X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=3a8c9f9e9c913dab5d51516487f3c73389eeb1cf;hb=3a5e7da51af0166273109f98bdf942e733105233;hp=014633270e72413098b4cbc0ee0379f869f2c6de;hpb=a9cdd36deb407469663634981cba65f049da5e44;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index 0146332..3a8c9f9 100755
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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
+ - Automatically hide introns when opening a gene/transcript view
+ - Uniprot Sequence fetcher Free Text Search dialog
+ - 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
+ - Upgrade to EMBL XML 1.2 for record retrieval via ENA rest API
- Support for ENA CDS records with reverse complement operator
+ - Update to groovy-2.4.6-indy - for faster groovy script execution
- 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
+ - Database selection dialog always shown before sequence fetcher is opened
- 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
+ - Displayed columns for PDBe and Uniprot querying stored in preferences
+ - Pagination for displaying PDBe and Uniprot search results
+ - Tooltips shown on database chooser
+ - Reverse complement function in calculate menu for nucleotide sequences
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+ Alignment sort by feature scores and feature counts preserves alignment ordering (and debugged for complex feature sets).
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Applet
@@ -94,7 +115,7 @@
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
+ 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
@@ -107,7 +128,40 @@
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
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+ Cannot create groups on an alignment from from a tree when t-coffee scores are shown
+ Cannot import and view PDB structures with chains containing negative resnums (4q4h)
+ ArithmeticExceptions raised when parsing some structures
+ 'Empty' alignment blocks added to Clustal, PIR and PileUp output
+ Reordering sequence features that are not visible causes alignment window to repaint
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+ Threshold sliders don't work in
+ graduated colour and colour by annotation row for e-value
+ scores associated with features and annotation rows
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+ amino acid physicochemical conservation
+ calculation should be case independent
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+ Remove annotation also updates hidden
+ columns
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+ FER1_ARATH and FER2_ARATH mislabelled in example file (uniref50.fa, feredoxin.fa, unaligned.fa, exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
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+ Null pointer exceptions and redraw problems when reference sequence defined and 'show non-conserved' enabled
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+ Quality and Conservation are now shown on load even when Consensus calculation is disabled
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Application
@@ -122,12 +176,68 @@
- Cannot save/restore representative sequence from project when only one sequence is represented
- 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
+ - View mapping in structure view shows mappings between sequence and all chains in a PDB file
+ - PDB and Uniprot FTS dialogs format columns correctly, don't display array data, sort columns according to type
+ - Export complete shown after destination file chooser is cancelled during an image export
+ - Error when querying PDB Service with sequence name containing special characters
+ - Manual PDB structure querying should be case insensitive
+ - Large tooltips with broken HTML formatting don't wrap
+ - Figures exported from wrapped view are truncated so L looks like I in consensus annotation
+ - Export features should only export the currently displayed features for the current selection or view
+ - Enable 'Get Cross-References' in menu after fetching cross-references
+ - Mouseover of a copy of a sequence is not followed in the structure viewer
+ - Titles for individual alignments in splitframe not restored from project
+ -
+ missing autocalculated annotation at trailing end of protein alignment in transcript/product splitview when pad-gaps not enabled by default
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+ -
+ amino acid physicochemical conservation is case dependent
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+ -
+ RSS reader doesn't stay hidden after last article has been read (reopened issue due to internationalisation problems)
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+ - Only offer PDB structures in structure viewer based on sequence name, PDB and Uniprot cross-references
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+ No progress bar shown during export of alignment as HTML
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+ Improved warning messages when DB Ref Fetcher fails to match, or otherwise updates sequence data from external database records.
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+ Structures not always superimposed after multiple structures are shown for one or more sequences.
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+ Reference sequence characters should not be replaced with '.' when 'Show unconserved' format option is enabled.
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+ Cannot specify chain code when entering specific PDB id for sequence
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+ File->Export->.. as doesn't work when 'Export hidden sequences' is enabled, but 'export hidden columns' is disabled.
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+ - Best Quality option in structure chooser selects lowest rather than highest resolution structures for each sequence
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+ Incorrect start and end reported for PDB to sequence mapping in 'View Mappings' report
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Applet
- Incorrect columns are selected when hidden columns present before start of sequence
+ - Missing dependencies on applet pages (JSON jars)
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+ Overview pixel size changes when sequences are hidden in applet
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+ - Updated instructions for applet deployment on examples pages.
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