Alignment Window Menus

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=7102fd740ba47d30f6b6ea14f736d070e0b5b62f;hb=141040cac1e8570634a25ad6a5550a56558041fb;hp=8156e9347b7d7918ccca1735eb72f09462602eda;hpb=0696cffbccbb537be78d9fc2410589adbcd7be35;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 8156e93..7102fd7 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,504 +1,632 @@ + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> 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 + +

+ 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.
  - 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.
+