JAL-3253 temporary branch SwingJS upgrade with testNG fixes Java 8

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

diff --git a/src/jalview/gui/StructureViewer.java b/src/jalview/gui/StructureViewer.java
index b7767fa..17b786d 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;
@@ -45,14 +50,25 @@ import java.util.Map.Entry;
  */
 public class StructureViewer
 {
+
+  static
+  {
+    Platform.ensureJmol();
+  }
+
   private static final String UNKNOWN_VIEWER_TYPE = "Unknown structure viewer type ";
 
   StructureSelectionManager ssm;
 
+  /**
+   * decide if new structures are aligned to existing ones
+   */
+  private boolean superposeAdded = true;
+
   public enum ViewerType
   {
     JMOL, CHIMERA
-  };
+  }
 
   /**
    * Constructor
@@ -127,6 +143,7 @@ public class StructureViewer
             new SequenceI[seqsForPdbs.size()][]);
     if (sview != null)
     {
+      sview.setAlignAddedStructures(superposeAdded);
       new Thread(new Runnable()
       {
         @Override
@@ -152,11 +169,12 @@ public class StructureViewer
 
     if (viewerType.equals(ViewerType.JMOL))
     {
-      sview = new AppJmol(ap, pdbsForFile, theSeqs);
+      sview = new AppJmol(ap, superposeAdded, pdbsForFile, theSeqs);
     }
     else if (viewerType.equals(ViewerType.CHIMERA))
     {
-      sview = new ChimeraViewFrame(pdbsForFile, theSeqs, ap);
+      sview = new ChimeraViewFrame(pdbsForFile, superposeAdded, theSeqs,
+              ap);
     }
     else
     {
@@ -279,11 +297,14 @@ public class StructureViewer
   {
     if (sview != null)
     {
-      if (!sview.addAlreadyLoadedFile(seqsForPdb, null, ap, pdb.getId()))
+      sview.setAlignAddedStructures(superposeAdded);
+      String pdbId = pdb.getId();
+      if (!sview.addAlreadyLoadedFile(seqsForPdb, null, ap, pdbId))
       {
-        sview.addToExistingViewer(pdb, seqsForPdb, null, ap, pdb.getId());
+        sview.addToExistingViewer(pdb, seqsForPdb, null, ap, pdbId);
       }
       sview.updateTitleAndMenus();
+      sview.raiseViewer();
       return sview;
     }
     ViewerType viewerType = getViewerType();
@@ -373,4 +394,140 @@ public class StructureViewer
     return sview != null && sview.isVisible();
   }
 
+  public void setSuperpose(boolean alignAddedStructures)
+  {
+    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);
+  }
+
+  /**
+   * Launch a structure viewer with or without an open StructureChooser.
+   * 
+   * Moved from StructureChooser to enable JalviewJS startup with structure
+   * display.
+   * 
+   * @param ap
+   * @param pdbEntriesToView
+   * @param sequences
+   * @param superimpose
+   * @param theViewer
+   * @param pb
+   * @return
+   */
+  protected static StructureViewer launchStructureViewer(
+          final AlignmentPanel ap,
+          final PDBEntry[] pdbEntriesToView, SequenceI[] sequences,
+          boolean superimpose, StructureViewer theViewer,
+          IProgressIndicator pb)
+  {
+    final StructureSelectionManager ssm = ap.getStructureSelectionManager();
+    long progressId = sequences.hashCode();
+    if (pb != null)
+    {
+      pb.setProgressBar(MessageManager
+            .getString("status.launching_3d_structure_viewer"), progressId);
+    }
+    if (theViewer == null)
+    {
+      theViewer = new StructureViewer(ssm);
+    }
+    theViewer.setSuperpose(superimpose);
+  
+    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...
+    Desktop.getInstance().lastTargetedView = theViewer;
+    return theViewer;
+  }
+
 }