JAL-3210 Barebones gradle/buildship/eclipse. See README

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

diff --git a/src/jalview/gui/StructureViewer.java b/src/jalview/gui/StructureViewer.java
index dc5d77d..0c8354b 100644 (file)
--- a/src/jalview/gui/StructureViewer.java
+++ b/src/jalview/gui/StructureViewer.java
@@ -25,12 +25,7 @@ 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;
@@ -50,13 +45,6 @@ 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;
@@ -400,135 +388,4 @@ 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);
-  }
-
-  /**
-   * 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;
-  }
-
 }