X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=49d4c3f98f0f18b39693912d50c340231fee6aee;hb=refs%2Fheads%2Fbug%2FJAL-1698_Append-Structures;hp=8913a322187e8df056962543d134af1573f0056d;hpb=94984a3b8f740773ad70385c76cc20601ea328c7;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
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+++ b/help/html/releases.html
@@ -1,7 +1,7 @@
General
+ - Make selection for columns now works on marked columns
+ rather than columns in rubber-band selection region.
+
+ Application
+ Deployment and Documentation
+ Application Known issues
+ Applet Known Issues
+
+
+
+
+ |
+ General
+
+ - Updated Java code signing certificate donated by Certum.PL.
+ - Features and annotation preserved when performing pairwise
+ alignment
+ - RNA pseudoknot annotation can be
+ imported/exported/displayed
+ - 'colour by annotation' can colour by RNA and
+ protein secondary structure
Application
- - Update Jalview project format:
+
- Extract and display secondary structure for sequences with
+ 3D structures
+ - Support for parsing RNAML
+ - Annotations menu for layout
+ - sort sequence annotation rows by alignment
+ - place sequence annotation above/below alignment
+ annotation
-
-
- |
+ Output in Stockholm format
+ Internationalisation: improved Spanish (es) translation
+ Structure viewer preferences tab
+ Disorder and Secondary Structure annotation tracks shared
+ between alignments
+ UCSF Chimera launch and linked highlighting from Jalview
+ Show/hide all sequence associated annotation rows for all
+ or current selection
+ disorder and secondary structure predictions available as
+ dataset annotation
+ Per-sequence rna helices colouring
+
+
+ Sequence database accessions imported when fetching
+ alignments from Rfam
+ update VARNA version to 3.91
+
+ New groovy scripts for exporting aligned positions,
+ conservation values, and calculating sum of pairs scores.
+ Command line argument to set default JABAWS server
+ include installation type in build properties and console
+ log output
+ Updated Jalview project format to preserve dataset annotation
+
Application
+ - Distinguish alignment and sequence associated RNA
+ structure in structure->view->VARNA
+ - Raise dialog box if user deletes all sequences in an
+ alignment
+ - Pressing F1 results in documentation opening twice
+ - Sequence feature tooltip is wrapped
+ - Double click on sequence associated annotation selects
+ only first column
+ - Redundancy removal doesn't result in unlinked leaves
+ shown in tree
+ - Undos after several redundancy removals don't undo
+ properly
+ - Hide sequence doesn't hide associated annotation
+ - User defined colours dialog box too big to fit on screen
+ and buttons not visible
+ - author list isn't updated if already written to jalview
+ properties
+ - Popup menu won't open after retrieving sequence from
+ database
+ - File open window for associate PDB doesn't open
+ - Left-then-right click on a sequence id opens a browser
+ search window
+ - Cannot open sequence feature shading/sort popup menu in
+ feature settings dialog
+ - better tooltip placement for some areas of Jalview desktop
+ - Allow addition of JABAWS Server which doesn't pass
+ validation
+ - Web services parameters dialog box is too large to fit on
+ screen
+ - Muscle nucleotide alignment preset obscured by tooltip
+ - JABAWS preset submenus don't contain newly defined
+ user preset
+ - MSA web services warns user if they were launched with
+ invalid input
+ - Jalview cannot contact DAS Registy when running on Java 8
+ -
+
+ 'Superpose with' submenu not shown when new view created
+
- Applet
+ Deployment and Documentation
+
+ - 2G and 1G options in launchApp have no effect on memory
+ allocation
+ - launchApp service doesn't automatically open
+ www.jalview.org/examples/exampleFile.jar if no file is given
+ -
+
+ InstallAnywhere reports cannot find valid JVM when Java 1.7_055 is
+ available
+
+ Application Known issues
+
+ -
+
+ corrupted or unreadable alignment display when scrolling alignment
+ to right
+
+ -
+
+ retrieval fails but progress bar continues for DAS retrieval with
+ large number of ID
+
+ -
+
+ flatfile output of visible region has incorrect sequence start/end
+
+ -
+
+ rna structure consensus doesn't update when secondary
+ structure tracks are rearranged
+
+ -
+
+ invalid rna structure positional highlighting does not highlight
+ position of invalid base pairs
+
+ -
+
+ out of memory errors are not raised when saving jalview project
+ from alignment window file menu
+
+ -
+
+ Switching to RNA Helices colouring doesn't propagate to
+ structures
+
+ -
+
+ colour by RNA Helices not enabled when user created annotation
+ added to alignment
+
+ -
+
+ Jalview icon not shown on dock in Mountain Lion/Webstart
+
+ Applet Known Issues
+ -
+
+ JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
+
+ -
+
+ Jalview and Jmol example not compatible with IE9
+
+
+ - Sort by annotation score doesn't reverse order when
+ selected
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