X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=00a2ec405971542b021a483760a965ebf40be132;hb=refs%2Fheads%2Ffeatures%2FJAL-1793VCF;hp=24f823974882b16687a543dc217fbc542fbc527f;hpb=f3226d82fed697cb41c626a5204bb3b56add70c3;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 24f8239..00a2ec4 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -244,7 +244,7 @@ Selects all the sequences and residues in the alignment.
Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all. - +
  • Deselect All (Escape)
    Removes the current selection box (red dashed box) from the alignment window. All selected sequences, residues and @@ -279,12 +279,11 @@ columns in the alignment according to secondary structure, labels and values shown in alignment annotation rows.
  • Select Highlighted Columns
    Selects - the columns currently highlighted as a result of a find, mouse - over, or selection event from a linked structure viewer or other - application. Modifiers will work on some platforms: SHIFT will - add columns to selection, ALT will invert the highlighted set - before selection, and CTRL (or META) will toggle the selection. -
    • + the columns currently highlighted as a result of a find, mouse + over, or selection event from a linked structure viewer or other + application. Modifiers will work on some platforms: ALT will add + all but the highlighted set to the column selection, and CTRL + (or META) will toggle the selection.
  • View
    • @@ -542,44 +540,26 @@ viewer window.
    -
  • Calculate Tree
    Functions - for calculating trees on the alignment or the currently - selected region. See calculating - trees. - - Note: Since Version 2.8.1, a number of - additional similarity measures for tree calculation are - provided in this menu.
    • -
  • Pairwise Alignments
    Applies - Smith and Waterman algorithm to selected sequences. See pairwise - alignments. +
  • Calculate Tree or PCA ...
    Opens the + calculations dialog for + for calculating trees or + principle component analysis + plots on the alignment or the currently selected + region.
    • -
  • Principal Component Analysis
    Shows - a spatial clustering of the sequences based on similarity - scores calculated with the alignment. See Principal - Component Analysis. -
    • -
  • Extract Scores ... (optional)
    This - option is only visible if Jalview detects one or more - white-space separated values in the description line of the - alignment sequences.
    When selected, these numbers are - parsed into sequence associated annotation which can then be - used to sort the alignment via the Sort by→Score menu. -
    • -
  • Autocalculate Consensus
    For +
  • Pairwise Alignments
    Applies + Smith and Waterman algorithm to selected sequences. See pairwise + alignments. +
    • +
  • Extract Scores ... (optional)
    This + option is only visible if Jalview detects one or more + white-space separated values in the description line of the + alignment sequences.
    When selected, these numbers are + parsed into sequence associated annotation which can then be + used to sort the alignment via the Sort by→Score menu. +
    • +
  • Autocalculate Consensus
    For large alignments it can be useful to deselect "Autocalculate Consensus" when editing. This prevents the sometimes lengthy calculations performed after @@ -615,7 +595,7 @@ in Jalview 2.8.1
  • 'Standard Databases' will check sequences against - the EBI databases plus any active DAS sequence sources<
    • + the EBI databases plus any active DAS sequence sources Other sub-menus allow you to pick a specific source to query - sources are listed alphabetically according to their nickname. @@ -639,22 +619,22 @@
    • JPred Secondary Structure Prediction
      Secondary structure prediction by network - consensus. See the Jpred3 + consensus. See the Jpred client entry for more information. The behaviour of this calculation depends on the current selection:
      • If nothing is selected, and the displayed - sequences appear to be aligned, then a JNet prediction + sequences appear to be aligned, then a JPred prediction will be run for the first sequence in the alignment, using the current alignment. Otherwise the first sequence will be submitted for prediction.
      • If just one sequence (or a region on one sequence) has been selected, it will be submitted to - the automatic JNet prediction server for homolog + the automatic JPred prediction server for homolog detection and prediction.
      • If a set of sequences are selected, and they appear to be aligned, then the alignment will be used - for a Jnet prediction on the first + for a JPred prediction on the first sequence in the set (that is, the one that appears first in the alignment window).