X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=95dcad838c9f562f3ef5ab4a38a7c69b439c21f1;hb=b5d61763044c1d72f06ce0e50da2171422a3774b;hp=94faed935127949cd7d9a2199361d7b1abdba96f;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 94faed9..95dcad8 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 @@ -236,17 +236,21 @@ Any columns currently not selected will replace the current column selection.
    • -
  • Undefine Groups (Control U)
    The - alignment will be reset with no defined groups.
    WARNING: - This cannot be undone.     -
    • -
  • Make Groups
     The currently +
  • Create Group (Control G)
     + Create a group containing the currently selected sequences.
    • +
  • Remove Group (Shift Control G)
     + Ungroup the currently selected sequence group. (Create/Remove group new in Jalview 2.8.1)
    • +
  • Make Groups for selection
     The currently selected groups of the alignment will be subdivided according to the contents of the currently selected region.
    Use this to subdivide an alignment based on the different combinations of residues observed at specific positions. (new in jalview 2.5)
    • - +
  • Undefine Groups (Control U)
    The + alignment will be reset with no defined groups.
    WARNING: + This cannot be undone.     +
    • +
  • View
    • New View (Control T)
      @@ -273,38 +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 @@ -327,6 +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 @@ -480,14 +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 @@ -505,28 +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