X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=f23c1b76d378fec01f1c1ee5de8fc08b10edc403;hb=5b05749cab04092671551fbbcdc80406b53da7d0;hp=22a0bd7f472506ecc37c42e366c1630e8a414caa;hpb=d587f1aa61946dc14f6f089cf1dc2a3116cfb773;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 22a0bd7..f23c1b7 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,422 +1,504 @@ - - -Alignment Window Menus - - - -

Alignment Window Menus

-
  • 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 select known ids from + Uniprot, EMBL, EMBLCDS 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, 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.
        +
        • +
      +
      • +
    • 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.
        +
        • +
      +
      • +
    • Web Service
      +       +
      • 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.
        +
        • +
      + Selecting one of the following menu items starts a remote + service on compute facilities at the University of Dundee. You need a + continuous network connection in order to use these services through + Jalview. +
        +
      • Alignment +
          +
        • ClustalW Multiple Sequence Alignment
          + Submits all, or just the currently selected sequences for + alignment with clustal W.
          • +
        • ClustalW Multiple Sequence Alignment + Realign
          + Submits the alignment or currently selected region for + re-alignment with clustal W. Use this if you have added some new + sequences to an existing alignment.
          • +
        • MAFFT Multiple Sequence Alignment
          + Submits all, or just the currently selected region for + alignment with MAFFT.
          • +
        • Muscle Multiple Protein Sequence Alignment
          + Submits all, or just the currently selected sequences for + alignment using Muscle. Do not use this if you are working with + nucleic acid sequences.
          • +
        +
        • +
      • Secondary Structure Prediction +
          +
        • JPred Secondary Structure Prediction
          + Secondary structure prediction by network consensus. 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).
          • +
        +
        • +
      +
      • +
    + +