jalview.git
5 years agoinsignificant test file changes
hansonr [Fri, 10 May 2019 02:53:36 +0000 (21:53 -0500)]
insignificant test file changes

5 years agoJalview-JS/JAL-3253-applet Desktop fix for null desktopPane in testing
hansonr [Fri, 10 May 2019 02:51:19 +0000 (21:51 -0500)]
Jalview-JS/JAL-3253-applet Desktop fix for null desktopPane in testing

5 years agoJalview-JS/JAL-3253-applet does not recognize \r\n as OK
hansonr [Thu, 9 May 2019 19:10:47 +0000 (14:10 -0500)]
Jalview-JS/JAL-3253-applet does not recognize \r\n as OK

5 years agoMerge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview...
hansonr [Thu, 9 May 2019 19:05:58 +0000 (14:05 -0500)]
Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet

5 years agoJalview-JS/JAL-3253-applet
hansonr [Thu, 9 May 2019 18:54:03 +0000 (13:54 -0500)]
Jalview-JS/JAL-3253-applet

5 years agoMerge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview...
hansonr [Thu, 9 May 2019 18:54:03 +0000 (13:54 -0500)]
Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet

5 years agoJAL-3253/JAL-3258 FileLoader fix for use of file.separator
hansonr [Thu, 9 May 2019 18:24:30 +0000 (13:24 -0500)]
JAL-3253/JAL-3258  FileLoader fix for use of file.separator

5 years agoJAL-3253/JAL-3257
hansonr [Thu, 9 May 2019 18:24:30 +0000 (13:24 -0500)]
JAL-3253/JAL-3257
working on getting TestNG working with singletons

check for null property file in Cache.setProperty to avoid error message
in testng; fixes problems with FeatureFileTest and FeatureFile with
mixed or unconsidered line endings

5 years agoJAL-3253 preliminary static fixes for JavaScript part 4 of 3
hansonr [Thu, 9 May 2019 13:32:00 +0000 (08:32 -0500)]
JAL-3253 preliminary static fixes for JavaScript part 4 of 3

working on getting TestNG working with singletons

5 years agoJAL-3253 preliminary static fixes for JavaScript part 3 of 3
hansonr [Thu, 9 May 2019 03:35:47 +0000 (22:35 -0500)]
JAL-3253 preliminary static fixes for JavaScript part 3 of 3

More succinct singleton class instances stored in jalview.bin.Jalview.

All 2200 instances of "static" checked.

5 years agoJAL-3253 preliminary static fixes for JavaScript part 2
hansonr [Wed, 8 May 2019 21:42:23 +0000 (16:42 -0500)]
JAL-3253 preliminary static fixes for JavaScript part 2

Includes lazy dynamic loading of SequenceFetcher database options.

Note that if WebServices menu is enabled (Java, not JavaScript), then
all web-based database proxies are instantiated anyway.

5 years agoJAL-3253 preliminary static fixes for JavaScript
hansonr [Wed, 8 May 2019 11:29:37 +0000 (06:29 -0500)]
JAL-3253 preliminary static fixes for JavaScript

Desktop.instance and Desktop.getInstance()
Jalview.instance and Jalview.getInstance()
AlignmentSorter.instance and AlignmentSorter.getInstance()

ArgsParser static final options

*SoapBindingStub static final _operations

Clean up of headless business
Clean up of ArgsParser options

5 years agoJAL-3253 AppletParams class for processing applet-specific params
hansonr [Wed, 8 May 2019 02:42:57 +0000 (21:42 -0500)]
JAL-3253 AppletParams class for processing applet-specific params

5 years agoJAL-3226 removal of superseded changes
gmungoc [Fri, 26 Apr 2019 09:20:31 +0000 (10:20 +0100)]
JAL-3226 removal of superseded changes

5 years agoJAL-3010 borderless 'x' for "delete this filter condition"
gmungoc [Fri, 26 Apr 2019 09:17:09 +0000 (10:17 +0100)]
JAL-3010 borderless 'x' for "delete this filter condition"

