From 26501f76ef450657c530de489b8404356a98aca3 Mon Sep 17 00:00:00 2001 From: hansonr Date: Wed, 27 Jun 2018 11:25:33 +0100 Subject: [PATCH] JAL-3032 just the changes pulled already --- .ant-targets-build.xml | 31 + .classpath | 1 - .classpath.js | 75 ++ RELEASE | 4 +- THIRDPARTYLIBS | 5 +- build.xml | 109 ++- help/help.jhm | 2 - help/helpTOC.xml | 5 +- help/html/editing/index.html | 2 +- help/html/features/clarguments.html | 24 - help/html/features/dasfeatures.html | 77 -- help/html/features/dassettings.html | 74 -- help/html/features/preferences.html | 4 - help/html/features/search.html | 2 +- help/html/features/searchclearhist.png | Bin 21757 -> 35172 bytes help/html/features/seqfeatures.html | 5 +- help/html/features/seqfetch.html | 30 +- help/html/menus/alignmentMenu.html | 46 +- help/html/menus/alwview.html | 3 +- help/html/menus/wsmenu.html | 17 +- help/html/releases.html | 24 + help/html/webServices/dbreffetcher.html | 20 +- help/html/webServices/index.html | 14 +- lib/jdas-1.0.4.jar | Bin 249906 -> 0 bytes nbbuild.xml | 2 +- src/jalview/bin/Cache.java | 18 - src/jalview/bin/Jalview.java | 1 - src/jalview/gui/DasSourceBrowser.java | 864 ------------------ src/jalview/gui/FeatureSettings.java | 210 ----- src/jalview/gui/JDatabaseTree.java | 50 -- src/jalview/gui/OverviewPanel.java | 6 + src/jalview/gui/Preferences.java | 5 - src/jalview/gui/SequenceFetcher.java | 26 +- src/jalview/io/cache/JvCacheableInputBox.java | 82 +- src/jalview/jbgui/GPreferences.java | 10 - src/jalview/renderer/OverviewRenderer.java | 4 +- src/jalview/ws/DBRefFetcher.java | 65 +- src/jalview/ws/DasSequenceFeatureFetcher.java | 925 -------------------- src/jalview/ws/SequenceFetcher.java | 86 +- .../ws/dbsources/das/api/DasSourceRegistryI.java | 57 -- .../ws/dbsources/das/api/jalviewSourceI.java | 87 -- .../dbsources/das/datamodel/DasSequenceSource.java | 354 -------- .../dbsources/das/datamodel/DasSourceRegistry.java | 484 ---------- .../ws/dbsources/das/datamodel/JalviewSource.java | 384 -------- test/jalview/analysis/CrossRefTest.java | 6 +- test/jalview/ws/PDBSequenceFetcherTest.java | 2 +- test/jalview/ws/SequenceFetcherTest.java | 18 +- test/jalview/ws/dbsources/RemoteFormatTest.java | 4 +- test/jalview/ws/seqfetcher/DasSequenceFetcher.java | 49 -- 49 files changed, 338 insertions(+), 4035 deletions(-) create mode 100644 .classpath.js delete mode 100644 help/html/features/dasfeatures.html delete mode 100644 help/html/features/dassettings.html delete mode 100644 lib/jdas-1.0.4.jar delete mode 100644 src/jalview/gui/DasSourceBrowser.java delete mode 100644 src/jalview/ws/DasSequenceFeatureFetcher.java delete mode 100644 src/jalview/ws/dbsources/das/api/DasSourceRegistryI.java delete mode 100644 src/jalview/ws/dbsources/das/api/jalviewSourceI.java delete mode 100644 src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java delete mode 100644 src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java delete mode 100644 src/jalview/ws/dbsources/das/datamodel/JalviewSource.java delete mode 100644 test/jalview/ws/seqfetcher/DasSequenceFetcher.java diff --git a/.ant-targets-build.xml b/.ant-targets-build.xml index 7ef21f1..8dd03da 100644 --- a/.ant-targets-build.xml +++ b/.ant-targets-build.xml @@ -1,2 +1,33 @@ +build +build-site +buildPropertiesFile +buildTests +buildextclients +buildindices +castorbinding +clean +compileApplet +distclean +eclipse-install help +init +linkcheck +makeApplet +makedist +makefulldist +obfuscate +packageApplet +prepare +prepareTests +preparejnlp +prepubapplet_1 +pubapplet +runenv +signApplet +sourcedist +sourcedoc +sourcescrub +testclean +testng usage +writejnlpf diff --git a/.classpath b/.classpath index 0cdc4b9..d32799b 100644 --- a/.classpath +++ b/.classpath @@ -36,7 +36,6 @@ - diff --git a/.classpath.js b/.classpath.js new file mode 100644 index 0000000..5075b84 --- /dev/null +++ b/.classpath.js @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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..1e9964c 100755 --- a/build.xml +++ b/build.xml @@ -309,7 +309,9 @@ - + + + @@ -449,7 +451,7 @@ - + @@ -465,7 +467,7 @@ - j2se version="1.8+" + j2se version="1.8+" @@ -759,13 +761,17 @@ - + + + - + + + @@ -976,7 +982,98 @@ - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/help/help.jhm b/help/help.jhm index e4bf12c..78f86b6 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -70,8 +70,6 @@ - - diff --git a/help/helpTOC.xml b/help/helpTOC.xml index b218b88..77ddd88 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -60,8 +60,6 @@ - - @@ -78,8 +76,7 @@ - - + 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/dasfeatures.html b/help/html/features/dasfeatures.html deleted file mode 100644 index 1965e70..0000000 --- a/help/html/features/dasfeatures.html +++ /dev/null @@ -1,77 +0,0 @@ - - - -DAS Features - - - -

- DAS Sequence Feature Retrieval -

-

Jalview includes a client for retrieving sequences and their - features via the Distributed Annotation System.

-
    -
  1. Open the Feature Settings panel by selecting "View - -> Feature Settings..."
    2. -
  2. Click on the "DAS - Settings" tabbed pane. -
    3. -
  3. Select the sources to use for DAS feature retrieval, then - click the "Fetch DAS Features" button. -
      -
    • Cancelling Feature Retrieval
      Press the Cancel - Fetch button to immediately stop feature retrieval. This - will not remove any features already added to the alignment, - but will halt any outstanding DAS requests.The cancel - fetch button is of particular use when one or more DAS - annotation servers are not responding! -
    -
    4. -
-

- If your DAS source selection contains sources which use UniProt - accession ids, you will be asked whether Jalview should find UniProt - Accession ids for the given sequence names. It is important to - realise that many DAS sources only use UniProt accession ids, rather - than Swissprot/UniProt sequence names.
The database - reference fetcher documentation describes how Jalview discovers - what database references are appropriate for the sequences in the - alignment. -

    -
  • Note
    Please remember to save your - alignment if either the start/end numbering, or the sequence IDs - were updated during the ID retrieval process.
    • -
-

  -

- DAS support was introduced in Jalview Version 2.1. -

-
-

- The DAS registry at http://www.dasregistry.org was - decommissioned early in 2015. An unmaintained mirror is currently - hosted at http://www.ebi.ac.uk/das-srv/registry/. -

-

  - - diff --git a/help/html/features/dassettings.html b/help/html/features/dassettings.html deleted file mode 100644 index 9600070..0000000 --- a/help/html/features/dassettings.html +++ /dev/null @@ -1,74 +0,0 @@ - - - -DAS Settings - - - -

- DAS Settings -

-

- Jalview can retrieve sequences and features from many DAS sources. The DAS sources - that it uses are discovered and selected via the DAS - settings panel, opened either from the View→Feature Settings dialog - box from the alignment window's menu bar, or the Tools→Preferences - dialog box opened from the Desktop menu bar. -

-

- -

The available sources are listed in the table using each - source's Nickname as its identifier. Clicking on a source's entry in - the table reveals more information about that service in the panel - to the right. Select the tickbox in the "Use Source" - column for a source to add it to the set Jalview queries for - alignment and sequence features.

-

You can filter the visible DAS sources by authority, type and - "label". You should read the DAS documentation to - understand more about these values. -

- Updating the list of sources -

-

- When the DAS Settings panel is first opened, and when the 'Refresh - source' buton is pressed, a list of DAS sources is retrieved from - the DAS registry URL. Note that the registry hosted at - http://www.dasregistry.org/das/ was retired at the start of 2015. An - alternative service is currently hosted at - http://www.ebi.ac.uk/das-srv/registry/das/. To connect to this - service, ensure your .jalview_properties file includes the following - line:
DAS_REGISTRY_URL=http\://www.ebi.ac.uk/das-srv/registry/das/ -

-

- Adding your own DAS Sources -

-

You can add your own DAS source to the list by clicking the - "Add Local Source" button. Enter the URL and nickname of - your additional service. It should be noted that Jalview 2.1 will - not query additional sources for more information, but this will be - implemented in future editions. -

  - - diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html index 50f864b..52e88db 100755 --- a/help/html/features/preferences.html +++ b/help/html/features/preferences.html @@ -65,10 +65,6 @@ Preferences tab contains settings affecting the export of sequence alignments and EPS files. -

  • The "DAS - Settings" Preferences tab allows you to select which DAS - sources to use when fetching DAS Features. -
  • The "Web Service" Preferences tab allows you to configure the JABAWS 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

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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: