From: gmungoc Date: Mon, 13 Aug 2018 10:10:16 +0000 (+0100) Subject: update spikes/mungo from JAL-3076 patch branch X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2b618ede76f5a9d2f1be7db9aad8bb3a2b10e23b;p=jalview.git update spikes/mungo from JAL-3076 patch branch --- diff --git a/.classpath b/.classpath index 0cdc4b9..d32799b 100644 --- a/.classpath +++ b/.classpath @@ -36,7 +36,6 @@ - diff --git a/.gitignore b/.gitignore index 2a55560..f1d1cb4 100644 --- a/.gitignore +++ b/.gitignore @@ -1,5 +1,6 @@ .project /dist +/clover /classes /tests /test-reports @@ -12,4 +13,6 @@ TESTNG /jalviewApplet.jar /benchmarking/lib -*.class \ No newline at end of file +*.class +/site + diff --git a/RELEASE b/RELEASE index c61d86c..1960368 100644 --- a/RELEASE +++ b/RELEASE @@ -1,2 +1,2 @@ -jalview.release=releases/Release_2_10_4_Branch -jalview.version=2.10.4b1 +jalview.release=releases/Release_2_11_Branch +jalview.version=2.11.0 diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS index d0d9125..a0b8d94 100644 --- a/THIRDPARTYLIBS +++ b/THIRDPARTYLIBS @@ -30,7 +30,6 @@ httpclient-4.0.3.jar httpcore-4.0.1.jar httpmime-4.0.3.jar jaxrpc.jar -jdas-1.0.4.jar : Apache License - built from http://code.google.com/p/jdas/ (29th Feb 2012) jhall.jar jswingreader-0.3.jar : Apache license - built from http://jswingreader.sourceforge.net/ svn/trunk v12 log4j-1.2.8.jar @@ -39,8 +38,8 @@ miglayout-4.0-swing.jar BSD http://www.migcalendar.com/miglayout/versions/4.0/li min-jaba-client.jar regex.jar saaj.jar -spring-core-3.0.5.RELEASE.jar : Apache License: jdas runtime dependencies retrieved via maven -spring-web-3.0.5.RELEASE.jar : Apache License: jdas runtime dependencies retrieved via maven +spring-core-3.0.5.RELEASE.jar : Apache License: jdas runtime dependencies retrieved via maven - TODO: JAL-3035 remove if no longer needed ? +spring-web-3.0.5.RELEASE.jar : Apache License: jdas runtime dependencies retrieved via maven - TODO: JAL-3035 remove if no longer needed ? vamsas-client.jar wsdl4j.jar xercesImpl.jar diff --git a/build.xml b/build.xml index d826d83..454b994 100755 --- a/build.xml +++ b/build.xml @@ -20,6 +20,9 @@ + + + @@ -40,6 +43,7 @@ + @@ -130,7 +134,8 @@ - + + @@ -299,6 +304,7 @@ verbose="2"> + @@ -538,6 +544,9 @@ + + Ignoring request to build jalview distribution with clover-instrumented classes + diff --git a/help/help.jhm b/help/help.jhm index 6239272..78f86b6 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -70,8 +70,6 @@ - - @@ -127,7 +125,6 @@ - diff --git a/help/helpTOC.xml b/help/helpTOC.xml index ca86625..77ddd88 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -60,8 +60,6 @@ - - @@ -78,8 +76,7 @@ - - + @@ -154,7 +151,6 @@ - diff --git a/help/html/editing/index.html b/help/html/editing/index.html index fd8c5a3..b3600c9 100755 --- a/help/html/editing/index.html +++ b/help/html/editing/index.html @@ -61,7 +61,7 @@ Undo / redo - editing of sequences (insertion/removal of gaps, removal of sequences, trimming sequences etc) may be undone or redone at any time using the appropriate menu items from the edit - menu. The undo history list only allows a maximum of 10 actions. + menu.

Trimming alignment - First select a column by clicking the scale indicator (above the sequences) The alignment may then be diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html index e065494..fa273a5 100644 --- a/help/html/features/clarguments.html +++ b/help/html/features/clarguments.html @@ -122,30 +122,6 @@ -

-dasserver nickname=URL
- -
- Add and enable a DAS server - with given nickname (alphanumeric or underscores only) for - retrieval of features for all alignments
Sources that - also support the sequence command may be specified by - prepending the URL with 'sequence:'
e.g. - sequence:http://localdas.somewhere.org/das/source -
- - - - -
-fetchfrom nickname
- -
- Query a DAS source called - nickname for features for the alignments and display them -
- - - -
-groovy FILE/URL
Execute groovy script in FILE (where diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html index 5bca358..52e88db 100755 --- a/help/html/features/preferences.html +++ b/help/html/features/preferences.html @@ -62,14 +62,8 @@ sequence alignments and EPS files.
  • The "Editing" - Preferences tab contains settings affecting the behaviour of alignments as you edit them. -
    • -
  • The "HMMER" - Preferences tab allows you to configure locally installed HMMER tools. -
    • -
  • The "DAS - Settings" Preferences tab allows you to select which DAS - sources to use when fetching DAS Features. + Preferences tab contains settings affecting the export of + sequence alignments and EPS files.
  • The "Web Service" Preferences tab allows you to configure the Sort with New Tree - When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment.

