jalview.git
6 years agoJAL-3032 BrowserLauncher simplified for JS
hansonr [Sat, 23 Jun 2018 23:00:07 +0000 (00:00 +0100)]
JAL-3032 BrowserLauncher simplified for JS

window.open(url)

6 years agomoving SwingJS-site.zip to /swingjs/
hansonr [Sat, 23 Jun 2018 22:59:19 +0000 (23:59 +0100)]
moving SwingJS-site.zip to /swingjs/

6 years agoRELATIVE_URL
hansonr [Sat, 23 Jun 2018 17:01:20 +0000 (18:01 +0100)]
RELATIVE_URL

6 years agoMerge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git...
hansonr [Sat, 23 Jun 2018 16:59:46 +0000 (17:59 +0100)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026

6 years agoJAL-3026 JDesktop/JInternalFrames support + relative URL file loading
hansonr [Sat, 23 Jun 2018 16:57:20 +0000 (17:57 +0100)]
JAL-3026 JDesktop/JInternalFrames support + relative URL file loading

- preliminary
- no minimization to JDesktopIcon
- no maximization
- z-order not checked

See JalviewJS2.java

new SwingJS-site.zip

AlignFrame.java:

JS bypass for addServiceListeners()

AppletFormatAdapter.java:
DataSourceType.java:
FileParse.java:

adds DataSourceType.RELATIVE_URL

for indicating files relative to the HTML page.

Desktop.java:

JS bypass for Console, Dialog Thread, News, Vamsas, and URL links

Jalview.java

JS bypass forparsing h, help, nodisplay, nogui, jabaws, startup example.

6 years agoJAL-3032 avoid assignments on the same line as synchronized
gmungoc [Fri, 22 Jun 2018 15:06:37 +0000 (16:06 +0100)]
JAL-3032 avoid assignments on the same line as synchronized

6 years agoMerge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git...
gmungoc [Fri, 22 Jun 2018 13:49:22 +0000 (14:49 +0100)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026

6 years agoJAL-3030 size split frame taller
gmungoc [Fri, 22 Jun 2018 13:49:17 +0000 (14:49 +0100)]
JAL-3030 size split frame taller

6 years agoMerge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git...
hansonr [Fri, 22 Jun 2018 13:45:53 +0000 (14:45 +0100)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026

6 years agofix for no access-control-origin on jalview site
hansonr [Fri, 22 Jun 2018 13:45:10 +0000 (14:45 +0100)]
fix for no access-control-origin on jalview site

6 years agoJAL-3032 more informative failure message
gmungoc [Fri, 22 Jun 2018 10:04:04 +0000 (11:04 +0100)]
JAL-3032 more informative failure message

6 years agoJInternalFrame implemented as such; no need for JSInternalFrame
hansonr [Fri, 22 Jun 2018 09:00:54 +0000 (10:00 +0100)]
JInternalFrame implemented as such; no need for JSInternalFrame

6 years agoJAL-3032 adds JSInternalFrame
hansonr [Fri, 22 Jun 2018 07:26:06 +0000 (08:26 +0100)]
JAL-3032 adds JSInternalFrame

JSInternalFrame extends JFrame.

Motif involves coercing a JInternalFrame in Java to a JSInternalFrame in
JavaScript:

<code>
JInternalFrame f;

/**
 * @j2sNative
 *
 * f = Clazz.new_('javax.swing.JSInternalFrame');
 *
 */
{
 f = new JInternalFrame();
}
</code>

6 years agoMerge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git...
hansonr [Thu, 21 Jun 2018 22:30:09 +0000 (23:30 +0100)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026

6 years agoJAL-3032 transpiler and runtime fixes
hansonr [Thu, 21 Jun 2018 22:29:40 +0000 (23:29 +0100)]
JAL-3032 transpiler and runtime fixes

for(final int xxx....)
regex Matcher charSequence.subSequence$I$I

6 years agoJAL-3030 allow uncaught exceptions (for easier JS debuggin)
gmungoc [Thu, 21 Jun 2018 15:52:49 +0000 (16:52 +0100)]
JAL-3030 allow uncaught exceptions (for easier JS debuggin)

6 years agoJAL-3030 try to open a split frame if file and file2 are supplied
gmungoc [Thu, 21 Jun 2018 11:37:33 +0000 (12:37 +0100)]
JAL-3030 try to open a split frame if file and file2 are supplied

