Alignment Window Menus

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=e18e273bc6e63d17a8266460e4a4915b193850f3;hb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;hp=44ba59a3fdb1bdd53b17d51a600dd62ae1272baa;hpb=ac5cc638b08386985f91503c81b27263230046e3;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 44ba59a3..e18e273 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,320 +1,18 @@ - -Alignment Window Menus - - -

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 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. -
  - HTML
    - Create a web page - from your alignment.
  - EPS
    - Create an Encapsulated - Postscript file from your alignment.
  - PNG
    - Create a Portable Network - Graphics file from your 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.
  -
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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 is a tab separated list
  - NAME START_RES END_RES SEQUENCE
- 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. -
  -
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Search -
- Find
  - Select this to search - for residues, sequence name or residue position within the alignment. -
  -
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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.
- 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.
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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.
  -
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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.
  -
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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).
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