jprocter [Wed, 26 Jul 2006 13:32:37 +0000 (13:32 +0000)]
Implemented CIGAR representation of an Alignment view for passing to
analysis'.
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.
amwaterhouse [Wed, 26 Jul 2006 12:58:40 +0000 (12:58 +0000)]
Switch to new srs url
amwaterhouse [Wed, 26 Jul 2006 12:31:23 +0000 (12:31 +0000)]
seqs[j] replaces current
amwaterhouse [Wed, 26 Jul 2006 10:49:44 +0000 (10:49 +0000)]
moved to org.biojava
amwaterhouse [Wed, 26 Jul 2006 10:43:43 +0000 (10:43 +0000)]
back to org.biojava
amwaterhouse [Wed, 26 Jul 2006 10:43:06 +0000 (10:43 +0000)]
Back to org.biojava
amwaterhouse [Wed, 26 Jul 2006 10:11:56 +0000 (10:11 +0000)]
Column hide/show updated
amwaterhouse [Wed, 26 Jul 2006 10:11:41 +0000 (10:11 +0000)]
Calculate overlap hidden regions
amwaterhouse [Wed, 26 Jul 2006 08:56:08 +0000 (08:56 +0000)]
Remove left, right, empty cols work on hidden reps
amwaterhouse [Tue, 25 Jul 2006 15:51:25 +0000 (15:51 +0000)]
ColumnSelection moved to datamodel
amwaterhouse [Tue, 25 Jul 2006 15:50:56 +0000 (15:50 +0000)]
activeRow is -1
amwaterhouse [Tue, 25 Jul 2006 15:50:35 +0000 (15:50 +0000)]
Odd edit bug with represented seqs fixed
amwaterhouse [Tue, 25 Jul 2006 15:50:08 +0000 (15:50 +0000)]
Dont add pdb format here
amwaterhouse [Tue, 25 Jul 2006 15:49:42 +0000 (15:49 +0000)]
1.1 compatible
amwaterhouse [Tue, 25 Jul 2006 15:49:14 +0000 (15:49 +0000)]
Moved to datamodel
amwaterhouse [Tue, 25 Jul 2006 13:29:01 +0000 (13:29 +0000)]
Output menus added
amwaterhouse [Tue, 25 Jul 2006 12:57:59 +0000 (12:57 +0000)]
Repaint
amwaterhouse [Tue, 25 Jul 2006 12:57:48 +0000 (12:57 +0000)]
Dont make new image unless resize
amwaterhouse [Tue, 25 Jul 2006 12:57:37 +0000 (12:57 +0000)]
Reorder popupmenu
amwaterhouse [Tue, 25 Jul 2006 10:52:38 +0000 (10:52 +0000)]
Renamed files not to conflict with BIOJAVA
amwaterhouse [Tue, 25 Jul 2006 10:49:55 +0000 (10:49 +0000)]
jalview.biojava
amwaterhouse [Tue, 25 Jul 2006 10:25:59 +0000 (10:25 +0000)]
x < endres-startres
amwaterhouse [Tue, 25 Jul 2006 10:25:10 +0000 (10:25 +0000)]
x < endres-startres
amwaterhouse [Tue, 25 Jul 2006 09:45:04 +0000 (09:45 +0000)]
Add dbrefs to mouseover
amwaterhouse [Tue, 25 Jul 2006 09:44:08 +0000 (09:44 +0000)]
Must be 1.1 compliant
amwaterhouse [Tue, 25 Jul 2006 09:43:53 +0000 (09:43 +0000)]
Remove associate menu
amwaterhouse [Tue, 25 Jul 2006 09:38:52 +0000 (09:38 +0000)]
FileLoader replaces paste when Dropping files
amwaterhouse [Tue, 25 Jul 2006 09:37:53 +0000 (09:37 +0000)]
Associate pdb files
amwaterhouse [Tue, 25 Jul 2006 09:37:41 +0000 (09:37 +0000)]
pdb fetchDataAsFile
amwaterhouse [Tue, 25 Jul 2006 09:36:57 +0000 (09:36 +0000)]
PDB format added
amwaterhouse [Tue, 25 Jul 2006 09:36:16 +0000 (09:36 +0000)]
pdb stuff moved to popupmenu
amwaterhouse [Tue, 25 Jul 2006 09:34:11 +0000 (09:34 +0000)]
Can have local file
amwaterhouse [Tue, 25 Jul 2006 09:33:56 +0000 (09:33 +0000)]
If seq has a dataset, dont clear it
amwaterhouse [Tue, 25 Jul 2006 09:33:12 +0000 (09:33 +0000)]
Extends AlignFile, dataset has PDBEntry added
amwaterhouse [Tue, 25 Jul 2006 09:32:17 +0000 (09:32 +0000)]
Can load PDB file from disk
jprocter [Mon, 24 Jul 2006 08:43:12 +0000 (08:43 +0000)]
partly finished pods.
