X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=a2cb603453107140975be86f36a518c3b203963e;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=fdaa0233478ea7509f25278b8f387d8b0ec88dcb;hpb=7fd07d9b6a64aa33e3dcab2fa2f8bc20be189f2f;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index fdaa023..a2cb603 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,22 +1,24 @@ + --> Alignment Window Menus @@ -60,18 +62,16 @@ Select the format of the text by selecting one of the following menu items.
  • Print (Control P)
    Jalview will print the alignment using the current fonts and colours of @@ -110,7 +110,7 @@
  • Load Associated Tree
    Jalview can view trees - stored in the Newick file format, and associate them with the + stored in the Newick file format, and associate them with the alignment. Note: the ids of the tree file and your alignment MUST be the same.
  • Load Features / Annotations
    Load @@ -201,9 +201,9 @@ the last redundancy deletion.
  • Pad Gaps
    When selected, - the alignment will be kept at minimal width (so there no empty + the alignment will be kept at minimal width (so there are no empty columns before or after the first or last aligned residue) and all - sequences will be padded with gap characters to the before and + sequences will be padded with gap characters before and after their terminating residues.
    This switch is useful when making a tree using unaligned sequences and when working with alignment analysis programs which require 'properly aligned @@ -277,38 +277,10 @@ selected, the view will automatically scroll to display the highlighted sequence position corresponding to the position under the mouse pointer in a linked alignment or structure view.
    • -
  • Show Annotations
    If this - is selected the "Annotation Panel" will be displayed - below the alignment. The default setting is to display the - conservation calculation, quality calculation and consensus values - as bar charts. -
    • -
  • Autocalculated Annotation
    Settings - for the display of autocalculated annotation. -
  • Show Sequence Features
    Show or hide sequence features on this alignment.
    • -
  • Seqence +
  • Sequence Feature Settings...
    Opens the Sequence Feature Settings dialog box to control the colour and display of sequence features on the alignment, and configure and @@ -331,6 +303,61 @@ using the mouse.
    • +
  • Annotations (Since Jalview 2.8.2) +
      +
    • Show Annotations
      If this + is selected the "Annotation Panel" will be displayed + below the alignment. The default setting is to display the + conservation calculation, quality calculation and consensus values + as bar charts. +
      • +
    • Show Alignment Related
      + Show all annotations that are for the alignment as a whole (for example, Consensus, + or secondary structure prediction from alignment).
      • +
    • Hide Alignment Related
      + Hide all annotations that are for the alignment as a whole.
      • +
    • Show Sequence Related
      + Show all annotations that are for individual sequences.
      • +
    • Hide Sequence Related
      + Hide all annotations that are for individual sequences.
      • +
    • You can also selectively show or hide annotations from the Popup + or Annotation menus.
      • +
    • Sort by Sequence
      Sort sequence-specific annotations by sequence order in the alignment + (and within that, by label).
      • +
    • Sort by Label
      Sort sequence-specific annotations by label + (and within that, by sequence order). If neither sort order is selected, no sorting is applied, + allowing you to make a manual ordering of the annotations.
      • +
    • Autocalculated Annotation
      Settings + for the display of autocalculated annotation. +
        +
      • Show first
         + Show autocalculated annotations above sequence-specific annotations. + Note this also applies to other annotations for the alignment, for example secondary + structure prediction from alignment.
        • +
      • Show last
         + Show autocalculated / alignment annotations below sequence-specific annotations.
        • +
      • Apply to all groups
         When + ticked, any modification to the current settings will be applied + to all autocalculated annotation.
        • +
      • Show Consensus Histogram
         + Enable or disable the display of the histogram above the + consensus sequence.
        • +
      • Show Consensus Logo
         Enable + or disable the display of the Consensus Logo above the consensus + sequence.
        • +
      • Normalise Consensus Logo
        +         When enabled, scales all logo stacks to the same height, + making it easier to compare symbol diversity in highly variable + regions.
        • +
      • Group Conservation
         When + ticked, display a conservation row for all groups (only available + for protein alignments).
        • +
      • Group Consensus
         When + ticked, display a consensus row for all groups.
        • +
      +
      • +
    +
  • Alignment Window Format Menu
    • Font...
      Opens the