Merge branch 'develop' into releases/Release_2_11_2_Branch

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index a72f5ac..5479291 100755 (executable)
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -131,7 +131,7 @@
                </tocitem>
                <tocitem text="3D Structure Data" target="viewingpdbs" expand="false">
                        <tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
-                       <tocitem text="PDB Structure Chooser" target="pdbchooser" />
+                       <tocitem text="PDB &amp; 3D-Beacons Structure Chooser" target="pdbchooser" />
                        <tocitem text="Jmol Viewer" target="pdbjmol" />
                        <tocitem text="Chimera Viewer" target="chimera" />                      
                </tocitem>

diff --git a/help/help/html/features/3dbeacons_button.png b/help/help/html/features/3dbeacons_button.png
new file mode 100644 (file)
index 0000000..2dae1f6
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diff --git a/help/help/html/features/3dbeacons_structurechooser.png b/help/help/html/features/3dbeacons_structurechooser.png
new file mode 100644 (file)
index 0000000..cd7fdab
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diff --git a/help/help/html/features/3dstructuredata_popupmenu.png b/help/help/html/features/3dstructuredata_popupmenu.png
new file mode 100644 (file)
index 0000000..e5de4ca
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diff --git a/help/help/html/features/schooser_main.png b/help/help/html/features/schooser_main.png
index ca793fd..07a1a3c 100644 (file)
Binary files a/help/help/html/features/schooser_main.png and b/help/help/html/features/schooser_main.png differ

diff --git a/help/help/html/features/schooser_viewbutton.png b/help/help/html/features/schooser_viewbutton.png
new file mode 100644 (file)
index 0000000..f14481e
Binary files /dev/null and b/help/help/html/features/schooser_viewbutton.png differ

diff --git a/help/help/html/features/selectfetchdb.gif b/help/help/html/features/selectfetchdb.gif
index de0a7e6..6103b31 100644 (file)
Binary files a/help/help/html/features/selectfetchdb.gif and b/help/help/html/features/selectfetchdb.gif differ

diff --git a/help/help/html/features/seqfetch.html b/help/help/html/features/seqfetch.html
index 4e9a75f..7d4a389 100755 (executable)
--- a/help/help/html/features/seqfetch.html
+++ b/help/help/html/features/seqfetch.html
@@ -38,7 +38,7 @@
       the database you want to retrieve sequences</strong> from the database
     chooser.
   </p>
-  <img src="selectfetchdb.gif" align="left" width="480" height="204"
+  <img src="selectfetchdb.gif" align="left"
     alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)">
   <p>
     The databases are shown as a tree, and ordered alphabetically;
@@ -69,7 +69,10 @@
         accession ids</strong> (as a semi-colon separated list), or press the
       &quot;Example&quot; button to paste the example accession for the
       currently selected database into the retrieval box. Finally, press
-      &quot;OK&quot; to initiate the retrieval.</li>
+      &quot;OK&quot; to initiate the retrieval.
+      <br />
+      For the PDB and UniProt sequence fetchers, choose the "Retrieve IDs" tab
+      to search for accession ids.</li>
   </ol>
 
   <p>If you use the Sequence Fetcher, please remember to cite the

diff --git a/help/help/html/features/seqfetcher.gif b/help/help/html/features/seqfetcher.gif
index 03ddd79..6b9ff21 100644 (file)
Binary files a/help/help/html/features/seqfetcher.gif and b/help/help/html/features/seqfetcher.gif differ

diff --git a/help/help/html/features/structurechooser.html b/help/help/html/features/structurechooser.html
index 785c429..11cad6b 100644 (file)
--- a/help/help/html/features/structurechooser.html
+++ b/help/help/html/features/structurechooser.html
@@ -32,8 +32,11 @@
     The Structure Chooser allows you to select
     3D structures to view for the currently selected set of
     sequences. It is opened by selecting the <strong>"3D
-      Structure Data..."</strong> option from the Sequence ID panel's <a
-      href="../menus/popupMenu.html">pop-up menu</a>. The dialog
+      Structure Data..."</strong> option from the Sequence ID panel's
+      <a href="../menus/popupMenu.html">pop-up menu</a>. <br/>
+      <img src="3dstructuredata_popupmenu.png" alt="pop-up menu"/>
+      <br/>
+      The dialog
     provides:
   </p>
   <ul>
@@ -69,6 +72,9 @@
     associated with the sequence. It does this based on the sequence's
     ID string, and any other associated database IDs. <br />
     <br />
+    Since Jalview 2.11.2, you can also <a href="#3dbeaconssearch">initiate a search
+    of the 3D-Beacons Network</a>.
+  </p>
   <p>
     <strong><a name="cachedstructview">Viewing existing
         structures for your sequences</a></strong>
@@ -86,7 +92,7 @@
   </p>
   <p>Jalview can automatically select the best structures according
     to meta-data provided by the PDB. For alignments with no existing
-    structure data, the 'Best Quality' structure for each sequence will
+    structure data, the 'PDBe Best Quality' structure for each sequence will
     by default be selected, but clicking on the drop down menu allows
     other criteria to be chosen, including Resolution (only defined for
     X-Ray structures), Highest Protein Chain etc. When 'Invert' is
@@ -103,7 +109,39 @@
     <br>The screenshot above shows the Structure Chooser displayed after
     selecting all the sequences in the Jalview example project. If no
     structures were auto-discovered, options for manually associating
-    PDB records will be shown (see below).<p>
+    PDB records will be shown (see below).
+
+  <p>
+    <strong><a name="3dbeaconssearch">3D-Beacons Network Search</a></strong>
+  </p>
+  <p>
+    To initiate a search of the 3D-Beacons Network&mdash;which searches
+    across experimentally determined and predicted structure models from
+    several resources including PDBe, AlphaFold DB, SWISS-MODEL, PED, SASDB, Genome3D and
+    PDBe-KB&mdash;click on the <strong>3D-Beacons Search</strong> button at the top of the
+    Structure Chooser window.
+    <br/>
+    <img src="3dbeacons_button.png"/>
+    <br/>
+    The 3D-Beacons Network search requires UniProt references and Jalview will ask
+    to attempt to fetch these references for the selected sequences.
+    UniProt references might not always be found in which case you can revert to the PDB
+    search.
+    <br/>
+    <img src="3dbeacons_structurechooser.png"/>
+    <br/>
+    If structures are found through the 3D-Beacons network you can filter which structures
+    are shown using the drop-down filter at the top of the Structure Chooser window.
+    <br/>
+    You can view information about each related model, such as the resource providing
+    each model, in the columns displayed. You can sort the list of models by clicking on
+    column headings.
+    <br/>
+    Select and view the structures in the usual way using the <a href="viewingpdbs.html#afterviewbutton">open structure options</a> at
+    the bottom of the Structure Chooser window.
+  </p>
+
+  <p>
     <strong>Exploration of meta-data for available structures</strong>
   </p>
   <p>Information on each structure available is displayed in columns
@@ -135,4 +173,4 @@
       2.9. </em>
   </p>
 </body>
-</html>
\ No newline at end of file
+</html>

diff --git a/help/help/html/features/viewingpdbs.html b/help/help/html/features/viewingpdbs.html
index b1ad4ba..947b96b 100755 (executable)
--- a/help/help/html/features/viewingpdbs.html
+++ b/help/help/html/features/viewingpdbs.html
@@ -24,7 +24,7 @@
 </head>
 <body>
   <p>
-    <strong>Discovering and Viewing PDB Structures</strong>
+    <strong>Discovering and Viewing PDB and 3D-Beacons structures</strong>
   </p>
   Jalview can be used to explore the 3D structures of sequences in an
   alignment by following the steps below:
@@ -34,7 +34,7 @@
         menu</a> to open the <a href="structurechooser.html">Structure
         Chooser</a> dialog box.
       <ul>
-        <li>If one or more structures exists for the given
+        <li>If one or more structures exist in the PDB for the given
           sequence, the <a href="structurechooser.html">Structure
             Chooser</a> dialog will open with them listed in the results
           pane.
@@ -43,9 +43,17 @@
           href="structurechooser.html">Structure Chooser</a> interface
           will present options for manual association of PDB structures.
         </li>
+       <li>
+          Since Jalview 2.11.2 you can also search the 3D-Beacons Network
+         for structures.  The 3D-Beacons Network acts as a one-stop shop for protein
+         structures by combining and standardising data from several providers.
+         See <a href="structurechooser.html#3dbeaconssearch">3D-Beacons Search</a> for
+         instructions.
+       </li>
       </ul>
     </li>
-    <li><strong>Selecting Structures</strong><br />You can select
+    <li><strong>Selecting PDB Structures</strong><br />
+      If one or more structures have been found from the PDB, you can select
       the structures that you want to open and view by selecting them
       with the mouse and keyboard.<br />By default, if structures were
       discovered, then some will already be selected according to the
@@ -79,7 +87,8 @@
     <strong>Structure Viewers in the Jalview Desktop</strong><br /> The
     <a href="jmol.html">Jmol viewer</a> has been included since Jalview
     2.3. Jalview 2.8.2 included support for <a href="chimera.html">Chimera</a>,
-    provided it is installed and can be launched by Jalview. The default
+    provided it is installed and can be launched by Jalview. ChimeraX and PyMOL
+    support is included from Jalview 2.11.2. The default
     viewer can be configured in the <a href="preferences.html#structure">Structure
       tab</a> in the <strong>Tools&rarr;Preferences</strong> dialog box.
   
@@ -90,12 +99,14 @@
     for more information.
   </p>
   <p>
-    <img src="schooser_viewbutton.png"
-      style="width: 465px; height: 81px" /><br/> <strong><a
+    <strong><a
       name="afterviewbutton">Controlling where the new structures
         will be shown</a></strong>
+    <br/>
+    <img src="schooser_viewbutton.png" />
         <br />The Structure Chooser offers several options
-    for viewing a structure. <br/><strong>New View</strong> will open a new
+    for viewing a structure. <br/>
+    The <strong>Open new structure view</strong> button will open a new
     structure viewer for the selected structures, but if there are views
     already open, you can select which one to use, and press the <strong>Add</strong>
     button. Jalview can automatically superimpose new structures based

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index fe4d257..973e867 100755 (executable)
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -80,6 +80,9 @@ li:before {
             scale factors being set with buggy window-managers (linux
             only)
           </li>
+          <li>
+               <!-- JAL-3915 -->Removed RNAview checkbox and logic from Structure Preferences
+          </li>
         </ul> <em>Development</em>
         <ul>
           <li>Fixed non-fatal gradle errors during build</li>

diff --git a/resources/fts/tdbeacons_data_columns.txt b/resources/fts/tdbeacons_data_columns.txt
index 4ebcc1b..3e4d1c8 100644 (file)
--- a/resources/fts/tdbeacons_data_columns.txt
+++ b/resources/fts/tdbeacons_data_columns.txt
@@ -58,5 +58,6 @@ Sequence Identity;sequence_identity;double|T|1;g2;80;150;85;false;false
 Created Date;created;string;g3;80;150;85;true;false
 UniProt Accession;uniprot_accession;String;g1;50;400;95;false;true
 Url;model_url;String;g3;100;150;105;true;false
+Model Format;model_format;String;g3;20;60;20;true;false
 Page URL;model_page_url;String;g3;100;150;105;true;false
 Ensemble Sample Url;ensembl_sample_url;String;g3;100;150;105;false;false

diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index fc4ee46..adcefb3 100755 (executable)
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -50,7 +50,7 @@ public class PDBEntry
   {
     // TODO is FILE needed; if not is this enum needed, or can we
     // use FileFormatI for PDB, MMCIF?
-    PDB("pdb", "pdb"), MMCIF("mmcif", "cif"), FILE("?", "?");
+    PDB("pdb", "pdb"), MMCIF("mmcif", "cif"), BCIF("bcif","bcif"),FILE("?", "?");
 
     /*
      * file extension for cached structure file; must be one that

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 666fb4e..0f80dd5 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -551,7 +551,8 @@ public class Desktop extends jalview.jbgui.GDesktop
     if (Cache.getDefault(Preferences.ADD_SS_ANN, true)) {
       ssm.setAddTempFacAnnot(Cache.getDefault(Preferences.ADD_TEMPFACT_ANN, true));
       ssm.setProcessSecondaryStructure(Cache.getDefault(Preferences.STRUCT_FROM_PDB, true));
-      ssm.setSecStructServices(Cache.getDefault(Preferences.USE_RNAVIEW, true));
+      // JAL-3915 - RNAView is no longer an option so this has no effect
+      ssm.setSecStructServices(Cache.getDefault(Preferences.USE_RNAVIEW, false));
     } else {
       ssm.setAddTempFacAnnot(false);
       ssm.setProcessSecondaryStructure(false);

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index baed0df..d8eee6d 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -396,13 +396,11 @@ public class Preferences extends GPreferences
     /*
      * Set Structure tab defaults
      */
-    final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
+    final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, true);
     structFromPdb.setSelected(structSelected);
-    useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
-    useRnaView.setEnabled(structSelected);
-    addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
+    addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, true));
     addSecondaryStructure.setEnabled(structSelected);
-    addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
+    addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, true));
     addTempFactor.setEnabled(structSelected);
 
     /*
@@ -845,8 +843,6 @@ public class Preferences extends GPreferences
             Boolean.toString(addTempFactor.isSelected()));
     Cache.applicationProperties.setProperty(ADD_SS_ANN,
             Boolean.toString(addSecondaryStructure.isSelected()));
-    Cache.applicationProperties.setProperty(USE_RNAVIEW,
-            Boolean.toString(useRnaView.isSelected()));
     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
             Boolean.toString(structFromPdb.isSelected()));
     String viewer = structViewer.getSelectedItem().toString();

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index e400b51..ce57373 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -191,7 +191,7 @@ public class StructureChooser extends GStructureChooser
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        promptForTDBFetch();
+        promptForTDBFetch(false);
       }
     });
 
@@ -242,7 +242,11 @@ public class StructureChooser extends GStructureChooser
     updateCurrentView();
   }
 
-  private void promptForTDBFetch()
+  /**
+   * raises dialog for Uniprot fetch followed by 3D beacons search
+   * @param ignoreGui - when true, don't ask, just fetch 
+   */
+  public void promptForTDBFetch(boolean ignoreGui)
   {
     final long progressId = System.currentTimeMillis();
 
@@ -260,6 +264,9 @@ public class StructureChooser extends GStructureChooser
         // redo initial discovery - this time with 3d beacons
         // Executors.
         previousWantedFields=null;
+        lastSelected=(FilterOption) cmb_filterOption.getSelectedItem();
+        cmb_filterOption.setSelectedItem(null);
+        cachedPDBExists=false; // reset to initial
         initialStructureDiscovery();
         if (!isStructuresDiscovered())
         {
@@ -267,6 +274,7 @@ public class StructureChooser extends GStructureChooser
           btn_queryTDB.setToolTipText(MessageManager.getString("status.no_structures_discovered_from_3d_beacons"));
           btn_queryTDB.setEnabled(false);
         } else {
+          cmb_filterOption.setSelectedIndex(0); // select 'best'
           btn_queryTDB.setVisible(false);
           progressBar.setProgressBar(null, progressId);
         }
@@ -322,8 +330,13 @@ public class StructureChooser extends GStructureChooser
         }
       };
     };
+    if (ignoreGui)
+    {
+      Executors.defaultThreadFactory().newThread(discoverCanonicalDBrefs).start();
+      return;
+    }
     // need cancel and no to result in the discoverPDB action - mocked is
-    // 'cancel'
+    // 'cancel' TODO: mock should be OK
     JvOptionPane.newOptionDialog(this)
             .setResponseHandler(JvOptionPane.OK_OPTION,
                     discoverCanonicalDBrefs)

diff --git a/src/jalview/gui/structurechooser/TDBResultAnalyser.java b/src/jalview/gui/structurechooser/TDBResultAnalyser.java
index d3896a5..a453529 100644 (file)
--- a/src/jalview/gui/structurechooser/TDBResultAnalyser.java
+++ b/src/jalview/gui/structurechooser/TDBResultAnalyser.java
@@ -235,6 +235,8 @@ public class TDBResultAnalyser
     BitSet cover = new BitSet();
     cover.set(seq.getStart(), seq.getEnd());
     // walk down the list of structures, selecting some to add to selected
+    // TODO: could do simple DP - double loop to select largest number of
+    // structures covering largest number of sites
     for (FTSData structure : filteredStructures)
     {
       Object[] odata = structure.getSummaryData();

diff --git a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
index cdf456c..2890a01 100644 (file)
--- a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
+++ b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
@@ -4,7 +4,6 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.Comparator;
-import java.util.HashSet;
 import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Locale;
@@ -12,6 +11,7 @@ import java.util.Set;
 
 import javax.swing.JTable;
 
+import jalview.bin.Cache;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
@@ -44,8 +44,6 @@ public class ThreeDBStructureChooserQuerySource
 
   private static final String FILTER_SOURCE_PREFIX = "only_";
 
-  private static int MAX_QLENGTH = 7820;
-
   protected FTSRestRequest lastTdbRequest;
 
   protected FTSRestClientI tdbRestClient;
@@ -75,19 +73,9 @@ public class ThreeDBStructureChooserQuerySource
 
   public String buildQuery(SequenceI seq)
   {
-    boolean isPDBRefsFound = false;
-    boolean isUniProtRefsFound = false;
-    StringBuilder queryBuilder = new StringBuilder();
-    Set<String> seqRefs = new LinkedHashSet<>();
-
-    /*
-     * note PDBs as DBRefEntry so they are not duplicated in query
-     */
-    Set<String> pdbids = new HashSet<>();
-
     List<DBRefEntry> refs = seq.getDBRefs();
     int ib = checkUniprotRefs(refs);
-    if (ib>-1)
+    if (ib > -1)
     {
       return getDBRefId(refs.get(ib));
     }
@@ -96,8 +84,10 @@ public class ThreeDBStructureChooserQuerySource
 
   /**
    * Searches DBRefEntry for uniprot refs
+   * 
    * @param seq
-   * @return -2 if no uniprot refs, -1 if no canonical ref., otherwise index of Uniprot canonical DBRefEntry 
+   * @return -2 if no uniprot refs, -1 if no canonical ref., otherwise index of
+   *         Uniprot canonical DBRefEntry
    */
   public static int checkUniprotRefs(List<DBRefEntry> refs)
   {
@@ -129,7 +119,6 @@ public class ThreeDBStructureChooserQuerySource
    */
   static boolean isValidSeqName(String seqName)
   {
-    // System.out.println("seqName : " + seqName);
     String ignoreList = "pdb,uniprot,swiss-prot";
     if (seqName.length() < 3)
     {
@@ -181,13 +170,14 @@ public class ThreeDBStructureChooserQuerySource
     {
       FTSRestRequest tdbRequest = getTDBeaconsRequest(seq, wantedFields);
       resultList = tdbRestClient.executeRequest(tdbRequest);
-      
+
       lastTdbRequest = tdbRequest;
-      if (resultList!=null)
+      if (resultList != null)
       { // Query the PDB and add additional metadata
         FTSRestResponse pdbResponse = fetchStructuresMetaDataFor(
                 getPDBQuerySource(), resultList);
-        FTSRestResponse joinedResp = joinResponses(resultList, pdbResponse);
+
+        resultList = joinResponses(resultList, pdbResponse);
       }
       return resultList;
     }
@@ -250,8 +240,7 @@ public class ThreeDBStructureChooserQuerySource
   {
     if (tdbEntries != null && lastTdbRequest != null)
     {
-      int prov_idx = lastTdbRequest.getFieldIndex("Provider");
-      boolean hasPDBe=false;
+      boolean hasPDBe = false;
       for (FTSData _row : tdbEntries)
       {
         // tdb returns custom object
@@ -266,21 +255,24 @@ public class ThreeDBStructureChooserQuerySource
           tdBeaconsFilters.add(FILTER_SOURCE_PREFIX + provider);
           if ("PDBe".equalsIgnoreCase(provider))
           {
-            hasPDBe=true;
+            hasPDBe = true;
           }
         }
       }
       if (!hasPDBe)
       {
         // remove the PDBe options from the available filters
-        int op=0;
-        while (op<xtantOptions.size())
+        int op = 0;
+        while (op < xtantOptions.size())
         {
           FilterOption filter = xtantOptions.get(op);
-          if (filter.getQuerySource() instanceof PDBStructureChooserQuerySource)
+          if (filter
+                  .getQuerySource() instanceof PDBStructureChooserQuerySource)
           {
             xtantOptions.remove(op);
-          } else {
+          }
+          else
+          {
             op++;
           }
         }
@@ -370,8 +362,7 @@ public class ThreeDBStructureChooserQuerySource
     int urlColumnIndex = restable.getColumn("Url").getModelIndex();
     int typeColumnIndex = restable.getColumn("Provider").getModelIndex();
     int humanUrl = restable.getColumn("Page URL").getModelIndex();
-    int categoryColumnIndex = restable.getColumn("Model Category")
-            .getModelIndex();
+    int modelformat = restable.getColumn("Model Format").getModelIndex();
     final int up_start_idx = restable.getColumn("Uniprot Start")
             .getModelIndex();
     final int up_end_idx = restable.getColumn("Uniprot End")
@@ -408,6 +399,8 @@ public class ThreeDBStructureChooserQuerySource
               .toString();
       String modelPage = humanUrl < 1 ? null
               : (String) restable.getValueAt(row, humanUrl);
+      String strucFormat = restable.getValueAt(row, modelformat).toString();
+
       SequenceI selectedSeq = (SequenceI) restable.getValueAt(row,
               refSeqColIndex);
       selectedSeqsToView.add(selectedSeq);
@@ -421,11 +414,15 @@ public class ThreeDBStructureChooserQuerySource
       {
         pdbEntry = new PDBEntry();
         pdbEntry.setId(pdbIdStr);
-        boolean hasCif = urlStr.toLowerCase(Locale.ENGLISH).endsWith("cif");
-        boolean probablyPdb = urlStr.toLowerCase(Locale.ENGLISH)
-                .contains("pdb");
-        pdbEntry.setType(hasCif ? PDBEntry.Type.MMCIF
-                : probablyPdb ? PDBEntry.Type.PDB : PDBEntry.Type.FILE);
+        try
+        {
+          pdbEntry.setType(PDBEntry.Type.valueOf(strucFormat));
+        } catch (Exception q)
+        {
+          Cache.log.warn("Unknown filetype for 3D Beacons Model from: "
+                  + strucFormat + " - " + pdbIdStr + " - " + modelPage);
+        }
+
         if (!"PDBe".equalsIgnoreCase(typeColumn))
         {
           pdbEntry.setRetrievalUrl(urlStr);
@@ -516,7 +513,6 @@ public class ThreeDBStructureChooserQuerySource
             : -1;
     int tdbTitle_idx = getLastFTSRequest().getFieldIndex("Title");
 
-    List<FTSData> joinedRows = new ArrayList<FTSData>();
     for (final FTSData row : upResponse.getSearchSummary())
     {
       String id = (String) row.getSummaryData()[idx_modelId];
@@ -554,13 +550,15 @@ public class ThreeDBStructureChooserQuerySource
           Collection<FTSData> discoveredStructuresSet)
   {
     int idColumnIndex = restable.getColumn("Model id").getModelIndex();
-    
-    String modelId = (String) restable.getValueAt(selectedRow, idColumnIndex);
-    for (FTSData row:discoveredStructuresSet)
+
+    String modelId = (String) restable.getValueAt(selectedRow,
+            idColumnIndex);
+    for (FTSData row : discoveredStructuresSet)
     {
-      if (row instanceof TDB_FTSData && ((TDB_FTSData)row).getModelId().equals(modelId))
+      if (row instanceof TDB_FTSData
+              && ((TDB_FTSData) row).getModelId().equals(modelId))
       {
-        return ((TDB_FTSData)row);
+        return ((TDB_FTSData) row);
       }
     }
     return null;

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index e6efed6..debb2ab 100755 (executable)
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -175,8 +175,6 @@ public class GPreferences extends JPanel
 
   protected JCheckBox structFromPdb = new JCheckBox();
 
-  protected JCheckBox useRnaView = new JCheckBox();
-
   protected JCheckBox addSecondaryStructure = new JCheckBox();
 
   protected JCheckBox addTempFactor = new JCheckBox();
@@ -1652,7 +1650,6 @@ public class GPreferences extends JPanel
       {
         boolean selected = structFromPdb.isSelected();
         // enable other options only when the first is checked
-        useRnaView.setEnabled(selected);
         addSecondaryStructure.setEnabled(selected);
         addTempFactor.setEnabled(selected);
       }
@@ -1661,12 +1658,6 @@ public class GPreferences extends JPanel
 
     // indent checkboxes that are conditional on the first one
     ypos += lineSpacing;
-    useRnaView.setFont(LABEL_FONT);
-    useRnaView.setText(MessageManager.getString("label.use_rnaview"));
-    useRnaView.setBounds(new Rectangle(25, ypos, width, height));
-    structureTab.add(useRnaView);
-
-    ypos += lineSpacing;
     addSecondaryStructure.setFont(LABEL_FONT);
     addSecondaryStructure
             .setText(MessageManager.getString("label.autoadd_secstr"));

diff --git a/test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java b/test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
index ef079d1..f72ad89 100644 (file)
--- a/test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
+++ b/test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
@@ -77,7 +77,7 @@ public class TDBeaconsFTSRestClientTest
             .isEmpty());
     Assert.assertEquals(
             ftsRestClient.getAllDefaultDisplayedFTSDataColumns().size(),
-            14);
+            15);
   }
 
   @Test(groups = { "Functional" })
@@ -112,7 +112,7 @@ public class TDBeaconsFTSRestClientTest
     String actual = ftsRestClient
             .getDataColumnsFieldsAsCommaDelimitedString(wantedFields);
     Assert.assertEquals(actual,
-            "uniprot_start,uniprot_end,provider,model_identifier,model_category,model_title,resolution,confidence_avg_local_score,confidence_type,confidence_version,coverage,created,model_url,model_page_url");
+            "uniprot_start,uniprot_end,provider,model_identifier,model_category,model_title,resolution,confidence_avg_local_score,confidence_type,confidence_version,coverage,created,model_url,model_format,model_page_url");
   }
 
   @Test(groups = { "Functional" })
@@ -122,7 +122,7 @@ public class TDBeaconsFTSRestClientTest
             .getAllFTSDataColumns();
     Assert.assertNotNull(allFields);
     // System.out.println(allFields.size());
-    Assert.assertEquals(allFields.size(), 19);
+    Assert.assertEquals(allFields.size(), 20);
   }
 
   @Test(groups = { "Functional" })
@@ -279,7 +279,7 @@ public class TDBeaconsFTSRestClientTest
   }
 
   private static String[][] mocks = { { "P38398.json",
-      "{\"uniprot_entry\":{\"sequence_length\":1863,\"ac\":\"P38398\",\"id\":\"BRCA1_HUMAN\"},\"structures\":[{\"model_identifier\":\"4igk\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2012-12-17\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":1.75,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4igk_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4igk\"},{\"model_identifier\":\"1t15\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2004-04-15\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":1.85,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t15_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1t15\"},{\"model_identifier\":\"4ifi\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2012-12-14\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.2,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4ifi_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4ifi\"},{\"model_identifier\":\"1t29\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2004-04-20\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.3,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t29_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1t29\"},{\"model_identifier\":\"3pxb\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxb_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3pxb\"},{\"model_identifier\":\"4y2g\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2015-02-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4y2g_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4y2g\"},{\"model_identifier\":\"1y98\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2004-12-14\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1y98_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1y98\"},{\"model_identifier\":\"1jnx\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2001-07-26\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1jnx_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1jnx\"},{\"model_identifier\":\"3pxa\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.55,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxa_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3pxa\"},{\"model_identifier\":\"3k0h\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2009-09-24\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.7,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3k0h_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3k0h\"},{\"model_identifier\":\"3k0k\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2009-09-24\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.7,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3k0k_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3k0k\"},{\"model_identifier\":\"1n5o\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2002-11-06\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1n5o_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1n5o\"},{\"model_identifier\":\"3pxc\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxc_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3pxc\"},{\"model_identifier\":\"3pxd\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxd_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3pxd\"},{\"model_identifier\":\"1t2u\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2004-04-22\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t2u_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1t2u\"},{\"model_identifier\":\"3k15\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2009-09-25\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3k15_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3k15\"},{\"model_identifier\":\"3pxe\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.85,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxe_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3pxe\"},{\"model_identifier\":\"3k16\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2009-09-25\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.0,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3k16_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3k16\"},{\"model_identifier\":\"4ofb\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2014-01-14\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.05,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4ofb_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4ofb\"},{\"model_identifier\":\"3coj\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2008-03-28\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.21,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3coj_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3coj\"},{\"model_identifier\":\"7lyb\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2021-03-06\",\"sequence_identity\":100.0,\"uniprot_start\":1,\"uniprot_end\":100,\"resolution\":3.28,\"coverage\":5.37,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/7lyb_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"ELECTRON MICROSCOPY\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/7lyb\"},{\"model_identifier\":\"1t2v\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2004-04-22\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.3,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t2v_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1t2v\"},{\"model_identifier\":\"4y18\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2015-02-06\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4y18_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4y18\"},{\"model_identifier\":\"4jlu\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2013-03-13\",\"sequence_identity\":100.0,\"uniprot_start\":1649,\"uniprot_end\":1859,\"resolution\":3.5,\"coverage\":11.33,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4jlu_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4jlu\"},{\"model_identifier\":\"4u4a\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2014-07-23\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.51,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4u4a_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4u4a\"},{\"model_identifier\":\"2ing\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2006-10-07\",\"sequence_identity\":100.0,\"uniprot_start\":1649,\"uniprot_end\":1859,\"resolution\":3.6,\"coverage\":11.33,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/2ing_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/2ing\"},{\"model_identifier\":\"7jzv\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2020-09-02\",\"sequence_identity\":99.0,\"uniprot_start\":2,\"uniprot_end\":104,\"resolution\":3.9,\"coverage\":5.53,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/7jzv_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"ELECTRON MICROSCOPY\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/7jzv\"},{\"model_identifier\":\"6g2i\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2018-03-23\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":5.9,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/6g2i_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"ELECTRON MICROSCOPY\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/6g2i\"},{\"model_identifier\":\"1jm7\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2001-07-17\",\"sequence_identity\":100.0,\"uniprot_start\":1,\"uniprot_end\":110,\"resolution\":null,\"coverage\":5.9,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1jm7_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"SOLUTION NMR\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1jm7\"},{\"model_identifier\":\"1oqa\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2003-03-07\",\"sequence_identity\":100.0,\"uniprot_start\":1755,\"uniprot_end\":1863,\"resolution\":null,\"coverage\":5.85,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1oqa_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"SOLUTION NMR\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1oqa\"},{\"model_identifier\":\"614833627ca5054bb52d2f3f\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISS-MODEL\",\"created\":\"2021-09-20\",\"sequence_identity\":1.