    -

    - "HMMER" Preferences tab -

    -

    If you have installed HMMER tools (available from hmmer.org), - then you should specify on this screen the location of the installation (the path to the folder - containing binary executable programs). Double-click in the input field to open a file browser.

    -

    When this path is configured, the HMMER menu will be - enabled in the Alignment window.

    +

     

    +

     

    diff --git a/help/html/features/search.html b/help/html/features/search.html index 72e5bdf..eec68ee 100755 --- a/help/html/features/search.html +++ b/help/html/features/search.html @@ -159,7 +159,7 @@ td {

    The search history keeps up to 99 queries by default. To clear the history, or modify the size of the history, right-click the text box.

    - +

    Other dialogs that provide a query history

    diff --git a/help/html/features/searchclearhist.png b/help/html/features/searchclearhist.png index 200c4d3..29cc34f 100644 Binary files a/help/html/features/searchclearhist.png and b/help/html/features/searchclearhist.png differ diff --git a/help/html/features/seqfeatures.html b/help/html/features/seqfeatures.html index 3c9d2b8..eeb63f6 100755 --- a/help/html/features/seqfeatures.html +++ b/help/html/features/seqfeatures.html @@ -87,10 +87,7 @@ href="featuresettings.html">Sequence Feature Settings dialog box. Feature colour schemes and display parameters are unique to a particular alignment, so it is possible to colour the same - sequence features differently in different alignment views.
    - Since Jalview 2.1, it is possible to add DAS - features to an alignment via the DAS tabbed pane of the feature - settings window. + sequence features differently in different alignment views.

    View→Sequence ID Tooltip→Show diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html index 44aa1c2..e726c49 100755 --- a/help/html/features/seqfetch.html +++ b/help/html/features/seqfetch.html @@ -26,19 +26,13 @@

    Sequence Fetcher

    -

    - Jalview can retrieve sequences from certain databases using either - the DBFetch service provided by the EMBL European Bioinformatics - Institute, or, since Jalview 2.4, DAS servers capable of the sequence - command (configured in DAS settings). -

    -

    The Sequence Fetcher can be opened via the "File" +

    Jalview can retrieve sequences from a range of sequence, 3D + structure, genomic and domain family databases provided by EMBL-EBI.

    +

    The Sequence Fetcher can be opened via the "File" menu on the main desktop in order to retrieve sequences as a new alignment, or opened via the "File" menu of an existing alignment to import additional sequences. There may be a short delay - when the sequence fetcher is first opened, whilst Jalview compiles - the list of available sequence datasources from the currently - defined DAS server registry.

    + when the sequence fetcher is first opened, whilst Jalview contacts each database's web API.

    Every time a new fetcher is opened, you will need to select the database you want to retrieve sequences from the database @@ -51,11 +45,6 @@ tooltips are shown if you mouse over some sources, explaining what the database will retrieve. You can select one by using the up/down arrow keys and hitting return, or by double clicking with the mouse. -
    - If you have DAS sources enabled, then you may have several - sources for the same type of sequence identifier, and these will - be grouped together in a sub-branch branch labeled with the - identifier.

    Once you have selected a sequence database, its fetcher dialog will open. Jalview provides two types of dialog:

    @@ -82,17 +71,6 @@ currently selected database into the retrieval box. Finally, press "OK" to initiate the retrieval.
    • -

    - Only retrieving part of a sequence -

    -

    - When using DAS sources (indicated by a "(DAS)"), - you can append a range in addition to a sequence ID. For example, to - retrieve 50 residues starting at position 35 in UNIPROT sequence - P73137 using the UNIPROT DAS server, you would enter - "'P73137:35,84'.
    Full support for DAS range - queries was introduced in Jalview 2.8 -

    If you use the WSDBFetch sequence fetcher services (EMBL, UniProt, PFAM, and RFAM) in work for publication, please cite:

    diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 00a2ec4..f3ab75d 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -314,9 +314,7 @@ href="../features/featuresettings.html">Sequence 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. + and display of sequence features on the alignment.
  • Sequence ID Tooltip (application only)
    This submenu's options allow the inclusion or exclusion of non-positional sequence features @@ -579,28 +577,26 @@ is dynamic, and may contain user-defined web service entries in addition to any of the following ones:
      -
    • Fetch DB References
      This - submenu contains options for accessing 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 - sequence start/end positions and retrieve all database cross - references and PDB ids associated with all or just the - selected sequences in the alignment. -
        -
      • 'Trim Retrieved Sequences' - when checked, Jalview - will discard any additional sequence data for accessions - associated with sequences in the alignment.
        Note: - Disabling this could cause out of memory errors when - working with genomic sequence records !
        Added - in Jalview 2.8.1 -
        • -
      • 'Standard Databases' will check sequences against - the EBI databases plus any active DAS sequence sources
        • -
      Other sub-menus allow you to pick a specific source to query - - sources are listed alphabetically according to their - nickname. -
      • -
    +
  • Fetch DB References
    This + submenu contains options for accessing any of the database + services that Jalview is aware of (e.g. those provided by + EMBL-EBI) to verify sequence start/end positions and retrieve all + database cross references and PDB ids associated with all or just + the selected sequences in the alignment. +
      +
    • 'Trim Retrieved Sequences' - when checked, Jalview will + discard any additional sequence data for accessions associated + with sequences in the alignment.
      Note: + Disabling this could cause out of memory errors when working + with genomic sequence records !
      Added + in Jalview 2.8.1 +
      • +
    • 'Standard Databases' will check sequences against the + EBI databases.
      • +
    Other sub-menus allow you to pick a specific source to query - + sources are listed alphabetically according to their nickname. +
    • +

    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 diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html index 2028304..33ec77f 100755 --- a/help/html/menus/alwview.html +++ b/help/html/menus/alwview.html @@ -53,8 +53,7 @@

  • Sequence 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 features on the alignment.
  • Sequence ID Tooltip (application only)
    This submenu's options allow the inclusion or exclusion of non-positional sequence features or database cross diff --git a/help/html/menus/wsmenu.html b/help/html/menus/wsmenu.html index b71bc1a..b8b357e 100755 --- a/help/html/menus/wsmenu.html +++ b/help/html/menus/wsmenu.html @@ -29,14 +29,13 @@ dynamic, and may contain user-defined web service entries in addition to any of the following ones:
      -
    • Fetch DB References
      This - submenu contains options for accessing 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 sequence - start/end positions and retrieve all database cross references - and PDB ids associated with all or just the selected sequences - in the alignment. -
        +
      • Fetch DB References
        This submenu + contains options for accessing any of the database services that + Jalview is aware of (e.g services provided by the EBI) to verify + sequence start/end positions and retrieve all database cross + references and PDB ids associated with all or just the selected + sequences in the alignment. +
        • 'Retrieve full Sequence' - when checked, Jalview will retrieve the full sequence for any accessions associated with sequences in the alignment.
          Note: @@ -45,7 +44,7 @@ in Jalview 2.8.1
        • 'Standard Databases' will check sequences against the - EBI databases plus any active DAS sequence sources<
          • + EBI databases
        Other submenus allow you to pick a specific source to query - sources are listed alphabetically according to their nickname.
        • diff --git a/help/html/releases.html b/help/html/releases.html index 3c1d73c..efe6520 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -67,6 +67,30 @@ li:before {
    • + + +
    + 2.11.0
    + 8/09/2018     +
    + +
    + +
      +
    • + +
      • +
    +
    +
    + +
      +
    • + DAS sequence retrieval and annotation capabilities removed from the Jalview Desktop +
      • +
    +
    +
    diff --git a/help/html/webServices/dbreffetcher.html b/help/html/webServices/dbreffetcher.html index 83c80ba..1f61dea 100644 --- a/help/html/webServices/dbreffetcher.html +++ b/help/html/webServices/dbreffetcher.html @@ -30,8 +30,7 @@ ID, and can be viewed in full via the Sequence Details window. . Jalview also uses references for the retrieval of - PDB structures and DAS features, and for + PDB structures, and for retrieving sequence cross-references such as the protein products of a DNA sequence.

    @@ -40,21 +39,18 @@ application provides three ways to access the retrieval function. Either:
      -
    • select the Discover PDB IDs option from the - structure submenu of the sequence's popup menu -
      • -
    • Choose one of the options from the 'Fetch DB Refs' submenu in +
    • select the Structure Chooser... option from + the Sequence ID popup menu. +
      • +
    • Choose one of the options from the 'Fetch DB Refs' submenu in the alignment window's Web Services menu:
        -
      • Standard Databases will fetch references from - the EBI databases plus currently selected DAS sources
        • -
      • The other entries submenus leading to lists of individual +
      • Standard Databases will fetch references from EBI + databases appropriate for the sequence type (Nucleotide or Protein)
        • +
      • The other entries submenus leading to lists of individual database sources that Jalview can access.
      • -
    • Answer 'Yes' when asked if you wish to retrieve database - references for your sequences after initiating a DAS Sequence - Feature fetch.

    Jalview discovers references for a sequence by generating a set of ID queries from the ID string of each sequence in the alignment. It diff --git a/help/html/webServices/index.html b/help/html/webServices/index.html index d0b497c..8f36013 100755 --- a/help/html/webServices/index.html +++ b/help/html/webServices/index.html @@ -36,15 +36,11 @@ 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 +
  • The Database Reference + Fetcher transfers database references and annotation from the public + sequence databases. +
    • +
  • The Web Services menu in each alignment window also provides access to the following: