From ab7509436f09413b122dace2ecd6692f6f06d347 Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 20 Sep 2011 16:44:37 +0100 Subject: [PATCH] help documentation for Jalview 2.7 --- help/help.jhm | 4 +- help/helpTOC.xml | 13 +- help/html/features/clarguments.html | 20 +- help/html/features/groovy.html | 109 ++-- help/html/menus/alignmentMenu.html | 1015 ++++++++++++++++++---------------- help/html/menus/wsmenu.html | 125 +++-- help/html/releases.html | 259 ++++++++- help/html/webServices/clustalw.html | 46 -- help/html/webServices/index.html | 155 +++--- help/html/webServices/mafft.html | 36 -- help/html/webServices/msaclient.html | 38 +- help/html/webServices/muscle.html | 32 -- help/html/webServices/shmr.html | 65 +++ 13 files changed, 1077 insertions(+), 840 deletions(-) delete mode 100755 help/html/webServices/clustalw.html delete mode 100644 help/html/webServices/mafft.html delete mode 100755 help/html/webServices/muscle.html create mode 100755 help/html/webServices/shmr.html diff --git a/help/help.jhm b/help/help.jhm index 0ed676c..6ed0d7b 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -15,10 +15,8 @@ - - - + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 3e41ba3..a1cf057 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -21,10 +21,9 @@ - - - - + + + @@ -48,13 +47,11 @@ - - - - + + diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html index 9ca64a6..88657f8 100644 --- a/help/html/features/clarguments.html +++ b/help/html/features/clarguments.html @@ -30,12 +30,12 @@ -
-props FILE
+
-props FILE/URL
Use the given Jalview properties file instead of users default.
-
-features FILE
+
-features FILE/URL

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

+
-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.
      - -
    • -
    • 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.
          +
        • +
        • 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: + +

        + 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

    +

    +

    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. + +

    + + -- 1.7.10.2