JAL-1400 numeric version numbers only for minimum jre compatibility

[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 4ac247c..f31272a 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -357,8 +357,21 @@ public abstract class JalviewJmolBinding implements StructureListener,
       return;
     }
     StringBuffer selectioncom = new StringBuffer();
-    
-
+    // 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++)
     {
@@ -403,8 +416,9 @@ 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++)
         {
@@ -469,6 +483,13 @@ 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
@@ -534,11 +555,6 @@ 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)
@@ -550,7 +566,7 @@ 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} {");