jalview.git
18 years agoSmoother drawing
amwaterhouse [Thu, 10 Aug 2006 14:57:52 +0000 (14:57 +0000)]
Smoother drawing

18 years agoCheck selection size before making tree
amwaterhouse [Thu, 10 Aug 2006 14:57:40 +0000 (14:57 +0000)]
Check selection size before making tree

18 years agogroup.getSize should be ab.alignment.getGroups
amwaterhouse [Thu, 10 Aug 2006 14:57:13 +0000 (14:57 +0000)]
group.getSize should be ab.alignment.getGroups

18 years agoCheck alAndColSel are not null
amwaterhouse [Thu, 10 Aug 2006 14:56:21 +0000 (14:56 +0000)]
Check alAndColSel are not null

18 years agoControl and shift for col selection
amwaterhouse [Thu, 10 Aug 2006 13:40:59 +0000 (13:40 +0000)]
Control and shift for col selection

18 years agoReset button added
amwaterhouse [Thu, 10 Aug 2006 13:18:12 +0000 (13:18 +0000)]
Reset button added

18 years agoRight mouse works with cursor mode
amwaterhouse [Thu, 10 Aug 2006 13:17:54 +0000 (13:17 +0000)]
Right mouse works with cursor mode

18 years agoOnly add 1 feature settings table
amwaterhouse [Thu, 10 Aug 2006 13:17:29 +0000 (13:17 +0000)]
Only add 1 feature settings table

18 years agoComment out start and end refs
amwaterhouse [Thu, 10 Aug 2006 12:58:00 +0000 (12:58 +0000)]
Comment out start and end refs

18 years ago1.1 compatible
amwaterhouse [Thu, 10 Aug 2006 09:50:14 +0000 (09:50 +0000)]
1.1 compatible

18 years agofile: is a URL
amwaterhouse [Thu, 10 Aug 2006 09:48:51 +0000 (09:48 +0000)]
file: is a URL

18 years agoInvert column selection
amwaterhouse [Thu, 10 Aug 2006 09:48:32 +0000 (09:48 +0000)]
Invert column selection

18 years agonew SequenceI method for making a sub sequence from a range on the
jprocter [Wed, 9 Aug 2006 16:21:36 +0000 (16:21 +0000)]
new SequenceI method for making a sub sequence from a range on the
current sequence.

18 years agoalignment from seqCigars will correctly mark deleted residues as
jprocter [Wed, 9 Aug 2006 16:20:41 +0000 (16:20 +0000)]
alignment from seqCigars will correctly mark deleted residues as
isolated insertions.

18 years agorefactored hidden regions methods and made an AlignmentView preserve
jprocter [Wed, 9 Aug 2006 16:19:24 +0000 (16:19 +0000)]
refactored hidden regions methods and made an AlignmentView preserve
the alignment in hidden regions.

18 years agofixed multiple shifts bug.
jprocter [Wed, 9 Aug 2006 16:12:58 +0000 (16:12 +0000)]
fixed multiple shifts bug.

18 years agoMust save all the feature settings
amwaterhouse [Wed, 9 Aug 2006 15:56:48 +0000 (15:56 +0000)]
Must save all the feature settings

18 years agoCheck if groups have already been added or not
amwaterhouse [Wed, 9 Aug 2006 15:56:32 +0000 (15:56 +0000)]
Check if groups have already been added or not

18 years agoFix for local sources with no capabilities
amwaterhouse [Wed, 9 Aug 2006 15:56:05 +0000 (15:56 +0000)]
Fix for local sources with no capabilities

18 years agoIcon drawing updated
amwaterhouse [Wed, 9 Aug 2006 15:55:43 +0000 (15:55 +0000)]
Icon drawing updated

18 years agoNull hidden cols check
amwaterhouse [Wed, 9 Aug 2006 15:55:26 +0000 (15:55 +0000)]
Null hidden cols check

18 years agoNo need to re repaint
amwaterhouse [Wed, 9 Aug 2006 15:54:58 +0000 (15:54 +0000)]
No need to re repaint

18 years agoHeight and info message
amwaterhouse [Wed, 9 Aug 2006 15:54:45 +0000 (15:54 +0000)]
Height and info message

18 years agoTransparency
amwaterhouse [Wed, 9 Aug 2006 15:54:26 +0000 (15:54 +0000)]
Transparency

18 years agoEndres check for wrap alignment
amwaterhouse [Wed, 9 Aug 2006 15:54:07 +0000 (15:54 +0000)]
Endres check for wrap alignment

