X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=4a1a200377de05d2c1849d08be7d1aace67497f3;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=ef2b98983413fce772f0c2f3a23ba981d641234d;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index ef2b989..4a1a200 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,7 +1,7 @@ +--> Alignment Window Menus -

Alignment Window Menus

-
  • File +

    + Alignment Window Menus +

    +
  • File +
    • +
  • Edit +
    • +
  • Select +
    • +
  • View +
    • +
  • Alignment Window Format 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.
      • -
    • 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.
      • -
    -
    • -
  • 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 + +
      • Colour +
        • +
      • 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. +
            • +
          • +
      -
      • -
    • 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.
        -
        • -
      -
      • -
    • Web Service
      -       -
      • 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.
        -
        • -
      - 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.
          • -
        • MAFFT Multiple Sequence Alignment
          - Submits all, or just the currently selected region for - alignment with MAFFT.
          • -
        • Muscle Multiple Protein Sequence Alignment
          - Submits all, or just 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 in the set (that is, the one - that appears first in the alignment window).
          • -
        -
        • -
      -
      • -
    +