5 years ago[JAL-3226] problem that JavaScript (or Java) may consolidate multiple
hansonr [Tue, 23 Apr 2019 03:48:49 +0000 (22:48 -0500)]
[JAL-3226] problem that JavaScript (or Java) may consolidate multiple
repaint() requests in unpredictable ways. In this case, the issue was
that in response to a CTRL-C/CTRL-V paste request, in Java a fast
repaint request preceded two full requests, thus resulting
in a full request for paint. In constrast, in JavaScript, the three
requests were bundled together into one, so the fastPaint flag was
still present for the second and third request.

This resulted in incomplete painting.

The solution was to set seqCanvas.fastPaint and idCanvas.fastPaint false
in PaintRefresher when the target to be painted is one of those two
components.

BH 2019.04.22

5 years agoupdate of SwingJS -- no changes known.
hansonr [Mon, 22 Apr 2019 17:10:09 +0000 (12:10 -0500)]
update of SwingJS -- no changes known.

5 years agominor code clean up
hansonr [Thu, 18 Apr 2019 18:15:55 +0000 (13:15 -0500)]
minor code clean up

5 years agominor code clean up
hansonr [Thu, 18 Apr 2019 18:15:24 +0000 (13:15 -0500)]
minor code clean up

5 years ago// BH 2018.04.18 comment: addNotify() is not appropriate here. We
hansonr [Thu, 18 Apr 2019 17:59:40 +0000 (12:59 -0500)]
// BH 2018.04.18 comment: addNotify() is not appropriate here. We
    // are not changing ancestors, and keyboard action listeners do
    // not need to be reset. addNotify() is a very expensive operation,
    // requiring a full re-layout of all parents and children.
    // Note in JComponent:
    // This method is called by the toolkit internally and should
    // not be called directly by programs.
    // I note that addNotify() is called in several areas of Jalview.

5 years agoAdds check for gap padding to disallow fast paint upon pasting if
hansonr [Thu, 18 Apr 2019 17:55:55 +0000 (12:55 -0500)]
Adds check for gap padding to disallow fast paint upon pasting if
alignment has been modified.

5 years agoremoves unnecessary clearFastPaint
hansonr [Thu, 18 Apr 2019 17:54:46 +0000 (12:54 -0500)]
removes unnecessary clearFastPaint

5 years agoCorrects incorrect calls to ViewportRanges.setEndSeq()
hansonr [Thu, 18 Apr 2019 17:54:08 +0000 (12:54 -0500)]
Corrects incorrect calls to ViewportRanges.setEndSeq()

This function has the limit of height - 1, not height. Also adds safety
for start < 0 in ViewportRanges.setEndSeq();

5 years agopushing again, just comments
hansonr [Thu, 18 Apr 2019 15:03:30 +0000 (10:03 -0500)]
pushing again, just comments

5 years agohack for fastpaint Java bug upshifting one line after a sequence
hansonr [Thu, 18 Apr 2019 14:32:42 +0000 (09:32 -0500)]
hack for fastpaint Java bug upshifting one line after a sequence
selection paste. Covered in Java by a full paint by ConsensusThread.

5 years agoreverting seqPanel.seqCanvas.clearFastPaint();
hansonr [Thu, 18 Apr 2019 11:53:00 +0000 (06:53 -0500)]
reverting     seqPanel.seqCanvas.clearFastPaint();

5 years agoMerge branch 'develop' into Jalview-JS/develop
gmungoc [Thu, 18 Apr 2019 08:36:57 +0000 (09:36 +0100)]
Merge branch 'develop' into Jalview-JS/develop

5 years agoJAL-3193 dbSource always "ENSEMBL"
gmungoc [Thu, 18 Apr 2019 08:36:28 +0000 (09:36 +0100)]
JAL-3193 dbSource always "ENSEMBL"

