X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=a5144125e5eafb5df51a07d7dc5ce5cb9beb161f;hb=713db61b4724485414159cfc145f9ffa4a24bb6d;hp=a15ad235c254f605e59d59e17e37c13340bdaaa4;hpb=3ec000e099e35b359996b824aabeaee632628deb;p=jalview.git
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-
Menus
+Alignment Window Menus
-Alignment Menu
+Alignment Window Menus
- - 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
- 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 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
+ - 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.
+ - 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).
+
+
+
+
-
-
- - 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. It
- DOES NOT undo colour changes or adjustments to group sizes affect 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. The
- format of copied residues is NAME<tab>START_RES<tab>END_RES<tab>SEQUENCE
-
- Use <CTRL> and C (<APPLE> and C on MacOSX) to copy.
-
- - 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 making
- a copy of them first.
-
- - 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 contain purely gap characters ("-",
- ".") will be deleted.
- You may set the default gap character in preferences.
-
-
- - Remove All Gaps
- All gap characters ("-", ".") will be deleted from
- the alignment.
- 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 two sequences exceeds this
- value one of the sequences (the shorter) is discarded. Press the "Apply"
- button to remove redundant sequences.
-
- - Pad Gaps
- If the sequences in an alignment window are not all the same
- length they can all be set to the length of the longest sequence by selecting
- "Pad Gaps." Any sequences which are shorter than the longest sequence
- in an alignment will have gap characters ("-" or ".")
- appended to the beginning or end to make them equal length.
- You may set the default gap character in preferences.
-
-
-
-
-
-
- - Find
- Select this to search
- for residues, sequence name or residue position within the alignment.
-
-
-
-
-
- - Font
- Change the font of the display. The default font can be set
- from the "Choose Font" window, which is shown when the "Font
- Menu" is selected.
-
- - Wrap
- The default alignment display shows sequences in a single horizontal
- row. If your alignment has only a few sequences you may wish to "Wrap"
- the alignment so that the sequences are shown on multiple horizontal rows.
- 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: In the current version the wrap alignment should be used for viewing,
- not editing.
-
- - 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 to enable the residue to be read.
-
- - Show Gaps
- If this is selected gap characters will be displayed as "."
- or "-". If unselected 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.
-
- - 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.
-
-
-
-
-
- - Apply Colour To All Groups
- If this is selected, any changes made to the background colour
- will be applied to all currently defined groups.
-
- - 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.
- - 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.
-
-
-
-
-
- - 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.
-
-
-
- - Calculate Tree
-
- - Average Distance Using % Identity
- - Neighbour Joining Using % Identity
- - Average Distance Using Blosum62
- - Neighbour Joining Using Blosum62
- See calculating trees.
-
-
-
-
- - Pairwise Alignments
- See pairwise alignments.
-
- - Principal Component Analysis
- See Principal Component Analysis.
-
-
- - Web Service
-
-
- Selecting one of the following menu items will start a remote service
- on the high powered computing facility at the University of Dundee. You
- will need a continuous network connection in order to use these services.
-
- - Clustal Alignment
- - Clustal Realign
- - JPred
- - Muscle Alignment
-
-
-
-
-