X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=4a1a200377de05d2c1849d08be7d1aace67497f3;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=22a0bd7f472506ecc37c42e366c1630e8a414caa;hpb=d587f1aa61946dc14f6f089cf1dc2a3116cfb773;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 22a0bd7..4a1a200 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,422 +1,575 @@ - - -Alignment Window Menus - - - -

Alignment Window Menus

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

    + Alignment Window Menus +

    +
      +
    • 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. +
        • +
      • Undefine Groups (Control U)
        The + alignment will be reset with no defined groups.
        WARNING: + This cannot be undone.         +
        • +
      • Make Groups
         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)         +
        • +
      • +
    • 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 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 + 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 +
      +
    • Apply Colour To All Groups
      If + this is selected, any changes made to the background colour will + be applied to all currently defined groups.
       +
      • +
    • Colour + Text...
      Opens the Colour Text dialog box to + set a different text colour for light and dark background, and the + intensity threshold for transition between them.       +
      • +
    • Colour Scheme options: None, ClustalX, + Blosum62 Score, Percentage Identity, Zappo, Taylor, + Hydrophobicity, Helix Propensity, Strand Propensity, Turn + Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User Defined
       See + colours for a + description of all colour schemes.
      • +
    • By Conservation
      See Colouring by + Conservation.
      • +
    • Modify Conservation Threshold
      Use + this to display the conservation threshold slider window. Useful + if the window has been closed, or if the 'by conservation' option + appears to be doing nothing!
      • +
    • Above Identity Threshold
      See + Above Percentage + Identity .
       +
      • +
    • Modify Identity Threshold
      Use + this to set the threshold value for colouring above Identity. + Useful if the window has been closed.
       +
      • +
    • By Annotation
      Colours + the alignment on a per-column value from a specified annotation. + See Annotation + Colouring.
      • +
    • By RNA Helices
      + Colours the helices of an RNA alignment loaded from a Stockholm file. See + RNA Helices + Colouring.
      +
      • +
    • +
  • Calculate +
      +
    • Sort +
        +
      • by ID
        This will sort + the sequences according to sequence name. If the sort is + repeated, the order of the sorted sequences will be inverted.         +
        • +
      • by Length
        This will + sort the sequences according to their length (excluding gap + characters). If the sort is repeated, the order of the sorted + sequences will be inverted.
        • +
      • by Group
        This + will sort the sequences according to sequence name. If the sort + is repeated, the order of the sorted sequences will be inverted. +
        • +
      • by Pairwise Identity
        This + will sort the selected sequences by their percentage identity to + the consensus sequence. The most similar sequence is put at the + top.
        • +
      • The Sort + menu will have some additional options if you have just done a + multiple alignment calculation, or opened a tree viewer window.
        +
        • +
      +
      • +
    • Calculate Tree
      Functions + for calculating trees on the alignment or the currently selected + region. See calculating + trees. +
        +
      • Average Distance Using % Identity
        • +
      • Neighbour Joining Using % Identity
        • +
      • Average Distance Using Blosum62
        • +
      • Neighbour Joining Using Blosum62
        +
        • +
      +
      • +
    • 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 + 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 + large alignments it can be useful to deselect "Autocalculate + Consensus" when editing. This prevents the sometimes lengthy + calculations performed after each sequence edit.
      +
      • +
    • Sort With New Tree
      When + enabled, Jalview will automatically sort the alignment when a new + tree is calculated or loaded onto it.
      • +
    • + +
  • 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.
      • +
    +

    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. +

    +
      +
    • Alignment
      Align the currently + selected sequences or all sequences in the alignment, or re-align + unaligned sequences to the aligned sequences. Entries in this menu + provide access to the various alignment programs supported by JABAWS. See the Multiple Sequence + Alignment webservice client entry for more information.
      • +
    • Secondary Structure Prediction +
        +
      • JPred Secondary Structure Prediction
        + Secondary structure prediction by network consensus. See + the Jpred3 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 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 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 sequence in the set + (that is, the one that appears first in the alignment window). +
          • +
        +
      • +
    • Analysis
      +
        +
      • Multi-Harmony
        Performs + functional residue analysis on a protein family alignment with + sub-families defined on it. See the Multi-Harmony service entry for more + information. +
        • +
      • +
    • + + + +