X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=f23c1b76d378fec01f1c1ee5de8fc08b10edc403;hb=c53aeee9a688f68d64106a968876e542f701fbc6;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index e18e273..f23c1b7 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -16,3 +16,489 @@ * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . --> + +Alignment Window Menus + + + +

Alignment Window Menus

+
  • File + +
    • +
  • Edit + +
    • +
  • Select + +
    • +
  • View + +
    • +
  • 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.
        +
        • +
      +
      • +
    • 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).
          • +
        +
        • +
      +
      • +
    + +