'no sources selected' calls method on feature settings dialog to prompt user.
fixed never-ending das feature retrieval bug.
0 lines of code changed in:
fixed deadlock
28 lines of code changed in:
setVisible replaces show
7 lines of code changed in:
Version 11.0.2
0 lines of code changed in:
REmoved
0 lines of code changed in:
rebuild sort by scores menu when new annotation is available
4 lines of code changed in:
pad should leave null annotations array null
2 lines of code changed in:
convenient creation of 'score only' annotation.
12 lines of code changed in:
parse alignment properties and add annotation rows for general alignment position annotation.
0 lines of code changed in:
alignment properties and embedded newick strings can be retrieved from parsed files
33 lines of code changed in:
dssp 7-state to three state lookup
38 lines of code changed in:
javadoc
1 lines of code changed in:
remove excessive painting
8 lines of code changed in:
REmove excessive painting
7 lines of code changed in:
Repaint after feature added
5 lines of code changed in:
Prevent err when editing and overview drawing
1 lines of code changed in:
FeatureRenderer mixups fixed
10 lines of code changed in:
Remove system.out�AppletPDBViewer.java
0 lines of code changed in:
Check pdbid size >0
3 lines of code changed in:
Trouble with featureRenderers fixed
14 lines of code changed in:
Move repaint in thread
7 lines of code changed in:
Put alignmentProperties in scrollpane
3 lines of code changed in:
Check feature group is visible for mouse over features
6 lines of code changed in:
remove System.out
1 lines of code changed in:
Add param to Jmol path
2 lines of code changed in:
padGaps moved
4 lines of code changed in:
Make sure mainContainer and owner are not null
0 lines of code changed in:
Must check that featureGroup is visible for mouse over features
8 lines of code changed in:
amendFeatures
1 lines of code changed in:
paintAlignment(true)
2 lines of code changed in:
Place new feature on top of existing features
32 lines of code changed in:
Make sure sequence is in mouse over alignment
2 lines of code changed in:
Amend Features
1 lines of code changed in:
ColourByStructure not ready yet
9 lines of code changed in:
newlines in alignment properties converted to <br>
18 lines of code changed in:
blc header lines inserted as 'comment' alignment property
14 lines of code changed in:
parsers can generate alignment properties
56 lines of code changed in:
getProperties returns nullk for no properties
1 lines of code changed in:
documentation and getProperties method
21 lines of code changed in:
aligned boxes
4 lines of code changed in:
ThresholdIsMin available in applet
33 lines of code changed in:
Set black if colour null
19 lines of code changed in:
Alignment properties available
104 lines of code changed in:
hide the initial window after selection made
0 lines of code changed in:
one colour flag in annotation export
0 lines of code changed in:
bugfix for deleted annotation undo
1 lines of code changed in:
Annotation gradient will use direct colours if no graph exists
45 lines of code changed in:
Allow threshold to be min/max
44 lines of code changed in:
hide annotation colouring options
40 lines of code changed in:
Dont colour labels
1 lines of code changed in:
added/tested sort by scores menu and added basic extractScores function.
1944 lines of code changed in:
use hasScore method to test presence of score in annotation.
5 lines of code changed in:
added 'sort by sequence associated annotation score'
554 lines of code changed in:
bug fixed basic score extraction by regex on description method
4 lines of code changed in:
get annotation by label string
43 lines of code changed in:
fix '\0' bug from score-only positional annotation
2 lines of code changed in:
score is a double, fix bugs for score only annotation not being associated with sequences
7 lines of code changed in:
double sort functions
183 lines of code changed in:
total annotation score is a double for maximum precision.
1 lines of code changed in:
check for null ss character
42 lines of code changed in:
colourText = false
2 lines of code changed in:
score and visible copy construction
6 lines of code changed in:
Edit seqs
53 lines of code changed in:
quick fix for verbose fortranesque comments in preamble of AMPS BLC files (lines were being recognised as JPred concise files)
10 lines of code changed in:
fixed bug in prefix extraction for application
9 lines of code changed in:
basic methods for adding scores extracted from description
16 lines of code changed in:
fix for null annotations
3 lines of code changed in:
groovy support without compile-time dependency.