18 years agoSet the start res and start seq
amwaterhouse [Wed, 9 Aug 2006 15:53:44 +0000 (15:53 +0000)]
Set the start res and start seq

18 years agoCopy hidden cols to new alignment
amwaterhouse [Wed, 9 Aug 2006 15:53:22 +0000 (15:53 +0000)]
Copy hidden cols to new alignment

18 years agoRemove system.out
amwaterhouse [Wed, 9 Aug 2006 08:51:07 +0000 (08:51 +0000)]
Remove system.out

18 years agoMake sure link menu is displayed
amwaterhouse [Wed, 9 Aug 2006 08:50:57 +0000 (08:50 +0000)]
Make sure link menu is displayed

18 years agoSave links and scores and keyValues for features
amwaterhouse [Wed, 9 Aug 2006 08:50:36 +0000 (08:50 +0000)]
Save links and scores and keyValues for features

18 years agoKeyValue pairs for features
amwaterhouse [Wed, 9 Aug 2006 08:50:07 +0000 (08:50 +0000)]
KeyValue pairs for features

18 years agoInput Data...
amwaterhouse [Tue, 8 Aug 2006 15:45:20 +0000 (15:45 +0000)]
Input Data...

18 years agoCapitals
amwaterhouse [Tue, 8 Aug 2006 15:44:59 +0000 (15:44 +0000)]
Capitals

18 years agoOut by 1 error on show columns
amwaterhouse [Tue, 8 Aug 2006 15:44:36 +0000 (15:44 +0000)]
Out by 1 error on show columns

18 years agoApplet has hidden regions
amwaterhouse [Tue, 8 Aug 2006 15:44:08 +0000 (15:44 +0000)]
Applet has hidden regions

18 years agoremoved extraneous classes.
jprocter [Tue, 8 Aug 2006 11:04:58 +0000 (11:04 +0000)]
removed extraneous classes.

18 years agolocally modified biojava-dasobert package is now org.biojava.dasobert
jprocter [Tue, 8 Aug 2006 09:47:26 +0000 (09:47 +0000)]
locally modified biojava-dasobert package is now org.biojava.dasobert

18 years agoUse idCanvas highlight system
amwaterhouse [Mon, 7 Aug 2006 15:25:42 +0000 (15:25 +0000)]
Use idCanvas highlight system

18 years ago1.1 compatible
amwaterhouse [Mon, 7 Aug 2006 15:25:34 +0000 (15:25 +0000)]
1.1 compatible

18 years agoUse idCanvas highlight system
amwaterhouse [Mon, 7 Aug 2006 15:14:13 +0000 (15:14 +0000)]
Use idCanvas highlight system

18 years ago1.1 compatible
amwaterhouse [Mon, 7 Aug 2006 15:13:47 +0000 (15:13 +0000)]
1.1 compatible

18 years agoSet wrapped mode even if false
amwaterhouse [Mon, 7 Aug 2006 14:46:45 +0000 (14:46 +0000)]
Set wrapped mode even if false

18 years agocatch out of memory error for consensus when loading groups
amwaterhouse [Mon, 7 Aug 2006 14:37:33 +0000 (14:37 +0000)]
catch out of memory error for consensus when loading groups

18 years agoadded commented out seqStrings comment.
jprocter [Mon, 7 Aug 2006 12:20:12 +0000 (12:20 +0000)]
added commented out seqStrings comment.

18 years agorecover original data for tree and pca as alignment view.
jprocter [Fri, 4 Aug 2006 14:28:05 +0000 (14:28 +0000)]
recover original data for tree and pca as alignment view.

18 years agoShow reveal all menu
amwaterhouse [Fri, 28 Jul 2006 16:06:51 +0000 (16:06 +0000)]
Show reveal all menu

18 years agofindSeq in SeqPanel is used
amwaterhouse [Fri, 28 Jul 2006 16:06:33 +0000 (16:06 +0000)]
findSeq in SeqPanel is used

18 years agoResize image if id width changes
amwaterhouse [Fri, 28 Jul 2006 16:06:10 +0000 (16:06 +0000)]
Resize image if id width changes

18 years agoNo need for count
amwaterhouse [Fri, 28 Jul 2006 16:05:47 +0000 (16:05 +0000)]
No need for count

18 years agoResize inactive when mouse exited and no dragEvent
amwaterhouse [Fri, 28 Jul 2006 16:05:31 +0000 (16:05 +0000)]
Resize inactive when mouse exited and no dragEvent

18 years agogetIndex replaced with findSeq in seqPanel
amwaterhouse [Fri, 28 Jul 2006 16:04:58 +0000 (16:04 +0000)]
getIndex replaced with findSeq in seqPanel

