Merge remote-tracking branch 'origin/merge/Jalview-JS/develop_feature/JAL-3690_callba...

[jalview.git] / src / jalview / gui / StructureViewer.java

diff --git a/src/jalview/gui/StructureViewer.java b/src/jalview/gui/StructureViewer.java
index 0c8354b..e7a30f9 100644 (file)
--- a/src/jalview/gui/StructureViewer.java
+++ b/src/jalview/gui/StructureViewer.java
@@ -25,7 +25,12 @@ import jalview.bin.Cache;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.StructureViewerModel;
+import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.DBRefFetcher;
+import jalview.ws.sifts.SiftsSettings;
 
 import java.awt.Rectangle;
 import java.util.ArrayList;
@@ -45,6 +50,16 @@ import java.util.Map.Entry;
  */
 public class StructureViewer
 {
+  
+  static
+  {
+    Platform.loadStaticResource("core/core_jvjmol.z.js",
+            "org.jmol.viewer.Viewer");
+  }
+
+
+  
+  
   private static final String UNKNOWN_VIEWER_TYPE = "Unknown structure viewer type ";
 
   StructureSelectionManager ssm;
@@ -388,4 +403,119 @@ public class StructureViewer
     superposeAdded = alignAddedStructures;
   }
 
+  /**
+   * Launch a minimal implementation of a StructureViewer.
+   * 
+   * @param alignPanel
+   * @param pdb
+   * @param seqs
+   * @return
+   */
+  public static StructureViewer launchStructureViewer(
+          AlignmentPanel alignPanel, PDBEntry pdb, SequenceI[] seqs)
+  {
+    return launchStructureViewer(alignPanel, new PDBEntry[] { pdb }, seqs,
+            false, null, null);
+  }
+
+  /**
+   * Adds PDB structures to a new or existing structure viewer
+   * 
+   * @param ssm
+   * @param pdbEntriesToView
+   * @param alignPanel
+   * @param sequences
+   * @return
+   */
+  protected static StructureViewer launchStructureViewer(
+          final AlignmentPanel ap, final PDBEntry[] pdbEntriesToView,
+          SequenceI[] sequences, boolean superimpose,
+          StructureViewer theViewer, IProgressIndicator pb)
+  {
+    final StructureSelectionManager ssm = ap.getStructureSelectionManager();
+    if (theViewer == null)
+      theViewer = new StructureViewer(ssm);
+    long progressId = sequences.hashCode();
+    if (pb != null)
+      pb.setProgressBar(MessageManager.getString(
+              "status.launching_3d_structure_viewer"), progressId);
+    theViewer.setSuperpose(superimpose);
+  
+    /*
+     * remember user's choice of superimpose or not
+     */
+    Cache.setProperty(StructureChooser.AUTOSUPERIMPOSE,
+            Boolean.valueOf(superimpose).toString());
+  
+    if (pb != null)
+      pb.setProgressBar(null, progressId);
+    if (SiftsSettings.isMapWithSifts())
+    {
+      List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>();
+      int p = 0;
+      // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
+      // real PDB ID. For moment, we can also safely do this if there is already
+      // a known mapping between the PDBEntry and the sequence.
+      for (SequenceI seq : sequences)
+      {
+        PDBEntry pdbe = pdbEntriesToView[p++];
+        if (pdbe != null && pdbe.getFile() != null)
+        {
+          StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
+          if (smm != null && smm.length > 0)
+          {
+            for (StructureMapping sm : smm)
+            {
+              if (sm.getSequence() == seq)
+              {
+                continue;
+              }
+            }
+          }
+        }
+        if (seq.getPrimaryDBRefs().isEmpty())
+        {
+          seqsWithoutSourceDBRef.add(seq);
+          continue;
+        }
+      }
+      if (!seqsWithoutSourceDBRef.isEmpty())
+      {
+        int y = seqsWithoutSourceDBRef.size();
+        if (pb != null)
+          pb.setProgressBar(MessageManager.formatMessage(
+                  "status.fetching_dbrefs_for_sequences_without_valid_refs",
+                  y), progressId);
+        SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
+                .toArray(new SequenceI[y]);
+        DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
+        dbRefFetcher.fetchDBRefs(true);
+  
+        if (pb != null)
+          pb.setProgressBar("Fetch complete.", progressId); // todo i18n
+      }
+    }
+    if (pdbEntriesToView.length > 1)
+    {
+      if (pb != null)
+        pb.setProgressBar(MessageManager.getString(
+                "status.fetching_3d_structures_for_selected_entries"),
+                progressId);
+      theViewer.viewStructures(pdbEntriesToView, sequences, ap);
+    }
+    else
+    {
+      if (pb != null)
+        pb.setProgressBar(MessageManager.formatMessage(
+                "status.fetching_3d_structures_for",
+                pdbEntriesToView[0].getId()), progressId);
+      theViewer.viewStructures(pdbEntriesToView[0], sequences, ap);
+    }
+    if (pb != null)
+      pb.setProgressBar(null, progressId);
+    // remember the last viewer we used...
+    StructureChooser.lastTargetedView = theViewer;
+    return theViewer;
+  }
+
 }