Alignment Window Menus

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=7102fd740ba47d30f6b6ea14f736d070e0b5b62f;hb=141040cac1e8570634a25ad6a5550a56558041fb;hp=0795189676bc7b73ce0f7f0e95044a15164ae7e3;hpb=bb105fcca41253815982584f4c8f6fae1f8e10a3;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 0795189..7102fd7 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,425 +1,632 @@ + Alignment Window Menus -

Alignment Window Menus

File + +
+ 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.
    - 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.
    -
  - 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)
      - All hidden Columns / Sequences will be revealed.
    - Hide→(all Columns / Sequences)
      - Hides the all the currently selected Columns / Sequences
    - 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 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.
    -
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