From: tcofoegbu Date: Tue, 8 Sep 2015 16:01:41 +0000 (+0100) Subject: updated helpTOC to include recently added features, updated menus and outdated screen... X-Git-Tag: Release_2_10_0~466 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=354963d0c9d69f28fa5aa642c1f13627676ff4ae;p=jalview.git updated helpTOC to include recently added features, updated menus and outdated screenshots --- diff --git a/help/help.jhm b/help/help.jhm index a450473..fe465ec 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -107,7 +107,6 @@ - @@ -138,6 +137,11 @@ + + + + + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 4ce9892..75ff4c4 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -31,7 +31,11 @@ - + + + + + diff --git a/help/html/calculations/AnnotationColumnSelectionWithSM.gif b/help/html/features/AnnotationColumnSelectionWithSM.gif similarity index 100% rename from help/html/calculations/AnnotationColumnSelectionWithSM.gif rename to help/html/features/AnnotationColumnSelectionWithSM.gif diff --git a/help/html/calculations/AnnotationColumnSelectionWithoutSM.gif b/help/html/features/AnnotationColumnSelectionWithoutSM.gif similarity index 100% rename from help/html/calculations/AnnotationColumnSelectionWithoutSM.gif rename to help/html/features/AnnotationColumnSelectionWithoutSM.gif diff --git a/help/html/calculations/columnFilterByAnnotation.html b/help/html/features/columnFilterByAnnotation.html similarity index 100% rename from help/html/calculations/columnFilterByAnnotation.html rename to help/html/features/columnFilterByAnnotation.html diff --git a/help/html/features/schooser_enter-id.png b/help/html/features/schooser_enter-id.png index dc5aa93..f551c50 100644 Binary files a/help/html/features/schooser_enter-id.png and b/help/html/features/schooser_enter-id.png differ diff --git a/help/html/features/schooser_main.png b/help/html/features/schooser_main.png index fe9e5dc..ab69427 100644 Binary files a/help/html/features/schooser_main.png and b/help/html/features/schooser_main.png differ diff --git a/help/html/features/structurechooser.html b/help/html/features/structurechooser.html index 1bf9f32..7db8083 100644 --- a/help/html/features/structurechooser.html +++ b/help/html/features/structurechooser.html @@ -32,7 +32,7 @@ selecting PDB structures to view in Jalview by querying readily available meta-data of structures. The Interface can be invoked by selecting the - "View Structure" option from a sequence's + "3D Structure Data.." option from a sequence's pop-up menu. Some of the main features it provides are listed below:
    diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index 44a07cc..3586083 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -104,7 +104,7 @@ structure is selected, one of the following will happen:

    Importing PDB Entries or files in PDB format
    You can retrieve sequences from the PDB using the Sequence Fetcher. Any sequences retrieved with + href="pdbsequencefetcher.html">Sequence Fetcher. Any sequences retrieved with this service are automatically associated with their source database entry. For PDB sequences, simply select PDB as the database and enter your known PDB id (appended with ':' and a chain code, if desired).
    diff --git a/help/html/menus/alwfile.html b/help/html/menus/alwfile.html index 9d2ad33..87582f8 100755 --- a/help/html/menus/alwfile.html +++ b/help/html/menus/alwfile.html @@ -64,7 +64,8 @@

  • PileUp
  • AMSA
  • STH
    • -
  • Phylip
    • +
  • PHYLIP
    • +
  • JSON
  • Page Setup ...
    @@ -94,6 +95,8 @@ Graphics file from your alignment.
  • SVG
    Create a Scalable Vector Graphics file from your alignment for embedding in web pages.
    • +
  • BioJS
    +     Create a BioJS MSA Viewer HTML file from your alignment.
  • Export Features
    diff --git a/help/html/menus/alwselect.html b/help/html/menus/alwselect.html index dc2b8a1..578a53e 100644 --- a/help/html/menus/alwselect.html +++ b/help/html/menus/alwselect.html @@ -54,6 +54,7 @@
  • Undefine Groups (Control U)
    The alignment will be reset with no defined groups.
    WARNING: This cannot be undone.
    • +
  • Select/Hide Columns by Annotation...
    Select or hide columns of an alignment by filtering with properties of any annotation row added to that alignment
    • diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html index f84922e..9d6a0c6 100755 --- a/help/html/menus/popupMenu.html +++ b/help/html/menus/popupMenu.html @@ -158,14 +158,13 @@ based URL links that matched the description line.
    -
  • View Structure This menu is only - visible if you right-click on a sequence name. If the - sequence has an associated PDB file(s), Jalview will open a 'Structure Chooser' - dialogue with options to select the structure which will eventually be opened in +
  • 3D Structure Data... This menu is + visible when you right-click on a sequence name. When this option is clicked, Jalview will open a 'Structure Chooser' + dialogue with options to select the structure which will eventually be opened in a 3D interactive view.
    These entries will only be present if the sequence - has associated PDB - structures.
    If the sequence or alignment has RNA structure, - then 2D RNA entries will also be present enabling + has associated PDB structures. +
    If the sequence or alignment has RNA structure, + then VARNA 2D Structure entries will also be present enabling you to open a linked view of the RNA structure in VARNA.