Groovy Shell

Use the given file to add sequence features to an alignment. See Features @@ -55,7 +55,7 @@ -

-annotations FILE

-annotations FILE/URL

Add precalculated annotations to the alignment. See Annotation File @@ -63,7 +63,7 @@ -

-tree FILE

-tree FILE/URL

Load the given newick format tree file onto the alignment

@@ -117,7 +117,7 @@ -

-groovy FILE

-groovy FILE/URL

Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other arguments have been processed

@@ -125,7 +125,7 @@ -

-vdoc VAMSAS DOCUMENT FILE or URL

-vdoc VAMSAS DOCUMENT FILE/URL

Import the given vamsas document into a new session.
New in 2.5

@@ -139,14 +139,6 @@ -

-groovy FILE

- -

Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other - arguments have been processed

- - - -

-fasta FILE

diff --git a/help/html/features/groovy.html b/help/html/features/groovy.html index d9aa13f..4f571dc 100644 --- a/help/html/features/groovy.html +++ b/help/html/features/groovy.html @@ -16,52 +16,79 @@ * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . --> -Groovy Shell + +Groovy Shell + -

The Groovy Shell

Groovy is an "agile and dynamic -language for the Java platform". The groovy scripting language makes it -extremely easy to programmatically interact with Java programs, in much the same -way that Javascript is used to generate and interact with applets and other -objects on the page.

Getting Groovy...
-Jalview Groovy support is only possible if the core groovy -jars which include the GroovyShell are present on the CLASSPATH -when Jalview is started.

The jars are obtained from the -embedded directory within the groovy -distribution. The easiest way of adding them to the -Jalview classpath is to download and build jalview from -it's source distribution, and then add the groovy-all-*.jar -to the lib directory whose path is given in the java.ext.dirs property.

Opening Jalview's Groovy Console
If groovy is available, then the -Tools→Groovy Console... menu entry will be available -from the Jalview Desktop's drop-down menu. Selecting this will open the -Groovy Console which -allows you to interactively execute Groovy scripts within the Jalview run-time environment.

Executing groovy scripts on Jalview startup
-The -groovy <script> option on the -Jalview command line will execute the contents of -<script>. <script> may be a file, or alternatively if it is "STDIN" -then the standard input will be used.

Access to Jalview's functions from Groovy Scripts
-There is as yet no properly defined scripting interface to Jalview, but all the -public methods of the jalview class hierarchy can be called from Groovy scripts. -The access point for this is the Jalview object defined in -the groovy environent which corresponds to the

jalview.gui.Desktop

object which -manages all the Jalview windows.

-Here's an example to get you started:
-

Getting the title, alignment and first sequence from the current alignFrame
-

+	
+		The Groovy Shell
+	
+	
+		Groovy is an "agile
+			and dynamic language for the Java platform". The groovy
+		scripting language makes it extremely easy to programmatically
+		interact with Java programs, in much the same way that Javascript is
+		used to generate and interact with applets and other objects on the
+		page.
+	
+	
+		Getting Groovy...
+		
 Jalview Groovy support is only possible if the core groovy
+		jars which include the GroovyShell are present on the CLASSPATH when
+		Jalview is started.
+	
+	
+		The jars are obtained from the embedded directory within the
+		groovy
+			distribution. The easiest way of adding them to the Jalview classpath
+		is to download and build jalview from it's source distribution, and
+		then add the groovy-all-*.jar to the lib directory whose path is given
+		in the java.ext.dirs property.
+	
+	
+		Opening Jalview's Groovy Console
If groovy is
+		available, then the Tools→Groovy Console...
+		menu entry will be available from the Jalview Desktop's drop-down
+		menu. Selecting this will open the Groovy Console
+		which allows you to interactively execute Groovy scripts within the
+		Jalview run-time environment.
+	
+	
+		Executing groovy scripts on Jalview startup

+		The -groovy <script> option on the 
+		Jalview command line will execute the contents of <script>.
+		<script> may be a file, a URL, or alternatively if it is
+		"STDIN" then the standard input will be used.

