From 7b3105fb21bff8b9ce42b5eff5145ec45cf8d15f Mon Sep 17 00:00:00 2001 From: jprocter Date: Sat, 1 May 2010 17:31:24 +0000 Subject: [PATCH] jalview 2.5 documentation (still) --- help/help.jhm | 1 + help/helpTOC.xml | 6 ++++-- help/html/features/annotation.html | 2 +- help/html/features/featuresFormat.html | 2 +- help/html/jalviewjnlp.html | 4 ++-- help/html/menus/popupMenu.html | 5 +++-- help/html/webServices/index.html | 23 ++++++++++++++--------- 7 files changed, 26 insertions(+), 17 deletions(-) diff --git a/help/help.jhm b/help/help.jhm index c575a5f..865013b 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -17,6 +17,7 @@ + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index feafc0f..f0403e7 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -20,9 +20,10 @@ + + + - - @@ -51,6 +52,7 @@ + diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html index 95e233b..00beb2f 100755 --- a/help/html/features/annotation.html +++ b/help/html/features/annotation.html @@ -98,7 +98,7 @@ User defined annotation is stored and retrieved using Jalview Archives.

Current Limitations

-

As of version 2.4, the Jalview user interface does not support the +

As of version 2.5, the Jalview user interface does not support the creation and editing quantitative annotation (histograms and line graphs), or to create annotation associated with a specific sequence. It is also incapable of annotation grouping or changing the style of existing annotation (to change between line or bar charts, or to make multiple line graphs). These annotation capabilities are only possible by the import of an diff --git a/help/html/features/featuresFormat.html b/help/html/features/featuresFormat.html index b802c63..93ce408 100755 --- a/help/html/features/featuresFormat.html +++ b/help/html/features/featuresFormat.html @@ -105,7 +105,7 @@ in order to attach it to the whole sequence. Non-positional features are shown in a tooltip when the mouse hovers over the sequence ID panel, and any embedded links can be accessed from the popup menu. Scores
-Scores can be associated with sequence features, and used to sort sequences or shade the alignment (this was added in jalview 2.4.X). The score field is optional, and malformed scores will be ignored. +Scores can be associated with sequence features, and used to sort sequences or shade the alignment (this was added in jalview 2.5). The score field is optional, and malformed scores will be ignored.

Feature annotations can be collected into named groups by prefixing definitions with lines of the form:

startgroup	groupname
.. diff --git a/help/html/jalviewjnlp.html b/help/html/jalviewjnlp.html index 0eacdb4..0c68bfb 100755 --- a/help/html/jalviewjnlp.html +++ b/help/html/jalviewjnlp.html @@ -47,7 +47,7 @@ <!-- the additional memory parameters are here --> <j2se version="1.4+" initial-heap-size="500M" max-heap-size="1000M"/> <jar href="jalview.jar"/> - <jar href="JGoogleAnalytics_0.2.jar"/> + <jar href="JGoogleAnalytics-0.2.1-SNAPSHOT.jar"/> <jar href="Jmol-11.0.2.jar"/> <jar href="activation.jar"/> <jar href="axis.jar"/> @@ -64,7 +64,7 @@ <jar href="wsdl4j.jar"/> <jar href="xercesImpl.jar"/> <jar href="xml-apis.jar"/> - <property name="jalview.version" value="2.4.0.b2"/> + <property name="jalview.version" value="2.5"/> </resources> <application-desc main-class="jalview.bin.Jalview"/> </jnlp> diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html index 8f03c9a..30d9033 100755 --- a/help/html/menus/popupMenu.html +++ b/help/html/menus/popupMenu.html @@ -88,7 +88,8 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).

-
  • Group Links
    +
  • Sequence Id
    This menu is only visible if you right-click on a sequence name. diff --git a/help/html/webServices/index.html b/help/html/webServices/index.html index 6425e9c..8e785dc 100755 --- a/help/html/webServices/index.html +++ b/help/html/webServices/index.html @@ -26,12 +26,16 @@

    Jalview includes clients for a variety of web services for both bioinformatic data retrieval and analysis.

      -
    • The Sequence Fetcher +
    • 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 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.
    • Jalview SOAP Web Services for sequence and alignment analysis are provided by the University of Dundee, and are available from the Alignment window's Web Service menu.
      • @@ -43,12 +47,13 @@ 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

      -

      Jalview 2.5 includes 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 members of ENFIN.

      -
      +

      Jalview 2.5 includes 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 members of ENFIN.

      +

      Web Service Dialog Box

      This dialog box is displayed when a web service job is submitted. -- 1.7.10.2