5 years agoMerge branch 'develop' into Jalview-JS/develop
gmungoc [Thu, 18 Apr 2019 08:31:17 +0000 (09:31 +0100)]
Merge branch 'develop' into Jalview-JS/develop

5 years agoexplicit Hashtable objects
hansonr [Thu, 18 Apr 2019 03:54:33 +0000 (22:54 -0500)]
explicit Hashtable objects

5 years agoadds an explicit clearing of the SeqCanvas fastPaint flag upon viewport
hansonr [Thu, 18 Apr 2019 03:53:59 +0000 (22:53 -0500)]
adds an explicit clearing of the SeqCanvas fastPaint flag upon viewport
adjustment

5 years agoJAL-3026 fix bug loading Jalview Project (in Java)
gmungoc [Wed, 17 Apr 2019 15:34:58 +0000 (16:34 +0100)]
JAL-3026 fix bug loading Jalview Project (in Java)

5 years agoJAL-3111 fix 2.11 html anchor in docs
Jim Procter [Wed, 17 Apr 2019 14:34:59 +0000 (15:34 +0100)]
JAL-3111 fix 2.11 html anchor in docs

5 years agoMerge branch 'documentation/JAL-3111_release_211' into develop
Jim Procter [Wed, 17 Apr 2019 14:32:58 +0000 (15:32 +0100)]
Merge branch 'documentation/JAL-3111_release_211' into develop

5 years agoJAL-3111 Jalview 2.11 what’s New and estimated release date
Jim Procter [Wed, 17 Apr 2019 14:32:36 +0000 (15:32 +0100)]
JAL-3111 Jalview 2.11 what’s New and estimated release date

5 years agoJAL-3111 tweak PCA documentation
Jim Procter [Wed, 17 Apr 2019 14:32:07 +0000 (15:32 +0100)]
JAL-3111 tweak PCA documentation

5 years agoMerge branch 'develop' into documentation/JAL-3111_release_211
Jim Procter [Wed, 17 Apr 2019 12:53:16 +0000 (13:53 +0100)]
Merge branch 'develop' into documentation/JAL-3111_release_211

5 years agoMerge branch 'develop' into Jalview-JS/develop
gmungoc [Wed, 17 Apr 2019 10:48:28 +0000 (11:48 +0100)]
Merge branch 'develop' into Jalview-JS/develop

5 years agobetter resource loading/file caching
hansonr [Tue, 16 Apr 2019 22:29:07 +0000 (17:29 -0500)]
better resource loading/file caching

5 years agocaching of DnD files dropped
hansonr [Tue, 16 Apr 2019 22:28:14 +0000 (17:28 -0500)]
caching of DnD files dropped

5 years agojmol-app updated for SwingJS ZipTools upgrade
hansonr [Tue, 16 Apr 2019 21:07:20 +0000 (16:07 -0500)]
jmol-app updated for SwingJS ZipTools upgrade

5 years agolocalizes Thread colourby so that it does not cause ThreadStateException
hansonr [Tue, 16 Apr 2019 21:06:36 +0000 (16:06 -0500)]
localizes Thread colourby so that it does not cause ThreadStateException
in Java

5 years agocomments only
hansonr [Tue, 16 Apr 2019 21:05:41 +0000 (16:05 -0500)]
comments only

5 years agomissing check for JavaScript in client response for String (Java) vs.
hansonr [Tue, 16 Apr 2019 13:39:31 +0000 (08:39 -0500)]
missing check for JavaScript in client response for String (Java) vs.
Map (JavaScript) -- since JavaScript has already done the conversion to
a Map and needs no further JSON parsing.

