X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=9339b33d5644db3785b74ec41187bc1f4bbb51c7;hb=0d50ab3cdf86523b239e7dcccc551164ed197467;hp=0837cb08f4a655e09e5e112b8f755eca49cad70b;hpb=04cc755a023a86c4a21c27bfbf17cee869635929;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index 0837cb0..9339b33 100755
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@@ -47,32 +47,41 @@
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General
- - Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and better PDB parsing.
+ - Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and better PDB parsing.
- Alignment ruler shows positions relative to reference sequence
- Position/residue shown in status bar when mousing over sequence associated annotation
+ - Default RNA SS symbol to 'matching bracket' for manual entry
+ - RNA Structure consensus indicates wc-only '()', canonical '[]' and invalid '{}' base pair populations for each column
+ - Feature settings popup menu options for showing or hiding columns containing a feature
+ - Edit selected group by double clicking on group and sequence associated annotation labels
+ - Sequence name added to annotation label in select/hide columns by annotation and colour by annotation dialogs
Application
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+ - UniProt - PDB protein structure mappings with the EMBL-EBI PDBe SIFTS database
+ - Updated download sites used for Rfam and Pfam sources to xfam.org
+ - Disabled Rfam(Full) in the sequence fetcher
- Show residue labels in Chimera when mousing over sequences in Jalview
- 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
+ - Support for ENA CDS records with reverse complement operator
+ - New 'execute Groovy script' option in an alignment window's Calculate menu
+ - Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode
+ - Support for creating new alignment calculation workers from groovy scripts
- Store/restore reference sequence in Jalview projects
- - Chain codes for a sequence's PDB associations are now saved/restored from project
- - Double click on an entry in Jalview's database chooser opens a sequence fetcher
- - Free-text search client for UniProt using the UniProt web API
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+ - Chain codes for a sequence's PDB associations are now saved/restored from project
+ - Double click on an entry in Jalview's database chooser opens a sequence fetcher
+ - Free-text search client for UniProt using the UniProt REST API
+ - -nonews command line parameter to prevent the news reader opening
+
Applet
@@ -85,13 +94,20 @@
- 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
+ - 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
- Alignment column in status incorrectly shown as "Sequence position" when mousing over annotation
+ - Incorrect column numbers in ruler when hidden columns present
+ - Colour by RNA Helices not enabled when user created annotation added to alignment
+ - RNA Structure consensus only computed for '()' base pair annotation
+ - Enabling 'Ignore Gaps' results in zero scores for all base pairs in RNA Structure Consensus
+ - Extend selection with columns containing feature not working
+ - Pfam format writer puts extra space at beginning of sequence
+ - Incomplete sequence extracted from pdb entry 3a6s
Application
@@ -105,12 +121,14 @@
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
Cannot save/restore representative sequence from project when only one sequence is represented
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+ Disabled 'Best Uniprot Coverage' option in Structure Chooser
+ Modifying 'Ignore Gaps' on consensus or structure consensus didn't refresh annotation panel
+ View mapping in structure view shows mappings between sequence and all chains in a PDB file
Applet
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+ - Incorrect columns are selected when hidden columns present before start of sequence
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