years agoCheck colourScheme is not null - jalview prior 2.5 incompatibility
amwaterhouse [Fri, 18 Aug 2006 16:54:54 +0000 (16:54 +0000)]
Check colourScheme is not null - jalview prior 2.5 incompatibility

18 years agodont remove all representative seqs on delete groups
amwaterhouse [Fri, 18 Aug 2006 14:02:52 +0000 (14:02 +0000)]
dont remove all representative seqs on delete groups

18 years agoremove all representative seqs on delete groups
amwaterhouse [Fri, 18 Aug 2006 13:57:14 +0000 (13:57 +0000)]
remove all representative seqs on delete groups

18 years agotreeFile = treeFile
amwaterhouse [Fri, 18 Aug 2006 09:23:25 +0000 (09:23 +0000)]
treeFile = treeFile

18 years agoOnly discover DAS sources if panel shown
amwaterhouse [Fri, 18 Aug 2006 08:53:07 +0000 (08:53 +0000)]
Only discover DAS sources if panel shown

18 years agoonly set new layout if 2 buttons visible
amwaterhouse [Fri, 18 Aug 2006 08:52:28 +0000 (08:52 +0000)]
only set new layout if 2 buttons visible

18 years agoJalview features format adds links as hrefs
amwaterhouse [Fri, 18 Aug 2006 08:51:58 +0000 (08:51 +0000)]
Jalview features format adds links as hrefs

18 years agoH key updates
amwaterhouse [Thu, 17 Aug 2006 14:06:02 +0000 (14:06 +0000)]
H key updates

18 years agoOptionPane invokeLater
amwaterhouse [Thu, 17 Aug 2006 13:51:56 +0000 (13:51 +0000)]
OptionPane invokeLater

18 years agoIf no annotation exists
amwaterhouse [Thu, 17 Aug 2006 13:41:37 +0000 (13:41 +0000)]
If no annotation exists

18 years agoSet bg white
amwaterhouse [Thu, 17 Aug 2006 13:41:10 +0000 (13:41 +0000)]
Set bg white

18 years agoHold onto selected region when hiding all columns only
amwaterhouse [Thu, 17 Aug 2006 13:40:57 +0000 (13:40 +0000)]
Hold onto selected region when hiding all columns only

18 years agomoved visible sub-alignment extraction and update from MsaWSThread to
jprocter [Thu, 17 Aug 2006 13:33:59 +0000 (13:33 +0000)]
moved visible sub-alignment extraction and update from MsaWSThread to
an AlignmentView method, refactored JPredClient to new abstraction and
added flags for canMergeResults and openResultsImmediatly to web
service gui.

18 years agojavadoc
jprocter [Thu, 17 Aug 2006 13:31:23 +0000 (13:31 +0000)]
javadoc

18 years agoMonospace check
amwaterhouse [Thu, 17 Aug 2006 12:34:07 +0000 (12:34 +0000)]
Monospace check

18 years ago1 more pixel allowed between chars and graph
amwaterhouse [Thu, 17 Aug 2006 12:33:55 +0000 (12:33 +0000)]
1 more pixel allowed between chars and graph

18 years agoKeys update
amwaterhouse [Thu, 17 Aug 2006 10:14:00 +0000 (10:14 +0000)]
Keys update

18 years agocontrol and shift
amwaterhouse [Thu, 17 Aug 2006 10:11:48 +0000 (10:11 +0000)]
control and shift

18 years agoDont set group null hideCOls
amwaterhouse [Thu, 17 Aug 2006 10:08:46 +0000 (10:08 +0000)]
Dont set group null hideCOls

18 years agoOptionPanes invokeLater
amwaterhouse [Thu, 17 Aug 2006 10:08:18 +0000 (10:08 +0000)]
OptionPanes invokeLater

18 years agoControl and alt for toggle hide
amwaterhouse [Thu, 17 Aug 2006 10:08:02 +0000 (10:08 +0000)]
Control and alt for toggle hide

18 years agoFire alignment changed if seqs hidden / revealed
amwaterhouse [Wed, 16 Aug 2006 08:05:35 +0000 (08:05 +0000)]
Fire alignment changed if seqs hidden / revealed

18 years agoCorrect title for sequence parameter applets
amwaterhouse [Tue, 15 Aug 2006 12:47:04 +0000 (12:47 +0000)]
Correct title for sequence parameter applets

18 years agoSequences can be added as parameter
amwaterhouse [Tue, 15 Aug 2006 12:36:11 +0000 (12:36 +0000)]
Sequences can be added as parameter

18 years agoH key added
amwaterhouse [Tue, 15 Aug 2006 11:14:25 +0000 (11:14 +0000)]
H key added

18 years agomake annotation label font size follow alignment font size.
jprocter [Tue, 15 Aug 2006 11:10:03 +0000 (11:10 +0000)]
make annotation label font size follow alignment font size.

