Merge branch 'features/r2_11_2/JAL-3829_3dbeacons' into develop

diff --git a/resources/fts/tdbeacons_data_columns.txt b/resources/fts/tdbeacons_data_columns.txt
index dd6bec5..4ebcc1b 100644 (file)
--- a/resources/fts/tdbeacons_data_columns.txt
+++ b/resources/fts/tdbeacons_data_columns.txt
@@ -58,5 +58,5 @@ 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
-Page URL;model_page_url;String;g3;100;150;105;false;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/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 4bc88e8..fabd577 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -512,6 +512,11 @@ label.load_tree_file = Load a tree file
 label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences = Retrieve and parse sequence database records for the alignment or the currently selected sequences
 label.standard_databases = Standard Databases
 label.fetch_embl_uniprot = Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources
+label.fetch_uniprot_references = Fetch Uniprot references
+label.search_3dbeacons = Find models with 3D-Beacons
+label.3dbeacons = 3D-Beacons
+label.fetch_references_for = Fetch database references for {0} sequences ?
+label.fetch_references_for_3dbeacons = 3D Beacons needs Uniprot References. Fetch database references for {0} sequences ?
 label.reset_min_max_colours_to_defaults = Reset min and max colours to defaults from user preferences.
 label.align_structures_using_linked_alignment_views = Superpose structures using {0} selected alignment view(s)
 label.threshold_feature_display_by_score = Threshold the feature display by score.

diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index 672a59e..fc4ee46 100755 (executable)
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -38,6 +38,8 @@ public class PDBEntry
 
   private static final int PDB_ID_LENGTH = 4;
 
+  private static final String FAKED_ID = "faked_pdbid";
+
   private String file;
 
   private String type;
@@ -384,21 +386,40 @@ public class PDBEntry
       return false; // shouldn't happen
     }
 
-    /*
-     * id has to match (ignoring case)
-     */
-    if (!getId().equalsIgnoreCase(newId))
-    {
-      return false;
-    }
+    boolean idMatches = getId().equalsIgnoreCase(newId);
 
     /*
      * Don't update if associated with different structure files
      */
     String newFile = newEntry.getFile();
-    if (newFile != null && getFile() != null && !newFile.equals(getFile()))
+    if (newFile != null && getFile() != null)
     {
-      return false;
+      if (!newFile.equals(getFile()))
+      {
+        return false;
+      }
+      else
+      {
+        // files match.
+        if (!idMatches)
+        {
+          // this shouldn't happen, but could do if the id from the
+          // file is not the same as the id from the authority that provided
+          // the file
+          if (!newEntry.fakedPDBId())
+          {
+            return false;
+          } // otherwise we can update
+        }
+      }
+    }
+    else
+    {
+      // one has data, one doesn't ..
+      if (!idMatches)
+      {
+        return false;
+      } // otherwise maybe can update
     }
 
     /*
@@ -453,6 +474,11 @@ public class PDBEntry
        */
       String key = newProps.nextElement();
       Object value = newEntry.getProperty(key);
+      if (FAKED_ID.equals(key))
+      {
+        // we never update the fake ID property
+        continue;
+      }
       if (!value.equals(getProperty(key)))
       {
         setProperty(key, value);
@@ -461,16 +487,58 @@ public class PDBEntry
     return true;
   }
   
+  /**
+   * set when Jalview has manufactured the ID using a local filename
+   * @return
+   */
+  public boolean fakedPDBId()
+  {
+    if (_hasProperty(FAKED_ID))
+    {
+      return true;
+    }
+    return false;
+  }
+  public void setFakedPDBId(boolean faked)
+  {
+    if (faked)
+    {
+      setProperty(FAKED_ID, Boolean.TRUE);
+    }
+    else 
+    {
+      if (properties!=null) {
+        properties.remove(FAKED_ID);
+      }
+    }
+  }
+
+  private boolean _hasProperty(final String key)
+  {
+    return (properties != null && properties.containsKey(key));
+  }
+
+  private static final String RETRIEVE_FROM = "RETRIEVE_FROM";
+
+  private static final String PROVIDER = "PROVIDER";
+
+  private static final String MODELPAGE = "PROVIDERPAGE";
 
-  private static final String RETRIEVE_FROM="RETRIEVE_FROM";
   /**
    * Permanent URI for retrieving the original structure data
+   * 
    * @param urlStr
    */
   public void setRetrievalUrl(String urlStr)
   {
     setProperty(RETRIEVE_FROM, urlStr);
   }
+
+  public boolean hasRetrievalUrl()
+  {
+    return _hasProperty(RETRIEVE_FROM);
+  }
+
   /**
    * get the Permanent URI for retrieving the original structure data
    */
@@ -479,8 +547,50 @@ public class PDBEntry
     return (String) getProperty(RETRIEVE_FROM);
   }
 
-  public boolean hasRetrievalUrl()
+  /**
+   * Data provider name - from 3D Beacons
+   * 
+   * @param provider
+   */
+  public void setProvider(String provider)
+  {
+    setProperty(PROVIDER, provider);
+  }
+
+  /**
+   * Get Data provider name - from 3D Beacons
+   * 
+   */
+  public String getProvider()
+  {
+    return (String) getProperty(PROVIDER);
+  }
+
+  /**
+   * Permanent URI for retrieving the original structure data
+   * 
+   * @param urlStr
+   */
+  public void setProviderPage(String urlStr)
+  {
+    setProperty(MODELPAGE, urlStr);
+  }
+
+  /**
+   * get the Permanent URI for retrieving the original structure data
+   */
+  public String getProviderPage()
+  {
+    return (String) getProperty(MODELPAGE);
+  }
+
+  public boolean hasProviderPage()
+  {
+    return _hasProperty(MODELPAGE);
+  }
+
+  public boolean hasProvider()
   {
-    return (properties!=null && properties.containsKey(RETRIEVE_FROM));
+    return _hasProperty(PROVIDER);
   }
 }

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 552349f..d52e049 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1799,13 +1799,30 @@ public class Sequence extends ASequence implements SequenceI
   public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
           String label)
   {
+    return getAlignmentAnnotations(calcId, label, null, true);
+  }
+
+  @Override
+  public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+          String label, String description)
+  {
+    return getAlignmentAnnotations(calcId, label, description, false);
+  }
+
+  private List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+          String label, String description, boolean ignoreDescription)
+  {
     List<AlignmentAnnotation> result = new ArrayList<>();
     if (this.annotation != null)
     {
       for (AlignmentAnnotation ann : annotation)
       {
-        if (ann.calcId != null && ann.calcId.equals(calcId)
-                && ann.label != null && ann.label.equals(label))
+        if ((ann.calcId != null && ann.calcId.equals(calcId))
+                && (ann.label != null && ann.label.equals(label))
+                && ((ignoreDescription && description == null)
+                        || (ann.description != null
+                                && ann.description.equals(description))))
+
         {
           result.add(ann);
         }

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 933f332..7c3eb41 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -446,6 +446,17 @@ public interface SequenceI extends ASequenceI
           String label);
 
   /**
+   * Returns a (possibly empty) list of any annotations that match on given
+   * calcId (source), label (type) and description (observation instance).
+   * Null values do not match.
+   * 
+   * @param calcId
+   * @param label
+   * @param description
+   */
+  public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+          String label, String description);
+  /**
    * create a new dataset sequence (if necessary) for this sequence and sets
    * this sequence to refer to it. This call will move any features or
    * references on the sequence onto the dataset. It will also make a duplicate

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index ae8ff7a..18d8e05 100644 (file)
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -160,7 +160,31 @@ public class JmolParser extends StructureFile implements JmolStatusListener
     return validator;
   }
 
