X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Freleases.html;h=0e7d02d3fc24282ccc0c4a236c70139c22b52122;hb=2c2992b8822b686f7f12022a66aa41f6969d06d0;hp=3c265faa4e3a0c97c84f7f641cf2382a22d501da;hpb=a49ce69b89678b3e6ba3c1a61b62d61cc9ee7342;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index 3c265fa..0e7d02d 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -45,6 +45,154 @@
+ |
+
+ |
+ General
+
+
+ - Alignment ruler shows positions relative to reference sequence
+ Application
+
+
+ - Support for reverse-complement coding regions in ENA and EMBL
+ - Upgrade to EMBL XML 1.2 for ENA record retrieval
+ - New 'execute Groovy script' option in an alignment window's Calculate menu
+ - Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode
+ - Store/restore reference sequence in Jalview projects
+
+ Applet
+ |
+
+
+ General
+
+ - reinstate CTRL-click for opening pop-up menu on OSX
+ - Export features in Jalview format (again) includes graduated colourschemes
+ - More responsive when working with big alignments and lots of hidden columns
+ - hidden column markers not always rendered at right of alignment window
+ - Tidied up links in help file table of contents
+ - Feature based tree calculation not shown for DNA alignments
+ - Hidden columns ignored during feature based tree calculation
+ - Alignment view stops updating when show unconserved enabled for group on alignment
+ - Cannot insert gaps into sequence when set as reference
+
+
+ Application
+
+
+ - Corrupt preferences for SVG, EPS & HTML output when running on non-gb/us i18n platforms
+ - URLs and links can imported by drag'n'drop on OSX webstart
+ - InstallAnywhere distribution fails when launching Chimera
+ - Jalview very slow to launch via webstart (also hotfix for 2.9.0b2)
+ - Cannot save project when view has a reference sequence defined
+ - Columns are suddenly selected in other alignments and views when revealing hidden columns
+ - Hide columns not mirrored in complement view in a cDNA/Protein splitframe
+
+
+ Applet
+
+ |
+
+
+ |
+
+ |
+ General
+
+ - Time stamps for signed Jalview application and applet
+ jars
+ |
+
+
+ Application
+
+ - Duplicate group consensus and conservation rows
+ shown when tree is partitioned
+ - Erratic behaviour when tree partitions made with
+ multiple cDNA/Protein split views
+
+ |
+
+
+ |
+
+ |
+ General
+
+ - Updated Spanish translations of localized text for
+ 2.9
+ Application
+
+
+ - Signed OSX InstallAnywhere installer
+ - Support for per-sequence based annotations in BioJSON
+ Applet
+
+ - Split frame example added to applet examples page
+ |
+
+
+ General
+
+ - Mapping of cDNA to protein in split frames
+ incorrect when sequence start > 1
+ - Broken images in filter column by annotation dialog
+ documentation
+ - Feature colours not parsed from features file
+ - Exceptions and incomplete link URLs recovered when
+ loading a features file containing HTML tags in feature
+ description
+
+
+ Application
+
+ - Annotations corrupted after BioJS export and
+ reimport
+ - Incorrect sequence limits after Fetch DB References
+ with 'trim retrieved sequences'
+ - Incorrect warning about deleting all data when
+ deleting selected columns
+ - Patch to build system for shipping properly signed
+ JNLP templates for webstart launch
+ - EMBL-PDBe fetcher/viewer dialogs do not offer
+ unreleased structures for download or viewing
+ - Tab/space/return keystroke operation of EMBL-PDBe
+ fetcher/viewer dialogs works correctly
+ - Disabled 'minimise' button on Jalview windows
+ running on OSX to workaround redraw hang bug
+ - Split cDNA/Protein view position and geometry not
+ recovered from jalview project
+ - Initial enabled/disabled state of annotation menu
+ sorter 'show autocalculated first/last' corresponds to
+ alignment view
+ - Restoring of Clustal, RNA Helices and T-Coffee
+ color schemes from BioJSON
+
+ Applet
+
+ - Reorder sequences mirrored in cDNA/Protein split
+ frame
+ - Applet with Jmol examples not loading correctly
+
+ |
+
+
|
@@ -65,7 +213,7 @@
Jmol integration updated to Jmol v14.2.14
Import and export of Jalview alignment views as BioJSON
+ href="features/bioJsonFormat.html">BioJSON
New alignment annotation file statements for
reference sequences and marking hidden columns
Reference sequence based alignment shading to
@@ -280,27 +428,6 @@
- |
-
- |
-
-
- |
-
-
-
- - Reinstated the display of default example file on
- startup
- - All pairs shown in Jalview window when viewing
- result of pairwise alignment
-
- |
-
-
|
@@ -606,7 +733,7 @@
|
@@ -1245,6 +1372,7 @@
- URL links generated from description line for
regular-expression based URL links (applet and application)
+
- Non-positional feature URL links are shown in link
menu
@@ -1288,10 +1416,7 @@
between different screens.
- New preference items for sequence ID tooltip and
consensus annotation
- - Client to submit sequences and IDs to Envision2
- Workflows
-
+ - Client to submit sequences and IDs to Envision2 Workflows
- Vamsas Capabilities
- Improved VAMSAS synchronization (Jalview archive
@@ -1699,6 +1824,7 @@
- Cancel button for DAS Feature Fetching
- PCA and PDB Viewers zoom via mouse roller
- User-defined sub-tree colours and sub-tree selection
+
- 'New Window' button on the 'Output to Text box'
@@ -1713,6 +1839,7 @@
- Fixed Remove Empty Columns Bug (empty columns at end
of alignment)
- Slowed DAS Feature Fetching for increased robustness.
+
- Made angle brackets in ASCII feature descriptions
display correctly
@@ -1724,6 +1851,7 @@
- WsDbFetch query/result association resolved
- Tree leaf to sequence mapping improved
- Smooth fonts switch moved to FontChooser dialog box.
+
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