+		Note: The groovy script will be executed after
+			any data is loaded, and before images or any output
+			files are written. This allows you to perform customised jalview
+			analysis workflows with groovy.
+	
+	
+		Access to Jalview's functions from Groovy Scripts

+		There is as yet no properly defined scripting interface to Jalview,
+		but all the public methods of the jalview class hierarchy can be
+		called from Groovy scripts. The access point for this is the Jalview
+		object defined in the groovy environent which corresponds to the
+	
jalview.gui.Desktop
+	object which manages all the Jalview windows.
+	
+	Here's an example to get you started:
+	

+	
+		Getting the title, alignment and first sequence from the
+			current alignFrame
  def alf = Jalview.getAlignframes();
 print alf[0].getTitle();
 def alignment = alf[0].viewport.alignment;
 def seq = alignment.getSequenceAt(0);
-
-
-
-
+

When running a groovy script from the command line, the alignment that was just loaded can be referred to like so:
```
+print currentAlFrame.getTitle();
```
+

diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 8156e93..c628cf1 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -21,484 +21,547 @@ -

Alignment Window Menus

File +

+ Alignment Window Menus +

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.
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.

-
Sequence ID Tooltip (application only) -
This submenu's options allow the inclusion or exclusion of - non-positional sequence features or database cross references - from the tooltip shown when the mouse hovers over the sequence ID panel.
-
Alignment Properties...
- Displays some simple statistics computed for the - current alignment view and any named properties defined on the - whole alignment.
-
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.
-

-
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).
-
+
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. +
+
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. +
+
Sequence ID Tooltip (application + only)
This submenu's options allow the inclusion or + exclusion of non-positional sequence features or database cross + references from the tooltip shown when the mouse hovers over the + sequence ID panel. +
+
Alignment Properties...
Displays + some simple statistics computed for the current alignment view and + any named properties defined on the whole alignment. +
+
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. +
+
+
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.
+
+
Sort With New Tree
When + enabled, Jalview will automatically sort the alignment when a new + tree is calculated or loaded onto it.
+
+ +
Web Service Menu
This menu + is dynamic, and may contain user-defined web service entries in + addition to any of the following ones: +
+
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.
'Standard Databases' will check + sequences against the EBI databases plus any active DAS sequence + sources, or you can verify against a specific source from one of + the sub-menus.
+
Envision2 Services
Submits one or + more sequences, sequence IDs or database references to analysis + workflows provided by the EnVision2 web + application. This allows Jalview users to easily access the EnCore + network of databases and analysis services developed by members of + ENFIN.
+
+
Selecting items from the following submenus will start a + remote service on compute facilities at the University of Dundee, or + elsewhere. You need a continuous network connection in order to use + these services through Jalview. +
+
+
Alignment
Align the currently + selected sequences or all sequences in the alignment, or re-align + unaligned sequences to the aligned sequences. Entries in this menu + provide access to the various alignment programs supported by JABAWS. See the Multiple Sequence + Alignment webservice client entry for more information.
+
Secondary Structure Prediction +
+
JPred Secondary Structure Prediction
+ Secondary structure prediction by network consensus. See + the Jpred3 client entry for + more information. 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). +
+
+
+
Analysis
+
+
Sequence Harmony Multi-Relief
Performs + functional residue analysis on a protein family alignment with + sub-families defined on it. See the SHMR client entry for more + information. +
+
+

-
-
+ diff --git a/help/html/menus/wsmenu.html b/help/html/menus/wsmenu.html index bac5a96..beb5443 100755 --- a/help/html/menus/wsmenu.html +++ b/help/html/menus/wsmenu.html @@ -19,63 +19,72 @@ Web Service Menu -
Web Service Menu
-
-
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. -
'Standard Databases' will check sequences against the EBI databases - plus any active DAS sequence sources, or you can verify against a specific - source from one of the sub-menus.
-
-
Envision2 Services
- Submits one or more sequences, sequence IDs or database references to analysis workflows provided -by the EnVision2 -web application. This allows Jalview users to easily access the EnCore network of -databases and analysis services developed by members of ENFIN. -
-
- 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. This enables you to align more 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).
-
-
-
-

+
Web Service Menu
This menu + is dynamic, and may contain user-defined web service entries in + addition to any of the following ones: +
+
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.
'Standard Databases' will check + sequences against the EBI databases plus any active DAS sequence + sources, or you can verify against a specific source from one of + the sub-menus.
+
Envision2 Services
Submits one or + more sequences, sequence IDs or database references to analysis + workflows provided by the EnVision2 web + application. This allows Jalview users to easily access the EnCore + network of databases and analysis services developed by members of + ENFIN.
+
+
Selecting items from the following submenus will start a + remote service on compute facilities at the University of Dundee, or + elsewhere. You need a continuous network connection in order to use + these services through Jalview. +
+
+
Alignment
Align the currently + selected sequences or all sequences in the alignment, or re-align + unaligned sequences to the aligned sequences. Entries in this menu + provide access to the various alignment programs supported by JABAWS. See the Multiple Sequence + Alignment webservice client entry for more information.
+
Secondary Structure Prediction +
+
JPred Secondary Structure Prediction
+ Secondary structure prediction by network consensus. See + the Jpred3 client entry for + more information. 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). +
+
+
+
Analysis
+
+
Sequence Harmony Multi-Relief
Performs + functional residue analysis on a protein family alignment with + sub-families defined on it. See the SHMR client entry for more + information. +
+
+
diff --git a/help/html/releases.html b/help/html/releases.html index 92cc453..19ff3e7 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -33,35 +33,236 @@
Issues Resolved
- - -
2.6.1
- 15/11/2010
- - Application -
-
New warning dialog when the Jalview Desktop cannot contact web services
-
JABA service parameters for a preset are shown in service job window
-
JABA Service menu entries reworded
-
- - -
-
Modeller PIR IO broken - cannot correctly import a pir file emitted by jalview
-
Existing feature settings transferred to new alignment view created from cut'n'paste
-
Improved test for mixed amino/nucleotide chains when parsing PDB files
-
Consensus and conservation annotation rows occasionally become blank for all new windows
-
Exception raised when right clicking above sequences in wrapped view mode
-
- Application -
-
multiple multiply aligned structure views cause cpu usage to hit 100% and computer to hang
-
Web Service parameter layout breaks for long user parameter names
-
Jaba service discovery hangs desktop if Jaba server is down
-
- - - + + +
+ 2.7 +
20/09/2011 +
+ Application +
+
tweaked default layout of web services menu
+
view/alignment association menu to enable user to easily + specify which alignment a multi-structure view takes its + colours/correspondences from
+
allow properties file location to be specified as URL
+
extend jalview project to preserve associations between + many alignment views and a single Jmol display
+
Store annotation row height in jalview project file
+
annotation row column label formatting attributes stored + in project file
+
annotation row order for auto-calculated annotation rows + preserved in jalview project file
+
visual progress indication when Jalview state is saved + using Desktop window menu
+
visual indication that command line arguments are still + being processed
+
groovy script execution from URL
+
colour by annotation default min and max colours in + preferences
+
automatically associate PDB files dragged onto an + alignment with sequences that have high similarity and matching + IDs
+
update JGoogleAnalytics to latest release (0.3)
+
'view structures' option to open many structures + in same window
+
Sort associated views menu option for tree panel
+
group all JABA and non-JABA services for a particular + analysis function in its own submenu
+
Applet +
+
userdefined and autogenerated annotation rows for groups
+
adjustment of alignment annotation pane height
+
annotation scrollbar for annotation panel
+
drag to reorder annotation rows in annotation panel
+
'automaticScrolling' parameter
+
allow sequences with partial ID string matches to be + annotated from GFF/jalview features files
+
sequence logo annotation row in applet
+
Absolute paths relative to host server in applet + parameters are treated as such
+
New in the JalviewLite javascript API: +
+
jalviewLite.js javascript library
+
Javascript callbacks for +
+
applet initialisation
+
sequence/alignment mouse-overs and selections
+
+
+
scrollTo row and column alignment scrolling functions
+
select sequence/alignment regions from javascript
+
javascript structure viewer harness to pass messages + between Jmol and Jalview when running as distinct applets
+
sortBy method
+
set of applet and application examples shipped with + documentation
+
new example to demonstrate jalviewLite and Jmol + javascript message exchange
+
+
General +
+