5 years agounused old SwingJS dependencies
hansonr [Tue, 16 Apr 2019 13:20:31 +0000 (08:20 -0500)]
unused old SwingJS dependencies

5 years agounused old SwingJS dependencies
hansonr [Tue, 16 Apr 2019 13:16:30 +0000 (08:16 -0500)]
unused old SwingJS dependencies

5 years agoAdds _j2sclasslist.txt to SwingJS distribution; fixes missing
hansonr [Tue, 16 Apr 2019 12:34:10 +0000 (07:34 -0500)]
Adds _j2sclasslist.txt to SwingJS distribution; fixes missing
menuListener

5 years agoMerge branch 'bug/JAL-3218scalePanelPopups' into develop
gmungoc [Tue, 16 Apr 2019 11:48:31 +0000 (12:48 +0100)]
Merge branch 'bug/JAL-3218scalePanelPopups' into develop

5 years agoJAL-3193 no separatge EnsemblGenomes source in SequenceFetcher
gmungoc [Mon, 15 Apr 2019 15:52:19 +0000 (16:52 +0100)]
JAL-3193 no separatge EnsemblGenomes source in SequenceFetcher

5 years agoMerge branch 'develop' into Jalview-JS/develop
gmungoc [Mon, 15 Apr 2019 08:47:50 +0000 (09:47 +0100)]
Merge branch 'develop' into Jalview-JS/develop

5 years agoJAL-3193 rest.ensemblgenomes.org merged to rest.ensembl.org
gmungoc [Wed, 10 Apr 2019 20:35:10 +0000 (21:35 +0100)]
JAL-3193 rest.ensemblgenomes.org merged to rest.ensembl.org

5 years agoJAL-3018 REST version updated to 10.0
gmungoc [Wed, 10 Apr 2019 20:20:22 +0000 (21:20 +0100)]
JAL-3018 REST version updated to 10.0

5 years agoJAL-3033 and more classes for examples core
Jim Procter [Wed, 10 Apr 2019 13:56:32 +0000 (14:56 +0100)]
JAL-3033 and more classes for examples core

5 years agoJAL-3033 http://www.jalview.org/jalview-js/JalviewJS.shtml?open%20http://www.jalview...
Jim Procter [Tue, 9 Apr 2019 13:23:56 +0000 (14:23 +0100)]
JAL-3033 jalview.org/jalview-js/JalviewJS.shtml?open%20http://www.jalview.org/examples/uniref50.fa

5 years agoJTable improvements
hansonr [Tue, 9 Apr 2019 04:41:36 +0000 (23:41 -0500)]
JTable improvements

- prevents loss of tool tip when clicking or editing

- corrects offset of center label in variable color option

- speed somewhat improved

5 years agobetter comment regarding setting recognized ajax-enabled sites
hansonr [Tue, 9 Apr 2019 04:39:28 +0000 (23:39 -0500)]
better comment regarding setting recognized ajax-enabled sites

5 years agoMerge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into...
hansonr [Tue, 9 Apr 2019 04:38:42 +0000 (23:38 -0500)]
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop

5 years agocode formatting only
hansonr [Tue, 9 Apr 2019 04:38:21 +0000 (23:38 -0500)]
code formatting only

5 years agoJAL-3033 more classes for the kitchen sink
Jim Procter [Mon, 8 Apr 2019 13:43:32 +0000 (14:43 +0100)]
JAL-3033 more classes for the kitchen sink

5 years agoJAL-3033 updated classlist for loading the example file (jim's kitchensink corefile)
Jim Procter [Mon, 8 Apr 2019 13:23:29 +0000 (14:23 +0100)]
JAL-3033 updated classlist for loading the example file (jim's kitchensink corefile)

5 years agoFile caching activated explicitly in Platform
hansonr [Fri, 5 Apr 2019 18:43:12 +0000 (13:43 -0500)]
File caching activated explicitly in Platform

5 years agoFix for #196 EBI does not allow AJAX on Tools/dbfetch - now they do.
hansonr [Fri, 5 Apr 2019 16:37:25 +0000 (11:37 -0500)]
Fix for #196  EBI does not allow AJAX on Tools/dbfetch  - now they do.

