From a69b975b0f7ba9d1004f9c7769ba6acc4140d074 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 31 Aug 2010 16:16:31 +0000
Subject: [PATCH] fixed various null pointer exceptions that occur when PDB
 files imported into Jmol which do not map to a sequence.
 Notes re JAL-623

---
 src/jalview/ext/jmol/JalviewJmolBinding.java |  191 ++++++++++++++++----------
 1 file changed, 120 insertions(+), 71 deletions(-)

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 80cc8af..5a36b7c 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -161,10 +161,12 @@ public abstract class JalviewJmolBinding implements StructureListener,
   public String getViewerTitle()
   {
     if (sequence == null || pdbentry == null || sequence.length < 1
-            || pdbentry.length < 1)
+            || pdbentry.length < 1 || sequence[0].length < 1)
     {
       return ("Jalview Jmol Window");
     }
+    // TODO: give a more informative title when multiple structures are
+    // displayed.
     StringBuffer title = new StringBuffer(sequence[0][0].getName() + ":"
             + pdbentry[0].getId());
 
@@ -229,7 +231,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
   public void colourByChain()
   {
     colourBySequence = false;
-    // TODO: colour by chain should colour each chain distinctly across all visible models 
+    // TODO: colour by chain should colour each chain distinctly across all
+    // visible models
     // TODO: http://issues.jalview.org/browse/JAL-628
     evalStateCommand("select *;color chain");
   }
@@ -266,32 +269,36 @@ public abstract class JalviewJmolBinding implements StructureListener,
   /**
    * superpose the structures associated with sequences in the alignment
    * according to their corresponding positions. ded)
+   * 
    * @param refStructure
    *          - select which pdb file to use as reference (default is -1 - the
    *          first structure in the alignment)
-   * @param hiddenCols TODO
+   * @param hiddenCols
+   *          TODO
    */
-  public void superposeStructures(AlignmentI alignment, int refStructure, ColumnSelection hiddenCols)
+  public void superposeStructures(AlignmentI alignment, int refStructure,
+          ColumnSelection hiddenCols)
   {
     String[] files = getPdbFile();
-    if (refStructure>=files.length)
+    if (refStructure >= files.length)
     {
-      System.err.println("Invalid reference structure value "+refStructure);
-      refStructure= -1;
+      System.err.println("Invalid reference structure value "
+              + refStructure);
+      refStructure = -1;
     }
-    if (refStructure<-1)
+    if (refStructure < -1)
     {
-      refStructure=-1;
+      refStructure = -1;
     }
     StringBuffer command = new StringBuffer(), selectioncom = new StringBuffer();
-    
+
     boolean matched[] = new boolean[alignment.getWidth()];
     for (int m = 0; m < matched.length; m++)
     {
-      
-      matched[m] = (hiddenCols!=null) ? hiddenCols.isVisible(m) : true;
+
+      matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
     }
-    
+
     int commonrpositions[][] = new int[files.length][alignment.getWidth()];
     String isel[] = new String[files.length];
     // reference structure - all others are superposed in it
@@ -413,13 +420,14 @@ public abstract class JalviewJmolBinding implements StructureListener,
           molsel.append(chainCd);
           molsel.append("}");
         }
-        selcom[pdbfnum] = molsel.toString(); 
+        selcom[pdbfnum] = molsel.toString();
         selectioncom.append("((");
-        selectioncom.append(selcom[pdbfnum].substring(1, selcom[pdbfnum].length()-1));
+        selectioncom.append(selcom[pdbfnum].substring(1,
+                selcom[pdbfnum].length() - 1));
         selectioncom.append(" )& ");
-        selectioncom.append(pdbfnum+1);
+        selectioncom.append(pdbfnum + 1);
         selectioncom.append(".1)");
-        if (pdbfnum<files.length-1)
+        if (pdbfnum < files.length - 1)
         {
           selectioncom.append("|");
         }
@@ -448,12 +456,13 @@ public abstract class JalviewJmolBinding implements StructureListener,
       command.append(" ROTATE TRANSLATE;\n");
     }
     System.out.println("Select regions:\n" + selectioncom.toString());
-    evalStateCommand("select *; cartoons off; backbone; select ("+selectioncom.toString()+"); cartoons; ");
+    evalStateCommand("select *; cartoons off; backbone; select ("
+            + selectioncom.toString() + "); cartoons; ");
     // selcom.append("; ribbons; ");
     System.out.println("Superimpose command(s):\n" + command.toString());
 
     evalStateCommand(command.toString());
-    
+
     // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString());
   }
 
@@ -662,19 +671,31 @@ public abstract class JalviewJmolBinding implements StructureListener,
     return -1;
   }
 
+  /**
+   * map between index of model filename returned from getPdbFile and the first
+   * index of models from this file in the viewer. Note - this is not trimmed -
+   * use getPdbFile to get number of unique models.
+   */
+  private int _modelFileNameMap[];
+
   // ////////////////////////////////
   // /StructureListener
   public synchronized String[] getPdbFile()
   {
     if (modelFileNames == null)
     {
+
       String mset[] = new String[viewer.getModelCount()];
-      int j=1;
+      _modelFileNameMap = new int[mset.length];
+      int j = 1;
       mset[0] = viewer.getModelFileName(0);
       for (int i = 1; i < mset.length; i++)
       {
-        // skip any additional models in the same file (NMR structures) 
-        if (!(mset[j] = viewer.getModelFileName(i)).equals(mset[j-1]))
+        mset[j] = viewer.getModelFileName(i);
+        _modelFileNameMap[j] = i; // record the model index for the filename
+        // skip any additional models in the same file (NMR structures)
+        if ((mset[j] == null ? mset[j] != mset[j - 1] : mset[j - 1] == null
+                || mset[j].equals(mset[j - 1])))
         {
           j++;
         }
@@ -781,6 +802,14 @@ public abstract class JalviewJmolBinding implements StructureListener,
   public void loadInline(String string)
   {
     loadedInline = true;
+    // TODO: re JAL-623
+    // viewer.loadInline(strModel, isAppend);
+    // could do this:
+    // construct fake fullPathName and fileName so we can identify the file
+    // later.
+    // Then, construct pass a reader for the string to Jmol.
+    // ((org.jmol.Viewer.Viewer) viewer).loadModelFromFile(fullPathName,
+    // fileName, null, reader, false, null, null, 0);
     viewer.openStringInline(string);
   }
 