524 lines of code changed in:
remove should be removeElement
2 lines of code changed in:
Alignment Properties required for annotation file
1 lines of code changed in:
moving word methods to MapList and begin bug-fix for single-residue codon span feature location (see TODOs)
76 lines of code changed in:
getContentPane().add alignmentProperties popup.
10 lines of code changed in:
properties + colours
0 lines of code changed in:
Show scores
27 lines of code changed in:
Export annotations with properties
2 lines of code changed in:
View Properties
64 lines of code changed in:
fix recent file type bug
1 lines of code changed in:
alignmentProperties added
35 lines of code changed in:
Functions for parsing free text properties on sequences, alignments and annotations.
116 lines of code changed in:
transfer of residue numbering as alignment annotation
51 lines of code changed in:
AlignmentAnnotation: added annotation score attribute and allowed for annotation[] array to be null
1377 lines of code changed in:
bugfix for sequence features mapped to multiple contigs on local sequence frame
1 lines of code changed in:
updated mapping for EMBL_Services_V1.1.xsd and tested with basic CDS feature detection.
56 lines of code changed in:
functions that operate on references to sequences in alignment rather than copies.
16 lines of code changed in:
distinct methods for getting references to selected sequences or getting new seuqence objects corresponding to selection.
26 lines of code changed in:
getColour method added
18 lines of code changed in:
Check for null displayCharacters
16 lines of code changed in:
Dbref fetcher takes sequences, not alignment
11 lines of code changed in:
getColour added to structures
56 lines of code changed in:
Test out new arrangement
52 lines of code changed in:
Get colour from structure added
8 lines of code changed in:
check dispalyChar is not null
23 lines of code changed in:
Check displayChar is not null
0 lines of code changed in:
Colour is null
2 lines of code changed in:
remove seqref annotations
4 lines of code changed in:
remove alignmentAnnotation added
14 lines of code changed in:
Only fetch refs for seelcted sequences
0 lines of code changed in:
fix null annotation values
17 lines of code changed in:
global dbref fetch option in web services menu.
21 lines of code changed in:
value only annotation
10 lines of code changed in:
adds annotation for display (with flag to set alignmentAnnotation as hidden initially)
15 lines of code changed in:
annotation and seqs vectors are protected members for use by file parsers for adding data for import.
174 lines of code changed in:
tfactor annotation description includes full sequenceID
1 lines of code changed in:
tfactor and occupancy extracted from PDB file, and tfactor added as sequence associated alignment annotation.
19 lines of code changed in:
bugfix
5 lines of code changed in:
fixed column selection cut/paste and self paste.
16 lines of code changed in:
sequence associated alignment annotation copy for column range selection
7 lines of code changed in:
ensure edit command gapChar is updated and used for padding when no alignmentI reference is available
11 lines of code changed in:
padGaps flag in copy constructor
2 lines of code changed in:
javadoc note on padding AlignmentAnnotation to alignment width
3 lines of code changed in:
copying sequenceMapping, restrict(alstart/end) and pad(alwidth) method.
91 lines of code changed in:
REPLACE added to edit command
134 lines of code changed in:
Only setDropTarget if Desktop is not null
8 lines of code changed in:
Validate range for all annotations
2 lines of code changed in:
Redundant code commented out
5 lines of code changed in:
hastext = false
3 lines of code changed in:
dont set seqref null if index incorrect
0 lines of code changed in:
featureGroups not null
3 lines of code changed in:
Pad gaps when annotation editing
14 lines of code changed in:
quality has text false
6 lines of code changed in:
Quality does not have text
5 lines of code changed in:
Alignment of labels and text
36 lines of code changed in:
checks for scrollbar height
7 lines of code changed in:
Disable memory checker for now
8 lines of code changed in:
adjustForAlignment on new seq ref
0 lines of code changed in:
Check values not null in copy constructor
12 lines of code changed in:
made compileApplet and obfuscate depend on the presence of a java 1.1 jdk to ensure that applet jar is properly 1.1 compliant.
26 lines of code changed in:
java 1.1 compliance
7 lines of code changed in:
bugfix for jalviewApplet run from command line.
1448 lines of code changed in:
bugfix.
5 lines of code changed in:
jmol lib dependency for proguard and castorbinding target.
