X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=2a65e4319ab97b80da3bbab76b46f3b5cb9e4fb0;hb=67473776389cd0a6024aa3e401819e503970082c;hp=22a0bd7f472506ecc37c42e366c1630e8a414caa;hpb=d587f1aa61946dc14f6f089cf1dc2a3116cfb773;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 22a0bd7..2a65e43 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,422 +1,639 @@ - - -Alignment Window Menus - - - -

Alignment Window Menus

-
  • File - -
    • -
  • Edit - -
    • -
  • Select - -
    • -
  • View - -
    • -
  • Alignment Window Format Menu - - - + + + + Alignment Window Menus + + + +

    Alignment Window Menus x

    + +
      + +
    • File +
        +
      • Fetch Sequence
        + Shows a dialog window in which you can retrieve known ids +from Uniprot, EMBL, EMBLCDS, PFAM, Rfam, or PDB database using Web +Services provided by the European Bioinformatics Institute. See Sequence Fetcher .
        • +
      • Add Sequences
        +Add sequences to the visible alignment from file, URL, or cut & +paste window
        • +
      • Reload
        +Reloads the alignment from the original file, if available.
        + Warning: This will delete any edits, analyses and +colourings applied since the alignment was last saved, and cannot be +undone.
        • +
      • Save (Control S)
        +Saves the alignment to the file it was loaded from (if available), in +the same format, updating the original in place.
        • +
      • Save As (Control Shift S)
        +         Save the alignment to local file. A file selection +window will open, use the "Files of type:" selection box to determine +which alignment format to save as. +
        • +
      • Output to Textbox
        +         The alignment will be displayed in plain text in a +new window, which you can "Copy and Paste" using the pull down menu, or +your standard operating system copy and paste keys. The output window +also has a "New Window" button to import the +(possibly edited) text as a new alignment.
        +Select the format of the text by selecting one of the following menu +items.         + +
          +
        • FASTA
          • +
        • MSF
          • +
        • CLUSTAL
          • +
        • BLC
          • +
        • PIR
          • +
        • PFAM
          • +
        +
        • +
      • Print (Control P)
        +         Jalview will print the alignment using the current +fonts and colours of your alignment. If the alignment has annotations +visible, these will be printed below the alignment. If the alignment is +wrapped the number of residues per line of your alignment will depend +on the paper width or your alignment window width, whichever is the +smaller.
        • +
      • Export Image
        +Creates an alignment graphic with the current view's annotation, +alignment background colours and group colours. If the alignment is wrapped, the output will also be +wrapped and will have the same visible residue width as the open +alignment.         + +
        • +
      • Export Features
        +All features visible on the alignment can be saved to file or displayed +in a textbox in either Jalview or GFF format
        • +
      • Export Annotations
        +All annotations visible on the alignment can be saved to file or +displayed in a textbox in Jalview annotations format.
        • +
      • Load Associated Tree
        +         Jalview can view trees 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 files describing precalculated sequence features or alignment annotations.
        • +
      • Close (Control W)
        + Close the alignment window. Make sure you have saved your +alignment before you close - either as a Jalview project or by using +the Save As menu.
        • +
      +
      • +
    • Edit +
        +
      • Undo (Control Z)
        +This will undo any edits you make to the alignment. This applies to +insertion or deletion of gaps, cutting residues or sequences from the +alignment or pasting sequences to the current alignment or sorting the +alignment. NOTE: It DOES NOT undo colour changes, +adjustments to group sizes, or changes to the annotation panel.
        • +
      • Redo (Control Y)
        +         Any actions which you undo can be redone using +redo.
        • +
      • Cut (Control X)
        +         This will make a copy of the currently selected +residues before removing them from your alignment. Click on a sequence +name if you wish to select a whole sequence.
        +Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.
        • +
      • Copy (Control C)
        + Copies the currently selected residues to the system +clipboard - you can also do this by pressing <CTRL> and C +(<APPLE> and C on MacOSX).
        +If you try to paste the clipboard contents to a text editor, you will +see the format of the copied residues FASTA.
        • +
      • Paste +
          +
        • To New Alignment (Control Shift V)
          +           A new alignment window will be created from +sequences previously copied or cut to the system clipboard.
          +Use <CTRL> and <SHIFT> and V(<APPLE> and +<SHIFT;> and and V on MacOSX) to paste.
          • +
        • Add To This Alignment (Control V)
          +           Copied sequences from another alignment window +can be added to the current Jalview alignment.
          • +
        +
        • +
      • Delete (Backspace)
        +         This will delete the currently selected residues +without copying them to the clipboard. Like the other edit operations, +this can be undone with Undo.
        • +
      • Remove Left (Control L)
        +         If the alignment has marked columns, the alignment +will be trimmed to the left of the leftmost marked column. To mark a +column, mouse click the scale bar above the alignment. Click again to +unmark a column, or select "Deselect All" to deselect all columns.
        • +
      • Remove Right (Control R)
        +         If the alignment has marked columns, the alignment +will be trimmed to the left of the leftmost marked column. To mark a +column, mouse click the scale bar above the alignment. Click again to +unmark a column, or select "Deselect All" to deselect all columns.
        • +
      • Remove Empty Columns (Control E)
        +         All columns which only contain gap characters +("-", ".") will be deleted.
        +You may set the default gap character in preferences.
        • +
      • Remove All Gaps (Control Shift E)
        + Gap characters ("-", ".") will be deleted from the selected +area of the alignment. If no selection is made, ALL the gaps in the +alignment will be removed.
        +You may set the default gap character in preferences.
        • +
      • Remove Redundancy (Control D)
