From 1a703959b2bfba03cf8117466f8f98f9aba1e77c Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Fri, 28 Nov 2014 16:01:03 +0000 Subject: [PATCH] JAL-1517 first stab at release notes... lots of documentation to go! --- help/html/na/index.html | 6 +- help/html/releases.html | 190 +++++++++++++++++++++++++++++++++++++++++------ help/html/whatsNew.html | 12 +-- 3 files changed, 180 insertions(+), 28 deletions(-) diff --git a/help/html/na/index.html b/help/html/na/index.html index f3c4a56..844b6b7 100644 --- a/help/html/na/index.html +++ b/help/html/na/index.html @@ -67,7 +67,7 @@ td { as LocaRNA output consensus RNA secondary structure lines in the line normally reserved for the Clustal consensus line in a clustal file. - +

RNAML Jalview can import RNAML files containing sequences and extended secondary structure annotation derived from RNA 3D structure

RNA Secondary Structure Visualization and Analysis
@@ -85,6 +85,10 @@ td { Visualization in VARNA - allows linked viewing of the consensus or an individual sequence's structure +

Pseudo-knots
+ Jalview 2.8.2 introduced limited support for working with structures including pseudoknots. Where possible, extended WUSS symbols (e.g. different types of parentheses, or upper and lower case letters) are preserved when parsing RNA structure annotation and will be shaded differently when displayed in the structure.
+ Extended WUSS annotation is also employed to distinguish different base pair interactions obtained from RNAML files.

Limitations when working with RNA in Jalview
Currently, Jalview is not able to export RNA secondary structure annotation in any format other than Jalview annotation
diff --git a/help/html/releases.html b/help/html/releases.html index 8913a32..1f5ca08 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -25,43 +25,191 @@

Release History

- - - - - + + + + + - +

Output in Stockholm format

Internationalisation: improved Spanish (es) translation

Structure viewer preferences tab

Disorder and Secondary Structure annotation tracks shared + between alignments

UCSF 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

+ + 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

+ Application Known issues +

+ + corrupted or unreadable alignment display when scrolling alignment + to right +
+ + 'Superpose with' submenu not shown when new view created +
+ + 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 +
+ + InstallAnywhere reports cannot find valid JVM when Java 1.7_055 is + available +
+ + invalid rna structure positional highlighting isn't useful +

+ + 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 JmolData jar dependencies +
+ + Jalview and Jmol example not compatible with IE9 +
Sort by annotation score doesn't reverse order when + selected

- Release -	- New Features -	- Issues Resolved -
+ + Release + +	+ + New Features + +	+ + Issues Resolved + +
2.8.2 18/11/2014	- - General +	General + 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 - - -	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 + Unable to add 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 dasregisty (Java 8) Applet - Other + General - -
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index ae45aae..4ca6e93 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -29,12 +29,12 @@ Jalview 2.8.2 is the first release produced by our new core development team. It incorporates many minor improvements and - bug-fixes, and also includes new features for working with 3D - structure data, shading alignments by secondary structure and - generation of alignment figures as Scalable Vector Graphics. As - ever, the highlights are detailed below, and the full list is given in - the Jalview 2.8.2 Release - Notes. + bug-fixes, and new features for working with 3D structure data, + shading alignments by secondary structure and generation of alignment + figures as Scalable Vector Graphics. + As ever, the highlights are detailed below, and the full list is + given in the + Jalview 2.8.2 Release Notes. -- 1.7.10.2