5 years agocommand line fix
hansonr [Fri, 5 Apr 2019 16:36:52 +0000 (11:36 -0500)]
command line fix

5 years agoMerge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into...
hansonr [Fri, 5 Apr 2019 16:13:42 +0000 (11:13 -0500)]
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop

5 years agofixes for Jalview command-line URI code
hansonr [Fri, 5 Apr 2019 16:13:21 +0000 (11:13 -0500)]
fixes for Jalview command-line URI code

5 years agoJAL-3204 update to uniprot schema
gmungoc [Fri, 5 Apr 2019 07:08:35 +0000 (08:08 +0100)]
JAL-3204 update to uniprot schema

5 years agoMerge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into...
hansonr [Thu, 4 Apr 2019 21:35:40 +0000 (16:35 -0500)]
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop

5 years agoj2sNative cleanup; fix for JTextArea preferred height miscalculation
hansonr [Thu, 4 Apr 2019 21:31:44 +0000 (16:31 -0500)]
j2sNative cleanup; fix for JTextArea preferred height miscalculation

5 years agoJAL-3220 j2sIgnore on 3 more main methods
gmungoc [Thu, 4 Apr 2019 19:45:19 +0000 (20:45 +0100)]
JAL-3220 j2sIgnore on 3 more main methods

5 years agoJAL-3220 j2sIgnore on main methods on test / utility classes
gmungoc [Thu, 4 Apr 2019 19:37:32 +0000 (20:37 +0100)]
JAL-3220 j2sIgnore on main methods on test / utility classes

5 years agoJAL-3220 unneeded main methods removed
gmungoc [Thu, 4 Apr 2019 15:00:54 +0000 (16:00 +0100)]
JAL-3220 unneeded main methods removed

5 years agoMerge branch 'develop' into Jalview-JS/develop
gmungoc [Thu, 4 Apr 2019 07:21:43 +0000 (08:21 +0100)]
Merge branch 'develop' into Jalview-JS/develop

5 years agoreplacing @j2sNative with @j2sIgnore where appropriate - requires NEW
hansonr [Wed, 3 Apr 2019 23:52:20 +0000 (18:52 -0500)]
replacing @j2sNative with @j2sIgnore where appropriate - requires NEW
TRANSPILER

5 years agoremoving early SplitPane SwingJS hack
hansonr [Wed, 3 Apr 2019 23:51:20 +0000 (18:51 -0500)]
removing early SplitPane SwingJS hack

5 years agoJAL-3021 show Sequence Details with cursor at top
gmungoc [Wed, 3 Apr 2019 15:43:19 +0000 (16:43 +0100)]
JAL-3021 show Sequence Details with cursor at top

5 years agoj2sNative clean-up. Fixes problem with second try of sequence fetching
hansonr [Wed, 3 Apr 2019 13:41:19 +0000 (08:41 -0500)]
j2sNative clean-up. Fixes problem with second try of sequence fetching
not retrieving (cached) data

5 years ago#210 Fixes Ensembl fetch problem (really)
hansonr [Tue, 2 Apr 2019 17:09:01 +0000 (12:09 -0500)]
#210 Fixes Ensembl fetch problem (really)

5 years agoJAL-3218 allow both Hide and Reveal in scale panel popup menu bug/JAL-3218scalePanelPopups
gmungoc [Tue, 2 Apr 2019 13:10:45 +0000 (14:10 +0100)]
JAL-3218 allow both Hide and Reveal in scale panel popup menu

5 years agoMerge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into...
hansonr [Mon, 1 Apr 2019 14:31:10 +0000 (09:31 -0500)]
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop

5 years agonote to self: Time to write a good interface and stop doing this secret
hansonr [Mon, 1 Apr 2019 14:30:53 +0000 (09:30 -0500)]
note to self: Time to write a good interface and stop doing this secret
calling of swingjs methods.