amwaterhouse [Fri, 21 Jul 2006 13:21:48 +0000 (13:21 +0000)]
correct icon draw bug
amwaterhouse [Fri, 21 Jul 2006 13:21:31 +0000 (13:21 +0000)]
Corrected hidden row feature render bug
amwaterhouse [Fri, 21 Jul 2006 13:20:53 +0000 (13:20 +0000)]
Put DBRefFether in a new thread
jprocter [Fri, 21 Jul 2006 12:43:12 +0000 (12:43 +0000)]
Item added to ignoreList
jprocter [Fri, 21 Jul 2006 12:42:35 +0000 (12:42 +0000)]
Item added to ignoreList
amwaterhouse [Fri, 21 Jul 2006 09:54:55 +0000 (09:54 +0000)]
Remove start end for now??
amwaterhouse [Fri, 21 Jul 2006 09:54:35 +0000 (09:54 +0000)]
Add pdb ref
amwaterhouse [Fri, 21 Jul 2006 09:27:20 +0000 (09:27 +0000)]
getViewAsString can ignore sequenceGroup
amwaterhouse [Fri, 21 Jul 2006 09:26:30 +0000 (09:26 +0000)]
this.seqs = seqs
amwaterhouse [Fri, 21 Jul 2006 08:48:31 +0000 (08:48 +0000)]
hidden seqs added
amwaterhouse [Fri, 21 Jul 2006 08:48:20 +0000 (08:48 +0000)]
dbrefs added
amwaterhouse [Fri, 21 Jul 2006 08:48:00 +0000 (08:48 +0000)]
show hide stuff moved from columnSelection
amwaterhouse [Fri, 21 Jul 2006 08:47:30 +0000 (08:47 +0000)]
Saves hidden seqs and DBRefs
amwaterhouse [Fri, 21 Jul 2006 08:47:13 +0000 (08:47 +0000)]
av.showHiddenMarkers check
amwaterhouse [Fri, 21 Jul 2006 08:46:41 +0000 (08:46 +0000)]
Show hide cols and rows
amwaterhouse [Fri, 21 Jul 2006 08:46:17 +0000 (08:46 +0000)]
Hide Selected Cols
amwaterhouse [Fri, 21 Jul 2006 08:45:54 +0000 (08:45 +0000)]
DBRefs now array
amwaterhouse [Fri, 21 Jul 2006 08:44:34 +0000 (08:44 +0000)]
getFullAlignment
amwaterhouse [Fri, 21 Jul 2006 08:44:12 +0000 (08:44 +0000)]
Remove note
amwaterhouse [Fri, 21 Jul 2006 08:43:57 +0000 (08:43 +0000)]
DBRef is an array, not vector
amwaterhouse [Fri, 21 Jul 2006 08:43:11 +0000 (08:43 +0000)]
DBRefs and HiddenRegions saved
jprocter [Fri, 21 Jul 2006 08:19:05 +0000 (08:19 +0000)]
Ignore list created
amwaterhouse [Fri, 21 Jul 2006 07:54:38 +0000 (07:54 +0000)]
Load tree from file constructor fixed
jprocter [Thu, 20 Jul 2006 17:41:32 +0000 (17:41 +0000)]
annotation label font size change in applet.
