Menus

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=d0f1052dd483f33c93f58782e1c5921e37a59e30;hb=0118e3685a087b37bb9d38d606f437638c9544d9;hp=a15ad235c254f605e59d59e17e37c13340bdaaa4;hpb=3ec000e099e35b359996b824aabeaee632628deb;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index a15ad23..d0f1052 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,329 +1,337 @@ -Menus +Alignment Window Menus -

Alignment Menu

Alignment Window Menus

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 - 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.
-
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
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.
- 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 graphic with the current 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.
  +
- 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 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.
- 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
  + Jalview load precalculated sequence + features or alignment + annotations.
- Close
  + 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
  + 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
  + 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 - 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
    + 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 + copying them to the clipboard. Like the other edit operations, this can + be undone with Undo.
- 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 only contain gap characters ("-", + ".") will be deleted.
  + You may set the default gap character in preferences. +
- Remove All Gaps
  + 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
  + 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
  + Adds gaps to the end of all the sequences so they are all + the same length. This is useful for making a tree using unaligned sequences.
  + 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 from the "Choose Font" + dialog box, which is shown when this item is selected.
- 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.
  + 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: When in wrapped alignment view, the alignment cannot + be edited or have regions selected on it.
- 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 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.
- 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.
- 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.
- Seqence Settings
  + If features have been added to the alignment then the priority of + rendering the features can be altered so that overlapping features can + be displayed or hidden. See Sequence + Features.
- 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.
- 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.
  +
+
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.
- Translate cDNA
  + If you are viewing a cDNA alignment a very simple translation service + is available. The translation ignores all gaps in the cDNA sequences. +
  +
+
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.
  - Muscle Multiple Protein Sequence Alignment
    + Submits all, or jut 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 selected in the set (that is, the one that was first clicked + on).
  +
+

-
-
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 remove 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 - calculation, 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. -
-
-
-
-
Pairwise 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 facility 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
-
-
-
-

-