X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=f8b6d2948752077f3562d452744429ac8999d307;hb=d79235eeb9913fa59f5f4e635a2a8c39d80c775b;hp=890f3438184681ca9ec2ededbc78328caa9fd98f;hpb=1718e104b60584336348531e51c8121d69ff6416;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index 890f343..f8b6d29 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 in v2.7 example file means
+ alignment appears unaligned when pad-gaps is not enabled
+ - 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 tooltips shown
+ on some platforms
+ - Chimera viewer 'View | Show Chain' menu is not
+ populated
+ - 'New View' fails with a Null Pointer Exception in
+ console 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
+ - Save as '.jar' option removed for saving Jalview
+ projects
+ - Colour by Sequence colouring in Chimera more
+ responsive
+ - 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
+
+ - Applet example pages appear different to the rest of
+ www.jalview.org
+
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
+ - Cannot disable consensus calculation independently of
+ quality and conservation
+ - Mouseover highlighting between cDNA and protein can
+ become sluggish with more than one splitframe shown
+
Applet Known Issues
+
+ - Core PDB parsing code requires Jmol
+ - Sequence canvas panel goes white when alignment
+ window is being resized
+
-
+
+
+
+
+ |
+
+ |
- 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
-
+
+
+ |
+
+
+ - Reinstated the display of default example file on startup
+ - All pairs shown in Jalview window when viewing result of pairwise alignment
+
+ |
@@ -88,7 +300,9 @@
RNA pseudoknot annotation can be
imported/exported/displayed
'colour by annotation' can colour by RNA and
- protein secondary structure
+ 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
@@ -142,7 +356,7 @@
- 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
+
- author list isn't updated if already written to Jalview
properties
- Popup menu won't open after retrieving sequence from
database
@@ -210,7 +424,7 @@
-
- out of memory errors are not raised when saving jalview project
+ out of memory errors are not raised when saving Jalview project
from alignment window file menu
-
@@ -296,7 +510,7 @@
- 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
@@ -321,7 +535,7 @@
- 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)
@@ -383,7 +597,7 @@
- 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