-
+  PDBEntry.Type jmolFiletype=null;
+  /**
+   * resolve a jmol filetype string and update the jmolFiletype field accordingly
+   * @param jmolIdentifiedFileType
+   * @return true if filetype was identified as MMCIF, PDB
+   */
+  public boolean updateFileType(String jmolIdentifiedFileType)
+  {
+    if (jmolIdentifiedFileType == null 
+            || jmolIdentifiedFileType.trim().equals(""))
+    {
+      return false;
+    }
+    if ("mmcif".equalsIgnoreCase(jmolIdentifiedFileType)) {
+      jmolFiletype = PDBEntry.Type.MMCIF;
+      return true;
+    }
+    if ("pdb".equalsIgnoreCase(jmolIdentifiedFileType))
+    {
+      jmolFiletype = PDBEntry.Type.PDB;
+      return true;
+    } 
+    return false;
+  }
+  
   public void transformJmolModelToJalview(ModelSet ms) throws IOException
   {
     try
@@ -171,8 +195,15 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       List<SequenceI> prot = new ArrayList<SequenceI>();
       PDBChain tmpchain;
       String pdbId = (String) ms.getInfo(0, "title");
-      String isMMCIF = (String) ms.getInfo(0, "fileType");
-
+      boolean isMMCIF = false;
+      String jmolFileType_String = (String) ms.getInfo(0, "fileType");
+      if (updateFileType(jmolFileType_String))
+      {
+        setStructureFileType(jmolFiletype.toString());
+      }
+      
+      isMMCIF = PDBEntry.Type.MMCIF.equals(jmolFiletype);
+      
       if (pdbId == null)
       {
         setId(safeName(getDataName()));
@@ -182,7 +213,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       {
         setId(pdbId);
         setPDBIdAvailable(true);
-        alphaFoldModel = alphaFold.search(pdbId) && isMMCIF!=null && isMMCIF.equalsIgnoreCase("mmcif");  
+        alphaFoldModel = alphaFold.search(pdbId) && isMMCIF;  
 
       }
       List<Atom> significantAtoms = convertSignificantAtoms(ms);
@@ -199,7 +230,13 @@ public class JmolParser extends StructureFile implements JmolStatusListener
           tmpchain.atoms.addElement(tmpatom);
         } else
         {
-          tmpchain = new PDBChain(getId(), tmpatom.chain,isAlphafoldModel());
+          String tempFString=null;
+          if (isAlphafoldModel())
+          {
+            tempFString = "Alphafold Reliability";
+          }
+
+          tmpchain = new PDBChain(getId(), tmpatom.chain,tempFString);
           getChains().add(tmpchain);
           tmpchain.atoms.addElement(tmpatom);
         }

diff --git a/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
index 08edcdf..c05306a 100644 (file)
--- a/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
+++ b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
@@ -127,22 +127,23 @@ public class TDBeaconsFTSRestClient extends FTSRestClient
     } catch (Exception e)
     {
       String exceptionMsg = e.getMessage();
-      if (exceptionMsg.contains("SocketException"))
+      if (exceptionMsg != null)
       {
-        // No internet connection
-        throw new Exception(MessageManager.getString(
-                "exception.unable_to_detect_internet_connection"));
-      }
-      else if (exceptionMsg.contains("UnknownHostException"))
-      {
-        // The server is unreachable
-        throw new Exception(MessageManager.formatMessage(
-                "exception.fts_server_unreachable", "3DB Hub"));
-      }
-      else
-      {
-        throw e;
+        if (exceptionMsg.contains("SocketException"))
+        {
+          // No internet connection
+          throw new Exception(MessageManager.getString(
+                  "exception.unable_to_detect_internet_connection"));
+        }
+        else if (exceptionMsg.contains("UnknownHostException"))
+        {
+          // The server is unreachable
+          throw new Exception(MessageManager.formatMessage(
+                  "exception.fts_server_unreachable", "3DB Hub"));
+        }
       }
+      throw e;
+      
     }
 
   }

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 6bcac24..849c278 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -21,11 +21,24 @@
 
 package jalview.gui;
 
+import java.awt.event.ItemEvent;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.concurrent.Executors;
+
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JTable;
+import javax.swing.SwingUtilities;
+import javax.swing.table.AbstractTableModel;
+
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.fts.api.FTSData;
@@ -37,6 +50,7 @@ import jalview.fts.core.FTSRestResponse;
 import jalview.fts.service.pdb.PDBFTSRestClient;
 import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
 import jalview.gui.structurechooser.StructureChooserQuerySource;
+import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
 import jalview.io.DataSourceType;
 import jalview.jbgui.FilterOption;
 import jalview.jbgui.GStructureChooser;
@@ -44,25 +58,10 @@ import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 import jalview.ws.DBRefFetcher;
+import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
+import jalview.ws.seqfetcher.DbSourceProxy;
 import jalview.ws.sifts.SiftsSettings;
 
-import java.awt.event.ItemEvent;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Objects;
-import java.util.Set;
-import java.util.Vector;
-
-import javax.swing.JCheckBox;
-import javax.swing.JComboBox;
-import javax.swing.JLabel;
-import javax.swing.JTable;
-import javax.swing.SwingUtilities;
-import javax.swing.table.AbstractTableModel;
-
 /**
  * Provides the behaviors for the Structure chooser Panel
  * 
@@ -75,6 +74,11 @@ public class StructureChooser extends GStructureChooser
 {
   private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE";
 
+  /**
+   * transient combo box choice for initiating 3db fetch
+   */
+  private static final String VIEWS_QUERYING_TDB = "QUERY_3DB";
+
   private SequenceI selectedSequence;
 
   private SequenceI[] selectedSequences;
@@ -99,25 +103,75 @@ public class StructureChooser extends GStructureChooser
 
   private Collection<FTSData> lastDiscoveredStructuresSet;
 
+  private boolean canQueryTDB = false;
+
+  private boolean notQueriedTDBYet = true;
+
+  List<SequenceI> seqsWithoutSourceDBRef = null;
+
   private static StructureViewer lastTargetedView = null;
 
   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
           AlignmentPanel ap)
   {
     // which FTS engine to use
-    data = StructureChooserQuerySource
-            .getQuerySourceFor(selectedSeqs);
+    data = StructureChooserQuerySource.getQuerySourceFor(selectedSeqs);
     initDialog();
-    
+
     this.ap = ap;
     this.selectedSequence = selectedSeq;
     this.selectedSequences = selectedSeqs;
     this.progressIndicator = (ap == null) ? null : ap.alignFrame;
     init();
-    
+
   }
 
   /**
+   * sets canQueryTDB if protein sequences without a canonical uniprot ref or at
+   * least one structure are discovered.
+   */
+  private void populateSeqsWithoutSourceDBRef()
+  {
+    seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
+    boolean needCanonical = false;
+    for (SequenceI seq : selectedSequences)
+    {
+      if (seq.isProtein())
+      {
+        int dbRef = ThreeDBStructureChooserQuerySource
+                .checkUniprotRefs(seq.getDBRefs());
+        if (dbRef < 0)
+        {
+          if (dbRef == -1)
+          {
+            // need to retrieve canonicals
+            needCanonical = true;
+            seqsWithoutSourceDBRef.add(seq);
+          }
+          else
+          {
+            // could be a sequence with pdb ref
+            if (seq.getAllPDBEntries() == null
+                    || seq.getAllPDBEntries().size() == 0)
+            {
+              seqsWithoutSourceDBRef.add(seq);
+            }
+          }
+        }
+      }
+    }
+    // retrieve database refs for protein sequences
+    if (!seqsWithoutSourceDBRef.isEmpty())
+    {
+      canQueryTDB = true;
+      if (needCanonical)
+      {
+        notQueriedTDBYet = false;
+      }
+    }
+  };
+
+  /**
    * Initializes parameters used by the Structure Chooser Panel
    */
   protected void init()
@@ -129,38 +183,138 @@ public class StructureChooser extends GStructureChooser
 
     chk_superpose.setSelected(Cache.getDefault(AUTOSUPERIMPOSE, true));
 
+    Executors.defaultThreadFactory().newThread(new Runnable()
+    {
+      public void run()
+      {
+        populateSeqsWithoutSourceDBRef();
+        initialStructureDiscovery();
+      }
+
+    }).start();
+
+  }
+
+  // called by init
+  private void initialStructureDiscovery()
+  {
+    // check which FTS engine to use
+    data = StructureChooserQuerySource.getQuerySourceFor(selectedSequences);
+
     // ensure a filter option is in force for search
     populateFilterComboBox(true, cachedPDBExists);
-    Thread discoverPDBStructuresThread = new Thread(new Runnable()
+
+    // looks for any existing structures already loaded
+    // for the sequences (the cached ones)
+    // then queries the StructureChooserQuerySource to
+    // discover more structures.
+    //
+    // Possible optimisation is to only begin querying
+    // the structure chooser if there are no cached structures.
+
+    long startTime = System.currentTimeMillis();
+    updateProgressIndicator(
+            MessageManager.getString("status.loading_cached_pdb_entries"),
+            startTime);
+    loadLocalCachedPDBEntries();
+    updateProgressIndicator(null, startTime);
+    updateProgressIndicator(
+            MessageManager.getString("status.searching_for_pdb_structures"),
+            startTime);
+    fetchStructuresMetaData();
+    // revise filter options if no results were found
+    populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
+    discoverStructureViews();
+    updateProgressIndicator(null, startTime);
+    mainFrame.setVisible(true);
+    updateCurrentView();
+  }
+
+  private void promptForTDBFetch()
+  {
+    final long progressId = System.currentTimeMillis();
+
+    // final action after prompting and discovering db refs
+    final Runnable strucDiscovery = new Runnable()
     {
       @Override
       public void run()
       {
-        // looks for any existing structures already loaded 
-        // for the sequences (the cached ones) 
-        // then queries the StructureChooserQuerySource to 
-        // discover more structures.
-        // 
-        // Possible optimisation is to only begin querying
-        // the structure chooser if there are no cached structures.
+        // TODO: warn if no accessions discovered
+        populateSeqsWithoutSourceDBRef();
+        // redo initial discovery - this time with 3d beacons
+        // Executors.
+        previousWantedFields=null;
         
-        long startTime = System.currentTimeMillis();
-        updateProgressIndicator(MessageManager
-                .getString("status.loading_cached_pdb_entries"), startTime);
-        loadLocalCachedPDBEntries();
-        updateProgressIndicator(null, startTime);
-        updateProgressIndicator(MessageManager.getString(
-                "status.searching_for_pdb_structures"), startTime);
-        fetchStructuresMetaData();
-        // revise filter options if no results were found
-        populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
-        discoverStructureViews();
-        updateProgressIndicator(null, startTime);
-        mainFrame.setVisible(true);
-        updateCurrentView();
+        initialStructureDiscovery();
       }
-    });
-    discoverPDBStructuresThread.start();
+    };
+
+    final FetchFinishedListenerI afterDbRefFetch = new FetchFinishedListenerI()
+    {
+      
+      @Override
+      public void finished()
+      {
+        // filter has been selected, so we set flag to remove ourselves
+        notQueriedTDBYet = false;
+        // new thread to discover structures - via 3d beacons
+        Executors.defaultThreadFactory().newThread(strucDiscovery).start();
+        
+      }
+    };
+    
+    // fetch db refs if OK pressed
+    final Runnable discoverCanonicalDBrefs = new Runnable() 
+    {
+      @Override
+      public void run()
+      {
+        populateSeqsWithoutSourceDBRef();
+
+        final int y = seqsWithoutSourceDBRef.size();
+        if (y > 0)
+        {
+          final SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
+                  .toArray(new SequenceI[y]);
+          DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef,
+                  progressBar, new DbSourceProxy[]
+                  { new jalview.ws.dbsources.Uniprot() }, null, false);
+          dbRefFetcher.addListener(afterDbRefFetch);
+          // ideally this would also gracefully run with callbacks
+          dbRefFetcher.fetchDBRefs(true);
+        } else {
+          // call finished action directly
+          afterDbRefFetch.finished();
+        }
+      }
+
+    };
+    final Runnable revertview = new Runnable() {
+      public void run() {
+        if (lastSelected!=null) {
+          cmb_filterOption.setSelectedItem(lastSelected);
+        }
+      };
+    };
+    // need cancel and no to result in the discoverPDB action - mocked is
+    // 'cancel'
+    JvOptionPane.newOptionDialog(this)
+            .setResponseHandler(JvOptionPane.OK_OPTION,
+                    discoverCanonicalDBrefs)
+            .setResponseHandler(JvOptionPane.CANCEL_OPTION, revertview)
+            .setResponseHandler(JvOptionPane.NO_OPTION, revertview)
+            .showDialog(
+                    MessageManager.formatMessage(
+                            "label.fetch_references_for_3dbeacons",
+                            seqsWithoutSourceDBRef.size()),
+                    MessageManager
+                            .getString("label.3dbeacons"),
+                    JvOptionPane.YES_NO_OPTION, JvOptionPane.PLAIN_MESSAGE,
+                    null, new Object[]
+                    { MessageManager.getString("action.ok"),
+                        MessageManager.getString("action.cancel") },
+                    MessageManager.getString("action.ok"));
   }
 
   /**
@@ -256,8 +410,9 @@ public class StructureChooser extends GStructureChooser
         resultList = data.fetchStructuresMetaData(seq, wantedFields,
                 selectedFilterOpt, !chk_invertFilter.isSelected());
         // null response means the FTSengine didn't yield a query for this
-        // consider designing a special exception if we really wanted to be OOCrazy
-        if (resultList==null)
+        // consider designing a special exception if we really wanted to be
+        // OOCrazy
+        if (resultList == null)
         {
           continue;
         }
@@ -282,9 +437,9 @@ public class StructureChooser extends GStructureChooser
     {
       getResultTable()
               .setModel(data.getTableModel(discoveredStructuresSet));
-      
+
       noOfStructuresFound = discoveredStructuresSet.size();
-      lastDiscoveredStructuresSet=discoveredStructuresSet;
+      lastDiscoveredStructuresSet = discoveredStructuresSet;
       mainFrame.setTitle(MessageManager.formatMessage(
               "label.structure_chooser_no_of_structures",
               noOfStructuresFound, totalTime));
@@ -357,8 +512,9 @@ public class StructureChooser extends GStructureChooser
           FTSRestResponse resultList;
           try
           {
-            resultList = data.selectFirstRankedQuery(seq, discoveredStructuresSet,wantedFields,
-                    fieldToFilterBy, !chk_invertFilter.isSelected());
+            resultList = data.selectFirstRankedQuery(seq,
+                    discoveredStructuresSet, wantedFields, fieldToFilterBy,
+                    !chk_invertFilter.isSelected());
 
           } catch (Exception e)
           {
@@ -383,7 +539,7 @@ public class StructureChooser extends GStructureChooser
           reorderedStructuresSet.addAll(discoveredStructuresSet);
           getResultTable()
                   .setModel(data.getTableModel(reorderedStructuresSet));
-          
+
           FTSRestResponse.configureTableColumn(getResultTable(),
                   wantedFields, tempUserPrefs);
           getResultTable().getColumn("Ref Sequence").setPreferredWidth(120);
@@ -457,6 +613,7 @@ public class StructureChooser extends GStructureChooser
   {
     populateFilterComboBox(haveData, cachedPDBExist, null);
   }
+
   /**
    * Populates the filter combo-box options dynamically depending on discovered
    * structures
@@ -464,45 +621,57 @@ public class StructureChooser extends GStructureChooser
   protected void populateFilterComboBox(boolean haveData,
           boolean cachedPDBExist, FilterOption lastSel)
   {
-    
+
     /*
      * temporarily suspend the change listener behaviour
      */
     cmb_filterOption.removeItemListener(this);
-    int selSet=-1;
+    int selSet = -1;
     cmb_filterOption.removeAllItems();
     if (haveData)
     {
-      List<FilterOption> filters = data.getAvailableFilterOptions(VIEWS_FILTER);
-      data.updateAvailableFilterOptions(VIEWS_FILTER, filters, lastDiscoveredStructuresSet);
-      int p=0;
-      for (FilterOption filter:filters)
+      List<FilterOption> filters = data
+              .getAvailableFilterOptions(VIEWS_FILTER);
+      data.updateAvailableFilterOptions(VIEWS_FILTER, filters,
+              lastDiscoveredStructuresSet);
+      int p = 0;
+      for (FilterOption filter : filters)
       {
-        if (lastSel!=null && filter.equals(lastSel)) {
-          selSet=p;
+        if (lastSel != null && filter.equals(lastSel))
+        {
+          selSet = p;
         }
         p++;
         cmb_filterOption.addItem(filter);
       }
     }
+
     cmb_filterOption.addItem(
             new FilterOption(MessageManager.getString("label.enter_pdb_id"),
-                    "-", VIEWS_ENTER_ID, false,null));
+                    "-", VIEWS_ENTER_ID, false, null));
     cmb_filterOption.addItem(
             new FilterOption(MessageManager.getString("label.from_file"),
-                    "-", VIEWS_FROM_FILE, false,null));
+                    "-", VIEWS_FROM_FILE, false, null));
+    if (canQueryTDB && notQueriedTDBYet)
+    {
+      FilterOption queryTDBOption = new FilterOption(
+              MessageManager.getString("label.search_3dbeacons"), "-",
+              VIEWS_QUERYING_TDB, false, null);
+      cmb_filterOption.addItem(queryTDBOption);
+    }
 
     if (cachedPDBExist)
     {
       FilterOption cachedOption = new FilterOption(
               MessageManager.getString("label.cached_structures"), "-",
-              VIEWS_LOCAL_PDB, false,null);
+              VIEWS_LOCAL_PDB, false, null);
       cmb_filterOption.addItem(cachedOption);
-      if (selSet==-1) {
+      if (selSet == -1)
+      {
         cmb_filterOption.setSelectedItem(cachedOption);
       }
     }
-    if (selSet>-1)
+    if (selSet > -1)
     {
       cmb_filterOption.setSelectedIndex(selSet);
     }
@@ -516,24 +685,45 @@ public class StructureChooser extends GStructureChooser
   {
     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
             .getSelectedItem());
+    
+    // first check if we need to rebuild dialog
+    if (selectedFilterOpt.getView() == VIEWS_QUERYING_TDB)
+    {
+      promptForTDBFetch();
+      return;
+    }
+    if (lastSelected == selectedFilterOpt)
+    {
+      // don't need to do anything, probably
+      return;
+    }
+    // otherwise, record selection
+    // and update the layout and dialog accordingly
+    lastSelected = selectedFilterOpt;
+
     layout_switchableViews.show(pnl_switchableViews,
             selectedFilterOpt.getView());
     String filterTitle = mainFrame.getTitle();
     mainFrame.setTitle(frameTitle);
     chk_invertFilter.setVisible(false);
+    
     if (selectedFilterOpt.getView() == VIEWS_FILTER)
     {
       mainFrame.setTitle(filterTitle);
       // TDB Query has no invert as yet
-      chk_invertFilter.setVisible(selectedFilterOpt.getQuerySource() instanceof PDBStructureChooserQuerySource);
-      
-      if (data!=selectedFilterOpt.getQuerySource() || data.needsRefetch(selectedFilterOpt)) 
+      chk_invertFilter.setVisible(selectedFilterOpt
+              .getQuerySource() instanceof PDBStructureChooserQuerySource);
+
+      if (data != selectedFilterOpt.getQuerySource()
+              || data.needsRefetch(selectedFilterOpt))
       {
         data = selectedFilterOpt.getQuerySource();
         // rebuild the views completely, since prefs will also change
         tabRefresh();
         return;
-      } else {
+      }
+      else
+      {
         filterResultSet(selectedFilterOpt.getValue());
       }
     }
@@ -672,7 +862,7 @@ public class StructureChooser extends GStructureChooser
   {
     validateSelections();
   }
-
+  private FilterOption lastSelected=null;
   /**
    * Handles the state change event for the 'filter' combo-box and 'invert'
    * check-box
@@ -780,7 +970,8 @@ public class StructureChooser extends GStructureChooser
           int[] selectedRows = restable.getSelectedRows();
           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
           List<SequenceI> selectedSeqsToView = new ArrayList<>();
-          pdbEntriesToView = data.collectSelectedRows(restable,selectedRows,selectedSeqsToView);
+          pdbEntriesToView = data.collectSelectedRows(restable,
+                  selectedRows, selectedSeqsToView);
 
           SequenceI[] selectedSeqs = selectedSeqsToView
                   .toArray(new SequenceI[selectedSeqsToView.size()]);
@@ -799,8 +990,9 @@ public class StructureChooser extends GStructureChooser
           List<SequenceI> selectedSeqsToView = new ArrayList<>();
           for (int row : selectedRows)
           {
-            PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
-                    pdbIdColIndex);
+            PDBEntry pdbEntry = ((PDBEntryTableModel) tbl_local_pdb
+                    .getModel()).getPDBEntryAt(row).getPdbEntry();
+
             pdbEntriesToView[count++] = pdbEntry;
             SequenceI selectedSeq = (SequenceI) tbl_local_pdb
                     .getValueAt(row, refSeqColIndex);
@@ -1101,7 +1293,7 @@ public class StructureChooser extends GStructureChooser
         public void run()
         {
           fetchStructuresMetaData();
-          //populateFilterComboBox(true, cachedPDBExists);
+          // populateFilterComboBox(true, cachedPDBExists);
 
           filterResultSet(
                   ((FilterOption) cmb_filterOption.getSelectedItem())
@@ -1159,7 +1351,7 @@ public class StructureChooser extends GStructureChooser
         value = entry.getSequence();
         break;
       case 1:
-        value = entry.getPdbEntry();
+        value = entry.getQualifiedId();
         break;
       case 2:
         value = entry.getPdbEntry().getChainCode() == null ? "_"
@@ -1200,6 +1392,15 @@ public class StructureChooser extends GStructureChooser
       this.pdbEntry = pdbEntry;
     }
 