        +         Selecting this option brings up a window asking +you to select a threshold. If the percentage identity between any two +sequences (under the current alignment) exceeds this value then one of +the sequences (the shorter) is discarded. Press the "Apply" button to +remove redundant sequences. The "Undo" button will undo the last +redundancy deletion.
        • +
      • Pad Gaps
        +         When selected, the alignment will be kept at +minimal width (so there 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 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 sequences' to be all the same length.
        +You may set the default for Pad Gaps in the preferences.
        • +
      +
      • +
    • Select +
        +
      • Find... (Control F) +
        +Opens the Find dialog box to search for residues, sequence name or +residue position within the alignment and create new sequence features +from the queries.
        • +
      • Select All (Control A)
        +         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 marked +columns will be deselected.
        +Use <ESCAPE> to deselect all.
        • +
      • Invert Sequence Selection (Control I)
        +         Any sequence ids currently not selected will +replace the current selection.
        • +
      • Invert Column Selection (Control Alt I)
        +         Any columns currently not selected will replace +the current column selection.
        • +
      • 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)
        +Creates a new view from the current alignment view.
        • +
      • Expand Views (X)
        +Display each view associated with the alignment in its own alignment +window, allowing several views to be displayed simultaneously.
        • +
      • Gather Views (G)
        +Each view associated with the alignment will be displayed within its +own tab on the current alignment window.
        • +
      • Show→(all Columns / Sequences / Sequences and Columns)
        +All hidden Columns / Sequences / Sequences and Columns will be +revealed.
        • +
      • Hide→(all Columns / Sequences / Selected Region / All +but Selected Region )
        +Hides the all the currently selected Columns / Sequences / Region or +everything but the selected Region.
        • +
      • Automatic Scrolling
        +         When 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 +Feature Settings...
        + Opens the Sequence Feature Settings dialog box to control +the colour and display of sequence features on the alignment, and +configure and retrieve features from DAS annotation servers.
        • + +
      • Sequence ID Tooltip (application +only)
        +This submenu's options allow the inclusion or exclusion of +non-positional sequence features or database cross references from the +tooltip shown when the mouse hovers over the sequence ID panel.
        • + +
      • Alignment Properties...
        +         Displays some simple statistics computed for the +current alignment view and any named properties defined on the whole +alignment.
        • + +
      • Overview +Window
        +         A scaled version of the alignment will be +displayed in a small window. A red box will indicate the currently +visible area of the alignment. Move the visible region using the mouse. +
        • + +
      +
      • + +
    • Alignment Window Format Menu +
        + +
      • Font...
        +         Opens the "Choose Font" dialog box, in order to +change the font of the display and enable or disable 'smooth fonts' +(anti-aliasing) for faster alignment rendering.
        • + +
      • Wrap
        +         When ticked, the alignment display is "wrapped" to the width of the +alignment window. This is useful if your alignment has only a few +sequences to view its full width at once.
        +Additional options for display of sequence numbering and scales are +also visible in wrapped layout mode:
        +         +
          + +
        • Scale Above
          + Show the alignment column position scale.
          • + +
        • Scale Left
          + Show the sequence position for the first aligned +residue in each row in the left column of the alignment.
          • + +
        • Scale Right
          + Show the sequence position for the last aligned +residue in each row in the right-most column of the alignment.
          • + +
        • Show Sequence Limits
          +           If this box is selected the sequence name will +have the start and end position of the sequence appended to the name, +in the format NAME/START-END
          • + +
        • Right Align Sequence ID
          +           If this box is selected then the sequence +names displayed in the sequence label area will be aligned against the +left-hand edge of the alignment display, rather than the left-hand edge +of the alignment window.
          • + +
        • Show Hidden Markers
          +           When this box is selected, positions in the +alignment where rows and columns are hidden will be marked by blue +arrows.
          • + +
        • Boxes
          +If this is selected the background of a residue will be coloured using +the selected background colour. Useful if used in conjunction with +"Colour Text."
          • + +
        • Text
          +           If this is selected the residues will be +displayed using the standard 1 character amino acid alphabet.
          • + +
        • Colour Text
          +           If this is selected the residues will be +coloured according to the background colour associated with that +residue. The colour is slightly darker than background so the amino +acid symbol remains visible.
          • + +
        • Show Gaps
          +           When this is selected, gap characters will be +displayed as "." or "-". If unselected, then gap characters will appear +as blank spaces.
          +You may set the default gap character in preferences.
          • + +
        • Centre Annotation Labels
          +           Select this to center labels along an +annotation row relative to their associated column (default is off, +i.e. left-justified).
          • + +
        • Show Unconserved
          +           When this is selected, all consensus sequence +symbols will be rendered as a '.', highlighting mutations in highly +conserved alignments.
          • + +
        +
        • + +
      +
      • + +
    + + +
  • Colour + +
    • + + +
  • Calculate + +
    • + + +
  • Web Service Menu
    + This menu is dynamic, and may contain user-defined web service +entries in addition to any of the following ones:     + + +

    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 use +these services through Jalview.

    + + +
    • + + + \ No newline at end of file