5 years agoJAL-3033 generalised publish-core-template ready to enable multiple templates/core...
Jim Procter [Mon, 1 Apr 2019 09:02:23 +0000 (10:02 +0100)]
JAL-3033 generalised publish-core-template ready to enable multiple templates/core-file html endpoints to be generated

5 years agoJAL-3033 always run the toJs core file build before building core files from classlis...
Jim Procter [Mon, 1 Apr 2019 09:00:43 +0000 (10:00 +0100)]
JAL-3033 always run the toJs core file build before building core files from classlist/*.txt

5 years agoJAL-3032 use small example Ensembl gene for JalviewJS
gmungoc [Mon, 1 Apr 2019 08:22:45 +0000 (09:22 +0100)]
JAL-3032 use small example Ensembl gene for JalviewJS

5 years agoupdated _j2sclasslist.txt adds a few more files (see end of file)
hansonr [Mon, 1 Apr 2019 02:57:39 +0000 (21:57 -0500)]
updated _j2sclasslist.txt adds a few more files (see end of file)

5 years agoembedded core-file demo for faster loading
hansonr [Mon, 1 Apr 2019 02:50:20 +0000 (21:50 -0500)]
embedded core-file demo for faster loading

5 years agoAjax enhancements
hansonr [Mon, 1 Apr 2019 02:42:17 +0000 (21:42 -0500)]
Ajax enhancements

5 years agofirst demo of embedding components as simple divs with known ids
hansonr [Mon, 1 Apr 2019 02:41:49 +0000 (21:41 -0500)]
first demo of embedding components as simple divs with known ids

5 years agojsmol2.php?? must have been just for testing
hansonr [Mon, 1 Apr 2019 02:41:20 +0000 (21:41 -0500)]
jsmol2.php?? must have been just for testing

5 years agoJSON refactoring of a few methods; fixing JavaScript issues
hansonr [Mon, 1 Apr 2019 02:40:37 +0000 (21:40 -0500)]
JSON refactoring of a few methods; fixing JavaScript issues

5 years agojalview-pca-div added
hansonr [Mon, 1 Apr 2019 02:39:35 +0000 (21:39 -0500)]
jalview-pca-div added

5 years agoMerge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into...
hansonr [Mon, 1 Apr 2019 02:38:34 +0000 (21:38 -0500)]
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop

5 years agoJAL-3033 build.xml:build-site runs build-site.xml to populate site/ with prebuilt...
Jim Procter [Sun, 31 Mar 2019 17:57:06 +0000 (18:57 +0100)]
JAL-3033 build.xml:build-site runs build-site.xml to populate site/ with prebuilt/deps

5 years agoadds TreePanel name jalview-tree
hansonr [Sun, 31 Mar 2019 17:21:52 +0000 (12:21 -0500)]
adds TreePanel name jalview-tree

5 years agoadds StructureViewer name jalview-structureviewer
hansonr [Sun, 31 Mar 2019 17:21:30 +0000 (12:21 -0500)]
adds StructureViewer name jalview-structureviewer

5 years agoadds SplitFrame name jalview-splitframe;
hansonr [Sun, 31 Mar 2019 17:20:31 +0000 (12:20 -0500)]
adds SplitFrame name jalview-splitframe;

5 years agoadds RnaStructureViewer name jalview-rnastructureviewer;
hansonr [Sun, 31 Mar 2019 17:20:07 +0000 (12:20 -0500)]
adds RnaStructureViewer name jalview-rnastructureviewer;

5 years agoadds Desktop name jalview-desktop;
hansonr [Sun, 31 Mar 2019 17:19:30 +0000 (12:19 -0500)]
adds Desktop name jalview-desktop;

5 years agoadds AlignFrame name jalview-alignment;
hansonr [Sun, 31 Mar 2019 17:19:07 +0000 (12:19 -0500)]
adds AlignFrame name jalview-alignment;

5 years agoclean up implicit object refs
hansonr [Sun, 31 Mar 2019 17:18:36 +0000 (12:18 -0500)]
clean up implicit object refs

5 years agoCache JS adds search of Info for jalview_xxx properties
hansonr [Sun, 31 Mar 2019 17:17:15 +0000 (12:17 -0500)]
Cache JS adds search of Info for jalview_xxx properties