Menus

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=22a0bd7f472506ecc37c42e366c1630e8a414caa;hb=df22dee52c85b43767658a079c87172d79c0af06;hp=280cce99f626bd829a61e2706a7cdcd6441fef7c;hpb=8891eedbf7430d8a98edc1cccb32fceac8e3a9bb;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 280cce9..22a0bd7 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,329 +1,422 @@ -Menus + +Alignment Window Menus + -

Alignment Menu

File

Save As
- 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.
-
Export
- Creates an alignment output maintaining the 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.
  -
-
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.
- Select the format of the text by selecting one of the following menu items. -
- FASTA
- MSF
- CLUSTAL
- BLC
- PIR
- PFAM
  -
-
Print
- Jalview will print the alignment using the current fonts and - coloursof 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.
-
Load Associated Tree
- Jalview can load in trees which are in the Newick file format - and associate them with a particular alignment. Note: the ids of the tree - file and your alignment MUST be the same.
-
Close
- Close the alignment window. Be aware that changes to your alignment - will not be save unless specifically actioned from the "Save As" - menu.
-

Edit

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 +
- 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.
+

+
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.
+
+
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 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.
+
+
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
+ 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).
+
+
+
+

-
-
-
Undo
- 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. It - DOES NOT undo colour changes or adjustments to group sizes affect the annotation - panel.
-
-
Redo
- Any actions which you undo can be redone using redo.
-
-
Cut
- 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
- Copies the currently selected residues to the system clipboard. The - format of copied residues is NAME<tab>START_RES<tab>END_RES<tab>SEQUENCE -
- Use <CTRL> and C (<APPLE> and C on MacOSX) to copy.
-
-
Paste -
-
To New Alignment
- A new alignment window will be created from sequences previously - copied or cut to the system clipboard.
- Use <CTRL> and V(<APPLE> and V on MacOSX) to paste.
-
Add To This Alignment
- Copied sequences from another alignment window can be added - to the current Jalview alignment.
-
-
-
-
Delete
- This will delete the currently selected residues without making - a copy of them first.
-
-
Select All
- Selects all the sequences and residues in the alignment.
- Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.
-
-
Deselect All
- 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 Selection
- Any sequence ids currently not selected will replace the current - selection.
-
-
Undefine Groups
- The alignment will be reset with no defined groups. WARNING: - This cannot be undone.
-
-
Remove Left
- 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
- 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
- All columns which contain purely gap characters ("-", - ".") will be deleted.
- You may set the default gap character in preferences. -
-
-
Remove All Gaps
- All gap characters ("-", ".") will be deleted from - the alignment.
- You may set the default gap character in preferences. -
-
-
Remove Redundancy
- Selecting this option brings up a window asking you to select - a threshold. If the percentage identity between two sequences exceeds this - value one of the sequences (the shorter) is discarded. Press the "Apply" - button to reomove redundant sequences.
-
-
Pad Gaps
- If the sequences in an alignment window are not all the same - length they can all be set to the length of the longest sequence by selecting - "Pad Gaps." Any sequences which are shorter than the longest sequence - in an alignment will have gap characters ("-" or ".") - appended to the beginning or end to make them equal length.
- You may set the default gap character in preferences. -
-
-
-
-
Search
-
-
-
-
Find
- Select this to search - for residues, sequence name or residue position within the alignment.
-
-
-
-
View
-
-
-
-
Font
- Change the font of the display. The default font can be set - from the "Choose Font" window, which is shown when the "Font - Menu" is selected.
-
-
Wrap
- The default alignment display shows sequences in a single horizontal - row. If your alignment has only a few sequences you may wish to "Wrap" - the alignment so that the sequences are shown on multiple horizontal rows. - Options are available to show the residue numbering at the start and/or - end of an alignment as well as showing the alignment position above each - sequence row.
- NOTE: In the current version the wrap alignment should be used for viewing, - not editing.
-
-
Show Full Sequence ID
- 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
-
-
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 to enable the residue to be read.
-
-
Show Gaps
- If this is selected gap characters will be displayed as "." - or "-". If unselected gap characters will appear as blank spaces. -
- You may set the default gap character in preferences.
-
-
Show Annotations
- If this is selected the "Annotation Panel" will be - displayed below the alignment. The default setting is to display the conservation - calulation, quality calculation and consensus values as bar charts.
-
-
Sequence Features
- If the sequence names are Swissprot entries Jalview will use - the names to retrieve sequence features from the EBI. Features which are - 1 residue in length are coloured red, sequences longer than 1 residue are - coloured blue. Move the mouse over a coloured feature to display the details - of the feature.
- Note: The retrieved information will update the sequence start and end labels - if they are incorrect.
-
-
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.
-
-
-
-
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.
-
-
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.
-
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.
-
-
-
-
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 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.
-
-
-
-
Calculate Tree -
-
Average Distance Using % Identity
-
Neighbour Joining Using % Identity
-
Average Distance Using Blosum62
-
Neighbour Joining Using Blosum62
- See calculating trees. -
-
-
-
-
Paiwise Alignments
- See pairwise alignments.
-
-
Principal Component Analysis
- See Principal Component Analysis. -
-
-
Web Service
- -
- Selecting one of the following menu items will start a remote service - on the high powered computing faciltiy at the University of Dundee. You - will need a continuous network connection in order to use these services. - -
Clustal Alignment
-
Clustal Realign
-
JPred
-
Muscle Alignment
-
-
-
-

-