X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=5f60ba52d6323b95055ab6742350fe4fc583404d;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=22a0bd7f472506ecc37c42e366c1630e8a414caa;hpb=d587f1aa61946dc14f6f089cf1dc2a3116cfb773;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 22a0bd7..5f60ba5 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,422 +1,678 @@ - - -Alignment Window Menus - - - -

Alignment Window Menus

-
  • File - -
    • -
  • Edit - -
    • -
  • Select - -
    • -
  • View - -
    • -
  • Alignment Window Format Menu - - - + + + +Alignment Window Menus + + + + +

    + 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.         +
        • +
      • 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 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 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.
        • +
      • +
    • 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, + and configure and retrieve features from DAS annotation + servers.
        • +
      • 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. + +
        +
      • Neighbour Joining Using PAM250
        • +
      • Neighbour Joining Using Sequence + Feature Similarity
        • +
      • Neighbour Joining Using Blosum62
        • +
      • Neighbour Joining Using % Identity
        • +
      • Average Distance Using PAM250
        • +
      • Average Distance Using Sequence + Feature Similarity
        • +
      • Average Distance Using Blosum62
        • +
      • Average Distance Using % Identity
        • +
      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. +
        +
      • '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. +
      • +
    +

    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. +
        • +
      • +
    • + + + +