6 years agoMerge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git...
hansonr [Thu, 21 Jun 2018 11:35:03 +0000 (12:35 +0100)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026

6 years agoToolTip fixed.
hansonr [Thu, 21 Jun 2018 11:34:37 +0000 (12:34 +0100)]
ToolTip fixed.

new SwingJS-site.zip
new Transpiler "for var var"

6 years agoJAL-3032 round Quality score for tooltip (as it becomes double in JalviewJS!)
gmungoc [Thu, 21 Jun 2018 09:22:24 +0000 (10:22 +0100)]
JAL-3032 round Quality score for tooltip (as it becomes double in JalviewJS!)

6 years agoJAL-3032 new SwingJS-site.zip
hansonr [Thu, 21 Jun 2018 08:15:27 +0000 (09:15 +0100)]
JAL-3032 new SwingJS-site.zip

JToolTip (still issues with HTML)

6 years agocore_jalview creation
hansonr [Thu, 21 Jun 2018 00:24:25 +0000 (01:24 +0100)]
core_jalview creation

6 years agoJAL-3032 for (var var
hansonr [Wed, 20 Jun 2018 23:38:30 +0000 (00:38 +0100)]
JAL-3032 for (var var

6 years agotemporary JSProgressBarUI
hansonr [Wed, 20 Jun 2018 22:49:10 +0000 (23:49 +0100)]
temporary JSProgressBarUI

6 years agofixes menubar closer issue
hansonr [Wed, 20 Jun 2018 22:31:01 +0000 (23:31 +0100)]
fixes menubar closer issue

6 years agoJS fix for JTooltip popup cache class error - new SwingJS-site.zip
hansonr [Wed, 20 Jun 2018 22:13:42 +0000 (23:13 +0100)]
JS fix for JTooltip popup cache class error - new SwingJS-site.zip

6 years agoSeqCanvas and OverviewCanvas
hansonr [Wed, 20 Jun 2018 17:51:07 +0000 (18:51 +0100)]
SeqCanvas and OverviewCanvas

It's important for us that these extend JPanel, not JComponent. This is
because we have slipped in a new subclass, JSComponent, that extends
JComponent and is a superclass of all Swing components in SwingJS.

6 years agoMerge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git...
hansonr [Wed, 20 Jun 2018 16:08:05 +0000 (17:08 +0100)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026

6 years agofixes broken MissingResourceException
hansonr [Wed, 20 Jun 2018 16:07:29 +0000 (17:07 +0100)]
fixes broken MissingResourceException

new SinwgJS-site.zip

6 years agoJAL-3032 simplified _LoadFileWaitTillLoaded with no thread
gmungoc [Wed, 20 Jun 2018 15:47:19 +0000 (16:47 +0100)]
JAL-3032 simplified _LoadFileWaitTillLoaded with no thread

6 years agonew SwingJS-site.zip
hansonr [Wed, 20 Jun 2018 13:01:30 +0000 (14:01 +0100)]
new SwingJS-site.zip

6 years agoJAL-3032 FileLoader fixes for SwingJS
hansonr [Wed, 20 Jun 2018 12:01:23 +0000 (13:01 +0100)]
JAL-3032 FileLoader fixes for SwingJS

SwingJS-site.zip for java.util.concurrent.locks.*

swingjs/j2s/java/awt/KeyboardFocusManager.js
was not found. (in JInternalFrame)

6 years agoadd java.util.concurrent.locks
hansonr [Wed, 20 Jun 2018 11:57:30 +0000 (12:57 +0100)]
add java.util.concurrent.locks

6 years agoupdate of javajs package; adds org.apache.harmony, org.xml.sax.helpers
hansonr [Wed, 20 Jun 2018 10:40:46 +0000 (11:40 +0100)]
update of javajs package; adds org.apache.harmony, org.xml.sax.helpers

File format identified as Fasta

6 years agoBob first commit JAL-3032
hansonr [Wed, 20 Jun 2018 09:59:05 +0000 (10:59 +0100)]
Bob first commit JAL-3032

- jalview/bin/cache.java
 propsAreReadable true for JS
 authordetails, builddetails "xxx" for JS for now
- org.apache.log4j -> jalview.javascript.log4j (minimal)
- jalview/util/MessageManager switch to org.apache.log4j

