notes re JAL-623 and JAL-583, new api methods for adding several structure/seq mappings at once
244 lines of code changed in:
notes re JAL-629
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fixed various null pointer exceptions that occur when PDB files imported into Jmol which do not map to a sequence. Notes re JAL-623
121 lines of code changed in:
fixed various null pointer exceptions that occur when PDB files imported into Jmol which do not map to a sequence
48 lines of code changed in:
added URL display for parameters/options and debugged parameter set switching
357 lines of code changed in:
utilities for cloning and manipulating JabaWS parameter objects.
79 lines of code changed in:
refactored seq/str binding methods and ensured that structures added to existing view get loaded first
251 lines of code changed in:
patch for structures with multiple models, and refactored seq/str binding methods
151 lines of code changed in:
1.2 compatibility
4 lines of code changed in:
revised sequence/structure binding so one structure associated with x-seuqenceI's, and bugfixed superposition code(See JAL-583)
320 lines of code changed in:
revised sequence/structure binding so one structure associated with x-seuqenceI's
5 lines of code changed in:
revised sequence/structure binding so one structure associated with x-seuqenceI's, and bugfixed superposition code(See JAL-583)
199 lines of code changed in:
patch re http://issues.jalview.org/browse/JAL-583 : hack to prevent chains being mapped to sequences with different chainspecs
26 lines of code changed in:
update to Jmol 12.1.5 (will become 12.2.X when released)
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applet now requires java 1.5 minimum (jmol 12.1.xx series is 1.5 only).
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update to Jmol 12.1.5 (will become 12.2.X when released)
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init Jmol with 'SmarterJmolAdapter'
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correct initing of JmolViewer to avoid security exception in unsigned applet moed
16 lines of code changed in:
excluded methods related to broken Jmol applet binding mechanism (JAL-621)
68 lines of code changed in:
correct initing of JmolViewer to avoid security exception in unsigned applet moed
2 lines of code changed in:
excluded methods related to broken Jmol applet binding mechanism (JAL-621) and implemented default 'search all alignment' mode when opening a new PDB structure view
34 lines of code changed in:
ensure template InstallAnywhere build file is always copied before file locations are updated
2 lines of code changed in:
avoid race condition by setting sequence logo flag directly rather than via accessor. See todo for further threadsafety
5 lines of code changed in:
rollback to 1.58 - since excludes are unnecessary
9 lines of code changed in:
broken xml ? (could be old ant issue)
1 lines of code changed in:
complete the sequence-structure mapping details. * JAL-582
11 lines of code changed in:
refactor jmol api so it doesn't clash with Swing component method. * JAL-582
15 lines of code changed in:
check that we have mappings before trying to broadcast mouseovers involving them
4 lines of code changed in:
(probably unnecessary) explicit inclusion of jalview/ext package
2 lines of code changed in:
refactored external structure viewer binding API calls so they do not reference Jmol classes (re-instate's Jmol free launch of JalviewLite).
124 lines of code changed in:
wrapped code from URL retrieval tester as a function to determine correct protocol to retrieve data of a certain type from a datasource string. note - not rigourously tested
182 lines of code changed in:
improved debug output when Jmol viewer creation fails
43 lines of code changed in:
extend jmol binding handles selection events and add in a 'refreshPdbEntries' step so the list of PDB entries jalview knows about can be updated before a Jmol notifyUpdate event is handled
129 lines of code changed in:
binding between JalviewLite alignment windows and some external Jmol viewer
124 lines of code changed in:
JAL-617 - new menu items for exporting current view or complete PCA pointset
135 lines of code changed in:
output the eigenvector matrix in full: JAL-616
11 lines of code changed in:
JAL-612 - catch hidden OOM related to filling in cut and paste text boxes
28 lines of code changed in:
new appletlib path for jars specific to the applet
3 lines of code changed in:
new appletlib path for jars specific to the applet
1 lines of code changed in:
source level now 1.5
4 lines of code changed in:
new appletlib path for jars specific to the applet
2 lines of code changed in:
update Jmol to 12.0.6
2 lines of code changed in:
1.5 annotation removal
0 lines of code changed in:
update jmol instance
2 lines of code changed in:
thread safe construction of Jmol instance and hack to translate invalid jmol state statements.
46 lines of code changed in:
refactor to abstract jmol/jalview binding and applet and application specific sequence structure binding.
782 lines of code changed in:
code design comment
1 lines of code changed in:
1.5 annotation fix and thread safe menu update
4 lines of code changed in:
refactor to jalview.api methods
22 lines of code changed in:
1.5 annotation fix
1 lines of code changed in:
colour menu items are in same radiobutton group
27 lines of code changed in:
1.5 annotation fix
0 lines of code changed in:
cutn'paste fix so rna residue chains are assembled correctly
1 lines of code changed in:
improved parameter set store/save/rename logic and debugged parameter/option display
353 lines of code changed in:
jaba ws client revision 2680
0 lines of code changed in:
reverted dodgy test code
12 lines of code changed in:
improved dialog layout and flow and fixed switching between presets. No preset save/load support yet.
390 lines of code changed in:
ask user if they want to run the JabaWS tester on new URLs
33 lines of code changed in:
render jnlp artefacts for 1G and 2G machines (jalview_1G and jalview_2G.jnlp)
284 lines of code changed in:
interactive/batch mode test for groovy scripting (See JAL-611)
32 lines of code changed in:
ensure that both null and undefined colourscheme names resolve to 'None' when the applied colour scheme is reflected in the gui
5 lines of code changed in:
reorganised colourscheme enumeration to make it easier to add hardwired schemes.
38 lines of code changed in:
jabaws is the new jaba!
1 lines of code changed in: