X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=58bba481587a6da743b068b0d49afa238ef56f03;hb=3325395b33ef3b52b4a62327621c5bddf12ee4e0;hp=5a9e382369288c89e3bb84a89a615deb9a139162;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 5a9e382..58bba48 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -1,31 +1,42 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.structure;
 
-import java.io.*;
-import java.util.*;
-
-import MCview.*;
-import jalview.analysis.*;
-import jalview.api.AlignmentViewPanel;
+import jalview.analysis.AlignSeq;
 import jalview.api.StructureSelectionManagerProvider;
-import jalview.datamodel.*;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+
+import java.io.PrintStream;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.IdentityHashMap;
+import java.util.Vector;
+
+import MCview.Atom;
+import MCview.PDBChain;
 
 public class StructureSelectionManager
 {
@@ -55,12 +66,26 @@ public class StructureSelectionManager
 
   Hashtable mappingData = new Hashtable();
 
+  private static StructureSelectionManager nullProvider = null;
+
   public static StructureSelectionManager getStructureSelectionManager(
           StructureSelectionManagerProvider context)
   {
-    if (context==null)
+    if (context == null)
     {
-      throw new Error("Implementation error. Structure selection manager's context is 'null'", new NullPointerException("SSM context is null"));
+      if (nullProvider == null)
+      {
+        if (instances != null)
+        {
+          throw new Error(MessageManager.getString("error.implementation_error_structure_selection_manager_null"),
+                  new NullPointerException(MessageManager.getString("exception.ssm_context_is_null")));
+        }
+        else
+        {
+          nullProvider = new StructureSelectionManager();
+        }
+        return nullProvider;
+      }
     }
     if (instances == null)
     {
@@ -69,7 +94,15 @@ public class StructureSelectionManager
     StructureSelectionManager instance = instances.get(context);
     if (instance == null)
     {
-      instances.put(context, instance = new StructureSelectionManager());
+      if (nullProvider != null)
+      {
+        instance = nullProvider;
+      }
+      else
+      {
+        instance = new StructureSelectionManager();
+      }
+      instances.put(context, instance);
     }
     return instance;
   }
@@ -156,9 +189,26 @@ public class StructureSelectionManager
      * the tried and tested MCview pdb mapping
      */
     MCview.PDBfile pdb = null;
+    boolean parseSecStr=true;
+    for (SequenceI sq:sequence)
+    {
+      SequenceI ds = sq;while (ds.getDatasetSequence()!=null) { ds = ds.getDatasetSequence();};
+      if (ds.getAnnotation()!=null)
+      {
+        for (AlignmentAnnotation ala:ds.getAnnotation())
+        {
+          // false if any annotation present from this structure
+          if (MCview.PDBfile.isCalcIdForFile(ala.getCalcId(), pdbFile))
+          {
+            parseSecStr = false;
+          }
+        }
+      }
+    }
     try
     {
-      pdb = new MCview.PDBfile(pdbFile, protocol);
+      pdb = new MCview.PDBfile(true, parseSecStr, pdbFile, protocol);
+      
     } catch (Exception ex)
     {
       ex.printStackTrace();
@@ -192,7 +242,9 @@ public class StructureSelectionManager
         }
       }
       else
+      {
         targetChain = "";
+      }
 
       int max = -10;
       AlignSeq maxAlignseq = null;
@@ -201,7 +253,7 @@ public class StructureSelectionManager
       boolean first = true;
       for (int i = 0; i < pdb.chains.size(); i++)
       {
-        PDBChain chain = ((PDBChain) pdb.chains.elementAt(i));
+        PDBChain chain = (pdb.chains.elementAt(i));
         if (targetChain.length() > 0 && !targetChain.equals(chain.id)
                 && !infChain)
         {
@@ -210,8 +262,8 @@ public class StructureSelectionManager
         // TODO: correctly determine sequence type for mixed na/peptide
         // structures
         AlignSeq as = new AlignSeq(sequence[s],
-                ((PDBChain) pdb.chains.elementAt(i)).sequence,
-                ((PDBChain) pdb.chains.elementAt(i)).isNa ? AlignSeq.DNA
+                pdb.chains.elementAt(i).sequence,
+                pdb.chains.elementAt(i).isNa ? AlignSeq.DNA
                         : AlignSeq.PEP);
         as.calcScoreMatrix();
         as.traceAlignment();
@@ -292,7 +344,9 @@ public class StructureSelectionManager
       }
 
       if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+      {
         pdbFile = "INLINE" + pdb.id;
+      }
 
       mappings[mappings.length - 1] = new StructureMapping(sequence[s],
               pdbFile, pdb.id, maxChainId, mapping,
@@ -327,7 +381,9 @@ public class StructureSelectionManager
     String[] handlepdbs;
     Vector pdbs = new Vector();
     for (int i = 0; i < pdbfiles.length; pdbs.addElement(pdbfiles[i++]))
+    {
       ;
+    }
     StructureListener sl;
     for (int i = 0; i < listeners.size(); i++)
     {
@@ -419,7 +475,9 @@ public class StructureSelectionManager
       {
         Object li = listeners.elementAt(i);
         if (li instanceof SequenceListener)
+        {
           ((SequenceListener) li).highlightSequence(results);
+        }
       }
     }
   }
@@ -443,7 +501,9 @@ public class StructureSelectionManager
     boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null;
     SearchResults results = null;
     if (index == -1)
+    {
       index = seq.findPosition(indexpos);
+    }
     StructureListener sl;
     int atomNo = 0;
     for (int i = 0; i < listeners.size(); i++)
@@ -661,9 +721,13 @@ public class StructureSelectionManager
           AlignedCodonFrame[] codonFrames)
   {
     if (!add && (seqmappings == null || seqmappings.size() == 0))
+    {
       return;
+    }
     if (seqmappings == null)
+    {
       seqmappings = new Vector();
+    }
     if (codonFrames != null && codonFrames.length > 0)
     {
       for (int cf = 0; cf < codonFrames.length; cf++)
@@ -701,8 +765,10 @@ public class StructureSelectionManager
             int[] nsr = new int[(seqmappingrefs == null) ? 1
                     : seqmappingrefs.length + 1];
             if (seqmappingrefs != null && seqmappingrefs.length > 0)
+            {
               System.arraycopy(seqmappingrefs, 0, nsr, 0,
                       seqmappingrefs.length);
+            }
             nsr[(seqmappingrefs == null) ? 0 : seqmappingrefs.length] = 1;
             seqmappingrefs = nsr;
           }