From d7c2b4706c0674a764a7e3568c0e23bc73a1d7aa Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 17 Nov 2014 17:14:23 +0000 Subject: [PATCH] JAL-1517 JAL-1587 JAL-674 secondary structure and annotation from prediction services documentation --- help/help.jhm | 2 ++ help/helpTOC.xml | 3 +++ help/html/features/annotation.html | 9 +++++++++ help/html/menus/popupMenu.html | 4 ++-- help/html/webServices/jnet.html | 3 ++- 5 files changed, 18 insertions(+), 3 deletions(-) diff --git a/help/help.jhm b/help/help.jhm index c6cc626..b6b0063 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -39,6 +39,7 @@ + @@ -54,6 +55,7 @@ + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 6ae5c78..1d45e7a 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -97,6 +97,9 @@ + + + diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html index 49128c2..a036bd5 100755 --- a/help/html/features/annotation.html +++ b/help/html/features/annotation.html @@ -39,6 +39,15 @@ and symbolic annotations can be added to an alignment via an Annotations File dragged into the alignment window or loaded from the alignment's file menu.

+

Sequence Reference Annotation +

+

+ Sequence reference annotation is created from 3D structure + data, and from the results of sequence based prediction of + secondary structure and disordered region + prediction methods. +

Interactive Alignment Annotation

Annotation rows are added using the Annotation Label diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html index 511b85f..63bb815 100755 --- a/help/html/menus/popupMenu.html +++ b/help/html/menus/popupMenu.html @@ -41,7 +41,7 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).

  • Hide Annotations...
    Choose to hide either All or a selected type of annotation for the selected sequences. (Since Jalview 2.8.2)
    • -
  • Add Reference Annotations...
    +
  • Add Reference Annotations
    Add to the alignment window any annotations on the selected sequences which have been read from reference sources or calculated (for example, secondary structure derived from 3D structure). (Since Jalview 2.8.2)
    • @@ -134,7 +134,7 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).

    window will be displayed asking for a new sequence name and sequence description to be entered. Press OK to accept your edit. To save sequence descriptions, you must save in Fasta, PIR or Jalview File format. -
    • +
  • Add Reference Annotations
    When enabled, copies any available alignment annotation for this sequence to the current view.
  • Represent Group With (Sequence Id)
    All sequences in the current selection group will be hidden, apart from (Sequence Id). Any edits performed on the visible representative diff --git a/help/html/webServices/jnet.html b/help/html/webServices/jnet.html index 9a7acd9..5555c73 100755 --- a/help/html/webServices/jnet.html +++ b/help/html/webServices/jnet.html @@ -110,10 +110,11 @@ The annotation bars below the alignment are as follows: invoked to rationalise significantly different primary predictions.

    • +JNet annotation created in Jalview 2.8.2 and later versions can be displayed on other alignments via the     Add reference annotation As of Jalview 2.6, the Jnet service accessed accessed via the 'Secondary structure prediction' submenu should be considered a legacy Jalview SOAP service, and will be replaced in the near future by a -JABAWS Jnet service. +JABAWS Jnet service (now available in the Jalview 2.9 development version). -- 1.7.10.2