@@ -989,6 +1018,9 @@ public abstract class JalviewJmolBinding implements StructureListener,
       refreshGUI();
       return;
     }
+    // TODO: deal sensibly with models loaded inLine:
+    // modelName will be null, as will fullPathName.
+
     // the rest of this routine ignores the arguments, and simply interrogates
     // the Jmol view to find out what structures it contains, and adds them to
     // the structure selection manager.
@@ -1038,65 +1070,82 @@ public abstract class JalviewJmolBinding implements StructureListener,
     for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++)
     {
       String fileName = modelfilenames[modelnum];
-      if (fileName != null)
+      boolean foundEntry = false;
+      MCview.PDBfile pdb = null;
+      String pdbfile = null, pdbfhash = null;
+      // model was probably loaded inline - so check the pdb file hashcode
+      if (loadedInline)
+      {
+        // calculate essential attributes for the pdb data imported inline.
+        // prolly need to resolve modelnumber properly - for now just use our 'best guess'
+        pdbfile = viewer.getData(""+(1+_modelFileNameMap[modelnum])+".0",
+                "PDB");
+        pdbfhash = "" + pdbfile.hashCode();
+      }
+      if (pdbentry != null)
       {
-        boolean foundEntry = false;
-        // search pdbentries and sequences to find correct pdbentry and
-        // sequence[] pair for this filename
-        if (pdbentry != null)
+        // search pdbentries and sequences to find correct pdbentry for this
+        // model
+        for (int pe = 0; pe < pdbentry.length; pe++)
         {
-          for (int pe = 0; pe < pdbentry.length; pe++)
+          boolean matches = false;
+          if (fileName == null)
           {
-            if (pdbentry[pe].getFile().equals(fileName))
+            if (false) 
+              // see JAL-623 - need method of matching pasted data up
             {
+              pdb = ssm.setMapping(sequence[pe], chains[pe], pdbfile,
+                      AppletFormatAdapter.PASTE);
+              pdbentry[modelnum].setFile("INLINE" + pdb.id);
+              matches = true;
               foundEntry = true;
-              MCview.PDBfile pdb;
-              if (loadedInline)
-              {
-                // TODO: replace with getData ?
-                pdb = ssm.setMapping(sequence[pe], chains[pe],
-                        pdbentry[pe].getFile(), AppletFormatAdapter.PASTE);
-                pdbentry[pe].setFile("INLINE" + pdb.id);
-              }
-              else
+            }
+          }
+          else
+          {
+            if (matches = pdbentry[pe].getFile().equals(fileName))
+            {
+              foundEntry = true;
+              // TODO: Jmol can in principle retrieve from CLASSLOADER but
+              // this
+              // needs
+              // to be tested. See mantis bug
+              // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
+              String protocol = AppletFormatAdapter.URL;
+              try
               {
-                // TODO: Jmol can in principle retrieve from CLASSLOADER but
-                // this
-                // needs
-                // to be tested. See mantis bug
-                // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
-                String protocol = AppletFormatAdapter.URL;
-                try
-                {
-                  File fl = new java.io.File(pdbentry[pe].getFile());
-                  if (fl.exists())
-                  {
-                    protocol = AppletFormatAdapter.FILE;
-                  }
-                } catch (Exception e)
-                {
-                } catch (Error e)
+                File fl = new java.io.File(pdbentry[pe].getFile());
+                if (fl.exists())
                 {
+                  protocol = AppletFormatAdapter.FILE;
                 }
-                ;
-                pdb = ssm.setMapping(sequence[pe], chains[pe],
-                        pdbentry[pe].getFile(), protocol);
-
+              } catch (Exception e)
+              {
+              } catch (Error e)
+              {
               }
+              ;
+              pdb = ssm.setMapping(sequence[pe], chains[pe],
+                      pdbentry[pe].getFile(), protocol);
 
-              pdbentry[pe].setId(pdb.id);
 
-              for (int i = 0; i < pdb.chains.size(); i++)
-              {
-                chainNames.addElement(new String(pdb.id + ":"
-                        + ((MCview.PDBChain) pdb.chains.elementAt(i)).id));
-              }
-              notifyLoaded = true;
             }
           }
+          if (matches)
+          {
+            pdbentry[pe].setId(pdb.id);
+            // add an entry for every chain in the model
+            for (int i = 0; i < pdb.chains.size(); i++)
+            {
+              chainNames.addElement(new String(pdb.id + ":"
+                      + ((MCview.PDBChain) pdb.chains.elementAt(i)).id));
+            }
+            notifyLoaded = true;
+          }
         }
-        if (!foundEntry && associateNewStructs)
-        {
+      }
+      if (!foundEntry && associateNewStructs)
+      {
           // this is a foreign pdb file that jalview doesn't know about - add
           // it to the dataset and try to find a home - either on a matching
           // sequence or as a new sequence.
@@ -1110,12 +1159,12 @@ public abstract class JalviewJmolBinding implements StructureListener,
 
         }
       }
-    }
     // FILE LOADED OK
     // so finally, update the jmol bits and pieces
     if (jmolpopup != null)
     {
-      jmolpopup.updateComputedMenus();
+      // potential for deadlock here:
+      // jmolpopup.updateComputedMenus();
     }
     if (!isLoadingFromArchive())
     {
@@ -1267,8 +1316,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
    * 
    * @returns the pdb entries added to the current set.
    */
-  public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe, SequenceI[][] seq,
-          String[][] chns)
+  public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
+          SequenceI[][] seq, String[][] chns)
   {
     int pe = -1;
     Vector v = new Vector();
-- 
1.7.10.2