X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=c628cf1fe94e98ce28c3aca93b1b86adb2331bc1;hb=ab7509436f09413b122dace2ecd6692f6f06d347;hp=d0f1052dd483f33c93f58782e1c5921e37a59e30;hpb=08b0ba966ee50a1668ca841afe8fe8ea6e6473fc;p=jalview.git
diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index d0f1052..c628cf1 100755
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -1,337 +1,567 @@
-
-
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.
- - 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 graphic with the current 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.
-
-
- - 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 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.
- - 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
- Jalview load precalculated sequence
- features or alignment
- annotations.
- - Close
- 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
- 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
- Any actions which you undo can be redone using redo.
- - Cut
- 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
- 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
- A new alignment window will be created from sequences
- previously copied or cut to the system clipboard.
- Use <CTRL> and V(<APPLE> and V on MacOSX) to paste.
- - Add To This Alignment
- Copied sequences from another alignment window can be
- added to the current Jalview alignment.
-
-
- - Delete
- This will delete the currently selected residues without
- copying them to the clipboard. Like the other edit operations, this can
- be undone with Undo.
- - Select All
- Selects all the sequences and residues in the alignment.
-
- Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.
- - Deselect All
- 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 Selection
- Any sequence ids currently not selected will replace the
- current selection.
- - Undefine Groups
- The alignment will be reset with no defined groups.
- WARNING: This cannot be undone.
- - Remove Left
- 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
- 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
- All columns which only contain gap characters ("-",
- ".") will be deleted.
- You may set the default gap character in preferences.
-
- - Remove All Gaps
- 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
- 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
- Adds gaps to the end of all the sequences so they are all
- the same length. This is useful for making a tree using unaligned sequences.
- You may set the default gap character in preferences.
-
-
-
-
- - Search
-
- - Find
- Select this to search
- for residues, sequence name or residue position within the alignment.
-
-
-
-
- - View
-
- - Font
- Change the font of the display from the "Choose Font"
- dialog box, which is shown when this item is selected.
- - 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.
- Options are available to show the residue numbering at the start and/or
- end of an alignment as well as showing the alignment position above each
- sequence row.
- NOTE: When in wrapped alignment view, the alignment cannot
- be edited or have regions selected on it.
- - Show Full Sequence ID
- 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
- - 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.
- - 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.
- - Sequence Features
- If the sequence names are Swissprot entries Jalview will
- use the names to retrieve sequence
- features from the EBI. Features which are 1 residue in length are
- coloured red, sequences longer than 1 residue are coloured blue. Move
- the mouse over a coloured feature to display the details of the feature.
-
- Note: The retrieved information will update the sequence start and end
- labels if they are incorrect.
- - Seqence Settings
- If features have been added to the alignment then the priority of
- rendering the features can be altered so that overlapping features can
- be displayed or hidden. See Sequence
- Features.
- - 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.
-
-
- - 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 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.
-
-
-
- - 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.
- - Translate cDNA
- If you are viewing a cDNA alignment a very simple translation service
- is available. The translation ignores all gaps in the cDNA sequences.
-
-
-
-
- - 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.
- - Muscle Multiple Protein Sequence Alignment
- Submits all, or jut 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 selected in the set (that is, the one that was first clicked
- on).
-
-
-
-
-
-
-
+
+
+
+Alignment Window Menus
+
+
+
+
+ Alignment Window Menus
+
+
+
+
+