JavaScript Status:

jalview.io.FileFormatException: Failed to read data from source: CANNOT
ACCESS DATA AT URL 'http://www.jalview.org/examples/uniref50.fa'
((intermediate value).toBIS$O is not a function

6 years agoMessageManager logger to log4j
hansonr [Wed, 20 Jun 2018 09:38:38 +0000 (10:38 +0100)]
MessageManager logger to log4j

6 years agoJAL-3032 load properties as "java.properties"
gmungoc [Wed, 20 Jun 2018 09:31:40 +0000 (10:31 +0100)]
JAL-3032 load properties as "java.properties"

6 years agoJAL-3030 suppress change that goes with JAL-3031
gmungoc [Wed, 20 Jun 2018 08:59:30 +0000 (09:59 +0100)]
JAL-3030 suppress change that goes with JAL-3031

6 years agoJAL-3030 reads features file, properties file
gmungoc [Wed, 20 Jun 2018 08:26:51 +0000 (09:26 +0100)]
JAL-3030 reads features file, properties file

6 years agoJAL-3030 added menu bar
gmungoc [Tue, 19 Jun 2018 11:16:22 +0000 (12:16 +0100)]
JAL-3030 added menu bar

6 years agoJAL-3030 first cut of JalviewJS.main entry point accepting 'file' parameter
gmungoc [Tue, 19 Jun 2018 11:02:52 +0000 (12:02 +0100)]
JAL-3030 first cut of JalviewJS.main entry point accepting 'file' parameter

6 years agoJAL-3026 adding javajs package
hansonr [Mon, 18 Jun 2018 14:18:02 +0000 (16:18 +0200)]
JAL-3026 adding javajs package

adding a general utility package for Java or JavaScript.

6 years agoJAL-3026 - adding README-BH
hansonr [Mon, 18 Jun 2018 11:36:44 +0000 (13:36 +0200)]
JAL-3026 - adding README-BH

first commit

6 years agoJAL-2755 correct Javadoc and error handling
gmungoc [Thu, 7 Jun 2018 14:40:11 +0000 (15:40 +0100)]
JAL-2755 correct Javadoc and error handling

6 years agoJAL-3013 ensure Chimera as a symlink gets resolved
gmungoc [Wed, 6 Jun 2018 14:16:50 +0000 (15:16 +0100)]
JAL-3013 ensure Chimera as a symlink gets resolved

6 years agoJAL-2808 update test for revised treatment of 'mixed type' attribute values
gmungoc [Mon, 4 Jun 2018 19:42:53 +0000 (20:42 +0100)]
JAL-2808 update test for revised treatment of 'mixed type' attribute values

6 years agoJAL-3019 correctly form toRange of 'traversed' MapList
gmungoc [Mon, 4 Jun 2018 19:40:07 +0000 (20:40 +0100)]
JAL-3019 correctly form toRange of 'traversed' MapList

6 years agoJAL-3018 updated REST versions to 6.3
gmungoc [Mon, 4 Jun 2018 14:06:21 +0000 (15:06 +0100)]
JAL-3018 updated REST versions to 6.3

6 years agoJAL-2808 don't capture or report min-max for mixed text/numeric attribute
gmungoc [Thu, 31 May 2018 13:20:50 +0000 (14:20 +0100)]
JAL-2808 don't capture or report min-max for mixed text/numeric attribute

6 years agoJAL-2808 pre-fill numeric inequality filter with min/max range value
gmungoc [Thu, 31 May 2018 10:43:40 +0000 (11:43 +0100)]
JAL-2808 pre-fill numeric inequality filter with min/max range value

6 years agoMerge branch 'bug/JAL-797' into develop
gmungoc [Mon, 28 May 2018 08:23:26 +0000 (09:23 +0100)]
Merge branch 'bug/JAL-797' into develop

6 years agoMerge remote-tracking branch 'origin/releases/Release_2_10_4_Branch' into develop
gmungoc [Mon, 28 May 2018 08:19:40 +0000 (09:19 +0100)]
Merge remote-tracking branch 'origin/releases/Release_2_10_4_Branch' into develop