amwaterhouse [Wed, 19 Jul 2006 15:33:16 +0000 (15:33 +0000)]
Make new seq[] when modifying hidden bits
amwaterhouse [Wed, 19 Jul 2006 15:32:49 +0000 (15:32 +0000)]
Remove b keystroke
amwaterhouse [Wed, 19 Jul 2006 15:22:39 +0000 (15:22 +0000)]
showTranslation is not a checkbox
amwaterhouse [Wed, 19 Jul 2006 15:22:07 +0000 (15:22 +0000)]
Merge new frame buttons added
amwaterhouse [Wed, 19 Jul 2006 15:20:52 +0000 (15:20 +0000)]
Output to text window added
amwaterhouse [Wed, 19 Jul 2006 15:20:34 +0000 (15:20 +0000)]
Correct highlighted res height
amwaterhouse [Wed, 19 Jul 2006 15:20:10 +0000 (15:20 +0000)]
Save output use whole alignment
amwaterhouse [Wed, 19 Jul 2006 15:19:42 +0000 (15:19 +0000)]
Original tree data output in PFAM format
amwaterhouse [Wed, 19 Jul 2006 10:57:43 +0000 (10:57 +0000)]
Count uniprot refs
amwaterhouse [Wed, 19 Jul 2006 10:41:23 +0000 (10:41 +0000)]
Highlight hidden columns after revealing
amwaterhouse [Wed, 19 Jul 2006 10:40:56 +0000 (10:40 +0000)]
datasetSeq bug
amwaterhouse [Wed, 19 Jul 2006 10:40:23 +0000 (10:40 +0000)]
Check for all gapped seqs
amwaterhouse [Wed, 19 Jul 2006 10:39:38 +0000 (10:39 +0000)]
Use Selection group to define sequence range to fetch features
amwaterhouse [Wed, 19 Jul 2006 08:11:16 +0000 (08:11 +0000)]
Copy works with selection area
amwaterhouse [Tue, 18 Jul 2006 15:50:18 +0000 (15:50 +0000)]
Modified for hidden region/group calculation
amwaterhouse [Tue, 18 Jul 2006 15:32:16 +0000 (15:32 +0000)]
Use selection area with hidden columns in calculations
amwaterhouse [Tue, 18 Jul 2006 15:31:51 +0000 (15:31 +0000)]
omitHiddenColumns
amwaterhouse [Tue, 18 Jul 2006 15:31:10 +0000 (15:31 +0000)]
Button to view original data
amwaterhouse [Tue, 18 Jul 2006 15:30:54 +0000 (15:30 +0000)]
Takes strings, not seqs
amwaterhouse [Tue, 18 Jul 2006 15:30:37 +0000 (15:30 +0000)]
getSelectionAsNewSequence added
amwaterhouse [Tue, 18 Jul 2006 15:30:08 +0000 (15:30 +0000)]
Takes a string, not sequence
amwaterhouse [Tue, 18 Jul 2006 15:29:35 +0000 (15:29 +0000)]
Works on strings, not seqs
amwaterhouse [Tue, 18 Jul 2006 15:28:43 +0000 (15:28 +0000)]
Takes string[] instead of seq[]
jprocter [Tue, 18 Jul 2006 14:12:45 +0000 (14:12 +0000)]
use of GapChars
amwaterhouse [Mon, 17 Jul 2006 10:02:34 +0000 (10:02 +0000)]
Towards an auto dbref fetcher
amwaterhouse [Mon, 17 Jul 2006 10:01:00 +0000 (10:01 +0000)]
Dasobert updates, labels and prefix changes
amwaterhouse [Fri, 14 Jul 2006 08:58:11 +0000 (08:58 +0000)]
Just fetch features for selected seqs
amwaterhouse [Thu, 13 Jul 2006 17:01:38 +0000 (17:01 +0000)]
DAS feature retrieval updated
amwaterhouse [Thu, 13 Jul 2006 17:00:47 +0000 (17:00 +0000)]
Selected DAS sources may differ from default
amwaterhouse [Thu, 13 Jul 2006 16:59:55 +0000 (16:59 +0000)]
Sequence is private
amwaterhouse [Wed, 12 Jul 2006 11:52:42 +0000 (11:52 +0000)]
Launch full app parameter takes servlet URL
amwaterhouse [Wed, 12 Jul 2006 11:22:05 +0000 (11:22 +0000)]
Das source browser
amwaterhouse [Wed, 12 Jul 2006 11:21:41 +0000 (11:21 +0000)]
Authority, type and labels
amwaterhouse [Wed, 12 Jul 2006 11:20:59 +0000 (11:20 +0000)]
sequences are private in SequenceGroup
amwaterhouse [Wed, 12 Jul 2006 11:19:11 +0000 (11:19 +0000)]
Append start and end
amwaterhouse [Fri, 7 Jul 2006 16:50:34 +0000 (16:50 +0000)]
Dont discard label if different to H or E
amwaterhouse [Fri, 7 Jul 2006 13:34:14 +0000 (13:34 +0000)]
Redundant Remove Redundancy Removed
amwaterhouse [Fri, 7 Jul 2006 13:30:38 +0000 (13:30 +0000)]
Sequence numbering maintained
amwaterhouse [Fri, 7 Jul 2006 13:09:38 +0000 (13:09 +0000)]
Changeable background colour
git://source.jalview.org / jalview.git / log