JAL-1432 updated copyright notices

[jalview.git] / src / jalview / ext / jmol / JalviewJmolBinding.java

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 257ca8c..8dfb9fd 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -14,6 +14,7 @@
  * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.ext.jmol;
 
@@ -323,9 +324,55 @@ public abstract class JalviewJmolBinding implements StructureListener,
   public void superposeStructures(AlignmentI[] _alignment,
           int[] _refStructure, ColumnSelection[] _hiddenCols)
   {
+    assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length);
+
     String[] files = getPdbFile();
+    // check to see if we are still waiting for Jmol files
+    long starttime=System.currentTimeMillis();
+    boolean waiting=true;
+    do {
+      waiting=false;
+      for (String file:files)
+      {
+        try {
+          // HACK - in Jalview 2.8 this call may not be threadsafe so we catch
+          // every possible exception
+          StructureMapping[] sm = ssm.getMapping(file);
+          if (sm == null || sm.length == 0)
+          {
+            waiting = true;
+          }
+        } catch (Exception x)
+        {
+          waiting = true;
+        } catch (Error q)
+        {
+          waiting = true;
+        }
+      }
+      // we wait around for a reasonable time before we give up
+    } while (waiting && System.currentTimeMillis()<(10000+1000*files.length+starttime));
+    if (waiting)
+    {
+      System.err.println("RUNTIME PROBLEM: Jmol seems to be taking a long time to process all the structures.");
+      return;
+    }
     StringBuffer selectioncom = new StringBuffer();
-    assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length);
+    // In principle - nSeconds specifies the speed of animation for each
+    // superposition - but is seems to behave weirdly, so we don't specify it.
+    String nSeconds = " ";
+    if (files.length > 10)
+    {
+      nSeconds = " 0.00001 ";
+    }
+    else
+    {
+      nSeconds = " " + (2.0 / files.length) + " ";
+      // if (nSeconds).substring(0,5)+" ";
+    }
+    // see JAL-1345 - should really automatically turn off the animation for
+    // large numbers of structures, but Jmol doesn't seem to allow that.
+    nSeconds = " ";
     // union of all aligned positions are collected together.
     for (int a = 0; a < _alignment.length; a++)
     {
@@ -370,8 +417,9 @@ public abstract class JalviewJmolBinding implements StructureListener,
         // RACE CONDITION - getMapping only returns Jmol loaded filenames once
         // Jmol callback has completed.
         if (mapping == null || mapping.length < 1)
-          continue;
-
+        {
+          throw new Error("Implementation error - Jmol seems to be still working on getting its data - report at http://issues.jalview.org/browse/JAL-1016");
+        }
         int lastPos = -1;
         for (int s = 0; s < sequence[pdbfnum].length; s++)
         {
@@ -436,6 +484,13 @@ public abstract class JalviewJmolBinding implements StructureListener,
           }
         }
       }
+      
+      // TODO: consider bailing if nmatched less than 4 because superposition
+      // not
+      // well defined.
+      // TODO: refactor superposable position search (above) from jmol selection
+      // construction (below)
+
       String[] selcom = new String[files.length];
       int nmatched = 0;
       // generate select statements to select regions to superimpose structures
@@ -501,11 +556,6 @@ public abstract class JalviewJmolBinding implements StructureListener,
           }
         }
       }
-      // TODO: consider bailing if nmatched less than 4 because superposition
-      // not
-      // well defined.
-      // TODO: refactor superposable position search (above) from jmol selection
-      // construction (below)
       for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
       {
         if (pdbfnum == refStructure)
@@ -517,7 +567,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
         command.append(chainNames[pdbfnum]);
         command.append(") against reference (");
         command.append(chainNames[refStructure]);
-        command.append(")\";\ncompare ");
+        command.append(")\";\ncompare "+nSeconds);
         command.append("{");
         command.append(1 + pdbfnum);
         command.append(".1} {");