X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=966c0053a7e4ecfff93c1337c396ba6ddbbe66a0;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=d53b3eb799f7436865dd10a3e904bf9710db5549;hpb=bda1b6a4412a73727de4613cfe3a6829b0fe0804;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index d53b3eb..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 @@ -59,18 +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 @@ -109,7 +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 @@ -200,9 +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 @@ -276,38 +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. -
      -
    • 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).
      • -
    • 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 @@ -330,6 +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 @@ -483,14 +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 @@ -508,28 +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