18 years agoRemove system.out
amwaterhouse [Fri, 28 Jul 2006 16:04:37 +0000 (16:04 +0000)]
Remove system.out

18 years agoScrolling fixed and selection in wrapped mode updated
amwaterhouse [Fri, 28 Jul 2006 16:04:16 +0000 (16:04 +0000)]
Scrolling fixed and selection in wrapped mode updated

18 years agogetIndex replaced by findSeq in Seqpanel
amwaterhouse [Fri, 28 Jul 2006 16:03:38 +0000 (16:03 +0000)]
getIndex replaced by findSeq in Seqpanel

18 years agoOut by one error on reveal columns
amwaterhouse [Fri, 28 Jul 2006 13:42:36 +0000 (13:42 +0000)]
Out by one error on reveal columns

18 years agoCheck height of featurePanel, not this for mousepresses
amwaterhouse [Fri, 28 Jul 2006 13:26:41 +0000 (13:26 +0000)]
Check height of featurePanel, not this for mousepresses

18 years ago1.1 compatible
amwaterhouse [Fri, 28 Jul 2006 13:19:43 +0000 (13:19 +0000)]
1.1 compatible

18 years agoApplet doesnt have hidden columns
amwaterhouse [Fri, 28 Jul 2006 13:17:15 +0000 (13:17 +0000)]
Applet doesnt have hidden columns

18 years agoDont set all feature descriptions on status bar
amwaterhouse [Fri, 28 Jul 2006 13:16:50 +0000 (13:16 +0000)]
Dont set all feature descriptions on status bar

18 years agoDont draw all the panel if just a mouse movement
amwaterhouse [Fri, 28 Jul 2006 13:16:27 +0000 (13:16 +0000)]
Dont draw all the panel if just a mouse movement

18 years agoIf colour hasnt been created, make a new one
amwaterhouse [Fri, 28 Jul 2006 13:16:05 +0000 (13:16 +0000)]
If colour hasnt been created, make a new one

18 years agoAdd transparency
amwaterhouse [Fri, 28 Jul 2006 11:08:54 +0000 (11:08 +0000)]
Add transparency

18 years agooutput source in gff file
amwaterhouse [Fri, 28 Jul 2006 11:08:11 +0000 (11:08 +0000)]
output source in gff file

18 years agoSend gapChar to print original Data
amwaterhouse [Thu, 27 Jul 2006 16:00:59 +0000 (16:00 +0000)]
Send gapChar to print original Data

18 years agoRemove immediate call to repaint when deleting
amwaterhouse [Thu, 27 Jul 2006 16:00:17 +0000 (16:00 +0000)]
Remove immediate call to repaint when deleting

18 years agoseq size cant be less than 2 for tree
amwaterhouse [Thu, 27 Jul 2006 15:59:51 +0000 (15:59 +0000)]
seq size cant be less than 2 for tree

18 years agoSends gapChar to seqData
amwaterhouse [Thu, 27 Jul 2006 15:58:56 +0000 (15:58 +0000)]
Sends gapChar to seqData

18 years agoremove unnecessary constructor
amwaterhouse [Thu, 27 Jul 2006 15:58:05 +0000 (15:58 +0000)]
remove unnecessary constructor

18 years agoRemove unnecessary imports
amwaterhouse [Thu, 27 Jul 2006 13:10:34 +0000 (13:10 +0000)]
Remove unnecessary imports

18 years agoReset das_registry_url if null or empty
amwaterhouse [Thu, 27 Jul 2006 13:10:17 +0000 (13:10 +0000)]
Reset das_registry_url if null or empty

18 years agoDont set pdb file if it doenst exist
amwaterhouse [Thu, 27 Jul 2006 13:09:30 +0000 (13:09 +0000)]
Dont set pdb file if it doenst exist

18 years agoNOR the <pre> tabs
amwaterhouse [Thu, 27 Jul 2006 10:57:32 +0000 (10:57 +0000)]
NOR the <pre> tabs

18 years agoUse DBRefSource.PDB
amwaterhouse [Thu, 27 Jul 2006 10:30:33 +0000 (10:30 +0000)]
Use DBRefSource.PDB

18 years agoSave PDB file to disk
amwaterhouse [Thu, 27 Jul 2006 10:29:45 +0000 (10:29 +0000)]
Save PDB file to disk

18 years agoReadline instead of bit by bit
amwaterhouse [Thu, 27 Jul 2006 07:53:41 +0000 (07:53 +0000)]
Readline instead of bit by bit

