From: Jim Procter
Date: Wed, 5 Sep 2018 10:06:54 +0000 (+0100)
Subject: Merge branch 'patch/VAqua_saveload_update_JAL-2988' into releases/Release_2_10_5_Branch
X-Git-Tag: Release_2_10_5~20
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=53a60c2b5970123bc8fcdfea42253e2c1dc99dfa;hp=573b3bad0aa40ce58c4dae6646523f9133b0564d;p=jalview.git
Merge branch 'patch/VAqua_saveload_update_JAL-2988' into releases/Release_2_10_5_Branch
---
diff --git a/.ant-targets-build.xml b/.ant-targets-build.xml
index 7ef21f1..15432a1 100644
--- a/.ant-targets-build.xml
+++ b/.ant-targets-build.xml
@@ -1,2 +1,31 @@
+build
+buildPropertiesFile
+buildTests
+buildextclients
+buildindices
+castorbinding
+clean
+compileApplet
+distclean
help
+init
+linkcheck
+makeApplet
+makedist
+makefulldist
+obfuscate
+packageApplet
+prepare
+prepareTests
+preparejnlp
+prepubapplet_1
+pubapplet
+runenv
+signApplet
+sourcedist
+sourcedoc
+sourcescrub
+testclean
+testng
usage
+writejnlpf
diff --git a/README b/README
index eaf226b..8172066 100755
--- a/README
+++ b/README
@@ -21,13 +21,18 @@ For more help, read the file doc/building.html
##################
-To run application:
+To run application...
+[ NOTE: when using the -classpath option with the '*' wildcard, the argument must be quoted to avoid shell expansion of the wildcard,
+ ALSO, the wildcard MUST be as DIR/* and not DIR/*.jar etc or it will not be interpreted correctly ]
-java -Djava.ext.dirs=JALVIEW_HOME/lib -cp JALVIEW_HOME/jalview.jar jalview.bin.Jalview
+on Windows use:
+ java -classpath "JALVIEW_HOME/lib/*;JALVIEW_HOME/jalview.jar" jalview.bin.Jalview
+and on MacOS or Linux:
+ java -classpath "JALVIEW_HOME/lib/*:JALVIEW_HOME/jalview.jar" jalview.bin.Jalview
Replace JALVIEW_HOME with the full path to Jalview Installation Directory. If building from source:
-java -Djava.ext.dirs=JALVIEW_BUILD/dist -cp JALVIEW_BUILD/dist/jalview.jar jalview.bin.Jalview
+ java -classpath "JALVIEW_BUILD/dist/*" jalview.bin.Jalview
##################
diff --git a/RELEASE b/RELEASE
index c61d86c..54b71f0 100644
--- a/RELEASE
+++ b/RELEASE
@@ -1,2 +1,2 @@
-jalview.release=releases/Release_2_10_4_Branch
-jalview.version=2.10.4b1
+jalview.release=releases/Release_2_10_5_Branch
+jalview.version=2.10.5
diff --git a/build.xml b/build.xml
index f9265dc..97f459d 100755
--- a/build.xml
+++ b/build.xml
@@ -395,7 +395,7 @@
-->
-
+
@@ -403,7 +403,7 @@
-
+
@@ -936,13 +936,13 @@
-
+
-
+
diff --git a/examples/rna_ss_test.stk b/examples/rna_ss_test.stk
new file mode 100644
index 0000000..429612e
--- /dev/null
+++ b/examples/rna_ss_test.stk
@@ -0,0 +1,6 @@
+# STOCKHOLM 1.0
+#=GF ID RNA.SS.TEST
+#=GF TP RNA;
+Test.sequence GUACAAAAAAAAAA
+#=GC SS_cons <(EHBheb(E)e)>
+//
diff --git a/examples/testdata/example_annot_file.jva b/examples/testdata/example_annot_file.jva
index 1779247..6b9faa4 100644
--- a/examples/testdata/example_annot_file.jva
+++ b/examples/testdata/example_annot_file.jva
@@ -18,5 +18,5 @@ SEQUENCE_GROUP Group_A 30 50 *
SEQUENCE_GROUP Group_B 1 351 2-5
SEQUENCE_GROUP Group_C 12 14 -1 seq1 seq2 seq3
PROPERTIES Group_A description=This is the description colour=Helix Propensity pidThreshold=0 outlineColour=red displayBoxes=true displayText=false colourText=false textCol1=black textCol2=black textColThreshold=0
-PROPERTIES Group_B outlineColour=red colour=None
+PROPERTIES Group_B outlineColour=green colour=None
PROPERTIES Group_C colour=Clustal
diff --git a/help/html/features/commandline.html b/help/html/features/commandline.html
index 9cffc51..92d9323 100644
--- a/help/html/features/commandline.html
+++ b/help/html/features/commandline.html
@@ -49,11 +49,11 @@
provided by InstallAnywhere any output from the application will be
sent to output.txt, not standard out.
The Jalview
application also requires a number of additional libraries on the
- class path. The command line below adds the Jalview installation's
- 'lib' directory to the list of directories that are searched for
- jars to be added to the classpath:
+ class path. The command line below adds all the jar files in the
+ Jalview installation's 'lib' directory to the classpath, as well as
+ the Jalview application jar file:
- java -Djava.ext.dirs=$INSTALL_DIR$/lib -cp $INSTALL_DIR$/jalview.jar jalview.bin.Jalview -open [FILE]
+ java -classpath "$INSTALL_DIR$/lib/*:$INSTALL_DIR$/jalview.jar" jalview.bin.Jalview -open [FILE]
Use '-help' to get more information on the command line arguments that
diff --git a/help/html/releases.html b/help/html/releases.html
index 75c8e06..38c0ae3 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -68,6 +68,89 @@ li:before {
+
+
+ |
+
+
+
+ -
+ Hidden sequence markers and representative
+ sequence bolding included when exporting alignment as EPS,
+ SVG, PNG or HTML. Display is configured via the
+ Format menu, or for command-line use via a jalview
+ properties file.
+
+ -
+ Ensembl client updated to Version 7 REST
+ API and sequence data now imported as JSON
+
+ -
+ Change in recommended way of starting
+ Jalview via a Java command line: add jars in lib directory
+ to CLASSPATH, rather than via the deprecated java.ext.dirs
+ property.
+
+
+ Development
+
+ -
+ Support added to execute test suite
+ instrumented with Open
+ Clover
+
+
+ |
+
+
+
+ -
+ Corrupted display when switching to
+ wrapped mode when sequence panel's vertical scrollbar is
+ visible.
+
+ -
+ Alignment is black in exported EPS file
+ when sequences are selected in exported view.
+
+ -
+ Groups with different coloured borders
+ aren't rendered with correct colour.
+
+ -
+ Jalview could hang when importing certain
+ types of knotted RNA secondary structure
+
+ -
+ Sequence highlight and selection in
+ trimmed VARNA 2D structure is incorrect for sequences that
+ do not start at 1
+
+ -
+ '.' inserted into RNA secondary structure
+ annotation when columns are inserted into an alignment,
+ and when exporting as Stockolm flatfile.
+
+ -
+ Jalview annotation rows containing upper
+ and lower-case 'E' and 'H' do not automatically get
+ treated as RNA secondary structure
+
+
+ Java 10 Issues
+
+ -
+ OSX - Can't save new files via the File
+ or export menus by typing in a name into the Save dialog
+ box.
+
+
+
+ |
+
+
2.10.4b1
@@ -111,7 +194,8 @@ li:before {
annotation added to view (Windows)
- Jalview Desktop is slow to start up when network connectivity is poor
+ Jalview Desktop is slow to start up when
+ network connectivity is poor
Drag URL from chrome, firefox, IE to
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index ed6f5c2..4dfc54e 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -24,57 +24,34 @@
- What's new in Jalview 2.10.4b1 ?
+ What's new in Jalview 2.10.5 ?
- This is the first patch release for Jalview 2.10.4. It includes
- the following new patches:
+ Jalview 2.10.5 is a minor release that includes critical
+ patches for users working with Ensembl, and RNA secondary structure
+ annotation.
- - HGVS nomenclature used for variant annotation retrieved
- from Uniprot
- - Uniprot import fails for some sequences (Cannot import
- features with multiple variant elements)
- - Clustal files with sequence positions in right-hand column
- are now parsed correctly
- - Wrap view - export to SVG - IDs shown but not alignment
- area in exported graphic
- - F2/Keyboard mode edits work when Overview window has input
- focus
- - Windows specific fixes:
-
- - Annotation panel set too high when annotation added to
- view
- - Updated search paths for Chimera default installation
- - Windows File Shortcuts can be dragged onto the Jalview
- Desktop
- - Drag URL from Chrome, Firefox, IE to Jalview desktop on
- Windows doesn't open file:
Dragging the currently open
- URL and links from a page viewed in Firefox or Chrome on
- Windows is now fully supported.
- If you are using Edge, only links in the page
- can be dragged.
- With Internet Explorer, only the currently open
- URL in the browser can be dropped onto Jalview.
-
-
+ - EPS, PNG and SVG export now includes hidden sequence
+ markers, and representative sequences are marked in bold.
+ - Ensembl Client updated for Ensembl Rest API v7.
The
+ latest Ensembl API is not backwards compatible with earlier
+ versions of Jalview, so if you require Ensembl functionality you
+ will need to install this release.
-
- Highlights in the 2.10.4 series include:
-
- - Numerous efficiency improvements in the renderer and overview when working with large alignments with lots of hidden columns
- - Use of HTTPS when connecting to Uniprot, Ensembl and other EBI web services
- - Critical patches for running Jalview on OSX with Java 10
- - Easier adjustment of the Alignment ID panel and Annotation panel
- - Improved support for mapping between 3D Structures and Uniprot Protein Sequences
- - Improved support for discovering CDS and transcripts for Proteins and Ensembl gene IDs
- - New buttons on the Structure Chooser for adding structures
- to an existing view, and disabling automatic superposition
- according to linked alignments
- - Annotation transfer between Chimera and Jalview (formerly only
- available in 'Experimental' mode)
+ - Improved support for VIENNA extended dot-bracket notation
+ for RNA secondary structure
+ - Positional and selected region highlighting in VARNA
+ 'trimmed sequence' view now more reliable
- The full list of bugs fixed in this release can be found in the 2.10.4
- Release Notes.
-
+ The full list of bugs fixed in this release can be found in the 2.10.5 Release Notes. The majority of improvement in 2.10.5 are due to Jalview users
+ contacting us via the jalview-discuss email list. Thanks to everyone
+ who took the time to do this !
+ Jalview and Java 10
+ This release addresses a critical bug for OSX users who are
+ running Jalview with Java 10 which can prevent files being saved
+ correctly through the 'Save As' dialog box. The 'Save As' dialog for
+ Jalview's Groovy Console remains affected - we hope to address this
+ in the next major release.
|