X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureViewer.java;h=189d490880ba8c563fe46180be6fa21db93e727b;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=22f12ea90cbabd403b45a8f5db047bc6a79b4d88;hpb=9b748cf747fedad98cb9c1f4e2f9aaf565c176cb;p=jalview.git

diff --git a/src/jalview/gui/StructureViewer.java b/src/jalview/gui/StructureViewer.java
index 22f12ea..189d490 100644
--- a/src/jalview/gui/StructureViewer.java
+++ b/src/jalview/gui/StructureViewer.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -24,9 +24,12 @@ import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.StructureViewerModel;
 import jalview.structure.StructureSelectionManager;
 
 import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.List;
 
 /**
  * proxy for handling structure viewers.
@@ -41,19 +44,19 @@ public class StructureViewer
 {
   StructureSelectionManager ssm;
 
-  public enum Viewer
+  public enum ViewerType
   {
     JMOL, CHIMERA
   };
 
-  public Viewer getViewerType()
+  public ViewerType getViewerType()
   {
     String viewType = Cache.getDefault(Preferences.STRUCTURE_DISPLAY,
-            Viewer.JMOL.name());
-    return Viewer.valueOf(viewType);
+            ViewerType.JMOL.name());
+    return ViewerType.valueOf(viewType);
   }
 
-  public void setViewerType(Viewer type)
+  public void setViewerType(ViewerType type)
   {
     Cache.setProperty(Preferences.STRUCTURE_DISPLAY, type.name());
   }
@@ -63,23 +66,86 @@ public class StructureViewer
     ssm = structureSelectionManager;
   }
 
-  public JalviewStructureDisplayI viewStructures(AlignmentPanel ap,
-          PDBEntry[] pr, SequenceI[][] collateForPDB)
+  /**
+   * View multiple PDB entries, each with associated sequences
+   * 
+   * @param pdbs
+   * @param seqsForPdbs
+   * @param ap
+   * @return
+   */
+  public JalviewStructureDisplayI viewStructures(PDBEntry[] pdbs,
+          SequenceI[][] seqsForPdbs, AlignmentPanel ap)
   {
-    return viewStructures(getViewerType(), ap, pr, collateForPDB);
+    JalviewStructureDisplayI viewer = onlyOnePdb(pdbs, seqsForPdbs, ap);
+    if (viewer != null)
+    {
+      return viewer;
+    }
+    return viewStructures(getViewerType(), pdbs, seqsForPdbs, ap);
+  }
+
+  /**
+   * A strictly temporary method pending JAL-1761 refactoring. Determines if all
+   * the passed PDB entries are the same (this is the case if selected sequences
+   * to view structure for are chains of the same structure). If so, calls the
+   * single-pdb version of viewStructures and returns the viewer, else returns
+   * null.
+   * 
+   * @param pdbs
+   * @param seqsForPdbs
+   * @param ap
+   * @return
+   */
+  private JalviewStructureDisplayI onlyOnePdb(PDBEntry[] pdbs,
+          SequenceI[][] seqsForPdbs, AlignmentPanel ap)
+  {
+    List<SequenceI> seqs = new ArrayList<SequenceI>();
+    if (pdbs == null || pdbs.length == 0)
+    {
+      return null;
+    }
+    int i = 0;
+    String firstFile = pdbs[0].getFile();
+    for (PDBEntry pdb : pdbs)
+    {
+      String pdbFile = pdb.getFile();
+      if (pdbFile == null || !pdbFile.equals(firstFile))
+      {
+        return null;
+      }
+      SequenceI[] pdbseqs = seqsForPdbs[i++];
+      if (pdbseqs != null)
+      {
+        for (SequenceI sq : pdbseqs)
+        {
+          seqs.add(sq);
+        }
+      }
+    }
+    return viewStructures(pdbs[0],
+            seqs.toArray(new SequenceI[seqs.size()]), ap);
   }
 
-  public JalviewStructureDisplayI viewStructures(Viewer viewerType,
-          AlignmentPanel ap, PDBEntry[] pr, SequenceI[][] collateForPDB)
+  public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
+          SequenceI[] seqsForPdb, AlignmentPanel ap)
   {
+    return viewStructures(getViewerType(), pdb, seqsForPdb, ap);
+  }
+
+  protected JalviewStructureDisplayI viewStructures(ViewerType viewerType,
+          PDBEntry[] pdbs, SequenceI[][] seqsForPdbs, AlignmentPanel ap)
+  {
+    PDBEntry[] pdbsForFile = getUniquePdbFiles(pdbs);
     JalviewStructureDisplayI sview = null;
-    if (viewerType.equals(Viewer.JMOL))
+    if (viewerType.equals(ViewerType.JMOL))
     {
-      sview = new AppJmol(ap, pr, ap.av.collateForPDB(pr));
+      sview = new AppJmol(ap, pdbsForFile, ap.av.collateForPDB(pdbsForFile));
     }
-    else if (viewerType.equals(Viewer.CHIMERA))
+    else if (viewerType.equals(ViewerType.CHIMERA))
     {
-      sview = new ChimeraViewFrame(ap, pr, ap.av.collateForPDB(pr));
+      sview = new ChimeraViewFrame(pdbsForFile,
+              ap.av.collateForPDB(pdbsForFile), ap);
     }
     else
     {
@@ -89,17 +155,47 @@ public class StructureViewer
     return sview;
   }
 