18 years agoCant have col less than 0
amwaterhouse [Thu, 27 Jul 2006 07:42:06 +0000 (07:42 +0000)]
Cant have col less than 0

18 years agoSave ref to pdb file
amwaterhouse [Thu, 27 Jul 2006 07:35:10 +0000 (07:35 +0000)]
Save ref to pdb file

18 years agoReadded
amwaterhouse [Thu, 27 Jul 2006 07:34:20 +0000 (07:34 +0000)]
Readded

18 years agoaccidental commit of a build
jprocter [Wed, 26 Jul 2006 17:40:04 +0000 (17:40 +0000)]
accidental commit of a build

18 years agoPDB file MUST have an id
amwaterhouse [Wed, 26 Jul 2006 16:15:32 +0000 (16:15 +0000)]
PDB file MUST have an id

18 years agonot used
amwaterhouse [Wed, 26 Jul 2006 16:14:44 +0000 (16:14 +0000)]
not used

18 years agoLoad and save PDB files
amwaterhouse [Wed, 26 Jul 2006 16:04:10 +0000 (16:04 +0000)]
Load and save PDB files

18 years agoAdd file ref for pdb files
amwaterhouse [Wed, 26 Jul 2006 16:03:51 +0000 (16:03 +0000)]
Add file ref for pdb files

18 years agoIgnore list created
jprocter [Wed, 26 Jul 2006 14:05:10 +0000 (14:05 +0000)]
Ignore list created

18 years agoCigars for representing alignment view as used for calculation.
jprocter [Wed, 26 Jul 2006 13:45:15 +0000 (13:45 +0000)]
Cigars for representing alignment view as used for calculation.

18 years agoCigarBase class and derivatives.
jprocter [Wed, 26 Jul 2006 13:43:24 +0000 (13:43 +0000)]
CigarBase class and derivatives.

18 years agoImplemented CIGAR representation of an Alignment view for passing to
jprocter [Wed, 26 Jul 2006 13:32:37 +0000 (13:32 +0000)]
Implemented CIGAR representation of an Alignment view for passing to
analysis'.

18 years agoCompact Idiosyncratic Gapped Alignment Representation objects for internal rep of...
jprocter [Wed, 26 Jul 2006 13:25:43 +0000 (13:25 +0000)]
Compact Idiosyncratic Gapped Alignment Representation objects for internal rep of hidden alignments and views.

18 years agoSwitch to new srs url
amwaterhouse [Wed, 26 Jul 2006 12:58:40 +0000 (12:58 +0000)]
Switch to new srs url

18 years agoseqs[j] replaces current
amwaterhouse [Wed, 26 Jul 2006 12:31:23 +0000 (12:31 +0000)]
seqs[j] replaces current

18 years agomoved to org.biojava
amwaterhouse [Wed, 26 Jul 2006 10:49:44 +0000 (10:49 +0000)]
moved to org.biojava

18 years agoback to org.biojava
amwaterhouse [Wed, 26 Jul 2006 10:43:43 +0000 (10:43 +0000)]
back to org.biojava

18 years agoBack to org.biojava
amwaterhouse [Wed, 26 Jul 2006 10:43:06 +0000 (10:43 +0000)]
Back to org.biojava

18 years agoColumn hide/show updated
amwaterhouse [Wed, 26 Jul 2006 10:11:56 +0000 (10:11 +0000)]
Column hide/show updated

18 years agoCalculate overlap hidden regions
amwaterhouse [Wed, 26 Jul 2006 10:11:41 +0000 (10:11 +0000)]
Calculate overlap hidden regions

18 years agoRemove left, right, empty cols work on hidden reps
amwaterhouse [Wed, 26 Jul 2006 08:56:08 +0000 (08:56 +0000)]
Remove left, right, empty cols work on hidden reps

18 years agoColumnSelection moved to datamodel
amwaterhouse [Tue, 25 Jul 2006 15:51:25 +0000 (15:51 +0000)]
ColumnSelection moved to datamodel

18 years agoactiveRow is -1
amwaterhouse [Tue, 25 Jul 2006 15:50:56 +0000 (15:50 +0000)]
activeRow is -1

18 years agoOdd edit bug with represented seqs fixed
amwaterhouse [Tue, 25 Jul 2006 15:50:35 +0000 (15:50 +0000)]
Odd edit bug with represented seqs fixed

18 years agoDont add pdb format here
amwaterhouse [Tue, 25 Jul 2006 15:50:08 +0000 (15:50 +0000)]
Dont add pdb format here