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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
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
-
-
+
+ - 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 or PCA ...
Opens the
+ calculations dialog for
+ for calculating trees or
+ principle component analysis
+ plots on the alignment or the currently selected
+ region.
+
+ - Pairwise Alignments
Applies
+ Smith and Waterman algorithm to selected sequences. See pairwise
+ alignments.
+
+ - 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.
+ - 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
+ 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 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 Jpred
+ 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 JPred 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 JPred 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 JPred 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.
+
+
+
+
+