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"coverage\":0.115,\"confidence_version\":\"4.2.0\",\"confidence_avg_local_score\":0.776,\"model_url\":\"https://swissmodel.expasy.org/3d-beacons/uniprot/P38398.pdb?range=1646-1859&template=6g2i.1.K&provider=swissmodel\",\"model_format\":\"PDB\",\"model_page_url\":\"https://swissmodel.expasy.org/repository/uniprot/P38398?provider=swissmodelrange=1646-1859&template=6g2i.1.K\",\"confidence_type\":\"QMEANDisCo\"},{\"model_identifier\":\"614833627ca5054bb52d2f43\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISS-MODEL\",\"created\":\"2021-09-20\",\"sequence_identity\":1.0,\"uniprot_start\":1,\"uniprot_end\":103,\"coverage\":0.055,\"confidence_version\":\"4.2.0\",\"confidence_avg_local_score\":0.655,\"model_url\":\"https://swissmodel.expasy.org/3d-beacons/uniprot/P38398.pdb?range=1-103&template=1jm7.1.A&provider=swissmodel\",\"model_format\":\"PDB\",\"model_page_url\":\"https://swissmodel.expasy.org/repository/uniprot/P38398?provider=swissmodelrange=1-103&template=1jm7.1.A\",\"confidence_type\":\"QMEANDisCo\"},{\"model_identifier\":\"AF-P38398-F1\",\"model_category\":\"DEEP-LEARNING\",\"provider\":\"AlphaFold DB\",\"created\":\"2021-07-01\",\"sequence_identity\":1.0,\"uniprot_start\":1,\"uniprot_end\":1863,\"coverage\":100.0,\"model_url\":\"https://alphafold.ebi.ac.uk/files/AF-P38398-F1-model_v1.cif\",\"model_format\":\"MMCIF\",\"model_page_url\":\"https://alphafold.ebi.ac.uk/entry/P38398\"}]}" },
+      "{\"uniprot_entry\":{\"sequence_length\":1863,\"ac\":\"P38398\",\"id\":\"BRCA1_HUMAN\"},\"structures\":[{\"model_identifier\":\"4igk\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2012-12-17\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":1.75,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4igk_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4igk\"},{\"model_identifier\":\"1t15\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2004-04-15\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":1.85,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t15_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1t15\"},{\"model_identifier\":\"4ifi\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2012-12-14\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.2,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4ifi_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4ifi\"},{\"model_identifier\":\"1t29\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2004-04-20\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.3,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t29_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY 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DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4y2g\"},{\"model_identifier\":\"1y98\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2004-12-14\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1y98_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1y98\"},{\"model_identifier\":\"1jnx\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2001-07-26\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1jnx_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY 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MICROSCOPY\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/6g2i\"},{\"model_identifier\":\"1jm7\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2001-07-17\",\"sequence_identity\":100.0,\"uniprot_start\":1,\"uniprot_end\":110,\"resolution\":null,\"coverage\":5.9,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1jm7_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"SOLUTION NMR\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1jm7\"},{\"model_identifier\":\"1oqa\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2003-03-07\",\"sequence_identity\":100.0,\"uniprot_start\":1755,\"uniprot_end\":1863,\"resolution\":null,\"coverage\":5.85,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1oqa_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"SOLUTION NMR\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1oqa\"},{\"model_identifier\":\"P38398_1646-1859:6g2i.1.K\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISS-MODEL\",\"created\":\"2021-11-05\",\"sequence_identity\":1.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"coverage\":0.115,\"confidence_version\":\"4.2.0\",\"confidence_avg_local_score\":0.776,\"model_url\":\"https://swissmodel.expasy.org/3d-beacons/uniprot/P38398.pdb?range=1646-1859&template=6g2i.1.K&provider=swissmodel\",\"model_format\":\"PDB\",\"model_page_url\":\"https://swissmodel.expasy.org/repository/uniprot/P38398?range=1646-1859&template=6g2i.1.K\",\"confidence_type\":\"QMEANDisCo\"},{\"model_identifier\":\"P38398_1-103:1jm7.1.A\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISS-MODEL\",\"created\":\"2021-11-05\",\"sequence_identity\":1.0,\"uniprot_start\":1,\"uniprot_end\":103,\"coverage\":0.055,\"confidence_version\":\"4.2.0\",\"confidence_avg_local_score\":0.655,\"model_url\":\"https://swissmodel.expasy.org/3d-beacons/uniprot/P38398.pdb?range=1-103&template=1jm7.1.A&provider=swissmodel\",\"model_format\":\"PDB\",\"model_page_url\":\"https://swissmodel.expasy.org/repository/uniprot/P38398?range=1-103&template=1jm7.1.A\",\"confidence_type\":\"QMEANDisCo\"},{\"model_identifier\":\"AF-P38398-F1\",\"model_category\":\"DEEP-LEARNING\",\"provider\":\"AlphaFold DB\",\"created\":\"2021-07-01\",\"sequence_identity\":1.0,\"uniprot_start\":1,\"uniprot_end\":1863,\"coverage\":100.0,\"model_url\":\"https://alphafold.ebi.ac.uk/files/AF-P38398-F1-model_v1.cif\",\"model_format\":\"MMCIF\",\"model_page_url\":\"https://alphafold.ebi.ac.uk/entry/P38398\"}]}" },
       { "P01308.json",null}};
 
   private static void setMockData()

diff --git a/test/jalview/fts/threedbeacons/p01308_tdb_resp.txt b/test/jalview/fts/threedbeacons/p01308_tdb_resp.txt
index 12f40ca..14a5d43 100644 (file)
--- a/test/jalview/fts/threedbeacons/p01308_tdb_resp.txt
+++ b/test/jalview/fts/threedbeacons/p01308_tdb_resp.txt
@@ -1 +1 @@
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