18 years agofirst stage of adapting JNet client to hidden regions and new WSClient
jprocter [Tue, 15 Aug 2006 10:59:31 +0000 (10:59 +0000)]
first stage of adapting JNet client to hidden regions and new WSClient
structure.

18 years agofixed alignment ordering name.
jprocter [Tue, 15 Aug 2006 10:57:59 +0000 (10:57 +0000)]
fixed alignment ordering name.

18 years agoensure that close widget is available for jobs that cannot be
jprocter [Tue, 15 Aug 2006 10:57:32 +0000 (10:57 +0000)]
ensure that close widget is available for jobs that cannot be
cancelled.

18 years agoAcknowledgement
amwaterhouse [Tue, 15 Aug 2006 10:35:37 +0000 (10:35 +0000)]
Acknowledgement

18 years agoSetselectiongroup null on hide
amwaterhouse [Tue, 15 Aug 2006 10:35:09 +0000 (10:35 +0000)]
Setselectiongroup null on hide

18 years agoH key to hide / reveal
amwaterhouse [Tue, 15 Aug 2006 10:34:56 +0000 (10:34 +0000)]
H key to hide / reveal

18 years agoAdd key listener to scalePanel and annotationPanel
amwaterhouse [Tue, 15 Aug 2006 10:34:29 +0000 (10:34 +0000)]
Add key listener to scalePanel and annotationPanel

18 years agoSelect revealed seqs
amwaterhouse [Tue, 15 Aug 2006 10:34:11 +0000 (10:34 +0000)]
Select revealed seqs

18 years agoWRITEABLE_FORMATS and READABLE_FORMATS string []
amwaterhouse [Tue, 15 Aug 2006 10:02:12 +0000 (10:02 +0000)]
WRITEABLE_FORMATS and READABLE_FORMATS string []

18 years agoMove features to dataset
amwaterhouse [Tue, 15 Aug 2006 09:59:24 +0000 (09:59 +0000)]
Move features to dataset

18 years agoStockholm parser added
amwaterhouse [Mon, 14 Aug 2006 16:10:00 +0000 (16:10 +0000)]
Stockholm parser added

18 years agoStockholm parser
amwaterhouse [Mon, 14 Aug 2006 16:09:17 +0000 (16:09 +0000)]
Stockholm parser

18 years agorefactored to create generic polling thread and subjobs
jprocter [Mon, 14 Aug 2006 15:23:07 +0000 (15:23 +0000)]
refactored to create generic polling thread and subjobs

18 years ago2.1 updates
amwaterhouse [Mon, 14 Aug 2006 15:22:36 +0000 (15:22 +0000)]
2.1 updates

18 years agofunction to indicate job has finished but no results are available.
jprocter [Mon, 14 Aug 2006 15:22:16 +0000 (15:22 +0000)]
function to indicate job has finished but no results are available.

18 years agoNew file
amwaterhouse [Mon, 14 Aug 2006 15:20:50 +0000 (15:20 +0000)]
New file

18 years agonew feature added
amwaterhouse [Mon, 14 Aug 2006 15:11:33 +0000 (15:11 +0000)]
new feature added

18 years agoStop loading must be before JOptionPane, 1.5 bug
amwaterhouse [Mon, 14 Aug 2006 15:11:12 +0000 (15:11 +0000)]
Stop loading must be before JOptionPane, 1.5 bug

18 years agoNo need to check selection group size
amwaterhouse [Mon, 14 Aug 2006 15:10:32 +0000 (15:10 +0000)]
No need to check selection group size

18 years agofindSequenceMatch returns multiple sequences
amwaterhouse [Mon, 14 Aug 2006 15:10:09 +0000 (15:10 +0000)]
findSequenceMatch returns multiple sequences