From: Jim Procter Date: Tue, 21 Apr 2020 13:10:22 +0000 (+0100) Subject: JAL-3567 JAL-3407 document sequence features report and the additional info provided... X-Git-Tag: Develop-2_11_2_0-d20201215~32 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2720003e4d3537f99f6c1643561cbdb3d0120d2d;hp=-c;p=jalview.git JAL-3567 JAL-3407 document sequence features report and the additional info provided for virtual features. Also bumped release date to 22st April --- 2720003e4d3537f99f6c1643561cbdb3d0120d2d diff --git a/help/help/help.jhm b/help/help/help.jhm index aecd1a4..99d010d 100755 --- a/help/help/help.jhm +++ b/help/help/help.jhm @@ -47,6 +47,7 @@ + diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml index 5802ddb..a0c7fe6 100755 --- a/help/help/helpTOC.xml +++ b/help/help/helpTOC.xml @@ -63,6 +63,7 @@ + diff --git a/help/help/html/features/seqfeaturereport.html b/help/help/html/features/seqfeaturereport.html new file mode 100644 index 0000000..340df5c --- /dev/null +++ b/help/help/html/features/seqfeaturereport.html @@ -0,0 +1,54 @@ + + + +Sequence Feature Reports + + +

+ Sequence Feature Reports
Sequence features + can carry a number of attributes. To view all the attributes for a + particular sequence feature, mouse over the feature and right-click + to open the Popup Menu and + select the feature's entry from the Feature Details + submenu. +

+ Full details for a particular Sequence Feature can be displayed as HTML in a report window +

+ Virtual Feature Reports
When a sequence feature + report is shown for features mapped between CDS and Protein + sequences, the report will include both the original and mapped + feature's location. +

+

+ Copying and pasting annotation to other programs
+ The File→Save option in the sequence + annotation report window allows the report to be saved as HTML, + which will preserve links and any other metadata. It is also + possible to copy and paste the text to other programs, but in some + cases, the HTML will not be preserved. In that case, you can toggle + the display of HTML source code with the Edit→Show + HTML Source drop down menu entry. +

+ Feature Reports were added in Jalview 2.11. + + diff --git a/help/help/html/features/seqfeaturesrep.png b/help/help/html/features/seqfeaturesrep.png new file mode 100644 index 0000000..f5995a1 Binary files /dev/null and b/help/help/html/features/seqfeaturesrep.png differ diff --git a/help/help/html/features/splitView.html b/help/help/html/features/splitView.html index 03b9ced..bb379ed 100644 --- a/help/help/html/features/splitView.html +++ b/help/help/html/features/splitView.html @@ -60,10 +60,14 @@ settings tabs and corresponding views showing 'Virtual Features' from each view overlaid on the other (created with Jalview 2.11.1.0).

-

When virtual features are enabled, they are also shown on any - linked 3D structure views when 'Colour by Sequence' is enabled, and +

+ When virtual features are enabled, they are also shown on any linked + 3D structure views when 'Colour by Sequence' is enabled, and exported as GFF and Jalview Features files (mapped to their - associated virtual coordinates).

+ associated virtual coordinates). Both the original and the mapped + locations are also included in Sequence + Feature Reports. +

Operations supported in Split Frame Mode

diff --git a/help/help/html/menus/popupMenu.html b/help/help/html/menus/popupMenu.html index 7625606..9c65e1a 100755 --- a/help/help/html/menus/popupMenu.html +++ b/help/help/html/menus/popupMenu.html @@ -27,14 +27,15 @@

Popup Menu
This menu is visible when right clicking either within a selected region on the - alignment or on a selected sequence name. It may not be accessible + alignment, on a sequence name, and also when right-clicking a sequence feature. It may not be accessible when in 'Cursor Mode' (toggled with the F2 key).
Mac Users: pressing CTRL whilst clicking the mouse/track pad is the same as a right-click. See your system's settings to configure your track-pad's corners to generate right-clicks.