311 lines of code changed in:
use of suffix string (filename.blc#suffixstring) to read a specified iteration from blc file.
250 lines of code changed in:
refactored to allow seeks on a FileParse datasource so IdentifyFile can be applied to an inputstream.
385 lines of code changed in:
javadoc
241 lines of code changed in:
ascii type
883 lines of code changed in:
paste adds or creates full copies of objects in clipboard, and properly copies sequence associated alignment annotation.
128 lines of code changed in:
pdb files are global to all alignments with new mapping mechanism.
5 lines of code changed in:
paste/cut now adds or removes associated AlignmentAnnotation.
702 lines of code changed in:
copy constructors and AlignmentAnnotation sequenceRef mechanisms for pasting sequences and annotation.
974 lines of code changed in:
copy constructor and ascii type change.
227 lines of code changed in:
proper copy constructor (not clone)
31 lines of code changed in:
Applet remembers PDBEntries, can launch multiple structures from popupmenu
43 lines of code changed in:
Add system.out for Mcview / Jmol detection
2 lines of code changed in:
Remove system.out
0 lines of code changed in:
drawSequence must be synchronized
2 lines of code changed in:
Too many calls to paintAlignment
4 lines of code changed in:
drawSequence must be synchronized
5 lines of code changed in:
FeatureRenderer takes alignmentPanel
101 lines of code changed in:
Check alignment has same sequence
1 lines of code changed in:
basic support for multi-exon CDS features
176 lines of code changed in:
Number pad keys can be used in cursor mode
20 lines of code changed in:
SetTargetColour before dialog.show
5 lines of code changed in:
Modified to compile applet with Jmol jar present
11 lines of code changed in:
fixed for display of 'null' group features
8 lines of code changed in:
fixed base lookup bug in dna pairwise alignment and ensured abiguous and non-standard aa and na codes are preserved in aligned sequences.
39 lines of code changed in:
Can add features with no group
13 lines of code changed in:
Adjustment for hidden columns
7 lines of code changed in:
Use same mouse events as scalePanel
15 lines of code changed in:
Amend features/annotations in applet
1338 lines of code changed in:
Used several places
79 lines of code changed in:
If hiddenColumns are null, then column is viisble
0 lines of code changed in:
featureAdded not in applet
2 lines of code changed in:
Paste menu item dispalyed on right click. Memory settings visible in this version
146 lines of code changed in:
Pasted file doesnt have title and not reloadable
9 lines of code changed in:
call getAllframes on desktop instance
2 lines of code changed in:
newFEatures flag for seq type
13 lines of code changed in:
Use newFeatures flag
17 lines of code changed in:
combobox for overlapping features
124 lines of code changed in:
paintALignment
3 lines of code changed in:
flag for dasCoordSysFound added
0 lines of code changed in:
Throw exception if pdb result size is zero
11 lines of code changed in:
doco change.
1 lines of code changed in:
update settings for new groups (always displayed) and new feature types (containing group is checked and type is checked and displayed on top)
63 lines of code changed in:
bugfix + create/amend whilst feature panel open (still fixing)
41 lines of code changed in:
typo fix.
2 lines of code changed in:
Allow for scroll bar height
5 lines of code changed in:
featuresAdded method introduced for consistency with application for notifying gui when features have been modified/created.
811 lines of code changed in:
fr==null check.
1158 lines of code changed in:
feature group state and type order preference storage/retrieval.
38 lines of code changed in:
featuresAdded call for transferred PDB features
7 lines of code changed in:
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.
401 lines of code changed in:
added feature type order preference attribute and visible feature group state element
201 lines of code changed in:
New seq feature name not added here
2 lines of code changed in:
getAllFeaturesAtRes replace by findFeaturesAtRes
7 lines of code changed in:
addElement
15 lines of code changed in:
destroy destroyed
0 lines of code changed in:
destroy destroyed
1 lines of code changed in:
Destroy alignment moved to finalize
2 lines of code changed in:
Chain might be null
3 lines of code changed in:
Destroy Alignment when closing frame
5 lines of code changed in:
Destroy aligment method added
15 lines of code changed in:
Must allow for scrollbar height
8 lines of code changed in: