From: jprocter Date: Thu, 29 Apr 2010 15:03:44 +0000 (+0000) Subject: 2.5 release doc X-Git-Tag: Release_2_5~16 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1d5612858f8384e57ff461990d8bafb149898073;p=jalview.git 2.5 release doc --- diff --git a/help/html/features/search.html b/help/html/features/search.html index 3d60858..037c938 100755 --- a/help/html/features/search.html +++ b/help/html/features/search.html @@ -1,100 +1,99 @@ - -Search - - - - -

Search

-

The search box is displayed by pressing Control and F or - selecting "Find..." from the "Search" menu.

- -

"Find next" will find the next occurence of the specified and adjust - the alignment window view to show it, and "Find all" highlights all - matches for a pattern. The "New Feature" is a quick way to highlight - and group residues matching the specified search pattern throughout the alignment. -

-

Creating Features from Search Results

-

- If "New Feature" is selected, the feature can be given a name from - a popup input box. Use the "Feature Settings" under the "View" - menu to change the visibility and colour of the new sequence feature.

-

A quick Regular Expression Guide

-

A regular expression is not just a simple text query - although it -can be used like one, the query is not parsed literally, but -interpreted like a series of instructions defining the features of the -match. For example, a simple query like "ACDED" would -match all occurences of that string, but "ACD+ED" matches -both 'ACDDED' and 'ACDDDDDDDDED'. More usefully, the query -"[ILGVMA]{;5,}" would find stretches of small, -hydrophobic amino acids of at least five residues in length. -

-

The table -below describes some of the regular expression syntax:

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Regular Expression ElementEffect
.Matches any single character
[]Matches any one of the characters in the brackets
^Matches at the start of an ID or sequence
$Matches at the end of an ID or sequence
*Matches if the preceding element matches zero or more times
?Matches if the preceding element matched once or not at all
+Matches if the preceding element matched at least once
{count}Matches if the preceding element matches a specified number of - times -
{min,} Matches of the preceding element matched at least the - specified number of times
{min,max} Matches if the preceding element matches min or at most max - number of times
- - + +Search + + + + +

Search

+

The search box is displayed by pressing Control and F or + selecting "Find..." from the "Search" menu.

+ +

"Find next" will find the next occurence of the specified and adjust + the alignment window view to show it, and "Find all" highlights all + matches for a pattern. The "New Feature" is a quick way to highlight + and group residues matching the specified search pattern throughout the alignment. +

+

Creating Features from Search Results

+

+ If "New Feature" is selected, the feature can be given a name from + a popup input box. Use the "Feature Settings" under the "View" + menu to change the visibility and colour of the new sequence feature.

+

A quick Regular Expression Guide

+

A regular expression is not just a simple text query - although it +can be used like one, the query is not parsed literally, but +interpreted like a series of instructions defining the features of the +match. For example, a simple query like "ACDED" would +match all occurences of that string, but "ACD+ED" matches +both 'ACDDED' and 'ACDDDDDDDDED'. More usefully, the query +"[ILGVMA]{;5,}" would find stretches of small, +hydrophobic amino acids of at least five residues in length. +

+

The table +below describes some of the regular expression syntax:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Regular Expression ElementEffect
.Matches any single character
[]Matches any one of the characters in the brackets
^Matches at the start of an ID or sequence
$Matches at the end of an ID or sequence
*Matches if the preceding element matches zero or more times
?Matches if the preceding element matched once or not at all
+Matches if the preceding element matched at least once
{count}Matches if the preceding element matches a specified number of + times +
{min,} Matches of the preceding element matched at least the + specified number of times
{min,max} Matches if the preceding element matches min or at most max + number of times
+ + diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index aceabce..b39bf25 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -215,17 +215,40 @@ 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.
    • -
  • 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.
  • 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 Sequence Features
    +
  • 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. + +
    • +
  • Show Sequence Features
    Show or hide sequence features on this alignment.
  • Seqence Feature Settings...
    @@ -236,7 +259,10 @@
    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 @@ -299,6 +325,10 @@
  • 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
      @@ -349,7 +379,10 @@
    • by ID
      This will sort the sequences according to sequence name. If the sort is repeated, the order of the sorted sequences will be inverted.
      • -
    • by Group
      +
    • 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.
      • diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html index 700ce51..6284264 100755 --- a/help/html/menus/alwcalculate.html +++ b/help/html/menus/alwcalculate.html @@ -9,6 +9,9 @@
    • 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. diff --git a/help/html/menus/alwformat.html b/help/html/menus/alwformat.html index 97cb88e..6e2f059 100644 --- a/help/html/menus/alwformat.html +++ b/help/html/menus/alwformat.html @@ -50,12 +50,13 @@ spaces.
      You may set the default gap character in preferences.
      • -
    • Show Unconserved
      -       When this is selected, all consensus sequence symbols will be rendered as a '.', highlighting mutations in highly conserved alignments. -
    • Centre Column Labels
      When this is selected, the text labels within each annotation row will be centred on the column that they are associated with.
      • +
    • Show Unconserved
      +       When this is selected, all consensus sequence symbols will be rendered as a '.', highlighting mutations in highly conserved alignments. +
      • +
    diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html index 85ffe36..b34e692 100755 --- a/help/html/menus/alwview.html +++ b/help/html/menus/alwview.html @@ -25,7 +25,7 @@
  • Autocalculated Annotation
    Settings for the display of autocalculated annotation.
    • Apply to all groups
       - When ticked, any settings will be applied to all autocalculated annotation. + When ticked, any modification to the current settings will be applied to all autocalculated annotation.
    • Show Consensus Histogram
       diff --git a/help/html/menus/desktopMenu.html b/help/html/menus/desktopMenu.html index 40cfff8..89f510a 100755 --- a/help/html/menus/desktopMenu.html +++ b/help/html/menus/desktopMenu.html @@ -37,7 +37,7 @@
    • -
  • Tools +
  • Tools
    • Preferences
      Change the default visual settings for opening new alignment @@ -49,11 +49,34 @@
    • Collect Garbage
       Selecting this will initiate the Java Virtual Machine garbage collector, which might help free up some memory... perhaps.
      • +
    • Java Console
       + Toggles the display of a the Jalview Java Console window. This setting will be remembered in your user preferences.
    • Groovy Console... (only available if groovy is on the classpath)
       Open's the Groovy Console for interactive scripting.
    • +
  • Vamsas + For more details, read the Jalview VAMSAS documentation.
    + When no session is active, the menu provides options for initiating a new VAMSAS session:     +
      +
    • Connect to
       + Connect to one of the existing sessions available.
      • +
    • New VAMSAS session
       + Initiates a new local VAMSAS session.
      • +
    • Load VAMSAS session...
       + Opens a file browser allowing you to choose a VAMSAS document to import into a new local session.
      • +
    + When Jalview is joined to a VAMSAS session, the menu contains the following: +
      +
    • Session Update
       + Sends alignment data in the Jalview desktop to the VAMSAS session.
      • +
    • Save VAMSAS Session...
       + Saves the current session to a VAMSAS document archive.
      • +
    • Stop VAMSAS Session
       + Disconnects from the current session. You may be asked if you want to save the current session's data if no other VAMSAS clients are connected.
      • +
    +
  • Help
    • About
      diff --git a/help/html/menus/wsmenu.html b/help/html/menus/wsmenu.html index 7ee893b..bf07dd7 100755 --- a/help/html/menus/wsmenu.html +++ b/help/html/menus/wsmenu.html @@ -8,7 +8,16 @@ 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.
      + 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 @@ -22,8 +31,7 @@ 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.
    • + 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.
    • diff --git a/help/html/releases.html b/help/html/releases.html index a81997e..6ee6480 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -20,7 +20,7 @@
    2.5
    - Not Yet Released
    + 30th April 2010 diff --git a/help/html/vamsas/index.html b/help/html/vamsas/index.html index 23b4ced..ab31958 100644 --- a/help/html/vamsas/index.html +++ b/help/html/vamsas/index.html @@ -4,54 +4,116 @@

    VAMSAS Interoperation

    -

    Jalview can interact with other applications using - "the VAMSAS Interoperation framework" - which is an experimental model for interoperation between - bioinformatics applications (Visualization - and Analysis of Molecular - Sequences, Alignements - and Structures). Currently, the only other VAMSAS enabled application is TOPALi - a user friendly program for phylogenetics and evolutionary analysis. -

    VAMSAS enabled applications access - a shared bioinformatics dataset containing sequences, alignments, - annotation and trees, which can be represented by an XML document - analogous to a Jalview - Project Archive.

    -
    Connecting to a VAMSAS session
    -The VAMSAS functionality in Jalview is accessed through the Desktop's Vamsas menu. The options available in this menu depend on whether the application is currently interacting with a VAMSAS dataset in a VAMSAS session. -When the application is not connected to a session is active, the menu options are as follows:
    - -
    - Once you have successfully connected to a VAMSAS session, any data made available by other VAMSAS applications will be automatically imported into Jalview. However, in order to share the data in Jalview with other VAMSAS applications, - you must manually select the Vamsas→"Session Update" entry that is visible when a session is active. Selecting this option will update the VAMSAS session document, with the data loaded into Jalview. Any new alignments, trees and annotation will be written to the session, in addition to any edits you have made to data originally stored in the document. -
    - Saving the current session
    - You can save the current session as a VAMSAS Session archive using the Vamsas→"Session Update". The file contains a snapshot of the current VAMSAS session, including data from any other applications connected to the session. - Leaving a VAMSAS session
    - A session can be disconnected from at any time using the Vamsas→"Stop Session" option. Selecting this option will only disconnect Jalview from the session - any other applications will remain connected to the session. If Jalview is the only application connected to the session and you have not yet saved the VAMSAS session then you will be prompted with an optional 'Save VAMSAS session...' dialog box, allowing the session to be saved and returned to at a later date. -
    - VAMSAS Session Persistence
    - VAMSAS sessions are persistent - this means that they exist independently of any VAMSAS applications that are connected to them. - This means that if something goes wrong with a VAMSAS application and it crashes or otherwise fails, the VAMSAS session it is connected to will (hopefully) be unaffected. For instance, if Jalview is killed or crashes whilst it is still connected to a session, that session can be recovered in a new Jalview instance using the Vamsas→"Existing session" sub menu.

    - A quick Demo
    - Jalview can talk to itself through VAMSAS. Simply start two copies of the application, create a new vamsas session in one, and connect to the new session in the other. Then load your data into one of the applications, and use the Vamsas→"Session Update" menu entry to try to propagate the data to the other application. -
    - - - - - - - -
    Data Sharing CapabilityJalview Version
    Alignments, sequences and annotation, trees, database references, cDNA/protein mappings.2.4
    Mouseover location across linked DNA, protein and structure positions.2.4
    Jalview project settings (Multiple views, groups, tree partitions, colouring, window positions)2.4.1
    Sequence region and column selections2.4.1
    - -

    - For further details about the VAMSAS framework, please check the VAMSAS website. The VAMSAS framework is implemented as a Java 1.4 Library and depends on a number of other open source projects. Its source is will be released under the LGPL license. -  

    +

    Jalview can interact with other applications using "the VAMSAS +Interoperation framework" which is an experimental model for +interoperation between bioinformatics applications (Visualization +and Analysis of Molecular Sequences, +Alignements and Structures). +Currently, the only other VAMSAS enabled application is TOPALi - a user friendly program for +phylogenetics and evolutionary analysis. +

    VAMSAS enabled applications access a shared bioinformatics +dataset containing sequences, alignments, annotation and trees, which +can be represented by an XML document analogous to a Jalview Project Archive.

    +
    +Connecting to a VAMSAS session
    +The VAMSAS functionality in Jalview is accessed through the Desktop's Vamsas +menu. The options available in this menu depend on whether the +application is currently interacting with a VAMSAS dataset in a VAMSAS +session. When the application is not connected to a session is active, +the menu options are as follows:
    + +
    +VAMSAS and Firewalls: VAMSAS uses sockets to +communicate between different programs. This means that after starting a +session, your firewall software may ask you whether to allow the java +executable access to the internet (port 53782). If you do not allow +this, messages will not be exchanged with other VAMSAS applications.
    +
    +Once you have successfully connected to a VAMSAS session, any data made +available by other VAMSAS applications will be automatically imported +into Jalview. However, in order to share the data in Jalview with other +VAMSAS applications, you must manually select the Vamsas→"Session +Update" entry that is visible when a session is active. Selecting +this option will update the VAMSAS session document, with the data +loaded into Jalview. Any new alignments, trees and annotation will be +written to the session, in addition to any edits you have made to data +originally stored in the document.
    +Saving the current session
    +You can save the current session as a VAMSAS Session archive using the Vamsas→"Session +Update". The file contains a snapshot of the current VAMSAS +session, including data from any other applications connected to the +session. Leaving a VAMSAS session
    +A session can be disconnected from at any time using the Vamsas→"Stop +Session" option. Selecting this option will only disconnect Jalview +from the session - any other applications will remain connected to the +session. If Jalview is the only application connected to the session and +you have not yet saved the VAMSAS session then you will be prompted with +an optional 'Save VAMSAS session...' dialog box, allowing the session to +be saved and returned to at a later date.
    +VAMSAS Session Persistence
    +VAMSAS sessions are persistent - this means that they exist +independently of any VAMSAS applications that are connected to them. +This means that if something goes wrong with a VAMSAS application and it +crashes or otherwise fails, the VAMSAS session it is connected to will +(hopefully) be unaffected. For instance, if Jalview is killed or crashes +whilst it is still connected to a session, that session can be recovered +in a new Jalview instance using the Vamsas→"Existing +session" sub menu.

    +A quick Demo +
    +Jalview can talk to itself through VAMSAS. Simply start two copies of +the application, create a new vamsas session in one, and connect to the +new session in the other. Then load your data into one of the +applications, and use the +Vamsas→"Session Update" +menu entry to try to propagate the data to the other application. +
    + + + + + + + + + + + + + + + + + + + + + +
    Data Sharing CapabilityJalview Version
    Alignments, sequences and annotation, trees, database + references, cDNA/protein mappings.2.4
    Mouseover location across linked DNA, protein and structure + positions.2.4
    Jalview project settings (Multiple views, groups, tree + partitions, colouring, window positions)2.5
    Sequence region and column selections2.5
    +
    +

    Version 0.2 of the VAMSAS client library is used in Jalview +2.4.1. For further details about the VAMSAS framework, please check the +VAMSAS website. The VAMSAS +framework is implemented as a Java 1.4 Library and depends on a number +of other open source projects. Its source is will be released under the +LGPL license.