Conflicts:
src/jalview/io/FeaturesFile.java

6 years agoJAL-2999 release date for 2.10.4b1 set for 27th May 2018
Jim Procter [Sat, 26 May 2018 12:36:41 +0000 (13:36 +0100)]
JAL-2999 release date for 2.10.4b1 set for 27th May 2018

6 years agoMerge branch 'documentation/JAL-2999_r2104b1' into releases/Release_2_10_4_Branch
Jim Procter [Fri, 25 May 2018 12:58:10 +0000 (13:58 +0100)]
Merge branch 'documentation/JAL-2999_r2104b1' into releases/Release_2_10_4_Branch

6 years agoMerge branch 'bug/JAL-2992panelHeight' into releases/Release_2_10_4_Branch
Jim Procter [Fri, 25 May 2018 12:58:01 +0000 (13:58 +0100)]
Merge branch 'bug/JAL-2992panelHeight' into releases/Release_2_10_4_Branch

6 years agoMerge branch 'bug/JAL-1460_dragndropWindows' into releases/Release_2_10_4_Branch
Jim Procter [Fri, 25 May 2018 12:56:34 +0000 (13:56 +0100)]
Merge branch 'bug/JAL-1460_dragndropWindows' into releases/Release_2_10_4_Branch

6 years agoJAL-2992 simpler heuristic for available height bug/JAL-2992panelHeight
gmungoc [Fri, 25 May 2018 12:49:33 +0000 (13:49 +0100)]
JAL-2992 simpler heuristic for available height

6 years agoMerge branch 'bug/JAL-2991_exporttosvgwrapview' into releases/Release_2_10_4_Branch
Jim Procter [Fri, 25 May 2018 10:19:58 +0000 (11:19 +0100)]
Merge branch 'bug/JAL-2991_exporttosvgwrapview' into releases/Release_2_10_4_Branch

6 years agoMerge branch 'feature/JAL-2994chimeraPath' into releases/Release_2_10_4_Branch
Jim Procter [Fri, 25 May 2018 10:10:20 +0000 (11:10 +0100)]
Merge branch 'feature/JAL-2994chimeraPath' into releases/Release_2_10_4_Branch

6 years agoJAL-1460 clarify release notes - and mention that shortcuts are now handled by Jalview
Jim Procter [Fri, 25 May 2018 10:09:33 +0000 (11:09 +0100)]
JAL-1460 clarify release notes - and mention that shortcuts are now handled by Jalview

6 years agoJAL-2994 add a few future release points for good measure in Chimera path search... feature/JAL-2994chimeraPath
Jim Procter [Fri, 25 May 2018 09:59:51 +0000 (10:59 +0100)]
JAL-2994 add a few future release points for good measure in Chimera path search on Windows

6 years agoJAL-1460 temp variable for clearer conditional and some extra brackets for readabilit... bug/JAL-1460_dragndropWindows
Jim Procter [Fri, 25 May 2018 09:47:32 +0000 (10:47 +0100)]
JAL-1460 temp variable for clearer conditional and some extra brackets for readability only


6 years agoJAL-1460 javadoc
Jim Procter [Fri, 25 May 2018 09:47:11 +0000 (10:47 +0100)]
JAL-1460 javadoc

6 years agoJAL-2995 tooltip on fields with double-click to browse for file
gmungoc [Fri, 25 May 2018 08:13:35 +0000 (09:13 +0100)]
JAL-2995 tooltip on fields with double-click to browse for file

6 years agoJAL-2994 temporary patch with paths to Chimera for Windows
gmungoc [Fri, 25 May 2018 08:13:00 +0000 (09:13 +0100)]
JAL-2994 temporary patch with paths to Chimera for Windows

6 years agoJAL-2999 issues resolved (or nearly so) for 2.10.4b1
Jim Procter [Thu, 24 May 2018 15:34:34 +0000 (16:34 +0100)]
JAL-2999 issues resolved (or nearly so) for 2.10.4b1

6 years agoJAL-2997 additional tests
gmungoc [Thu, 24 May 2018 14:59:49 +0000 (15:59 +0100)]
JAL-2997 additional tests

6 years agoJAL-1460 tidied up the use of windows link file parser
Jim Procter [Thu, 24 May 2018 13:38:59 +0000 (14:38 +0100)]
JAL-1460 tidied up the use of windows link file parser

6 years agoJAL-1460 more complete drag'n'drop debugging info and bugfixes
Jim Procter [Thu, 24 May 2018 12:52:32 +0000 (13:52 +0100)]
JAL-1460 more complete drag'n'drop debugging info and bugfixes

6 years agoJAL-1460 process .lnk files dragged to Jalview when on Windows using WindowsShortCutH...
Jim Procter [Thu, 24 May 2018 10:56:32 +0000 (11:56 +0100)]
JAL-1460 process .lnk files dragged to Jalview when on Windows using WindowsShortCutHandler class (thanks to StackOverFlow post..)


