X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=c628cf1fe94e98ce28c3aca93b1b86adb2331bc1;hb=ab7509436f09413b122dace2ecd6692f6f06d347;hp=aceabce6cff415f41d403479174de80961e2d074;hpb=aff93619ba53584f9b01970832558331951d9dbf;p=jalview.git
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Alignment Window Menus
-Alignment Window Menus
- File
+
+ Alignment Window Menus
+
- - 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.
- - 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.
- - 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 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.
-
- - 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).
-
- - 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 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.
-
-
-
+