+    public String getQualifiedId()
+    {
+      if (pdbEntry.hasProvider())
+      {
+        return pdbEntry.getProvider() + ":" + pdbEntry.getId();
+      }
+      return pdbEntry.toString();
+    }
+
     public SequenceI getSequence()
     {
       return sequence;
@@ -1241,6 +1442,18 @@ public class StructureChooser extends GStructureChooser
   protected void setFTSDocFieldPrefs(FTSDataColumnPreferences newPrefs)
   {
     data.setDocFieldPrefs(newPrefs);
-    
+
+  }
+
+  /**
+   * 
+   * @return true when all initialisation threads have finished and dialog is
+   *         visible
+   */
+  public boolean isDialogVisible()
+  {
+    return mainFrame != null && data != null && cmb_filterOption != null
+            && mainFrame.isVisible()
+            && cmb_filterOption.getSelectedItem() != null;
   }
 }

diff --git a/src/jalview/gui/structurechooser/PDBStructureChooserQuerySource.java b/src/jalview/gui/structurechooser/PDBStructureChooserQuerySource.java
index 0f38e9f..6651272 100644 (file)
--- a/src/jalview/gui/structurechooser/PDBStructureChooserQuerySource.java
+++ b/src/jalview/gui/structurechooser/PDBStructureChooserQuerySource.java
@@ -238,19 +238,19 @@ public class PDBStructureChooserQuerySource
   public List<FilterOption> getAvailableFilterOptions(String VIEWS_FILTER)
   {
     List<FilterOption> filters = new ArrayList<FilterOption>();
-    filters.add(new FilterOption(
+    filters.add(new FilterOption("PDBe "+
             MessageManager.getString("label.best_quality"),
             "overall_quality", VIEWS_FILTER, false,this));
-    filters.add(new FilterOption(
+    filters.add(new FilterOption("PDBe "+
             MessageManager.getString("label.best_resolution"),
             "resolution", VIEWS_FILTER, false,this));
-    filters.add(new FilterOption(
+    filters.add(new FilterOption("PDBe "+
             MessageManager.getString("label.most_protein_chain"),
             "number_of_protein_chains", VIEWS_FILTER, false,this));
-    filters.add(new FilterOption(
+    filters.add(new FilterOption("PDBe "+
             MessageManager.getString("label.most_bound_molecules"),
             "number_of_bound_molecules", VIEWS_FILTER, false,this));
-    filters.add(new FilterOption(
+    filters.add(new FilterOption("PDBe "+
             MessageManager.getString("label.most_polymer_residues"),
             "number_of_polymer_residues", VIEWS_FILTER, true,this));
   

diff --git a/src/jalview/gui/structurechooser/StructureChooserQuerySource.java b/src/jalview/gui/structurechooser/StructureChooserQuerySource.java
index b5646db..a4ae2c8 100644 (file)
--- a/src/jalview/gui/structurechooser/StructureChooserQuerySource.java
+++ b/src/jalview/gui/structurechooser/StructureChooserQuerySource.java
@@ -42,7 +42,7 @@ public abstract class StructureChooserQuerySource
 
   public static StructureChooserQuerySource getPDBfts()
   {
-          return new PDBStructureChooserQuerySource();
+    return new PDBStructureChooserQuerySource();
   }
 
   public static StructureChooserQuerySource getTDBfts()
@@ -65,7 +65,6 @@ public abstract class StructureChooserQuerySource
     return docFieldPrefs;
   }
 
-
   /**
    * Builds a query string for a given sequences using its DBRef entries
    * 
@@ -75,7 +74,6 @@ public abstract class StructureChooserQuerySource
    */
 
   public abstract String buildQuery(SequenceI seq);
-  
 
   /**
    * Remove the following special characters from input string +, -, &, !, (, ),
@@ -167,7 +165,8 @@ public abstract class StructureChooserQuerySource
    * 
    * @param seq
    *          - seq to generate a query for
-   * @param discoveredStructuresSet - existing set of entries - allows client side selection
+   * @param discoveredStructuresSet
+   *          - existing set of entries - allows client side selection
    * @param wantedFields
    *          - fields to retrieve
    * @param selectedFilterOpt
@@ -178,7 +177,8 @@ public abstract class StructureChooserQuerySource
    * @throws Exception
    */
   public abstract FTSRestResponse selectFirstRankedQuery(SequenceI seq,
-          Collection<FTSData> discoveredStructuresSet, Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
+          Collection<FTSData> discoveredStructuresSet,
+          Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
           boolean b) throws Exception;
 
   /**
@@ -200,15 +200,17 @@ public abstract class StructureChooserQuerySource
 
   /**
    * @param VIEWS_FILTER
-   *          - a String key that can be used by the caller to tag the returned filter
-   *          options to distinguish them in a collection
+   *          - a String key that can be used by the caller to tag the returned
+   *          filter options to distinguish them in a collection
    * @return list of FilterOption - convention is that the last one in the list
    *         will be constructed with 'addSeparator==true'
    */
-  public abstract List<FilterOption> getAvailableFilterOptions(String VIEWS_FILTER);
+  public abstract List<FilterOption> getAvailableFilterOptions(
+          String VIEWS_FILTER);
 
   /**
    * construct a structure chooser query source for the given set of sequences
+   * 
    * @param selectedSeqs
    * @return PDBe or 3DB query source
    */
@@ -216,22 +218,39 @@ public abstract class StructureChooserQuerySource
           SequenceI[] selectedSeqs)
   {
     ThreeDBStructureChooserQuerySource tdbSource = new ThreeDBStructureChooserQuerySource();
-    boolean hasUniprot=false;
-    boolean hasNA=false,hasProtein=false;
-    for (SequenceI seq:selectedSeqs)
+    boolean hasUniprot = false, hasCanonical = false;
+    boolean hasNA = false, hasProtein = false;
+    int protWithoutUni = 0;
+    int protWithoutCanon = 0;
+    for (SequenceI seq : selectedSeqs)
     {
-      hasNA|=!seq.isProtein();
+      hasNA |= !seq.isProtein();
       hasProtein |= seq.isProtein();
       if (seq.isProtein())
       {
-        String query = tdbSource.buildQuery(seq);
-        if (query!=null && query.length()>0)
+        int refsAvailable = ThreeDBStructureChooserQuerySource
+                .checkUniprotRefs(seq.getDBRefs());
+        if (refsAvailable > -2)
         {
-          hasUniprot=true;
+          if (refsAvailable > -1)
+          {
+            hasCanonical = true;
+          } else {
+            protWithoutCanon++;
+          }
+          hasUniprot = true;
+        } else {
+          protWithoutUni++;
+          
         }
       }
     }
-    if (hasProtein && hasUniprot && !hasNA)
+    //
+    // logic: all canonicals - no fetchdb
+    // some uniprot no canonicals: defer to PDB, user can optionally fetch
+    //
+    if (hasProtein && hasCanonical && !hasNA && protWithoutCanon == 0 && protWithoutUni == 0)
+
     {
       return tdbSource;
     }
@@ -239,17 +258,17 @@ public abstract class StructureChooserQuerySource
   }
 
   /**
-   * some filter options may mean the original query needs to be executed again. 
+   * some filter options may mean the original query needs to be executed again.
+   * 
    * @param selectedFilterOpt
    * @return true if the fetchStructuresMetadata method needs to be called again
    */
   public abstract boolean needsRefetch(FilterOption selectedFilterOpt);
 
-  
-  
   public void updateAvailableFilterOptions(String VIEWS_FILTER,
           List<FilterOption> xtantOptions, Collection<FTSData> lastFTSData)
   {
     // TODO Auto-generated method stub
-    
-  }}
\ No newline at end of file
+
+  }
+}
\ No newline at end of file

diff --git a/src/jalview/gui/structurechooser/TDBResultAnalyser.java b/src/jalview/gui/structurechooser/TDBResultAnalyser.java
index ffac9c4..9f57100 100644 (file)
--- a/src/jalview/gui/structurechooser/TDBResultAnalyser.java
+++ b/src/jalview/gui/structurechooser/TDBResultAnalyser.java
@@ -177,8 +177,8 @@ public class TDBResultAnalyser
                   return nonNullFirst(idx_mqual, o1data, o2data);
                 }
                 // models, so rank on qmean - b
-                float o1_mq = (Float) o1data[idx_mqual];
-                float o2_mq = (Float) o2data[idx_mqual];
+                double o1_mq = (Double) o1data[idx_mqual];
+                double o2_mq = (Double) o2data[idx_mqual];
                 return (o2_mq < o1_mq) ? 1 : (o2_mq == o1_mq) ? 0 : -1;
               }
             }
@@ -250,6 +250,10 @@ public class TDBResultAnalyser
         cover.andNot(scover);
       }
     }
+    if (selected.size()==0)
+    {
+      return selected;
+    }
     // final step is to sort on length - this might help the superposition
     // process
     Collections.sort(selected, new Comparator<FTSData>()

diff --git a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
index ff414dd..9b6d8e8 100644 (file)
--- a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
+++ b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
@@ -3,7 +3,6 @@ package jalview.gui.structurechooser;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
-import java.util.Collections;
 import java.util.Comparator;
 import java.util.HashSet;
 import java.util.LinkedHashSet;
@@ -26,7 +25,6 @@ import jalview.fts.core.FTSRestRequest;
 import jalview.fts.core.FTSRestResponse;
 import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
 import jalview.jbgui.FilterOption;
-import jalview.util.MessageManager;
 
 /**
  * logic for querying the 3DBeacons API for structures of sequences
@@ -87,26 +85,38 @@ public class ThreeDBStructureChooserQuerySource
     Set<String> pdbids = new HashSet<>();
 
     List<DBRefEntry> refs = seq.getDBRefs();
+    int ib = checkUniprotRefs(refs);
+    if (ib>-1)
+    {
+      return getDBRefId(refs.get(ib));
+    }
+    return null;
+  }
+
+  /**
+   * Searches DBRefEntry for uniprot refs
+   * @param seq
+   * @return -2 if no uniprot refs, -1 if no canonical ref., otherwise index of Uniprot canonical DBRefEntry 
+   */
+  public static int checkUniprotRefs(List<DBRefEntry> refs)
+  {
+    boolean hasUniprot = false;
     if (refs != null && refs.size() != 0)
     {
       for (int ib = 0, nb = refs.size(); ib < nb; ib++)
       {
         DBRefEntry dbRef = refs.get(ib);
-        if (isValidSeqName(getDBRefId(dbRef))
-                && queryBuilder.length() < MAX_QLENGTH)
+        if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
         {
-          if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT)
-                  && dbRef.isCanonical())
+          hasUniprot = true;
+          if (dbRef.isCanonical())
           {
-            // TODO: pick best Uniprot accession
-            isUniProtRefsFound = true;
-            return getDBRefId(dbRef);
-
+            return ib;
           }
         }
       }
     }
-    return null;
+    return hasUniprot ? -1 : -2;
   }
 
   /**
@@ -165,17 +175,19 @@ public class ThreeDBStructureChooserQuerySource
           FilterOption selectedFilterOpt, boolean b) throws Exception
   {
     FTSRestResponse resultList;
-    if (selectedFilterOpt!=null && tdBeaconsFilter(selectedFilterOpt.getValue()))
+    if (selectedFilterOpt != null
+            && tdBeaconsFilter(selectedFilterOpt.getValue()))
     {
       FTSRestRequest tdbRequest = getTDBeaconsRequest(seq, wantedFields);
       resultList = tdbRestClient.executeRequest(tdbRequest);
-
+      
       lastTdbRequest = tdbRequest;
-
-      // Query the PDB and add additional metadata
-      FTSRestResponse pdbResponse = fetchStructuresMetaDataFor(
-              getPDBQuerySource(), resultList);
-      FTSRestResponse joinedResp = joinResponses(resultList, pdbResponse);
+      if (resultList!=null)
+      { // Query the PDB and add additional metadata
+        FTSRestResponse pdbResponse = fetchStructuresMetaDataFor(
+                getPDBQuerySource(), resultList);
+        FTSRestResponse joinedResp = joinResponses(resultList, pdbResponse);
+      }
       return resultList;
     }
     // use the PDBFTS directly
@@ -183,7 +195,7 @@ public class ThreeDBStructureChooserQuerySource
             wantedFields, selectedFilterOpt, b);
     lastTdbRequest = getPDBQuerySource().lastPdbRequest;
     lastPdbRequest = lastTdbRequest; // both queries the same - indicates we
-                                     // rank using PDBe
+    // rank using PDBe
     return resultList;
 
   }
@@ -235,22 +247,39 @@ public class ThreeDBStructureChooserQuerySource
   public void updateAvailableFilterOptions(String VIEWS_FILTER,
           List<FilterOption> xtantOptions, Collection<FTSData> tdbEntries)
   {
-    if (tdbEntries !=null && lastTdbRequest != null)
+    if (tdbEntries != null && lastTdbRequest != null)
     {
       int prov_idx = lastTdbRequest.getFieldIndex("Provider");
-
+      boolean hasPDBe=false;
       for (FTSData row : tdbEntries)
       {
         String provider = (String) row.getSummaryData()[prov_idx];
-        FilterOption providerOpt = new FilterOption("3DB Provider - " + provider,
-                FILTER_SOURCE_PREFIX + provider, VIEWS_FILTER,
-                false, this);
+        FilterOption providerOpt = new FilterOption(
+                "3DB Provider - " + provider,
+                FILTER_SOURCE_PREFIX + provider, VIEWS_FILTER, false, this);
         if (!xtantOptions.contains(providerOpt))
         {
-          xtantOptions.add(1,
-                  providerOpt);
-          tdBeaconsFilters.add(FILTER_SOURCE_PREFIX+provider);
-
+          xtantOptions.add(1, providerOpt);
+          tdBeaconsFilters.add(FILTER_SOURCE_PREFIX + provider);
+          if ("PDBe".equalsIgnoreCase(provider))
+          {
+            hasPDBe=true;
+          }
+        }
+      }
+      if (!hasPDBe)
+      {
+        // remove the PDBe options from the available filters
+        int op=0;
+        while (op<xtantOptions.size())
+        {
+          FilterOption filter = xtantOptions.get(op);
+          if (filter.getQuerySource() instanceof PDBStructureChooserQuerySource)
+          {
+            xtantOptions.remove(op);
+          } else {
+            op++;
+          }
         }
       }
     }
@@ -280,8 +309,9 @@ public class ThreeDBStructureChooserQuerySource
   @Override
   public boolean needsRefetch(FilterOption selectedFilterOpt)
   {
-    return selectedFilterOpt==null || !tdBeaconsFilter(selectedFilterOpt.getValue())
-            && lastPdbRequest != lastTdbRequest;
+    return selectedFilterOpt == null
+            || !tdBeaconsFilter(selectedFilterOpt.getValue())
+                    && lastPdbRequest != lastTdbRequest;
   }
 
   /**
@@ -304,7 +334,7 @@ public class ThreeDBStructureChooserQuerySource
           Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
           boolean b) throws Exception
   {
-    if (fieldToFilterBy!=null && tdBeaconsFilter(fieldToFilterBy))
+    if (fieldToFilterBy != null && tdBeaconsFilter(fieldToFilterBy))
     {
       TDBResultAnalyser analyser = new TDBResultAnalyser(seq,
               collectedResults, lastTdbRequest, fieldToFilterBy,
@@ -336,6 +366,7 @@ public class ThreeDBStructureChooserQuerySource
     int idColumnIndex = restable.getColumn("Model id").getModelIndex();
     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();
     final int up_start_idx = restable.getColumn("Uniprot Start")
@@ -372,6 +403,8 @@ public class ThreeDBStructureChooserQuerySource
       String urlStr = restable.getValueAt(row, urlColumnIndex).toString();
       String typeColumn = restable.getValueAt(row, typeColumnIndex)
               .toString();
+      String modelPage = humanUrl < 1 ? null
+              : (String) restable.getValueAt(row, humanUrl);
       SequenceI selectedSeq = (SequenceI) restable.getValueAt(row,
               refSeqColIndex);
       selectedSeqsToView.add(selectedSeq);
@@ -386,12 +419,16 @@ 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);
+        boolean probablyPdb = urlStr.toLowerCase(Locale.ENGLISH)
+                .contains("pdb");
+        pdbEntry.setType(hasCif ? PDBEntry.Type.MMCIF
+                : probablyPdb ? PDBEntry.Type.PDB : PDBEntry.Type.FILE);
         if (!"PDBe".equalsIgnoreCase(typeColumn))
         {
           pdbEntry.setRetrievalUrl(urlStr);
         }
+        pdbEntry.setProvider(typeColumn);
+        pdbEntry.setProviderPage(modelPage);
         selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
       }
       pdbEntriesToView[count++] = pdbEntry;
@@ -443,7 +480,7 @@ public class ThreeDBStructureChooserQuerySource
   {
 
     String pdb_Query = buildPDBFTSQueryFor(upResponse);
-    if (pdb_Query.length()==0)
+    if (pdb_Query.length() == 0)
     {
       return null;
     }
@@ -456,7 +493,7 @@ public class ThreeDBStructureChooserQuerySource
     pdbRequest.setWantedFields(
             pdbquery.getDocFieldPrefs().getStructureSummaryFields());
     pdbRequest.setSearchTerm(pdb_Query + ")");
-    
+
     resultList = pdbquery.executePDBFTSRestRequest(pdbRequest);
 
     lastPdbRequest = pdbRequest;
@@ -466,11 +503,14 @@ public class ThreeDBStructureChooserQuerySource
   public FTSRestResponse joinResponses(FTSRestResponse upResponse,
           FTSRestResponse pdbResponse)
   {
+    boolean hasPdbResp = lastPdbRequest != null;
+
     int idx_provider = getLastFTSRequest().getFieldIndex("Provider");
     // join on
     int idx_modelId = getLastFTSRequest().getFieldIndex("Model id");
-    int pdbIdx = lastPdbRequest.getFieldIndex("PDB Id");
-    int pdbTitle_idx = lastPdbRequest.getFieldIndex("Title");
+    int pdbIdx = hasPdbResp ? lastPdbRequest.getFieldIndex("PDB Id") : -1;
+    int pdbTitle_idx = hasPdbResp ? lastPdbRequest.getFieldIndex("Title")
+            : -1;
     int tdbTitle_idx = getLastFTSRequest().getFieldIndex("Title");
 
     List<FTSData> joinedRows = new ArrayList<FTSData>();
@@ -480,15 +520,24 @@ public class ThreeDBStructureChooserQuerySource
       String provider = (String) row.getSummaryData()[idx_provider];
       if ("PDBe".equalsIgnoreCase(provider))
       {
-        for (final FTSData pdbrow : pdbResponse.getSearchSummary())
+        if (!hasPdbResp)
         {
-          String pdbid = (String) pdbrow.getSummaryData()[pdbIdx];
-          if (id.equalsIgnoreCase(pdbid))
+          System.out.println(
+                  "Warning: seems like we couldn't get to the PDBe search interface.");
+        }
+        else
+        {
+          for (final FTSData pdbrow : pdbResponse.getSearchSummary())
           {
-            row.getSummaryData()[tdbTitle_idx] = pdbrow
-                    .getSummaryData()[pdbTitle_idx];
+            String pdbid = (String) pdbrow.getSummaryData()[pdbIdx];
+            if (id.equalsIgnoreCase(pdbid))
+            {
+              row.getSummaryData()[tdbTitle_idx] = pdbrow
+                      .getSummaryData()[pdbTitle_idx];
+            }
           }
         }
+
       }
       else
       {

diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index 084f886..94a832b 100644 (file)
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -119,6 +119,7 @@ public abstract class StructureFile extends AlignFile
     pdbSequence.setName(getId() + "|" + pdbSequence.getName());
     PDBEntry entry = new PDBEntry();
     entry.setId(getId());
+    entry.setFakedPDBId(!isPPDBIdAvailable());
     entry.setType(getStructureFileType());
     if (chain.id != null)
     {

diff --git a/src/mc_view/PDBChain.java b/src/mc_view/PDBChain.java
index 60c289e..e1c90f3 100755 (executable)
--- a/src/mc_view/PDBChain.java
+++ b/src/mc_view/PDBChain.java
@@ -78,11 +78,27 @@ public class PDBChain
 
   public String pdbid = "";
 
-  public PDBChain(String thePdbid, String theId, boolean isAlphaFoldModel)
+  String tfacName = "Temperature Factor";
+
+
+  public PDBChain(String thePdbid, String theId, String tempFactorColumnName)
   {
     this.pdbid = thePdbid == null ? thePdbid : thePdbid.toLowerCase();
     this.id = theId;
-    this.alphaFoldModel = isAlphaFoldModel;
+    if (tempFactorColumnName!=null && tempFactorColumnName.length()>0)
+    {
+      tfacName = tempFactorColumnName;
+    }
+  }
+
+  /**
+   * import chain data assuming Temperature Factor is in the Temperature Factor column
+   * @param thePdbid
+   * @param theId
+   */
+  public PDBChain(String thePdbid, String theId)
+  {
+    this(thePdbid,theId, null);
   }
 
   /**
@@ -92,8 +108,6 @@ public class PDBChain
 
   public Mapping shadowMap;
 
-  private boolean alphaFoldModel;
-
   public void setNewlineString(String nl)
   {
     newline = nl;
@@ -493,23 +507,17 @@ public class PDBChain
         min = Math.min(min, annots[i].value);
         resAnnotation.setElementAt(null, i);
       }
-      String tfacName = "Temperature Factor";
-      if (isAlphaFoldModel())
-      {
-        tfacName = "Alphafold Reliability";
-      }
       AlignmentAnnotation tfactorann = new AlignmentAnnotation(
               tfacName, tfacName + " for " + pdbid + id,
               annots, min, max, AlignmentAnnotation.LINE_GRAPH);
+      
+      tfactorann.setCalcId(getClass().getName());
+
       tfactorann.setSequenceRef(sequence);
       sequence.addAlignmentAnnotation(tfactorann);
     }
   }
 
-  private boolean isAlphaFoldModel()
-  {
-    return alphaFoldModel;
-  }
 
   /**
    * Colour start/end of bonds by charge
@@ -627,8 +635,10 @@ public class PDBChain
 
         for (AlignmentAnnotation ana : shadow.getAnnotation())
         {
-          List<AlignmentAnnotation> transfer = sq
-                  .getAlignmentAnnotations(ana.getCalcId(), ana.label);
+          // match on calcId, label and description so annotations from
+          // different structures are preserved
+          List<AlignmentAnnotation> transfer = sq.getAlignmentAnnotations(
+                  ana.getCalcId(), ana.label, ana.description);
           if (transfer == null || transfer.size() == 0)
           {
             ana = new AlignmentAnnotation(ana);
@@ -648,8 +658,11 @@ public class PDBChain
         {
           for (AlignmentAnnotation ana : sequence.getAnnotation())
           {
+            // match on calcId, label and description so annotations from
+            // different structures are preserved
             List<AlignmentAnnotation> transfer = dsq
-                    .getAlignmentAnnotations(ana.getCalcId(), ana.label);
+                    .getAlignmentAnnotations(ana.getCalcId(), ana.label,
+                            ana.description);
             if (transfer == null || transfer.size() == 0)
             {
               ana = new AlignmentAnnotation(ana);

diff --git a/src/mc_view/PDBfile.java b/src/mc_view/PDBfile.java
index 24e0435..0eb14cd 100755 (executable)
--- a/src/mc_view/PDBfile.java
+++ b/src/mc_view/PDBfile.java
@@ -154,8 +154,8 @@ public class PDBfile extends StructureFile
             tmpchain.atoms.addElement(tmpatom);
           } else
           {
-            // PDBfile never handles alphafold models, so false
-            tmpchain = new PDBChain(getId(), tmpatom.chain, false);
+            // PDBfile never handles alphafold models
+            tmpchain = new PDBChain(getId(), tmpatom.chain);
             getChains().add(tmpchain);
             tmpchain.atoms.addElement(tmpatom);
           }

diff --git a/test/jalview/datamodel/PDBEntryTest.java b/test/jalview/datamodel/PDBEntryTest.java
index cf4294e..198cde3 100644 (file)
--- a/test/jalview/datamodel/PDBEntryTest.java
+++ b/test/jalview/datamodel/PDBEntryTest.java
@@ -208,7 +208,7 @@ public class PDBEntryTest
     assertTrue(pdb1.updateFrom(pdb2));
     assertEquals(pdb1.getFile(), "filePath");
     assertEquals(pdb1.getType(), Type.FILE.toString());
-
+    assertEquals(pdb1.getChainCode(),"B");
     /*
      * change of file is not allowed
      */

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 6d07113..5069759 100644 (file)
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -192,6 +192,35 @@ public class SequenceTest
     assertTrue(seq.getAlignmentAnnotations(null, null).isEmpty());
   }
 
+
+  @Test(groups = { "Functional" })
+  public void testGetAlignmentAnnotations_forCalcIdLabelAndDescription()
+  {
+    addAnnotation("label1", "desc1", "calcId1", 1f);
+    AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
+            1f);
+    addAnnotation("label2", "desc3", "calcId3", 1f);
+    AlignmentAnnotation ann4 = addAnnotation("label2", "desc3", "calcId2",
+            1f);
+    addAnnotation("label5", "desc3", null, 1f);
+    addAnnotation(null, "desc3", "calcId3", 1f);
+
+    List<AlignmentAnnotation> anns = seq.getAlignmentAnnotations("calcId2",
+            "label2", "desc3");
+    assertEquals(1, anns.size());
+    assertSame(ann4, anns.get(0));
+    /**
+     * null matching should fail
+     */
+    assertTrue(seq.getAlignmentAnnotations("calcId3", "label2",null).isEmpty());
+    
+    assertTrue(seq.getAlignmentAnnotations("calcId2", "label3",null).isEmpty());
+    assertTrue(seq.getAlignmentAnnotations("calcId3", "label5",null).isEmpty());
+    assertTrue(seq.getAlignmentAnnotations("calcId2", null,null).isEmpty());
+    assertTrue(seq.getAlignmentAnnotations(null, "label3",null).isEmpty());
+    assertTrue(seq.getAlignmentAnnotations(null, null,null).isEmpty());
+  }
+
   /**
    * Tests for addAlignmentAnnotation. Note this method has the side-effect of
    * setting the sequenceRef on the annotation. Adding the same annotation twice
@@ -1431,6 +1460,21 @@ public class SequenceTest
     seq.addPDBId(pdbe5);
     assertEquals(4, seq.getAllPDBEntries().size());
     assertSame(pdbe5, seq.getAllPDBEntries().get(3));
+    
+    // add with a fake pdbid 
+    // (models don't have an embedded ID)
+    String realId = "RealIDQ";
+    PDBEntry pdbe6 = new PDBEntry(realId,null,Type.PDB,"real/localpath");
+    PDBEntry pdbe7 = new PDBEntry("RealID/real/localpath","C",Type.MMCIF,"real/localpath");
+    pdbe7.setFakedPDBId(true);
+    seq.addPDBId(pdbe6);
+    assertEquals(5,seq.getAllPDBEntries().size());
+    seq.addPDBId(pdbe7);
+    assertEquals(5,seq.getAllPDBEntries().size());
+    assertFalse(pdbe6.fakedPDBId());
+    assertSame(pdbe6,seq.getAllPDBEntries().get(4));
+    assertEquals("C",pdbe6.getChainCode());
+    assertEquals(realId, pdbe6.getId());
   }
 
   @Test(

diff --git a/test/jalview/ext/jmol/JmolParserTest.java b/test/jalview/ext/jmol/JmolParserTest.java
index 2832135..10882d3 100644 (file)
--- a/test/jalview/ext/jmol/JmolParserTest.java
+++ b/test/jalview/ext/jmol/JmolParserTest.java
@@ -277,6 +277,10 @@ public class JmolParserTest
     assertEquals(structureData.getId(), "localstruct");
     assertNotNull(structureData.getSeqs());
     /*
+     * local structures have a fake ID
+     */
+    assertTrue(structureData.getSeqs().get(0).getAllPDBEntries().get(0).fakedPDBId());
+    /*
      * the ID is also the group for features derived from structure data 
      */
     String featureGroup = structureData.getSeqs().get(0)

diff --git a/test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java b/test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
index c1b4d1b..ef079d1 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(),
-            13);
+            14);
   }
 
   @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");
+            "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");
   }
 
   @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\",\"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\",\"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\",\"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\",\"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\",\"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\",\"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\",\"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\",\"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\",\"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\",\"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\",\"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\",\"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\",\"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\",\"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\",\"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\",\"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\",\"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\",\"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\",\"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\",\"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\",\"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\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1t2v\"},{\"model_identifier\":\"4y18\",\"model_category\":\"EXPERIMENTALLY 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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\"}]}" },
       { "P01308.json",null}};
 
   private static void setMockData()
@@ -308,6 +308,8 @@ public class TDBeaconsFTSRestClientTest
    * check that the mock request and response are the same as the response from
    * a live 3D-beacons endpoint
    * 
+   * Note - servers often have rapidly changing ids / URIs so this might fail, but the overall structure will remain. 
+   * 
    * @throws Exception
    */
   @Test(groups = { "Network", "Integration" })

diff --git a/test/jalview/fts/threedbeacons/p01308_tdb_resp.txt b/test/jalview/fts/threedbeacons/p01308_tdb_resp.txt
index 26d4abd..12f40ca 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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diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java
index 4685e4c..a87e1c6 100644 (file)
--- a/test/jalview/gui/StructureChooserTest.java
+++ b/test/jalview/gui/StructureChooserTest.java
@@ -131,6 +131,7 @@ public class StructureChooserTest
 
     SequenceI[] selectedSeqs = new SequenceI[] { seq };
     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
+    ThreadwaitFor(200, sc);
     
     // if structures are not discovered then don't
     // populate filter options
@@ -169,6 +170,9 @@ public class StructureChooserTest
     PDBFTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
     SequenceI[] selectedSeqs = new SequenceI[] { seq };
     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
+    // not mocked, wait for 2s 
+    ThreadwaitFor(2000, sc);
+    
     sc.fetchStructuresMetaData();
     Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
             "discoveredStructuresSet");
@@ -183,6 +187,8 @@ public class StructureChooserTest
     PDBFTSRestClientTest.setMock();
     SequenceI[] selectedSeqs = new SequenceI[] { upSeq };
     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
+    ThreadwaitFor(500, sc);
+    
     sc.fetchStructuresMetaData();
     Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
             "discoveredStructuresSet");
@@ -190,6 +196,22 @@ public class StructureChooserTest
     assertTrue(ss.size() > 0);
   }
 
+  private void ThreadwaitFor(int i, StructureChooser sc)
+  {
+    long timeout = i+System.currentTimeMillis();
+    while (!sc.isDialogVisible() && timeout > System.currentTimeMillis())
+    {
+      try {
+        Thread.sleep(50);
+      } catch (InterruptedException x)
+      {
+        
+      }
+    }
+    
+  }
+
+
   @Test(groups = { "Functional" })
   public void sanitizeSeqNameTest()
   {

diff --git a/test/mc_view/PDBChainTest.java b/test/mc_view/PDBChainTest.java
index 14ec1e7..0f748ce 100644 (file)
--- a/test/mc_view/PDBChainTest.java
+++ b/test/mc_view/PDBChainTest.java
@@ -68,7 +68,7 @@ public class PDBChainTest
   {
     System.out.println("setup");
     StructureImportSettings.setShowSeqFeatures(true);
-    c = new PDBChain("1GAQ", "A", false);
+    c = new PDBChain("1GAQ", "A");
   }
 
   @Test(groups = { "Functional" })