6 years agoJAL-1460 new data flavor for URLs added belt-and-braces URL drop code found in Marina...
Jim Procter [Thu, 24 May 2018 10:54:26 +0000 (11:54 +0100)]
JAL-1460 new data flavor for URLs added belt-and-braces URL drop code found in Marinacci and Adamson’s ’Swing Hacks’ (https://books.google.co.uk/books?id=oNbFfcyAtv4C&lpg=PA336&ots=hflsI561Dv&dq=java%20drag%20and%20drop%20url&pg=PA337#v=onepage&q=java%20drag%20and%20drop%20url&f=false ) plus OS X bug workaround.

6 years agoJAL-2993 AlignFrame listen for keystrokes in OverviewPanel
gmungoc [Wed, 23 May 2018 16:14:17 +0000 (17:14 +0100)]
JAL-2993 AlignFrame listen for keystrokes in OverviewPanel

6 years agoJAL-2997 unit test
gmungoc [Wed, 23 May 2018 15:49:53 +0000 (16:49 +0100)]
JAL-2997 unit test

6 years agofix for JAL-2991 - we could do better :/ bug/JAL-2991_exporttosvgwrapview
Jim Procter [Wed, 23 May 2018 15:19:56 +0000 (16:19 +0100)]
fix for JAL-2991 - we could do better :/

6 years agoJAL-2997 handle tab-delimited trailing column number when parsing
gmungoc [Wed, 23 May 2018 14:33:08 +0000 (15:33 +0100)]
JAL-2997 handle tab-delimited trailing column number when parsing

6 years agoJAL-2999 release notes and version bump for jalview 2.10.4b1
Jim Procter [Wed, 23 May 2018 14:18:52 +0000 (15:18 +0100)]
JAL-2999 release notes and version bump for jalview 2.10.4b1

6 years agoJAL-2895 replace $$Jalview-Version$$ in help.jhm with build version when indexing...
Jim Procter [Wed, 23 May 2018 14:17:45 +0000 (15:17 +0100)]
JAL-2895 replace $$Jalview-Version$$ in help.jhm with build version when indexing built in help pages

6 years agoJAL-797 Cmd-W act WHEN_IN_FOCUSED_WINDOW bug/JAL-797
gmungoc [Mon, 21 May 2018 14:31:34 +0000 (15:31 +0100)]
JAL-797 Cmd-W act WHEN_IN_FOCUSED_WINDOW

6 years agoJAL-2986 corrected findIndex for out of range residue value
gmungoc [Fri, 11 May 2018 11:19:52 +0000 (12:19 +0100)]
JAL-2986 corrected findIndex for out of range residue value

6 years agoJAL-2986 additional asserts for SequenceCursor updates
gmungoc [Fri, 11 May 2018 11:17:18 +0000 (12:17 +0100)]
JAL-2986 additional asserts for SequenceCursor updates

6 years agoJAL-2986 failing test added
gmungoc [Fri, 11 May 2018 10:57:56 +0000 (11:57 +0100)]
JAL-2986 failing test added

6 years agoJAL-2920 release notes Release_2_10_4
Jim Procter [Thu, 10 May 2018 10:49:14 +0000 (11:49 +0100)]
JAL-2920 release notes

6 years agoMerge branch 'bug/JAL-2920_uniprotvariantfeature' into releases/Release_2_10_4_Branch
Jim Procter [Thu, 10 May 2018 10:35:44 +0000 (11:35 +0100)]
Merge branch 'bug/JAL-2920_uniprotvariantfeature' into releases/Release_2_10_4_Branch

6 years agoJAL-2920 basic test for Description from features with/out description, variation...
Jim Procter [Thu, 10 May 2018 10:35:11 +0000 (11:35 +0100)]
JAL-2920 basic test for Description from features with/out description, variation and original attributes

6 years agoJAL-2920 simplified logic and added corner cases for missing attributes (probably...
Jim Procter [Thu, 10 May 2018 10:34:23 +0000 (11:34 +0100)]
JAL-2920 simplified logic and added corner cases for missing attributes (probably not needed but..)

