X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=966c0053a7e4ecfff93c1337c396ba6ddbbe66a0;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=ff741397db866eaf474431995df901a6b93c4d2f;hpb=1984126973e19bd10f39bb516d728c9226f2ba71;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index ff74139..966c005 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,21 +1,24 @@ + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> Alignment Window Menus @@ -28,8 +31,8 @@
  • File
    • +
  • Undefine Groups (Control U)
    The + alignment will be reset with no defined groups.
    WARNING: + This cannot be undone.     +
    • +
  • View
    • New View (Control T)
      @@ -272,34 +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. -
        -
      • 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 Profile
         Enable - or disable the display of the sequence logo above the consensus - sequence.
        • -
      • Group Conservation
         When - ticked, display a conservation row for all groups (only available - for protein alignments).
        • -
      • Apply to all groups
         When - ticked, display a consensus row for all groups.
        • -
    • 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 @@ -322,6 +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 @@ -391,6 +427,9 @@
    • + + +
  • Colour @@ -407,7 +446,7 @@
  • Colour Scheme options: None, ClustalX, Blosum62 Score, Percentage Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity, Turn - Propensity, Buried Index, Nucleotide, User Defined
     See + Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User Defined
     See colours for a description of all colour schemes.
  • By Conservation
    See Annotation Colouring.
    • +
  • By RNA Helices
    + Colours the helices of an RNA alignment loaded from a Stockholm file. See + RNA Helices + Colouring.
    +
  • Calculate
      @@ -467,14 +511,15 @@
    • Neighbour Joining Using Blosum62
    + 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.
  • Principal Component Analysis
    Shows - a spatial clustering of the sequences based on the BLOSUM62 scores - in the alignment. See Principal + a spatial clustering of the sequences based on similarity scores calculated with + the alignment. See Principal Component Analysis.
  • Extract Scores ... (optional)
    This @@ -492,28 +537,36 @@
  • Sort With New Tree
    When enabled, Jalview will automatically sort the alignment when a new tree is calculated or loaded onto it.
    • - +
  • Show Flanking Regions
    Opens + a new alignment window showing any additional sequence data either + side of the current alignment. Useful in conjunction with 'Fetch + Database References' when the 'Trim Retrieved Sequences' option is + disabled to retrieve full length sequences for a set of aligned + peptides.
    • +
  • Web Service Menu
    This menu is dynamic, and may contain user-defined web service entries in addition to any of the following ones:
    • Fetch DB References
      This - will use 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 the sequence and retrieve all database cross - references and PDB ids associated with all or just the selected - sequences in the alignment.
      'Standard Databases' will check - sequences against the EBI databases plus any active DAS sequence - sources, or you can verify against a specific source from one of - the sub-menus.
      • -
    • Envision2 Services
      Submits one or - more sequences, sequence IDs or database references to analysis - workflows provided by the EnVision2 web - application. This allows Jalview users to easily access the EnCore - network of databases and analysis services developed by members of - ENFIN.
      • + 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. +

    Selecting items from the following submenus will start a remote service on compute facilities at the University of Dundee, or