X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=f3ab75dfbbc55786166c79c35ee50254ede337c9;hb=7692386ccfe778075dd83a753d30a7a27fe507be;hp=24f823974882b16687a543dc217fbc542fbc527f;hpb=f3226d82fed697cb41c626a5204bb3b56add70c3;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 24f8239..f3ab75d 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 +538,26 @@ 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 @@ -599,28 +577,26 @@ is dynamic, and may contain user-defined web service entries in addition to any of the following ones:
      -
    • Fetch DB References
      This - submenu contains options for accessing any of the database - services that Jalview is aware of (e.g. DAS sequence servers - and the WSDBFetch service provided by the EBI) to verify - sequence start/end positions and retrieve all database cross - references and PDB ids associated with all or just the - selected sequences in the alignment. -
        -
      • 'Trim Retrieved Sequences' - when checked, Jalview - will discard any additional sequence data for accessions - associated with sequences in the alignment.
        Note: - Disabling this could cause out of memory errors when - working with genomic sequence records !
        Added - in Jalview 2.8.1 -
        • -
      • 'Standard Databases' will check sequences against - 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. -
      • -
    +
  • Fetch DB References
    This + submenu contains options for accessing any of the database + services that Jalview is aware of (e.g. those provided by + EMBL-EBI) to verify sequence start/end positions and retrieve all + database cross references and PDB ids associated with all or just + the selected sequences in the alignment. +
      +
    • 'Trim Retrieved Sequences' - when checked, Jalview will + discard any additional sequence data for accessions associated + with sequences in the alignment.
      Note: + Disabling this could cause out of memory errors when working + with genomic sequence records !
      Added + in Jalview 2.8.1 +
      • +
    • 'Standard Databases' will check sequences against the + EBI databases.
      • +
    Other sub-menus allow you to pick a specific source to query - + sources are listed alphabetically according to their nickname. +
    • +

    Selecting items from the following submenus will start a remote service on compute facilities at the University of Dundee, or elsewhere. You need a continuous network connection in order to @@ -639,22 +615,22 @@

    • 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).