6 years agoJAL-2906 update release date and release notes
Jim Procter [Wed, 9 May 2018 19:46:50 +0000 (20:46 +0100)]
JAL-2906 update release date and release notes

6 years agoJAL-2931 patch IA paths for new build box
Jim Procter [Wed, 9 May 2018 19:46:04 +0000 (20:46 +0100)]
JAL-2931 patch IA paths for new build box

6 years agoJAL-2984 add pdb as sequence(s) if associate structure is declined
gmungoc [Wed, 9 May 2018 13:59:14 +0000 (14:59 +0100)]
JAL-2984 add pdb as sequence(s) if associate structure is declined

6 years agoMerge branch 'patch/JAL-2976_vaqua4_fallback' into releases/Release_2_10_4_Branch
Jim Procter [Wed, 9 May 2018 09:39:51 +0000 (10:39 +0100)]
Merge branch 'patch/JAL-2976_vaqua4_fallback' into releases/Release_2_10_4_Branch

6 years agoJAL-2976 fixed bad equivalence check and implemented belt-and-braces check for quaqua...
Jim Procter [Wed, 9 May 2018 09:39:19 +0000 (10:39 +0100)]
JAL-2976 fixed bad equivalence check and implemented belt-and-braces check for quaqua in class name string of look and feel to decide when to fallback to violetlib-Aqua.

6 years agoJAL-2321 release notes
Jim Procter [Tue, 8 May 2018 09:59:37 +0000 (10:59 +0100)]
JAL-2321 release notes

6 years agoMerge branch 'patch/JAL-2321_addsecstrForDroppedPDBFile' into releases/Release_2_10_4...
Jim Procter [Tue, 8 May 2018 09:57:35 +0000 (10:57 +0100)]
Merge branch 'patch/JAL-2321_addsecstrForDroppedPDBFile' into releases/Release_2_10_4_Branch

6 years agoJAL-2321 patch test to ensure structures are actually annotated when loaded directly... patch/JAL-2321_addsecstrForDroppedPDBFile
Jim Procter [Mon, 7 May 2018 17:08:38 +0000 (18:08 +0100)]
JAL-2321 patch test to ensure structures are actually annotated when loaded directly to desktop

6 years agoJAL-2321 ensure default is ‘parseImmediately=true’
Jim Procter [Mon, 7 May 2018 17:08:11 +0000 (18:08 +0100)]
JAL-2321 ensure default is ‘parseImmediately=true’

6 years agoJAL-2321 use configured values for structure derived annotation
Jim Procter [Mon, 7 May 2018 16:43:56 +0000 (17:43 +0100)]
JAL-2321 use configured values for structure derived annotation

6 years agoJAL-2321 add secondary structure & temp factor if not already present on mapped sequences
Jim Procter [Mon, 7 May 2018 16:39:17 +0000 (17:39 +0100)]
JAL-2321 add secondary structure & temp factor if not already present on mapped sequences

6 years agoJAL-2321 use StructureImportSettings singleton settings when JmolParser.parse() calle...
Jim Procter [Mon, 7 May 2018 16:38:29 +0000 (17:38 +0100)]
JAL-2321 use StructureImportSettings singleton settings when JmolParser.parse() called from constructor

6 years agoJAL-2321 isParseImmediately() allows the parse() method to determine if it was called...
Jim Procter [Mon, 7 May 2018 16:36:28 +0000 (17:36 +0100)]
JAL-2321 isParseImmediately() allows the parse() method to determine if it was called by the constructor or after construction

6 years agoJAL-2321 allow JmolParser to be configured before parsing data
Jim Procter [Mon, 7 May 2018 16:35:18 +0000 (17:35 +0100)]
JAL-2321 allow JmolParser to be configured before parsing data

6 years agoJAL-2808 ensure test setUp/tearDown alwaysRun
gmungoc [Mon, 7 May 2018 14:16:42 +0000 (15:16 +0100)]
JAL-2808 ensure test setUp/tearDown alwaysRun