Alignment Window Menus

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=ff741397db866eaf474431995df901a6b93c4d2f;hb=1984126973e19bd10f39bb516d728c9226f2ba71;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index e18e273..ff74139 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,7 +1,7 @@ + +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 .
- 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. +
  - 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. +
- 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. +
- Make Groups
  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 observed at specific positions. (new in jalview 2.5) +
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 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. +
- Autocalculated Annotation
  Settings + for the display of autocalculated annotation. +
  - 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 Profile
    Enable + or disable the display of the sequence logo above the consensus + sequence.
  - Group Conservation
    When + ticked, display a conservation row for all groups (only available + for protein alignments).
  - Apply to all groups
    When + ticked, display a consensus row for all groups.
- 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. +

+
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, 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 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
+
+
+
+
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.
+
+
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.
+
+ +
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 + will use 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 the sequence and retrieve all database cross + references and PDB ids associated with all or just the selected + sequences in the alignment.
'Standard Databases' will check + sequences against the EBI databases plus any active DAS sequence + sources, or you can verify against a specific source from one of + the sub-menus.
+
Envision2 Services
Submits one or + more sequences, sequence IDs or database references to analysis + workflows provided by the EnVision2 web + application. This allows Jalview users to easily access the EnCore + network of databases and analysis services developed by members of + ENFIN.
+
+
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. +
+
+
+

+ + +