X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=f3ab75dfbbc55786166c79c35ee50254ede337c9;hb=a510e9b4726214441e4fdac8a1d6752263c4c73d;hp=f67faa969963e1f89863a931a18683f5e6761802;hpb=7c5e7c1c51a48eab1b217a221df82748c35b76b1;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index f67faa9..f3ab75d 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,7 +1,7 @@ +

+ Alignment Window Menus +

File +
- Fetch Sequence
  Shows + a dialog window in which you can retrieve known ids from + UniProt, EMBL, EMBLCDS, PFAM, Rfam, 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
  - PileUp
  - AMSA
  - STH
  - Phylip
  - JSON
- Page Setup ...
  Open + the printing system's Page Setup dialog box, to control page + size, layout and orientation.
- 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. +
  - 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. +
  - SVG
    + Create a Scalable + Vector Graphics file from your alignment for embedding + in web pages. +
  - BioJS
    + Create a BioJS MSA + Viewer HTML file from your 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 from the Desktop's Save + Project File menu option, 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 right of the rightmost 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 are no empty columns before or after the + first or last aligned residue) and all sequences will be + padded with gap characters 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.
- Create Group (Control G)
  Create + a group containing the currently selected sequences.
- Remove Group (Shift Control G)
  + Ungroup the currently selected sequence group.
- Make Groups for selection
  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 at marked + columns. +
- Undefine Groups (Control U)
  + The alignment will be reset with no defined groups.
  + WARNING: This cannot be undone. +
- Select/Hide + Columns by Annotation
  Select or Hide + columns in the alignment according to secondary structure, + labels and values shown in alignment annotation rows.
- Select Highlighted Columns
  Selects + the columns currently highlighted as a result of a find, mouse + over, or selection event from a linked structure viewer or other + application. Modifiers will work on some platforms: ALT will add + all but the highlighted set to the column selection, and CTRL + (or META) will toggle the selection.
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 Sequence Features
  Show + or hide sequence features on this alignment.
- Sequence + Feature Settings...
  Opens the + Sequence Feature Settings dialog box to control the colour + and display of sequence features on the alignment.
- 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.
Annotations (Since Jalview 2.8.2) +
- 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 Alignment Related
  + Show all annotations that are for the alignment as a whole + (for example, Consensus, or secondary structure prediction + from alignment).
- Hide Alignment Related
  + Hide all annotations that are for the alignment as a whole.
- Show Sequence Related
  + Show all annotations that are for individual sequences.
- Hide Sequence Related
  + Hide all annotations that are for individual sequences.
- You can also selectively show or hide + annotations from the Popup or + Annotation menus. +
- Sort by Sequence
  Sort + sequence-specific annotations by sequence order in the + alignment (and within that, by label).
- Sort by Label
  Sort + sequence-specific annotations by label (and within that, by + sequence order). If neither sort order is selected, no + sorting is applied, allowing you to make a manual ordering + of the annotations.
- Autocalculated Annotation
  + Settings for the display of autocalculated annotation. +
  - Show first
    Show + autocalculated annotations above sequence-specific + annotations. Note this also applies to other annotations + for the alignment, for example secondary structure + prediction from alignment.
  - Show last
    Show + autocalculated / alignment annotations below + sequence-specific annotations.
  - 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 Logo
    + Enable or disable the display of the Consensus + Logo above the consensus sequence.
  - Normalise Consensus Logo
    + When enabled, scales all logo stacks to the same + height, making it easier to compare symbol diversity in + highly variable regions.
  - Group Conservation
    + When ticked, display a conservation row for all + groups (only available for protein alignments).
  - Group Consensus
    + When ticked, display a consensus row for all + groups.
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, 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
  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
    -
  - Note: Since Version 2.8.1, a number of additional similarity measures for tree calculation are provided in this menu. -
- 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 similarity scores calculated with - 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.
  -
- 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. +
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
-
'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. +
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. those provided by + EMBL-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.
+
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 Jpred3 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 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). -
-
-
-
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. -
-
-
- +
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. +
+
+
+