X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=07d05ea6db6f3e20caf2e179ef6d874a934376bb;hb=9f48318d26fe985ea5e0445abb6625fe1e788bd5;hp=6b92a2c6b40295f16922c73be927b6e2b4fd15f9;hpb=e5cbd35e13f46ae1d59a08b0af1086677418141d;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index 6b92a2c..07d05ea 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -1,7 +1,7 @@
Application
+
+ - Escape should close any open find dialogs
+ - typo in select-by-features status report
+ - Consensus RNA secondary secondary structure
+ predictions are not highlighted in amber
+ - missing gap character means v2.7 example file appears
+ unaligned REVIEW
+ - First switch to RNA Helices colouring doesn't colour
+ associated structure views
+ - ID width preference option is greyed out when auto
+ width checkbox not enabled
+ - Stopped a warning dialog from being shown when
+ creating user defined colours
+ - 'View Mapping' in structure viewer shows sequence
+ mappings for just that viewer's sequences
+ - Workaround for superposing PDB files containing
+ multiple models in Chimera
+ - Report sequence position in status bar when hovering
+ over Jmol structure
+ - Cannot output gaps as '.' symbols with Selection ->
+ output to text box
+ - Flat file exports of alignments with hidden columns
+ have incorrect sequence start/end
+ - 'Aligning' a second chain to a Chimera structure from
+ Jalview fails
+ - Colour schemes applied to structure viewers don't
+ work for nucleotide
+ - Loading/cut'n'pasting an empty or invalid file leads
+ to a grey/invisible alignment window
+ - Exported Jpred annotation from a sequence region
+ imports to different position
+ - Space at beginning of sequence feature mouseover
+ tooltip on some platforms
+ - Chimera viewer 'View | Show Chain' menu is not
+ populated
+ - 'New View' fails with a Null Pointer Exception if
+ Chimera has been opened
+ - Mouseover to Chimera not working
+ - Miscellaneous ENA XML feature qualifiers not
+ retrieved
+ - NPE in annotation renderer after 'Extract Scores'
+ - If two structures in one Chimera window, mouseover of
+ either sequence shows on first structure
+ - 'Show annotations' options should not make
+ non-positional annotations visible
+ - subsequence secondary structure annotation not shown
+ in right place after 'view flanking regions'
+ - File Save As type unset when current file format is
+ unknown
+ - Native 'Quaqua' dialogs for saving and loading files
+ on OSX
+ - Save as '.jar' option removed for saving Jalview
+ projects
+ - Colour by Sequence colouring in Chimera more
+ responsive
+ - Can disable consensus calculation independently of
+ quality and conservation
+ - Cannot 'add reference annotation' for a sequence in
+ several views on same alignment
+ - Cannot show linked products for EMBL / ENA records
+ - Jalview's tooltip wraps long texts containing no
+ spaces
+
Applet
+ Jmol to JalviewLite mouseover/link not working
+ JalviewLite can't import sequences with ID descriptions
+ containing angle brackets
+ General
+
+ - Cannot export and reimport RNA secondary structure
+ via jalview annotation file
+ - Random helix colour palette for colour by annotation
+ with RNA secondary structure
+ - Mouseover to cDNA from STOP residue in protein
+ translation doesn't work.
+ - hints when using the select by annotation dialog box
+ - Jmol alignment incorrect if PDB file has alternate CA
+ positions
+ - FontChooser message dialog appears to hang after
+ choosing 1pt font
+ - Peptide secondary structure incorrectly imported from
+ annotation file when annotation display text includes 'e' or
+ 'h'
+ - Cannot set colour of new feature type whilst creating
+ new feature
+ - cDNA translation alignment should not be sequence
+ order dependent
+ - 'Show unconserved' doesn't work for lower case
+ sequences
+ - Nucleotide ambiguity codes involving R not recognised
+
Deployment and Documentation
+ Application Known issues
+
+ - Incomplete sequence extracted from PDB entry 3a6s
+ - Misleading message appears after trying to delete
+ solid column.
+ - Jalview icon not shown in dock after InstallAnywhere
+ version launches
+ - Fetching EMBL reference for an RNA sequence results
+ fails with a sequence mismatch
+ - Corrupted or unreadable alignment display when
+ scrolling alignment to right
+ - ArrayIndexOutOfBoundsException thrown when remove
+ empty columns called on alignment with ragged gapped ends
+ - auto calculated alignment annotation rows do not get
+ placed above or below non-autocalculated rows
+ - Jalview dekstop becomes sluggish at full screen in
+ ultra-high resolution
+
Applet Known Issues
+
+ - Core PDB parsing code requires Jmol
+ - Sequence canvas panel goes white when alignment
+ window is being resized
+
-
+
+
+
+ |
+
+ |
+
+
+
+ |
+
+
+ - Reinstated the display of default example file on startup
+ - All pairs shown in Jalview window when viewing result of pairwise alignment
+
+ |
+
+
+ |
+ 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
+ - Warn user if 'Find' regular expression is invalid (mentioned post-hoc with 2.9 release)
+
+ Application
+
+ - 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
+
+
+ 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
+
+ |
+
2.8.1
4/6/2014
@@ -89,7 +508,7 @@
Newly created RNA secondary structure line doesn't have
'display all symbols' flag set
T-COFFEE alignment score shading scheme and other
- annotation shading not saved in jalview project
+ annotation shading not saved in Jalview project
Local file cannot be loaded in freshly downloaded Jalview
Jalview icon not shown on dock in Mountain Lion/Webstart
Load file from desktop file browser fails
@@ -114,7 +533,7 @@
Not all working JABAWS services are shown in Jalview's
menu
- JAVAWS version of jalview fails to launch with 'invalid
+ JAVAWS version of Jalview fails to launch with 'invalid
literal/length code'
Annotation/RNA Helix colourschemes cannot be applied to
alignment with groups (actually fixed in 2.8.0b1)
@@ -176,7 +595,7 @@
Allow disorder predictions to be made on the current
selection (or visible selection) in the same way that JPred
works
- Groovy scripting for headless jalview operation
+ Groovy scripting for headless Jalview operation
Other improvements
- Upgrade desktop installer to InstallAnywhere 2013
|