enable Jmol displays to be associated with multiple + multiple alignments
+
Option to automatically sort alignment with new tree
+
user configurable link to enable redirects to a + www.jalview.org mirror
+
Jmol colours option for Jmol displays
+
configurable newline string when writing alignment and + other flat files
+
Allow alignment annotation description lines to contain + html tags
+
Documentation and Development +
+
add groovy test harness for bulk load testing to examples +
+
groovy script to load and align a set of sequences using a + web service before displaying the result in the Jalview desktop
+
restructured javascript and applet api documentation
+
ant target to publish example html files with applet archive
+
netbeans project for building jalview from source
+
ant task to create online javadoc for jalview source
+
+ Application +
+
user defined colourscheme throws exception when current + built in colourscheme is saved as new scheme
+
AlignFrame->Save in application pops up save dialog for + valid filename/format
+
cannot view associated structure for uniprot sequence
+
pdb file association breaks for Uniprot sequence P37173
+
associate PDB from file dialog does not tell you which + sequence is to be associated with the file
+
find All raises null pointer exception when query only + matches sequence IDs
+
pre 2.6 jalview project cannot be loaded into v2.6
+
Jalview project with Jmol views created with Jalview 2.4 + cannot be loaded
+
filetype associations not installed for webstart launch
+
two or more chains in a single PDB file associated with + sequences in different alignments do not get coloured by their + associated sequence
+
visibility status of autocalculated annotation row not + preserved when project is loaded
+
tree bootstraps are not preserved when saved as a jalview + project
+
envision2 workflow tooltips are corrupted
+
enabling show group conservation also enables colour by + conservation
+
duplicate group associated conservation or consensus + created on new view
+
annotation scrollbar not displayed after 'show all + hidden annotation rows' option selected
+
alignment quality not updated after alignment annotation + row is hidden then shown
+
preserve colouring of structures coloured by sequences in pre + jalview 2.7 projects
+
Web service job parameter dialog is not laid out properly +
+
web services menu not refreshed after 'reset + services' button is pressed in preferences
+
annotation off by one in jalview v2_3 example project
+
structures imported from file and saved in project get + name like jalview_pdb1234.txt when reloaded
+
Jalview does not always retrieve progress of a JABAWS job + execution in full once it is complete
+
Applet +
+
alignment height set incorrectly when lots of annotation + rows are displayed
+
relative URLs in feature HTML text not resolved to + codebase
+
view follows highlighting does not work for positions in + sequences
+
<= shown as = in tooltip
+
export features raises exception when no features exist
+
separator string used for serialising lists of ids for + javascript api is modified when separator string provided as + parameter
+
null pointer exception when selecting tree leaves for + alignment with no existing selection
+
relative URLs for datasources assumed to be relative to + applet's codebase
+
status bar not updated after finished searching and search + wraps around to first result
+
StructureSelectionManager instance shared between several + jalview applets causes race conditions and memory leaks
+
hover tooltip and mouseover of position on structure not + sent from Jmol in applet
+
certain sequences of javascript method calls to applet API + fatally hang browser
+
General +
+
view follows structure mouseover scrolls beyond position + with wrapped view and hidden regions
+
Find sequence position moves to wrong residue with/without + hidden columns
+
Sequence length given in alignment properties window is + off by 1
+
InvalidNumberFormat exceptions thrown when trying to + import PDB like structure files
+
positional search results are only highlighted between + user-supplied sequence start/end bounds
+
end attribute of sequence is not validated
+
Find dialog only finds first sequence containing a given + sequence position
+
sequence numbering not preserved in MSF alignment output
+
Jalview PDB file reader does not extract sequence from + nucleotide chains correctly
+
annotation row height and visibility attributes not stored + in jalview project
+
structure colours not updated when tree partition changed + in alignment
+
sequence associated secondary structure not correctly + parsed in interleaved stockholm
+
colour by annotation dialog does not restore current state +
+
Hiding (nearly) all sequences doesn't work properly
+
sequences containing lowercase letters are not properly + associated with their pdb files
+
Documentation and Development +
+
schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright + tool
+
+ + + +
+ 2.6.1 +
15/11/2010 +
+ Application +
+
New warning dialog when the Jalview Desktop cannot contact + web services
+
JABA service parameters for a preset are shown in service + job window
+
JABA Service menu entries reworded
+
+ +
+
Modeller PIR IO broken - cannot correctly import a pir + file emitted by jalview
+
Existing feature settings transferred to new alignment + view created from cut'n'paste
+
Improved test for mixed amino/nucleotide chains when + parsing PDB files
+
Consensus and conservation annotation rows occasionally + become blank for all new windows
+
Exception raised when right clicking above sequences in + wrapped view mode
+
Application +
+
multiple multiply aligned structure views cause cpu usage + to hit 100% and computer to hang
+
Web Service parameter layout breaks for long user + parameter names
+
Jaba service discovery hangs desktop if Jaba server is + down
+
+ +
2.6
26/9/2010
diff --git a/help/html/webServices/clustalw.html b/help/html/webServices/clustalw.html deleted file mode 100755 index 81ccc4e..0000000 --- a/help/html/webServices/clustalw.html +++ /dev/null @@ -1,46 +0,0 @@ - - -ClustalW Alignment - -
ClustalW Alignments
-
ClustalW is a program for multiple sequence alignment. It works -with both DNA and protein sequences, and can also perform profile -profile alignments to align two or more multiple sequence -alignments.
-
-Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994)
-CLUSTAL W: improving the sensitivity of progressive multiple -sequence alignment through sequence weighting, position specific gap -penalties and weight matrix choice.
-Nucleic Acids Research 22 4673-4680 -
-
There are two versions of this alignment function, which will operate -on the selected region, if any, or the whole sequence set:
-
-
Web Service→Alignment→ClustalW Multiple Sequence Alignment
- Aligns using the clustalW program, ignoring any gaps in the submitted sequence - set.
-
Web Service→Alignment→ClustalW Mulitple Sequence Alignment - Realign
- Submits the sequences with existing gaps to clustalW, which will preserve - existing gaps and re-align those regions which are not optimal.
-
-As of Jalview 2.6, alignment services accessed via the 'Alignment' submenu should be considered legacy Jalview SOAP services. - - diff --git a/help/html/webServices/index.html b/help/html/webServices/index.html index 939db64..82a1902 100755 --- a/help/html/webServices/index.html +++ b/help/html/webServices/index.html @@ -21,94 +21,77 @@ Web Services -
Web services
+
+ Web services +
-
Jalview includes clients for a variety of web services for both -bioinformatic data retrieval and analysis. -
-
The Sequence Fetcher - utilises web services for sequence, alignment and structure retrieval - provided by the European Bioinformatics Institute (EBI) and Distributed - Annotation System servers that are capable of serving sequences.
-
The DAS Feature - Fetcher enables the retrieval and visualization of features from DAS - annotation sources
-
The Database Reference Fetcher - transfers database references from records available from DAS or the - public sequence databases.
-
The Web Services menu in each alignment - window also provides access to the following: +
Jalview includes clients for a variety of web services for both + bioinformatic data retrieval and analysis.
-
Jalview SOAP Web Services for sequence alignment and - secondary structure prediction based at the University of Dundee.
-
Services for submitting IDs and sequences to external - bioinformatics services such as Envision2.
-
Programs for multiple sequence alignment, made available via - Java Bioinformatic Analysis Web Service - (JABAWS) servers.
+
The Sequence Fetcher + utilises web services for sequence, alignment and structure retrieval + provided by the European Bioinformatics Institute (EBI) and + Distributed Annotation System servers that are capable of serving + sequences.
+
The DAS Feature + Fetcher enables the retrieval and visualization of features from DAS + annotation sources
+
The Database Reference + Fetcher transfers database references from records available from + DAS or the public sequence databases.
+
The Web Services menu in each alignment + window also provides access to the following: +
+
Programs for multiple sequence + alignment, made available via Java + Bioinformatic Analysis Web Service (JABAWS) servers.
+
Jalview SOAP Web Services for secondary + structure prediction based at the University of Dundee.
+
Services for alignment analysis, such as Sequence Harmony Multi Relief. +
Services for submitting IDs and sequences to external + bioinformatics services such as Envision2 (see below).
+
+
+ Web Service Dialog Box +
+
This dialog box is displayed when a web service job is + submitted. It gives the name of the service and any method citation + information, and monitors the progress of the calculation. The + cancel button will permanently cancel the job, but this is only + possible for some services.
The Web + Services Preference panel controls the display and appearance of the + submission and analysis services in the Web Services + menu.
+
If Jalview encounters problems accessing any services, it may + display a warning + dialog box (this can be turned off using the web services + preferences tab).

- The Web Services Preference panel - controls the display and appearance of the submission and analysis - services in the Web Services menu.
-
If Jalview encounters problems accessing any services, it may - display a warning dialog - box (this can be turned off using the web services preferences tab).
-
-
-
More about Jalview's Web Services
-Jalview's distributed computations are SOAP based services exposing -protein sequence alignment and secondary structure prediction programs. -These services actually run on the cluster based in the School of Life -Sciences, University of Dundee, and are maintained by the Barton group.
-
Envision2 Services
-
Since version 2.5, Jalview has included a client to enable the -user to submit one or more sequences or sequence IDs to analysis -workflows provided by the EnVision2 web -application. This allows Jalview users to easily access the EnCore -network of databases and analysis services developed by ENFIN (www.enfin.org).
-
-
Web Service Dialog Box
- -
This dialog box is displayed when a web service job is submitted. -It gives the name of the service and any method citation information, -and monitors the progress of the calculation. The cancel button will -permanently cancel the job, but this is only possible for some services. -
-
Current services: -
- Multiple Sequence - Alignment Services -
-
ClustalW Multiple Alignment and - re-alignment
- The clustal W service remains one of the more popular Jalview - features.
-
Muscle Multiple Alignment
- High Quality and High Throughput multiple alignments of proteins. This - method can sometimes be more accurate than ClustalW when dealing with - diverse sets of sequences.
-
MAFFT
- Multiple Alignment with Fast Fourier Transforms - a highly accurate - and high throughput dna and amino acid alignment method, performing at - least as well as ClustalW and Muscle.
-
Other alignment methods are also available via JABAWS. For more information about a - particular service, see the documentation available via the web services parameter dialog box.
-
- -
Secondary Structure Prediction -
-
JNet
- This is a front end to the JNet www server - allowing single sequence or profile based prediction.
-
-
-
-
- +
+
+ More about Jalview's Web Services
Jalview's + distributed computations utilise SOAP and REST + web services exposing sequence alignment, analysis, and secondary + structure prediction programs. Originally, Jalview 2's services were + maintained by the Barton group at the University of Dundee, and ran + programs on the Life Sciences High-performace Computing Cluster. With + the advent of JABAWS, + however, it is possible for anyone to host Jalview web services. +
+
+ Envision2 Services + +
+
+ Since version 2.5, Jalview has included a client to enable the user to + submit one or more sequences or sequence IDs to analysis workflows + provided by the EnVision2 + web application. This allows Jalview users to easily access the + EnCore network of databases and analysis services developed by ENFIN (www.enfin.org). +
diff --git a/help/html/webServices/mafft.html b/help/html/webServices/mafft.html deleted file mode 100644 index 052e565..0000000 --- a/help/html/webServices/mafft.html +++ /dev/null @@ -1,36 +0,0 @@ - - -MAFFT Multiple Sequence Alignments - -
MAFFT Multiple Sequence Alignments
-
Katoh, K., K. Kuma, K., Toh, H., and Miyata, T. (2005) "MAFFT version - 5: improvement in accuracy of multiple sequence alignment." Nucleic Acids - Research, 33 511-518
-
MAFFT is a program for the multiple alignment of nucleic acid or protein -sequences, and is available from the Web -Service→Alignment→MAFFT Multiple Sequence -Alignment entry in the web services menu.
-
MAFFT utilizes algorithms for spectral correlation to identify -homologous regions in a fast-fourier transform representation of each -sequence. The Jalview web service runs MAFFT using the -'--auto' option which picks optimal parameters -for the set of sequences to be aligned.
-As of Jalview 2.6, alignment services accessed via the 'Alignment' submenu should be considered legacy Jalview SOAP services. - - diff --git a/help/html/webServices/msaclient.html b/help/html/webServices/msaclient.html index 0d413fc..de12faa 100644 --- a/help/html/webServices/msaclient.html +++ b/help/html/webServices/msaclient.html @@ -21,14 +21,15 @@ Multiple Sequence Alignment Web Services -
Multiple sequence alignment services can be accessed from either -the Alignment or the JABAWS Alignment -submenu of the Alignment Window's Web Service menu. -When an entry from one of these menus is selected, either the currently -selected residues, or the whole sequence set (if there is no selection -or only one sequence is selected) will be submitted for multiple -sequence alignment.
-
There are two kinds of multiple sequence alignment operations +
+ Multiple sequence alignment services are accessed from the Alignment + submenu of the Alignment Window's Web Service menu. + When an entry from one of these menus is selected, either the + currently selected residues, or the whole sequence set (if there is no + selection or only one sequence is selected) will be submitted for + multiple sequence alignment. +
+
There are two kinds of multiple sequence alignment operations available:

