X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=22a0bd7f472506ecc37c42e366c1630e8a414caa;hb=4fe43371b9524afd658c97c8767cf7e6dc84459e;hp=00bca80edc6a3ebefd460129804c9db33f2c8024;hpb=c973cc268cbba93fa4ca9620c3910d30891a5abc;p=jalview.git
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@@ -1,176 +1,422 @@
-
Menus
+
+Alignment Window Menus
+
-Alignment Menu
-
- - File
-
- - Save As
- 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.
-
- - Export
- Creates an alignment output maintaining the 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.
-
-
-
- - 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.
- Select the format of the text by selecting one of the following menu items.
-
- - FASTA
- - MSF
- - CLUSTAL
- - BLC
- - PIR
- - PFAM
-
-
-
- - Print
- Jalview will print the alignment using the current fonts and
- coloursof 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.
- - Load Associated Tree
- Jalview can load in trees which are in the Newick file format
- and associate them with a particular alignment. Note: the ids of the tree
- file and your alignment MUST be the same.
- - Close
- Close the alignment window. Be aware that changes to your alignment
- will not be save unless specifically actioned from the "Save As"
- menu.
-
-
- - Edit
+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.
+
+
+ - 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)
+ All hidden Columns / Sequences will be revealed.
+ - Hide→(all Columns / Sequences)
+ Hides the all the currently selected Columns / Sequences
+ - 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.
+ - 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.
+ - 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.
+
+ - 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.
+
+ - 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
+ 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).
+
+
+
+
-
-
- - Undo
- 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, pasting
-
- - Redo
-
- - Cut
- - Copy
- - Paste
-
- - To New Alignment
- - Add To This Alignment
-
-
- - Delete
- - Select All
- - Deselect All
- - Invert Selection
- - Undefine Groups
- - Remove Left
- - Remove Right
- - Remove Empty Columns
- - Remove All Gaps
- - Remove Redundancy
- - Pad Gaps
-
-
-
-
-
-
-
-
-
- - Font
- - Wrap
- - Show Full Sequence ID
- - Boxes
- - Text
- - Colour Text
- - Show Gaps
- - Show Annotations
- - Sequence Features
- - Overview Window
-
-
-
-
-
- - Apply Colour To All Groups
- - None
- - ClustalX
- - Blosum62 Score
- - Percentage Identity
- - Zappo
- - Taylor
- - Hydrophobicity
- - Helix Propensity
- - Strand Propensity
- - Turn Propensity
- - Buried Index
- - Nucleotide
- - User Defined
- - By Conservation
- - Modify Conservation Threshold
- - Above Identity Threshold
- - Modify Identity Threshold
-
-
-
-
-
- - Sort
-
- - by ID
- - by Group
- - by Pairwise Identity
-
-
- - Calculate Tree
-
- - Average Distance Using % Identity
- - Neighbour Joining Using % Identity
- - Average Distance Using Blosum62
- - Neighbour Joining Using Blosum62
-
-
- - Paiwise Alignments
- - Principal Component Analysis
- - Web Service
-
- - Clustal Alignment
- - JPred
- - Muscle Alignment
-
-
-
-
-