-  public JalviewStructureDisplayI viewStructures(Viewer viewerType,
-          AlignmentPanel ap, PDBEntry pr, SequenceI[] collateForPDB)
+  /**
+   * Convert the array of PDBEntry into an array with no filename repeated
+   * 
+   * @param pdbs
+   * @return
+   */
+  static PDBEntry[] getUniquePdbFiles(PDBEntry[] pdbs)
+  {
+    if (pdbs == null)
+    {
+      return null;
+    }
+    List<PDBEntry> uniques = new ArrayList<PDBEntry>();
+    List<String> filesSeen = new ArrayList<String>();
+    for (PDBEntry entry : pdbs)
+    {
+      String file = entry.getFile();
+      if (file == null)
+      {
+        uniques.add(entry);
+      }
+      else if (!filesSeen.contains(file))
+      {
+        uniques.add(entry);
+        filesSeen.add(file);
+      }
+    }
+    return uniques.toArray(new PDBEntry[uniques.size()]);
+  }
+
+  protected JalviewStructureDisplayI viewStructures(ViewerType viewerType,
+          PDBEntry pdb, SequenceI[] seqsForPdb, AlignmentPanel ap)
   {
     JalviewStructureDisplayI sview = null;
-    if (viewerType.equals(Viewer.JMOL))
+    if (viewerType.equals(ViewerType.JMOL))
     {
-      sview = new AppJmol(pr, collateForPDB, null, ap);
+      sview = new AppJmol(pdb, seqsForPdb, null, ap);
     }
-    else if (viewerType.equals(Viewer.CHIMERA))
+    else if (viewerType.equals(ViewerType.CHIMERA))
     {
-      sview = new ChimeraViewFrame(pr, collateForPDB, null, ap);
+      sview = new ChimeraViewFrame(pdb, seqsForPdb, null, ap);
     }
     else
     {
@@ -109,30 +205,42 @@ public class StructureViewer
     return sview;
   }
 
-  public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
-          SequenceI[] sequenceIs, Object object, AlignmentPanel ap)
+  /**
+   * Create a new panel controlling a structure viewer.
+   * 
+   * @param type
+   * @param pdbf
+   * @param id
+   * @param sq
+   * @param alignPanel
+   * @param viewerData
+   * @param fileloc
+   * @param rect
+   * @param vid
+   * @return
+   */
+  public JalviewStructureDisplayI createView(ViewerType type,
+          String[] pdbf, String[] id, SequenceI[][] sq,
+          AlignmentPanel alignPanel, StructureViewerModel viewerData,
+          String fileloc, Rectangle rect, String vid)
   {
-    return viewStructures(getViewerType(), ap, pdb, sequenceIs);
-  }
+    final boolean useinViewerSuperpos = viewerData.isAlignWithPanel();
+    final boolean usetoColourbyseq = viewerData.isColourWithAlignPanel();
+    final boolean viewerColouring = viewerData.isColourByViewer();
 
-  public JalviewStructureDisplayI createView(Viewer viewer, String[] pdbf,
-          String[] id, SequenceI[][] sq, AlignmentPanel alignPanel,
-          boolean useinJmolsuperpos, boolean usetoColourbyseq,
-          boolean jmolColouring, String fileloc, Rectangle rect, String vid)
-  {
     JalviewStructureDisplayI sview = null;
-    switch (viewer)
+    switch (type)
     {
     case JMOL:
-      sview = new AppJmol(pdbf, id, sq, alignPanel, useinJmolsuperpos,
-              usetoColourbyseq, jmolColouring, fileloc, rect, vid);
+      sview = new AppJmol(pdbf, id, sq, alignPanel, usetoColourbyseq,
+              useinViewerSuperpos, viewerColouring, fileloc, rect, vid);
       break;
     case CHIMERA:
       Cache.log.error("Unsupported structure viewer type "
-              + viewer.toString());
+              + type.toString());
       break;
     default:
-      Cache.log.error("Unknown structure viewer type " + viewer.toString());
+      Cache.log.error("Unknown structure viewer type " + type.toString());
     }
     return sview;
   }