alignment - where a new alignment is constructed from @@ -37,9 +38,24 @@ available: used by the service to construct a profile based alignment of the remaining unaligned sequences.

-The JABAWS Alignment services also offer a -range of predefined alignment settings and the opportunity for you to -define your own set of parameters for running the alingment program.
+ JABAWS Alignment services
Most alignment services are + provided by the + JABAWS framework, which allows you to + customise the precise parameters used when running each alignment + prgoram. In addition to the 'Default settings', you may choose from a + range of alignment preset settings, or create your own using the + 'Edit Settings And Run ..' dialog + box. +
+
Alignment programs supported by JABAWS
+
ClustalW (version 2.0.12)
+
Mafft (version 6.713)
+
Muscle (version 3.7)
+
Tcoffee (version 8.14)
+
Probcons (version 1.12)
+
+
+
Multiple Alignments of Sequences with hidden columns
Multiple alignment services are 'column separable' analysis operations. diff --git a/help/html/webServices/muscle.html b/help/html/webServices/muscle.html deleted file mode 100755 index 1a3de9f..0000000 --- a/help/html/webServices/muscle.html +++ /dev/null @@ -1,32 +0,0 @@ - - -Muscle Alignment - -
Muscle Alignments
-
Muscle is a program for the alignment of many protein sequences.
-
-Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with high -accuracy and high throughput
-Nucleic Acids Research 32(5), 1792-97.
-
This alignment method is applied to the selected region, if any, or the whole - sequence set when the Web Service→Alignment→Muscle - Protein Sequence Alignment menu item is selected.
-As of Jalview 2.6, alignment services accessed via the 'Alignment' submenu should be considered legacy Jalview SOAP services. - - diff --git a/help/html/webServices/shmr.html b/help/html/webServices/shmr.html new file mode 100755 index 0000000..4051ac5 --- /dev/null +++ b/help/html/webServices/shmr.html @@ -0,0 +1,65 @@ + + + +Multi-Group Sequence Harmony and Multi-Relief + + + Functional residue analysis with Sequence Harmony and + Multi-Relief +
+ The Sequence Harmony and Multi-Relief (SHMR) service (Brandt, Feenstra and Heringa, 2010) available + from the Analysis sub-menu of the alignment window's web + services menu provides a method for the identification of significant + patterns of sub-family variation amongst the columns of an + alignment. +
+
+ Instructions for use
The service requires a + protein sequence multiple alignment that has been sub-divided into + groups containing at least two non-identical protein sequences. An + easy way to create groups is to use the built-in neighbour-joining or UPGMA tree + routines to calculate a tree for the alignment, and then click on the + tree to subdivide the alignment. +
+
+ The SHMR service operates on the currently selected visible region(s) + of the alignment. Once submitted, a job progress window will display + status information about your job, including a URL which allows you to + visit the status page on the + IBIVU SHMR server. +
+
When the job is complete, Jalview will automatically open a new + window containing the alignment and groups that were submitted for + analysis, with additional histograms added portraying the SHMR scores + for each column of the sub-grouped alignment.
+
+ If you use this service in your work, please cite :
Brandt, + B.W.*, Feenstra, K.A*. and Heringa, J. (2010) Multi-Harmony: detecting + functional specificity from sequence alignment. Nucleic + Acids Res. 38: W35-W40. (* joint first authors) +
+ Note: The SHMR service is implemented with Jalview's RESTful + web service client, first introduced in Jalview 2.7. + +
+ +